Σχεδιασμός Χημικών Προϊόντων

Σχεδιασμός Χημικών Προϊόντων
Δημήτρης Χατζηαβραμίδης Σχολή Χημικών Μηχανικών Εθνικό Μετσόβιο Πολυτεχνείο 14/2/2014 ΔΧ

Μοριακά Προϊόντα Φάρμακα: Φαρμακευτικά δραστικές ουσίες (Αctive Pharmaceutical Ingredients) Νανοϋλικά, νανοσωματίδια Βιολογικά μόρια 14/2/2014 ΔΧ

Νανοκλίμακα: 1 nm = 10-9 m = 10-3 mm = 10 Å
Νανοσωματίδια Νανοκλίμακα: 1 nm = 10-9 m = 10-3 mm = 10 Å Ατομική κλίμακα (~ Å ) < Νανοκλίμακα (~ nm) < Mακροκλίμακα (> 1 mm ) Γιατί είναι σπουδαία; Γιατί: Κβαντομηχανικές (κυμματικές) ιδιότητες των ηλεκτρονίων μέσα στο υλικό επιρρεάζονται από διακυμάνσεις στη νανοκλίμακα ⇒ είναι δυνατό να μεταβληθούν μακροσκοπικές ιδιότητες του υλικού (π.χ., ειδική θερμότητα, θερμοικρασία τήξης, μαγνητική επαγωγή, κλπ.) χωρίς να αλλάξει η σύσταση Κύριο χαρακτηριστικό των βιολογικών συστημάτων είναι η οργάνωση της ύλης σε νανοκλίμακα ⇒ να κατασκευστούν νέα υλικά κάνοντας χρήση της αυτοδιάταξης (self-assembly) της φύσης Τα διάφορα στοιχεία συστημάτων σε νανοκλίμακα έχουν πολύ υψηλό λόγο επιφάνειας προς όγκο ⇒ ιδανικά για χρήση σε σύνθετα (composite) υλικά, αντιδρώντα συστήματα, χορήγηση φαρμάκων (drug delivery), αποθήκευση χημικής ενέργειας (υδρογόνο, φυσικό αέριο) Συστήματα που αποτελούνται από νανοδομές μπορεί να έχουν υψηλότερες πυκνότητες και αγωγιμότητες από αυτές συστημάτων με μικροδομές Οι μακροσκοπικές ιδιότητες (μηχανικές, θερμικές, οπτικές, μαγνητικές, ηλεκτρικές, κλπ.) για συστήματα σε νανοκλίμακα είναι αρκετά διαφορετικές από εκείνες μακροσκοπικών ή ογκώδη (bulk) συστήματα 14/2/2014 ΔΧ

Interparticle Potentials for prediction of macroscopic properties
NANOPARTICLES Nanotechnology: The technology to build macro and micro materials and structures with atomic precision According to Feynman (1959), the laws of nature do not limit our ability to work at the molecular level, atom by atom; instead, it was our lack of appropriate equipment and techniques for doing so ⇒ challenge for miniaturization Scientists at IBM (1999) used a nanotechnology tool called Atomic Force Microscope to perform Dip Pen Nanolithography (AFM tip coated with molecular ink and brought into contact with surface to be patterned) Thermodynamics and Statistical Mechanics of small systems, introduced by T. L. Hill in the 1963 to deal with colloidal particles, macromolecules and their mixtures, after formulation of key concepts for nonextensive systems, i.e., systems away from the thermodynamic limit (N → ∞ , V → ∞ , N / V = rN finite), (C. Tsallis, 1988), became Nanothermodynamics Interparticle Potentials for prediction of macroscopic properties Atoms or simple molecules - quantum mechanical ab initio calculations Macrosystems classical potentials, e.g.,Coulomb, LJ, for ( 1023 particles) covalent and noncovalent interactions Nanosystems - experimental and theoretical development ( finite number of particles) 14/2/2014 ΔΧ

Molecular Building Blocks Diamondoids Buckyballs Carbon nanotubes
NANOPARTICLES Molecular Building Blocks Diamondoids Buckyballs Carbon nanotubes Cyclodextrins Liposomes Monoclonal Antibodies Diamondoids, also known as cage hydrocarbons, are saturated, polycyclic hydrocarbons with diamond-like fused structures (nanostructures that can be superimposed upon a diamond lattice) and highly unusual physical and chemical properties. The common formula for the group is C4n+6H4n+12 , n=1 for adamantane, n=2 for diamantane, n=3 for trimentane, n=4 for tetramentane, etc. First 3 compounds of the group do not possess isomeric forms When n>4, the number of isomers increases significantly Chirality occurs first in tetramantane Divided into (a) lower diamondoids, diameter 1-2 nm, and (b) higher diamondoids, diameter > 2 nm In solid state, diamondoids melt at much higher temperatures than other hydrocarbon molecules (adamantane, Tm= oC; diamantane Tm= oC) with the same number of carbon atoms They possess high density and low-strain energy, and are more stable and stiff iso anti skew 14/2/2014 ΔΧ

Diamondoid Applications
NANOPARTICLES Diamondoids exist as physical components in crude oil, discovered in 1933 in Czechoslovakia . Adamantine can be synthesized with zeolites as catalysts Diamondoid Applications Three adamantane derivatives, amantadine (1-adamantaneamine hydrochloride), rimantadine (a-methyl-1-adamantane methylamine hydrochloride) and memantine (1-amino-3,5-dimethyladamantane) have been used as antiviral drugs, e.g., prevention and treatment of influenza A viral infections. Also used in treatment of Parkinson’s disease and inhibition of hepatitis C virus (HCV). Reported to be effective in slowing progression of Alzheimer disease. Half-life of derivatives is long (adamandine h; rimandine h) Monocationic and dicationic adamantane derivatives block AMPA (A-Amino-3-Hydroxy-5-Methyl-4-Isoxazolepropionic Acid; receptor for glutamatefast synaptic transmission), NMDA (N-methyl D-aspartate mimics action of glutamate on receptor ) and 5-HT3 (5-Hydroxytryptamine3; serotonin inhibitor) receptors. Attaching short peptide chains to adamantane makes it possible to design antagonists, e.g., Bradykinin and vasopressin receptor antagonists Adamantane derivatives can be employed as carriers for drug delivery and targeting systems. Due to their high lipophilicity, attachment of diamondoids to drugs with low hydrophobicity would lead to increase of drug solubility in lipid membranes and thus increase in drug uptake 14/2/2014 ΔΧ

Diamondoid Applications
NANOPARTICLES Diamondoid Applications Short peptide sequences, lipids and polysaccharides bound to adamantine and provide a binding site for connection of macromolecular drugs and small molecules. Ex. Brain delivery drugs that can pass Brain Blood Barrier, 1-Adamantyl moiety attached to AZT (azidothymidine) drugs (for AIDS) via ester spacer Adamantane derivatives attached to nucleic acid sequences via an amide linker used for gene delivery (which has problems with low uptake of nucleic acids by cells, and instabilities in blood stream). DNA and RNA exhibit binding selectivity to polyamine adamantane derivatives (DNA and RNA can be stabilized by binding) DNA fragments, because of DNA’s unique feature for site-selective immobilization, are used as linkers in DNA-adamantane-protein nanaostructures. Knowledge of protein folding and conformations in biological systems can help us design nanostructures with desired and predictable conformation in a biomimetic way. Thus, adamantane can be used to construct peptide scaffolding and in synthesis of artificial proteins 14/2/2014 ΔΧ

most popular discovery in Nanotechnology
NANOPARTICLES Buckyballs A Buckyball or Buckminster fullerene molecule, an allotropic form of carbon, is the most popular discovery in Nanotechnology For this discovery, Kroto and Smalley were awarded the 1996 Nobel Prize in Chemistry Buckyballs are Cn clusters with n>20 ( most common C60 , C70 ; later fullerenes C76 , C80 , C240 , etc). Originally made by laser evaporation of graphite. More efficient and less expensive methods for making them found later A molecule should have at least 2 linking groups to be considered as M(olecular) B(uilding) B(lock). The presence of 3 linking groups would lead to 2-D or a tubular structure formation. Presence of 4 or more linking groups lead to a 3-D structure. Molecules with 5 linking groups can form a 3-D solid structure; those with 6 linking groups can be attached in a cubic structure. Functionalization of buckyballs with 6 functional groups (for positional or robotic assembly) is presently possible 14/2/2014 ΔΧ

range, from one to several mm
NANOPARTICLES Carbon Nanotubes discovered by Iijima in He used an electron microscope while studying cathodic material deposition through vaporizing carbon graphite in an electric arc-evaporation reactor under an inert atmosphere during synthesis of fullerenes They appeared to be made of a perfect network of hexagonal graphite rolled up to form a hollow tube The nanotube diameter range, from one to several nm, is much smaller than its length range, from one to several mm Laser ablation chemical vapor deposition joined with metal-catalyzed disproportionation of suitable carbonaceous feedstock are often used to produce carbon nanotubes Carbon nanotubes exhibit unusual photochemical, electronic, thermal and mechanical properties Single-Walled Carbon NanoTubes could behave as metallic, semi-metallic, or semiconductive 1-D objects. They have high tensile strength, ~ 100 times that of steel 14/2/2014 ΔΧ

NANOPARTICLES Cyclodextrins
are cyclic oligosaccharides in the shape of a truncated cone with a relatively hydrophobic interior. They have the ability to form inclusion complexes with a wide range of substrates in aqueous solutions ⇒ encapsulation of drugs for drug delivery Liposomes Spherical synthetic lipid bilayer vesicles, created by dispersion of a phospholipid in aqueous salt solutions. Quite similar to micelles with an internal aqueous compartment Used as carriers for a variety of drugs, small molecules, proteins, nucleotides (has nitrogenous base, sugar and phosphate group), even plasmids (extrachromosomal DNA molecule having ability to replicate independently of chromosomal DNA), to tissues and into cells 14/2/2014 ΔΧ

Monoclonal Antibodies
NANOPARTICLES Monoclonal Antibodies A monoclonal antibody protein molecule consists of four protein chains, two heavy and two light, which are folded to form a Y-shaped structure. The small size, 10 nm in diameter, ensures that intravenously administered monoclonal antibodies can penetrate small capillaries and reach cells in tissues where they are needed. Nanostructures smaller than 20 nm can transit out of blood vessels 14/2/2014 ΔΧ

Nano Thermodynamics and Statistical Mechanics
NANOPARTICLES Nano Thermodynamics and Statistical Mechanics The principles of thermodynamics and statistical mechanics are well defined for macroscopic systems and relations between macroscopic properties and molecular characteristics can be derived Basic concepts in Thermodynamics for macroscopic systems are System & Surroundings State of the System & Equilibrium Process & Reversibility / Irreversibility Energy, Heat and Work Properties (extensive and intensive) & Relations among them Axiomatic Basis, i.e., Laws of Thermodynamics Degrees of Freedom of a System Phase Transitions Basic concepts in Statistical Mechanics for macroscopic systems are Ensembles and Averaging Ergodicity PhaseSpace (coordinates) Ground State Correlated and Interacting Systems 14/2/2014 ΔΧ

Differences between Macroscopic and Nanoscale systems Macroscopic systems can be in any of the three states of matter, gas, liquid, and solid. Nanoscale systems, i.e., isolated nanostructures and their assemblies, small drops, bubbles, clusters, aggregates, nanocrystals, nanowires, etc., are made of condensed (liquid or solid) matter Macroscopic system size: > 1 mm; 1023 particles in 1 cm3 (thermodynamic limit: N → ∞ , V → ∞ , N / V = rN finite) Nanoscale system size: > 1 nm; N = finite Thermodynamic properties, e.g., temperature, for macroscopic systems are well-defined and their fluctuations in time and space are negligible. This is not the case for nanoscale systems the size of which is of the same order as the size of fluctuations. Pressure in nanosystems is not isotropic and must be treated as a tensor Because of the large size fluctuations in properties, static equilibrium cannot be defined in nanosystems as in macroscopic systems. The states of a nanoscale system can only be in dynamic equilibrium Because of the large size fluctuations in properties, over short periods of time, processes in nanosystems cannot be reversible as in macroscopic systems However, over long periods of time, processes in nanosystems are expected to be closer to reversibility than those in macroscopic systems 14/2/2014 ΔΧ

Differences between Macroscopic and Nanoscale systems The definitions of extensive, i.e., system-size-dependent, and intensive , i.e., system-size-independent, properties for macroscopic systems don’t seem to be satisfied in nanosystems Thermodynamic property relations in macroscopic systems are independent of their surroundings (environment); they are environment-dependent for nanosystems, e.g., depend on the geometry, size and walls of the confining structure Energy and mass are mutually interchangeable and the laws of their conservation are combined into the First Law of Thermodynamics which is universal. Energy measures the ability of the system to induce a change which is visible at the scale of the system. Work and heat, on the other hand, are means of energy exchange between the system and its surroundings. Transfer of energy through work or heat is a visible phenomenon in macroscopic systems but not in nanosystems ⇒ conversion of thermal to mechanical energy in nanosystems ??? Entropy definition for macroscopic systems cannot be extended to nanosystems If a macroscopic system is divided into parts, the sum of the entropies of its parts is equal to the entropy of the original system. This is not the case for nanosystems. Macroscopic systems are extensive; nanosystems are nonextensive 14/2/2014 ΔΧ

S L Nano Thermodynamics and Statistical Mechanics
SOPT FOPT S Nano Thermodynamics and Statistical Mechanics Differences between Macroscopic and Nanoscale systems Phase transitions in macroscopic systems are different than in nanosystems In first order phase transitions (FOPT) in macroscopic systems, we observe abrupt changes (discontinuities) in entropy and energy associated with the phases, and physically, there is a distinct separating boundary (meniscus in the case of liquid and vapor transition) apparent between the phases. Second order transitions (SOPT), on the other hand, do not exhibit discontinuities in entropy and energy but in their derivatives, e.g., heat capacity = derivative of energy w.r.t. temperature L L 14/2/2014 ΔΧ

Nanothermodynamics and Statistical Mechanics
Differences between Macroscopic and Nanoscale systems First Order Phase Transitions in macroscopic systems are different than in nanosystems Small system Large system 14/2/2014 ΔΧ

Differences between Macroscopic and Nanoscale systems Phase transitions in nanosystems also include Fragmentation, a real phase transition of the first order in nuclei, e.g., boiling, liquid fragmentation when the ratio of viscous-to-capillary forces exceeds a critical value, and Self-assembly, a process in which a set of components or constituents spontaneously forms an ordered aggregate through their global energy minimization 14/2/2014 ΔΧ

The Laws of Thermodynamics Zeroth Law: establishment of an absolute temperature scale Temperature in a macroscopic system is a well defined property, its fluctuations are negligible and it is a measure of thermal equilibrium or lack of it In nanosystems, space and time fluctuations cannot be neglected In view of temporal scale ~ N (number of particles) spatial scale ~ N logN, accuracy scale ~ N7 to N! Fluctuations in nanosystems are not yet correlated to their properties Customary in Statistical Mechanics to express fluctuations in properties in terms of distribution functions or as derivatives of other properties First Law: combination of conservation of mass and energy, both of which are interchangeable In macroscopic systems, reversibility is equivalent to thermal equilibrium Nanosystems may be reversible but not in thermal equilibrium Similar to macro systems, nanosystems can be open, closed, adiabatic, isothermal, isochoric (constant volume) or isobaric (constant pressure) 14/2/2014 ΔΧ

The Laws of Thermodynamics First Law: combination of conservation of mass and energy, both of which are interchangeable dE = dQ + dW (1) Macroscopic systems: dQ = cdT dW = p dV (2a) Nanosystems: dW = tij deij dij V (2b) (tij external stress tensor; eij deformation tensor; dij Kronecker delta, dij = 1 iff i = j) Second Law: For a closed system entropy production is always nonnegative dS – dQ / Tex > 0 (3) Applies both to macroscopic and nano systems, if the concept of entropy is redefined to include nonextensive systems Boltzmann defined the entropy of the systems as S = kB lnW (4) where W is the number of possible configurations of a system of particles consistent with the properties of the system. The Boltzmann entropy has two important features: Non-decrease, i.e. if no heat enters or leaves the system its entropy cannot decrease, Additivity, i.e, the entropy of systems taken together is the sum of their individual entropies 14/2/2014 ΔΧ

The Laws of Thermodynamics Entropy The Boltzmann entropy, otherwise called entropy of a coarse-grain distribution is for a macroscopic state over a statistical ensemble with equiprobability. For non- equiprobability, Gibbs consider a system of a large number of particles (e.g., molecules), N, distributed in W classes (e.g., energy states) with non equal probability. If pi = Wi / W (SWi = W), is the probability of the distribution of i particles in the system, the entropy of the system is given by the Boltzmann-Gibbs formula With equiprobability, pi = 1 / W, Eq.(5) reduces to Eq.(4), i.e., the Gibbs-defined entropy becomes the Boltzmann-defined entropy The problem with these definitions of entropy is that they apply to homogeneous systems with a large number of particles. i.e., systems at the thermodynamic limit. For those systems, the notions of extensivity (additivity) and intensivitiy (averaging) of thermodynamic properties also apply Nanosystems, consist of a finite number of particles and their spatial scale is of the same order of magnitude as the correlation length for their thermodynamic properties 14/2/2014 ΔΧ

The Laws of Thermodynamics Entropy A new formulation of entropy to include extensive (e.g., macroscopic) as well nonextensive (e.g., nanosystems) was introduced by Tsallis (1988) We need to start with the definition of homogeneous function of degree l f(tx1 , tx2 , tx3 , …, txr) = tl f(x1 , x2 , x3 , …, xr) (6) and Euler’s theorem x1(∂ f / ∂ x1 ) + x2(∂ f / ∂ x2 ) + … + xr(∂ f / ∂ xr ) = l f (7) A thermodynamic variable is intensive when l = 0 , and extensive if l = 1 Tsallis (1988) expressed the entropy as 14/2/2014 ΔΧ

The Laws of Thermodynamics Entropy q is called entropic index; q >1 represents frequent events; q < 1 represents rare events (piq < pi ) q is also called extensivity index; q >1 represents superextensivity (superadditivity), q = 1 represents extensivity (additivity of entropy), and q < 1 represents subextensivity (subadditivity) Depending on the entropic index q, Eq.(8) ⇒ For q > 0, Sq > 0, i.e., entropy is always positive For q→ 1, , i.e., the Gibbs-Boltzmann formula For q = 1, S1 = k lnW , i.e., the Boltzmann formula Also For equiprobability, i.e., pi = 1 / W, Eq.(8) ⇒ 2. In the case of certainty, i.e., all but one probabilities vanish, p1 =1, pi = 0 for i>1, Eq.(8) ⇒ entropy is zero, Sq = 0 14/2/2014 ΔΧ

The Laws of Thermodynamics Entropy When two (statistically) independent systems A and B join, Eq.(8) ⇒ If the set of possibilities W is arbitrarily separated into two subsets WL and WM (WL+WM = W), Eq.(8) ⇒ 14/2/2014 ΔΧ

The Laws of Thermodynamics Entropy The Tsallis entropy has two more additional properties: Can be tested under translation as well as under dilation The Boltzmann-Gibbs formula satisfies Eq.(8) ⇒ Is always convex, when q<0, and always concave, when q > 0 This is not the case for other definitions of entropy, e.g., Renyi definition of entrolpy for fractal geometries does not have this property for all values of q 14/2/2014 ΔΧ

Microcanonical Ensemble for Nonextensive Systems Consider a nanosystem at fixed N, V and T, isolated (no energy exchange) from its surroundings . The entropy of this system, which is given by the Tsallis formula, becomes maximum when the probabilities pi are all equal. If W = W (e ) is the number of states with energies centered around e, then pi = 1 / W . For this system, W is called degeneracy and is related to entropy through When the system is at equilibrium, dU = T dS – p dV (12) From (11) and (12) ⇒ i.e., k T W q ∂W is related to the energy change dU. Eq.(13) is a fundamental equation of Statistical Mechanics for nonextensive systems 14/2/2014 ΔΧ

Canonical Ensemble for Nonextensive Systems Consider now a nanosystem at fixed N, V and T, exchanging energy with its surroundings. We’d like to maximize the entropy of this system, under the constraint that the average energy of the system is constant For a nonextensive system, the internal energy constraint is The other constraint on the system is We employ the method of Lagrange multipliers to minimize the function where b has units of inverse temperature and q is dimensionless. Minimization ⇒ 14/2/2014 ΔΧ

Canonical Ensemble for Nonextensive Systems Consider now a nanosystem at fixed N, V and T, exchanging energy with its surroundings. We’d like to maximize the entropy of this system, under the constraint that the average energy of the system is constant Eq.(16) ⇒ where Zq is the canonical ensemble partition function for nonextensive systems Intermolecular Potentials The database of intermolecular potentials of simple fluids and solids to be used in predicting properties of macroscopic systems is rather complete. These potentials cannot be used for predictions of properties of nanosystems The nature and role of intermolecular interactions, needed for formulation of intermolecular potentials, in nanostructures is challenging and not well understood Direct measurements of interparticle force vs. distance data and quantum mechanical ab initio calculations are needed to generate intermolecular poltentials for nanosystems consisting of a few hundred to a few thousand particles 14/2/2014 ΔΧ

Simulation Methods for Nanosystems
Monte Carlo (MC) simulations generally follow the evolution of a system in which change proceeds not in a predefined but rather a random manner Considering the fact that there are several thousands of atoms or molecules in a 10 nm cube, there are significant challenges in using MC techniques to predict the properties of nanosystems Molecular Dynamics simulations consist of the numerical solution of Newton’s equation of motion for a system of particles (atoms, molecules, aggregates, etc.) to obtain information about their time-dependent properties. MD are an ideal to relate the collective dynamics of a finite number of particles in nanosystems to single-particle Dynamics Optimization methods help us achieve several goals, (a) to develop a controlled simulation scheme to obtain different nanostructures, (b) to study the most stable conditions for nanosystems 14/2/2014 ΔΧ

Experimental Tools in Nanotechnology
S(canning) T(unneling) M(icroscope) discovered by Binning and Rohrer at IBM Zurich (Binning and Rohrer received the Nobel prize in 1986). It allows imaging of solid surfaces with atomic scale precision. Its operation is based on tunneling current which is initiated when a tip mounted on a piezoelectric scanner approaches a conducting surface at a distance of 1 nm It was followed by the S(canning) P(robe) M(icroscope) and the A(tomi) F(orce) M(icroscope) The AFM enables one to study non-conducting surfaces, as it scans van der Waals forces with its “atomic” tips 14/2/2014 ΔΧ

Experimental Tools in Nanotechnology
Both the STM and AFT are used for positional or robotic assembly, the ultimate goal of which is to build with molecules nanostructures in the same way we build macroscopic structures with macroscopic building blocks, e.g., bricks If we achieve sufficient control over the positioning of the right molecules in the right places, we may be able to alter materials to those with desired properties Assemblers or positional devices are made to position and hold Molecular Building Blocks in positional assemblies. The most basic form of an assembler is the Stewart Platform, a rigid and flexible polyhedron with all its faces being triangular. Two of the faces, designated as base and platform, and are connected by six struts of varying length. Changing the lengths of the struts changes the orientation and position of the platform with respect to the base To restore MBBs to their desired positions, assemblers utilize a spring force, F = s x where x is the distance between the original and the desired position of the MBB and s is the stiffness of the spring The positional uncertainty (mean error in position), e, is given by e2 = kB T / s The STM has s ~ 10 nm, hence, e ~ 0.02 nm 14/2/2014 ΔΧ

interface, and (2)occurring in the bulk of a fluid phase
Self-Assembly This is a remarkable property of systems at the nanoscale. It is believed to be the basic process that led up to the evolution of the biological world from inanimate matter. There two kinds of self-assembly, (1) occurring on a fluid / solid interface, and (2)occurring in the bulk of a fluid phase An example of self assembly occurring in the bulk of a fluid phase is the micellization of asphaltene macromolecules, followed by self assembly of micelles into micelle- coacervates Asphaltene Micelle Micelle Coacervate Self-assembly on a fluid / solid interface involves immobilization molecules in the fluid as an assembly on a solid surface. It can be achieved via covalent or noncovalent interactions between molecules in the fluid and the molecules of the solid surface 14/2/2014 ΔΧ

biomolecule by formation of a complex with metal ions)
Self-Assembly Covalent bonds, e.g., between a sulfide and a noble metal, produce irreversible, thus stable, immobilization at all stages. Immobilization through noncovalent bonds is reversible, thus unstable, at the onset of the self assembly process but it achieves stability upon appreciable growth of the assembly. Some common noncovalent bonds involve (1) affinity coupling via antibodies (glycoproteins produced by the immune system in response to invasion of foreign substances called antigens), (2) affinity coupling by biotin-streptavidin (avidin, a glycoprotein, combines with Biotin, a vitamin B; STreptaVidin is a tetrameric protein which has four binding sites for biotin), and (3) Immobilized Metal Ion Complexation (non-covalent binding of biomolecule by formation of a complex with metal ions) Divalent metal ion 14/2/2014 ΔΧ

ΝΑΝΟΣΥΝΘΕΤΑ ΠΟΛΥΜΕΡΙΚΗΣ ΜΗΤΡΑΣ
ΝΑΝΟΣΥΝΘΕΤΑ ΠΟΛΥΜΕΡΙΚΗΣ ΜΗΤΡΑΣ Mήτρα: Άμορφο πολυμερές Πληρωτικό: Σφαιρικά νανοσωματίδια, ακτίνας Rn  1 nm Κλάσμα όγκου: Συγκέντρωση σωματιδίων: Διεπιφάνεια ανά μονάδα όγκου: Area of American football field = square meters. 10^6 m^-1 equals 187 American football fields per cubic meter. Payne (decrease of the dynamic moduli at large strain amplitudes) and Mullins (hysteretic stress-softening of filled rubbers subjected to large cyclic deformations) effects. Απόσταση επιφανειών γειτον. σωματιδίων: Γυροσκοπική ακτίνα αλυσίδων: 14/2/2014 ΔΧ

ΚΛΙΜΑΚΕΣ ΜΗΚΟΥΣ ΚΑΙ ΧΡΟΝΟΥ ΣΤΑ ΠΟΛΥΜΕΡΗ
ΚΛΙΜΑΚΕΣ ΜΗΚΟΥΣ ΚΑΙ ΧΡΟΝΟΥ ΣΤΑ ΠΟΛΥΜΕΡΗ Μήκη δεσμών, ατομικές ακτίνες ~ 0.1 nm Μήκος στατιστικού τμήματος (Kuhn) b ~ 1 nm Γυροσκοπική ακτίνα αλυσίδας ~ 10 nm Μέγεθος περιοχών σε φασικά διαχω-ρισμένο υλικό ~ 1 m Δονητικές κινήσεις 10-14 s Μεταπτώσεις διαμόρφωσης 10-11 s Μέγιστος χρόνος χα-λάρωσης 10-3 s Διαχωρισμός σε φάσεις/ μικροφάσεις  1 s Φυσική γήρανση (Τ < Τg-20οC)  1 yr Τήγμα Υαλώδης κατάσταση 14/2/2014 ΔΧ

IΕΡΑΡΧΙΚΗ ΣΤΡΑΤΗΓΙΚΗ ΓΙΑ ΤΗΝ ΥΠΟΛΟΓΙΣΤΙΚΗ ΕΠΙΣΤΗΜΗ ΚΑΙ ΤΕΧΝΙΚΗ ΤΩΝ ΥΛΙΚΩΝ
Επεξεργασία Μορφολογία Μικροδομή Αδροποι- ημένες παράμετροιαλληλεπί-δρασης π.χ. Σταθερές ρυθμού, συντελε- στές τριβής Μεσοσκο- πικές Προσομοι-ώσεις Κινητική Monte Carlo, Θεωρίες αυτo-συνεπούς πεδίου, Dynamic density functional theory, Dissipative particle dynamics Ιδιότητες Υλικού Καταστ. Εξισώσεις, Υλικές Σχέσεις Μοριακή οργάνωση και κίνηση Μικροσκοπικοί μηχανισμοί υπεύθυνοι για μακροσκοπική συμπεριφορά Μοριακές Προσομοι-ώσεις, Εφαρμ. Στατιστική Μηχανική π.χ. Monte Carlo, Μοριακή δυναμική, Μοριακή μηχανική, Θεωρία μεταβατικών καταστάσεων Μακροσκο-πικοί Υπολογισμοί, Σχεδιασμός π.χ. Εφαρμοσμένη θερμοδυναμική, Φαινόμενα μεταφοράς, Χημική κινητική, Μηχανική του συνεχούς, Ηλεκτρομαγνη- τική θεωρία Επιδόσεις υλικού υπό συγκε-κριμένες συνθήκες εφαρμογής Κβαντο- μηχανι-κοί Υπολο-γισμοί Μοριακή γεωμετρία, Ηλεκτρο- νικές ιδιότητες Πεδία δυνάμεων μοριακών αλληλεπι-δράσεων χημική σύσταση Οι υπολογισμοί κατευθύνουν και συμπληρώνουν πειραματικές προσπάθειες για την ανάπτυξη νέων υλικών, διεργασιών και προϊόντων. 14/2/2014 ΔΧ

NAΝΟΣΥΝΘΕΤΑ: EΠΙΠΕΔΑ ΜΟΝΤΕΛΟΠΟΙΗΣΗΣ
Ατομιστικό (~10-10 m) Προσομοιώσεις MD Λεπτομέρειες δομής, τοπική δυναμική Δυναμικά Hamaker για αλληλεπιδράσεις νανοσωματιδίου-νανοσωματιδίου και νανοσωματιδίου–πολυμ. τμήματος Αδροποιημένο (~10-9 m) Monte Carlo μεταβλητής συνδετικότητας Καλά εξισορροπημένες διαμορφώσεις σε συστήματα μακριών αλυσίδων Εμπνευσμένο από τη θεωρία πεδίου (FTiMC) (~10-7 m) Προσομοιώσεις Monte Carlo με απλοποιημένη Χαμιλτονιανή Μεγάλα νανοσωματίδια, πολλά νανοσωματίδια 14/2/2014 ΔΧ

ΕΞΙΣΟΡΡΟΠΗΣΗ ΠΥΚΝΩΝ ΠΟΛΥΜΕΡΙΚΩΝ ΦΑΣΕΩΝ :MONTE CARLO
Κινήσεις μεμονωμένων τμημάτων: Περιστροφή εσωτερικού ατόμου (FLIP) Ερπυσμός (REPT) Τοπικές ανακατατάξεις διαμόρφωσης: Μεροληψία απεικόνισης (CB) Συντονισμένη περιστροφή (CONROT) [1] Μεταβολές συνδετικότητας: Διπλή γεφύρωση (DB) [2] Ενδομοριακή διπλή αναγεφύρωση (IDR) [2] Διακύμανση όγκου FLIP REPT CB CONROT new chain jch’ is formed new chain ich’ is formed DB IDR L.R. Dodd, T.D. Boone, DNT, Mol. Phys., 78, 961 (1993) N. Karayiannis, V.G. Mavrantzas , DNT, Phys. Rev. Lett. 88, (2002) 14/2/2014 ΔΧ

ΕΞΙΣΟΡΡΟΠΗΣΗ ΠΟΛΥΣΤΥΡΕΝΙΟΥ (PS)
Rg R αυξάνει μονότονα προς μία ασυμπτωτική τιμή. Εξαιρετική συμφωνία με σκέδαση νετρονίων σε μικρές γωνίες (SANS). T. Spyriouni, C. Tzoumanekas, DNT, F. Müller-Plathe, G. Milano, Macromolecules 40, 3876 (2007) G. G. Vogiatzis and DNT, Macromolecules 47, (2014), in press. DOI: /ma402214r 14/2/2014 ΔΧ

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αδροποιημένο μοντέλο ατομιστικό από αντίστρ. απεικόνιση Van der Waals diameter of fullerene: approximately 1.01 nm. At coarse-grained level, represented as spherical shell. Πεδίο δυνάμεων ενοποιημένων ατόμων για πολυστυρένιο: A.V. Lyulin, M.A.J. Michels, Macromolecules 35, 1463 (2002). Πεδίο δυνάμεων C60: S.L. Mayo, B.D. Olafson, W.A. Goddard, J. Phys. Chem. 94, 8897 (1990); L.A. Girifalco, J. Phys. Chem. 96, 858 (1992). 14/2/2014 ΔΧ

ΔΥΝΑΜΙΚΗ ΤΜΗΜΑΤΩΝ: ΤΗΓΜΑ PS συγκρινόμενο με ΝΑΝΟΣΥΝΘΕΤΟ PS-C60
Προσαρμογή σε τροποποιημένη έκφραση Kohlrausch – Williams – Watts (mKWW): Χρόνος συσχέτισης για τμηματική κίνηση δίνεται από το ολοκλήρωμα: 14/2/2014 ΔΧ G. G. Vogiatzis and DNT, Macromolecules 47, (2014), in press. DOI: /ma402214r

Προσαρμογή εμπειρικής εξίσωσης Williams–Landel–Ferry (WLF)[1]: Συντελεστές WLF σε πολύ καλή συμφωνία με το πείραμα [2]. Πειραματικό σημείο υαλώδους μετάπτωσης ατακτ. πολυστυρενίου: – K [3]. Σύστημα πολυστυρενίου – C60 επιδεικνύει λίγο υψηλότερο Tg από ό,τι το καθαρό πολυστυρένιο. Ανύψωση του Tg κατά 1 Κ έχει αναφερθεί από τους Green και συνεργάτες [4]. Fit τg, Tg, C1, C2, ensuring τg is realistic, or Use universal C1, C2 from the literature and fit τg, Tg Get very similar results. J.D. Ferry, Viscoelastic Properties of Polymers, 3rd ed., Wiley, New York, 1980. S.K. Kumar, R.H. Colby, S.H. Anastasiadis, G. Fytas, J. Chem. Phys. 105, 3777 (1996). J. Hintermeyer, A. Herrmann, R. Kahlau, C. Goiceanu, E.A. Rössler, Macromolecules 41, 9335 (2008). J.M. Kropka, V.G. Sakai, P.F. Green, Nano Lett. 8, 1061 (2008). 14/2/2014 ΔΧ

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Αλυσίδες: τυχαίοι περίπατοι από στατιστικά τμήματα Kuhn. Κάθε τμήμα Kuhn αντιστοιχεί σε 7 μονομερή PS. Δεσμικές αλληλεπιδράσεις λαμβάνονται υπόψη μέσω του σταθερού μήκους του τμήματος Kuhn (b=18.3 Å). Μή δεσμικές αλληλεπιδράσεις: Πολυμερούς-πολυμερούς (όπως στη θεωρία πεδίου) Πολυμερούς-νανοσωματιδίου (ολοκλήρωση Hamaker των ατομιστικών δυναμικών) Νανοσωματιδίου-νανοσωματιδίου (Hamaker) Τοπική πυκνότητα πολυμερούς παρακολουθείται χρησιμοποιώντας τρισδιάστατο πλέγμα. Απεικόνιση αλυσίδων και νανοσωμα τιδίων μεταβάλλεται με κινήσεις MC. Χρησιμοποιούνται και μετακινήσεις του πλέγματος. 60 nm 14/2/2014 ΔΧ

G.G. Vogiatzis and DNT Macromolecules 46, 4670 (2013)
14/2/2014 G.G. Vogiatzis and DNT Macromolecules 46, 4670 (2013) ΔΧ

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- Silica nanoparticles, Rn=8 nm Μήτρα ατακτικού πολυστυρενίου Αραιή διασπορά Mg= 20kg/mol Mf=100kg/mol Ακτινική κατανομή πυκνότητας, Μεταβολές στη θέση και το πάχος της περιοχής αλληλεπικάλυψης εμφυτευμένων και ελεύθερων αλυσίδων συναρτήσει: Μοριακής μάζας εμφυτευμένων αλυσίδων Επιφανειακής πυκνότητας εμφύτευσης 14/2/2014 G.G. Vogiatzis and DNT Macromolecules 46, 4670 (2013) ΔΧ

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G.G. Vogiatzis and DNT, Macromolecules 46, 4670 (2013) Καλή συμφωνία με πειράματα σκέδασης νετρονίων σε μικρές γωνίες (SANS).[1] Καλή συμφωνία με θεωρία Daoud-Cotton: [2] SiO2 σε PS, Rn=8 nm Mf=100 kg/mol Mathias Meyer, Ph. D. thesis, Westfälische Wilhelms-Universität Münster, 2012. M. Daoud, J. Cotton, J. Phys. France 43, 531 (1982). 14/2/2014 ΔΧ

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SiO2 in PS, Rn=13 nm Mg = 25 kg/mol, σ = 0.5 nm-2 SiO2 in PS, Rn=8 nm Mg = 20 kg/mol, Mf = 100 kg/mol Πειράματα: C. Chevigny, J. Jestin, D. Gigmes, R. Schweins, E. Di-Cola, F. Dalmas, D. Bertin, F. Boué, Macromolecules, 43, (2010). 14/2/2014 ΔΧ

ΔΙΑΧΥΤΟΤΗΤΑ ΑΡΩΜΑΤΙΚΩΝ ΜΟΡΙΩΝ ΣΤΟ ΖΕΟΛΙΘΟ ΣΙΛΙΚΑΛΙΤΗ-1
ΔΙΑΧΥΤΟΤΗΤΑ ΑΡΩΜΑΤΙΚΩΝ ΜΟΡΙΩΝ ΣΤΟ ΖΕΟΛΙΘΟ ΣΙΛΙΚΑΛΙΤΗ-1 Ζεόλιθοι MFI (Mobil Five): ευρεία χρήση στην πετροχημική βιομηχανία ZSM-5: Καταλύτης για μετατροπές αλκυλαρωματικών μορίων Τερεφθαλικό οξύ Οξείδωση PET Σιλικαλίτης-1: Μοριακό κόσκινο για διαχωρισμό π-ξυλολίου από άλλα μόρια στη νάφθα, όπως βενζόλιο, τολουόλιο, ο- και m-ξυλόλιο. Ο Σιλικαλίτης-1 είναι η καθαρά πυριτική μορφή του ZSM-5. ZSM-5: Καταλύτης για μετατροπή μεθανόλης σε βενζίνη. 14/2/2014 ΔΧ

ΣΙΛΙΚΑΛΙΤΗΣ-1 x y z a b c Μοναδιαία κυψελίδα Si96O192 Pnma a = Å b = Å c = Å (δείχνονται  3  3 κυψελίδες) Αποτελείται από τετράεδρα SiO4 που μοιράζονται κορυφές. Ευθύγραμμα (S) και ημιτονοειδή (Z) κανάλια διαμέτρου ≈ 5.5 Å Περιοχές διασταύρωσης καναλιών (I) διαμέτρου ≈ 9 Å 14/2/2014 ΔΧ

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x z y Αρωματικό μόριο βρίσκεται υπό ισχυρό περιορισμό στα κανάλια. Προτιμά να εντοπίζεται σε ενεργειακά ευνοϊκές «θέσεις ρόφησης» και σπάνια εκτελεί άλματα μεταξύ αυτών των θέσεων. Πειραματικός συντελεστής αυτοδιάχυσης, βενζόλιο/Σιλικαλίτης-1 (300 K) H. Jobic. M. Bée, S. Pouget J. Phys. Chem.B 104, 7130 (2000). Τόσο χαμηλές διαχυτότητες δεν μπορούν να υπολογιστούν με MD. 14/2/2014 ΔΧ 51

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Σταθερά ρυθμού kij : Πιθανότητα ανά μονάδα χρόνου να επιτελεστεί μετάβαση προς την κατάσταση j ,προϋποτιθεμένου ότι το σύστημα βρίσκεται αρχικά στην κατάσταση i. i j state διαχωριστική επιφάνεια μεταξύ καταστάσεων i και j Ελεύθερη ενέργεια ως συνάρτηση των βαθμών ελευθερίας r που συμμετέχουν στη μετάβαση. TST: Μπορεί να υπολογιστεί ένας δυναμικός παράγοντας διόρθωσης για το kij, που ενσωματώνει την επίπτωση φαινομένων αναδιασταύρωσης της διαχωριστικής επιφάνειας, μέσω σύντομων προσομοιώσεων MD που ξεκινούν από τη διαχωριστική επιφάνεια. 14/2/2014 ΔΧ J. Kärger, D. Ruthven, DNT, Diffusion in Nanoporous Materials, Volume 1, Wiley-VCH, 2012, Chap.9 52

Προσδιορισμός A(r): Το ροφημένο μόριο εξαναγκάζεται να δειγματοληπτήσει μικρές αλληλεπικαλυπτόμενες περιοχές μέσα στους πόρους. Χρήση MD παρουσία περιοριστικών «τοίχων». Length of a confined simulation: 15 ns. P.D. Kolokathis, E. Pantatosaki, C.-A. Gatsiou, H. Jobic, G.K. Papadopoulos, DNT Molecular Simulation 40, (2014). 14/2/2014 ΔΧ

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Θερμοκρασία Σταθερές ρυθμού TST (s-1) 300K 465K 555K I → S 5.24  105 3.314 107 1.13  108 S → I 1.887  107 1.09  109 3.72  109 I → Zb 9.382  104 9.51  106 3.295  107 Zb → I 1.617  107 4.97  108 1.41  109 I → Za 1.76 106 6.18 107 2.01  108 Za → I 3.04  108 3.22  109 8.66  109 14/2/2014 Δυναμικοί παράγοντες διόρθωσης: 0.81 έως 0.91 ΔΧ 54

Bενζόλιο και π-ξυλόλιο στο Σιλικαλίτη-1, T=300 K
Μονοδιάστατα προφίλ ελεύθερης ενέργειας στο ευθύγραμμο κανάλι: -6 -12 S I S Κάθετα προς δακτύλιο Μίσχος μεθυλίου (κύριος άξονας) 10.5 X(Å) 9.5 ξ(Å) 2 Κατανομή ελεύθερης ενέργειας προσανατολισμού σε διάφορες θέσεις: Χρωματικός κώδικας 14/2/2014 ΔΧ

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Εξίσωση Master για τη χρονική εξέλιξη των πιθανοτήτων κατάληψης των καταστάσεων: Άνυσμα πιθανοτήτων κατάληψης καταστάσεων Πίνακας σταθερών ρυθμού Ld Cell 1 Cell 2 Cell 2ν -1 Cell 2ν Cell 2ν-1 +1 Cell 2ν-1 Επίλυση της εξίσωσης Master μέσω αναδρομικής ελάττωσης της διαστατικότητας (MESoRReD) σε σύστημα 2ν μοναδιαίων κυψελίδων με περιοδικές οριακές συνθήκες στα άκρα: 14/2/2014 P.D. Kolokathis and DNT J. Chem. Phys 137, (2012) ΔΧ 56

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ΣΥΝΤΕΛΕΣΤΕΣ ΑΥΤΟΔΙΑΧΥΣΗΣ ΣΤΟ ΣΙΛΙΚΑΛΙΤΗ-1 Τεχνική Neutron Spin-Echo Προσομοιώσεις 14/2/2014 ΔΧ

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 Η μοριακή προτυποποίηση και προσομοίωση μπορούν να βοηθήσουν σημαντικά στην κατανόηση των ιδιοτήτων νανοδομημένων υλικών.  Η πολλαπλότητα των κλιμάκων μήκους και χρόνου επιβάλλει την ανάπτυξη στρατηγικών προσομοίωσης σε πολλές κλίμακες.  Προσομοιώσεις Μonte Carlo μεταβλητής συνδετικότητας, μαζί με αδροποίηση και αντίστροφη απεικόνιση, εξισορροπούν πλήρως πολυμερικά τήγματα μεγάλου μοριακού βάρους.  Η επίπτωση νανοσωματιδίων στην τμηματική δυναμική νανοσυνθέτων C60-πολυστυρενίου ποσοτικοποιείται με προσομοιώσεις MD.  Προσομοιώσεις Monte Carlo εμπνευσμένες από τη θεωρία πεδίου προβλέπουν τη διαμόρφωση αλυσίδων εμφυτευμένων σε νανοσωματίδια ακτίνων 8 και 13 nm μέσα σε τήγματα πολυστυρενίου.  Υπολογισμός των προφίλ ελεύθερης ενέργειας κατά μήκος των πόρων, σε συνδυασμό με θεωρία μεταβατικών καταστάσεων και MESoRReD, δίνει εκτιμήσεις διαχυτοτήτων αρωματικών μορίων στο Σιλικαλίτη-1.  Το π-ξυλόλιο διαχέεται ταχύτερα από ό,τι το βενζόλιο μέσα στο Σιλικαλίτη-1. Η δυνατότητα αναπροσανατολισμού στις διασταυρώσεις των καναλιών δημιουργεί υψηλότερο φράγμα ελεύθερης ενέργειας εντροπικής προέλευσης για το βενζόλιο. 14/2/2014 ΔΧ

Είναι επίσηςγνωστά ως Φαρμακευτικά βασισμένα στη Βιοτεχνολογία
Βιοφαρμακευτικά Είναι επίσηςγνωστά ως Φαρμακευτικά βασισμένα στη Βιοτεχνολογία Από το 1980 περισσότερα από 90 ανασυνδυασμένα (recombinant) φάρμακα έχουν εγκριθεί και 369 έχουν σειρά για έγκριση (are in the pipeline). H πλειονότητα αυτών των φαρμάκων είναι ανασυνδυασμένες εκδοχές πρωτεϊνών που υπάρχουν in vivo Χρησιμοποιούνται (1) για Θεραπεία αντικατάστασης (replacement therapy), e.g., insulin and growth hormone, (2) σαν συμπλήρωμα (supplement) την αύξηση της επίδρασης ενδογενών πρωτεϊνών, (3) για να ενεργοποιήσουν υποδοχείς (receptors) που είναι σε ιούς υπό στόχευση, (4) σαν θεραπευτικά αντισώματα (antibodies), (5) σαν μεταφορείς σε εξειδικευμένη θέση τοξικών φαρμάκων, και (6) σαν παράγοντες απεικόνισης Χρήση θεραπευτικών πρωτεϊνών για να αντικαταστήσουν ή να συμπληρώσουν μόρια ενδογενών πρωτεϊνών έχει εδώ και καιρό καθιερωθεί σαν θεραπευτική αγωγή (modality) για ασθένειες όπως ο διαβήτης, ανεπάρκεια αυξητικής ορμόνης (growth hormone deficiency), και αιμοφιλία. Η θεραπεία συχνά περιορίζονταν από (1) αντιδράσεις του ανοσιοποιητικού συστήματος (immunlogical responses) σε μόρια ετερόλογων πρωτεϊνών, (2) μόλυνση (contamination) πρωτεϊνών που εξάγονται από πολύπλοκες φυσικές πηγές, και (3) δυσκολία and έξοδα για ανάκτηση χρήσιμων ποσοτήτων υλικού με ανθρώπινη και ζωϊκή προέλευση Σήμερα οι τεχνικές ανασυνδυασμένου DNA και υβριδώματος (hybridoma) είναι ικανές να παράγουν μόρια με καλά καθορισμένη χημική σύσταση και σε μέσα κυτταροκαλλιέργειας (cell culture media) που μπορεί να ελεγχούν ενδελεχώς. 14/2/2014 ΔΧ

Biopharmaceuticals DNA, because of its role in the replication of new structures and characteristics of living organisms, has widespread use in recapitulating, via viral or non-viral vectors, both desirable and undesirable characteristics of a species to achieve characteristic change or to counteract effects caused by genetic or imposed disorders that affect cellular or organismal processes. Recombinant DNA is a form of artificial DNA that is engineered through the combination or insertion of one or more DNA strands, thereby combining DNA sequences that would not normally occur together. In terms of genetic modification, recombinant DNA is produced through the addition of relevant DNA into an existing organismal genome, such as the plasmid of bacteria, to code for or alter different traits for a specific purpose, such as immunity. Genetic modification differs from genetic recombination, in that it does not occur through processes within the cell or ribosome, but is exclusively engineered. The recombinant DNA technique was engineered by Stanley Norman Cohen and Herbert Boyer in They published their findings in a 1974 which described a technique to isolate and amplify genes or DNA segments and insert them into another cell with precision, creating a transgenic bacterium. Recombinant DNA technology was made possible by the discovery of restriction endonucleases by Werner Arber, Daniel Nathan, and Hamilton Smith, for which they received the 1978 Nobel Prize in Medicine 14/2/2014 ΔΧ

Biopharmaceuticals Antibodies are highly specific proteins that bind to antigens, and produced by stimulated B-lymphocytes, each of which secretes antibodies of only one specificity. Polyclonal antibodies are mixtures of many different antibodies of many different specificities, produced in vivo. Monoclonal antibodies are produced from a mixture of antibodies, by isolating B-lymphocytes in tissue culture, growing the isolated B-lymphocytes, and producing clones of identical B-cells. Problems encountered with this procedure are that isolated B-lymphocytes will often not remain viable in culture, don't divide very rapidly, and produce very little antibody. If we combine the properties of a B-lymphocyte, which produces antibodies, and a tumor cell, which exhibits tissue viability and rapid cell division, i.e., we “fuse” a B-lymphocyte and a tumor cell into one cell, this “hybrid" cell continues to grow indefinitely in culture, and undergoes rapid cell division (produces one "clone"). In the same culture, antibody production by one [mono] clone is initiated and large amounts of antibodies can be produced. The hybridoma technique can manipulate genetics of isolated lymphocytes, can select antibodies with certain biological properties, and is much less expensive than maintaining animals that produce antibodies 14/2/2014 ΔΧ

Biopharmaceuticals Recombinant DNA technology or Genetic Engineering involves the isolation of cellular DNA fragments that code for proteins of therapeutic interest DNA fragments are inserted into cellular hosts that, by normal replication, make multiple copies of the original sequence. This amplification of the original sequence enables the production of useful quantities of protein in the cell culture medium. By using established biochemical purification techniques, the protein may be isolated in highly purified form Monoclonal antibodies were one of the first proteins, derived from recombinant DNA technology, administered to humans. In the early days, monoclonal antibodies were derived from murine strains using hybridoma techniques. Administration of the murine-derived antibodies elicited a human immune response with the production of endogenous antibodies to neutralize the administered antibody and a short serum half life for the latter. With Genetic Engineering tools developed later, monoclonal antibodies expressing greater sequence homology to endogenous antibodies have been produced. Two main technologies have emerged for production of fully “humanized” proteins, (1) from transgenic animals, and (2) from phage display 14/2/2014 ΔΧ

Biopharmaceuticals The most efficient and popular expression systems for recombinantly derived biopharmaceuticals are mammalian cell lines such as Chinese Hamster Ovary and mouse myeloma cells (NSO) Prokaryotic cell lines derived from Escherichia coli and yeast strains are also used to express proteins of therapeutic interest Mammalian expression systems, as opposed to those of nonmammalian origin, have the biochemical machinery to glycosylate proteins during posttranslational biosynthetic events. Recombinantly derived monoclonal antibodies require glycosylation to exhibit a complete spectrum of biological activity. Glycosylation of recombinant antibodies can be controlled during fermentation by adjusting carbohydrate levels in the cell culture where cells are growing. Fermentation conditions for these cell types can also be adapted to express high titers of the therapeutic antibody, at > 1 g/L, which is important for developing efficient and economic processes One can enhance overall product yield of therapeutic proteins by using transgenic animals, e.g., sheep, goats, or pigs Specialized serum-free cell nutritional media, free of bovine-derived products, to remove any possibility of contamination by trace levels of Bovine Spongiform Encephalopathy (BSE), have been developed 14/2/2014 ΔΧ

Defined only in terms of its properties:
Some Biology What is Life? Defined only in terms of its properties: Cellular organization, assemblages of molecules enclosed within membranes, Sensitivity, ability to respond to stimuli, Growth, assimilate energy and use it to grow (metabolism), Development, systematic gene-directed changes as organisms grow and mature, Reproduction, passing traits to next generation, Regulation, organisms have mechanisms that regulate internal processes, Homeostasis, organisms maintain relatively constant internal conditions, different from their environment Building blocks of life Molecules → Cells → Tissues → Organs → Organisms Cell - smallest living entity, basic unit of organization of all organisms; contains DNA, the hereditary molecule; enclosed and separated from its surroundings by plasma membrane 14/2/2014 ΔΧ

Cells are of two types, (1) procaryotic, i. e
Cells are of two types, (1) procaryotic, i.e., cells that have no nuclear membrane, no organelles, a single chromosome (DNA molecule), and (2) eucaryotic, i.e., cells that have complex internal structure, with a nuclear membrane, a variety of organelles, including mitochondria, endoplasmic reticulum, golgi apparatus and others, and more than one chromosomes in the nucleus Cellular organisms are classified into eucaryotes (have eucaryotic cells) and bacteria (have procaryotic cells). Eucaryotes can be multicellular (extensive differentiation of cells and tissues), e.g., plants, or unicellular (little or no differentiation of cells and tissues), e.g., animals and protists (algae,fungi, protozoa) Bacteria can be divided into eubacteria (most of the bacteria; their cell chemistry is similar to eucaryotes) and archaebacteria (ex. methanogens, halophiles,thermo- acidophiles; have distinctive cell chemistry) Viruses cannot be classified under any category; are very small ( nm) and obligate parasites (not free-living cells) of other cells; contain either DNA or RNA as genetic material and use either RNA or DNA to decode genetic information (in free-living cells all genetic information is contained in DNA). RNA viruses are called retroviruses, e.g., HIV virus 14/2/2014 ΔΧ

eukaryotic cells, cytoplasm contains specialized membrane-
Some Biology Cell In prokaryotes (bacteria), most of genetic material lies in a single molecule of DNA which resides in area close to cell center, nucleotid; this area in not segregated from the rest of cell’s interior by membranes In eukaryotes, DNA is contained in nucleus which is surrounded by two membranes, (a) A semi-fluid matrix, cytoplasm, fills interior of cell, exclusive of nucleus (eukaryotes) or nucleotid (prokaryotes). Contains sugars, amino acids and proteins for cell’s activities. In eukaryotic cells, cytoplasm contains specialized membrane- bounded compartments, called organelles, and (b) A phospholipid bilayer , plasma membrane, which separates the cell from its surroundings 14/2/2014 ΔΧ

Eukaryotic cell structures
Some Biology Eukaryotic cell structures Cell wall – only in plant cells for protection and support, Cytoskeleton – array of fibrous proteins for structural support and cell movement, Plasma membrane – phospholipid bilayer (hydrophobic end interior, hydrophilic end exterior) regulates what passes in and out of cell, Endoplasmic reticulum - network of membranes in which glycoproteins and lipids are synthesized Nucleus – houses most of cellular DNA; directs protein synthesis and cell reproduction Golgi - packages proteins for export from cell; forms secretory vesicles, 8. Lysosomes - contain enzymes, digest worn-out organelles and cell debris 9. Microbodies - contain enzymes, isolate particular activities from rest of cell, 10. Mitohondria - bacteria-like elements; sites of oxidative metabolism, 11. Chloroplasts - sites of photosynthesis in plant cells, 12. Chromosomes - DNA and protein complex assemblies, contain hereditary information (total DNA in chromosomes of organism is its genome), 13. Nucleolus - site of genes for rRNA synthesis, assembles ribosomes, 14. Ribosomes - complex assemblies of protein and RNA, often found in endoplasmic reticulum; sites of protein synthesis 14/2/2014 ΔΧ

Nucleotide Nucleic Acid Sugar Polysaccharides
Some Biology Molecules of Life Water, inorganic ions, and relatively small organic molecules (e.g., sugars, vitamins, fatty acids) account for 75 – 80% of living matter by weight. Water is most abundant. Water, ions and many small organic molecules are imported into cells. Cells also make and alter many small organic molecules Remaining 20 – 25% of living matter are macromolecules (polymers) ,including proteins, polysaccharides, and nucleic acids, e.g., DNA (deoxyribonucleic acid), RNA (ribonucleic acid). Cells can acquire macromolecules only by making them Monomer Polymer Amino acid Protein Nucleotide Nucleic Acid Sugar Polysaccharides 14/2/2014 ΔΧ

Amino acids Contain at least one carboxylic group, -COOH, one a-amino group, -NH2, and a side group, R. H | H2N - C - COOH R Building blocks of proteins are 20 common amino acids which, on the basis of side group, R, are classified as: Nonpolar - R groups contain –CH2 or –CH3: alanine, valine, leucine, isoleucine, Polar uncharged - R groups contain O or only H: glycine, serine, threonine, asparagine, glutamine, Ionizable - R groups contain acids or bases: glutamic acid, aspartic acid, histildine, lysine, arginine, Aromatic - R groups contain C rings with alternating single and double bonds: phenylalanine, tryptophan, and Special-function: methionine, proline (causes kinks in chains), cysteine (links chains together) 14/2/2014 ΔΧ

zwitterion Amino acids
Are optically active and occur in two isomeric forms, L and D H H | | H2N - C - COOH HOOC - C - NH | | R R L-amino acid D-amino acid In gas state are neutral; in liquid state exist as dipolar molecules of the form H | H3N+ - C - COO- R zwitterion The pH value at which an amino acid has no net charge is called isoelectric point 14/2/2014 ΔΧ

larger amino acid chains are proteins
are the most abundant organic molecules in living cells, 40 – 70% of their dry weight. They are condensation polymers of a-amino acids, joined by peptide bonds. A peptide bond forms when –NH2 end of one amino acid joins to the -COOH of another The peptide bond is planar. Peptides contain two or more amino acids linked by peptide bonds. Polypeptides are chains containing less than 50 amino acids and larger amino acid chains are proteins Only L amino acids are found in proteins. D amino acids are rare in nature; they are found in the cell walls of some microorganisms and in some antibiotics Conjugated proteins contain organic and/or inorganic components, other than amino acids, which are called prosthetic groups, e.g., hemoglobin is a conjugated protein with four heme groups, i.e., iron-containing organometallic complexes R | H2N - C - C - | || H O H R΄ | | N - C - COOH | H 14/2/2014 ΔΧ

Structural, e.g., glycoproteins, collagen, keratin,
There are two major types of protein conformation, (1) fibrous, and (2) globular Based on their diverse biological functions, proteins can be classified in 5 major classes: Structural, e.g., glycoproteins, collagen, keratin, Catalytic, e.g., enzymes, Transport, e.g., hemoglobin, serum albumin, Regulatory, e.g., hormones (insulin, growth hormone), and Protective, e.g., antibodies, thrombin Enzymes, over 2000 different kinds known, represent the largest class. Most enzymes are globular proteins, with extraordinary catalytic power and high specificity in their function. Every molecule of an enzyme has an active site to which its specific substrate is bound during catalysis Antibodies (Ab) or immunoglobulins (IgG, IgA, IgD, IgE, and IgM), MW = 150 – 900 kD, are found in the blood serum and certain cells of the vertebrae and bind to Antigens (Ag), foreign molecules, to form an Ab-Ag complex. The formation of the complex is called immune response. They are highly specific to foreign proteins that induce their formation. They have 4 polypeptide chains, 2 heavy (430 amino acids) and 2 light (214 amino acids), linked together by disulfide bonds into a Y- shape, flexible structure. Each chain has constant and variable amino-acid-sequence regions. The variable sequence regions of the light and heavy chains compose the binding sites 14/2/2014 ΔΧ

described at 4 different levels:
Proteins The 3-D structure of proteins, which is critical to their biological activity, can be described at 4 different levels: Primary structure - a unique linear sequence of amino acids with defined composition, Secondary structure - arises from hydrogen bonding of neighboring amino acids, i.e., hydrogen bonds on the same chain form a helix, hydrogen bonds across chains form b-pleated sheet (sheet structure is more stable than the helix structure), Tertiary structure – folding or bending of amino acid chains as a result of covalent, disulfide, or hydrogen bond, or hydrophilic and hydrophobic interactions between R groups (disulfide bonds critical to proper folding), and Quaternary structure – arises from interactions (disulfide bonds or weak interactions) between peptide chains 14/2/2014 ΔΧ

Hemagluttinin: consists of 3 identical subunits, each
Proteins Hemagluttinin: consists of 3 identical subunits, each composed of 2 chains, HA1 & HA2 Primary structure - sequence of amino acid residues 68 – 195 of HA1 (used by influenza virus to bind to animal cells); one-letter amino acid code. Secondary structure - regions of polypeptide chain folded into a-helices (cylinders), b-sheets or strands (arrows), and random coils (bold lines) Tertiary structure - folding of helices and sheets in each subunit; domains with globular (membrane-distal domain), and fibrous conformation (membrane-proximal domain) Quaternary structure – consists of 3 subunits of HA and is stabilized by lateral interactions between subunits 14/2/2014 ΔΧ

Carbohydrate - contain C:H:O in molar ratio 1:2:1
Polysaccharides Carbohydrate - contain C:H:O in molar ratio 1:2:1 C-H bonds release energy when broken Sugars - carbohydrates consisting of six-carbon rings (Fructose, glucose and galactose, isomers with empirical formula C6H12O6 ) Polysaccharides – polymers of sugar Organisms convert most of the glucose into fat to store energy over long periods of time Lipids Molecules insoluble in water Fat - composite molecules which consists of glycerol (a 3-C alcohol with each C bearing a OH- group) and 3 fatty acids (long hydrocarbon chains ending in -COOH group); most contain more than 40 C atoms but ratio of energy-storing C-H bonds to C atoms more than twice that of carbohydrates Saturated fats contain maximum possible number of H atoms; unsaturated fats contain double bonds between one or more pairs of successive C atoms; polyunsaturated fats contain more than one double bonds, have low melting point (fatty acid chains bend at double bond preventing molecules from aligning closely with one another) and are usually liquid at room temperature 14/2/2014 ΔΧ

down to its descendants
Nucleic acids Nucleic acids - polymers of nucleotides; information storage devices of cells; serve as template to produce precise copies of them-selves, so that information that specifies what an organism is can be copied and passed down to its descendants Nucleotide - consists of (1) a 5-C sugar (ribose in RNA and deoxyribose in DNA), (2) a phosphate group, -PO4 , and (3) an organic N-containing base. When a nucleic acid polymer forms, the phosphate group of one nucleotide binds to the hydroxyl group of another, releasing water and forming a phosphodiester bond. Nucleotides contain two types of organic bases: (1) purines, large double- ring molecules found in both DNA and RNA, e.g., adenine (A) and guanine (G), and (2) pyrimidines, smaller single-ring molecules, e.g., cytosine (C, in both DNA and RNA), thymine (T, in DNA only), and uracil (U, in RNA only) Adenine key component of Adenosine TriPhosphate, energy currency of cell; also in Nicotinamide Adenine Dinucleotide (NAD+) and Flavin Adenine Dinucleotide (FAD+), carry electrons whose energy is used to make ATP Code of DNA consists of different combinations of 4 nucleotides, A, C, G, T 14/2/2014 ΔΧ

Nucleic Acids Double-stranded DNA replicating Nucleotides 14/2/2014 ΔΧ

RNA molecules are always single-stranded
Nucleic acids DNA - deoxyribonucleic acid; contains deoxyribose sugar in which –OH is replaced by –H; stores hereditary information as a specific sequence of nucleotide bases; information is used to assemble proteins in a way similar to which letters on a page encode information RNA - ribonucleic acid; contains ribose sugar in which number 2 C is bonded to –OH; similar in structure to DNA; made as a transcript copy of portions of DNA and used by cells to read the DNA-encoded information and direct synthesis of proteins; utilizes uracil instead of thymine in DNA; uracil has same structure as thymine, except one of its C atoms lacks a –CH3 DNA molecules exist not as single chains (exceptions viruses) but as double chains wound around each other like the outside and inside rails of a circular staircase (double helix) Each step of DNA’s helical staircase is a base-pair, consisting of a base in one chain attracted by hydrogen bonds to a base opposite to it on the other chain RNA molecules are always single-stranded 14/2/2014 ΔΧ

Properties of biological molecules (proteins, peptides, nucleic acids)
The diffusion coefficients of particles, of a regular or close to regular shape and size from molecular (in Å ) upwards, in a liquid, with the particles-liquid system being either a suspension or a solution, are given by the Stokes-Einstein equation where Dpl is the diffusion coefficient of the particles in the liquid, kB is the Boltzman constant equal to 1.38x10-16 erg molecule-1 oK-1 In the dilute regime, where the volumetric fraction of the particles in the particles- liquid sytem is small (< 0.10), such as those found in most biological systems, the motion of particles is caused by thermal energy transferred from the liquid molecules during random collisions between them and particles. This transfer of energy leads to fluid motion which is retarded by the drag of the liquid on the particles. For particles with a characteristic dimension about 10 times greater than that of the solvent molecules, the drag force can be approximated using low-Reynolds-number hydrodynamics, as FD = K . vp (2) where FD is the drag force (vector) acting on a single particle, K is the translation tensor (symmetric, i.e., Kij = Kji ) , and vp the velocity of the particle The symmetric tensor K, by appropriate choice of the coordinate axes, can be made so that it has fij = 0 if i ≠ j and fij ≠ 0 if i = j. The nonzero main diagonal components of K are called principal friction coefficients and, for the case of isotropic particle, are f1 = f2 = f3 = f 14/2/2014 ΔΧ

Proteins under physiological conditions assume their distinctive tertiary structure, native conformation, of minimum free energy, which is a prerequisite for biological function. The native biologically active form of a protein molecule is globular (in synthetic polymers, the random chains may also be coiled into globular structures called spherulites), but protein molecules cannot be treated adequately as spheres. This is clear from the values of the ratios f ̅/ f0 and the structures and sizes of X-ray Crystallography In solution, a protein is hydrated due to electrostatic and electrodynamic interactions. If hydration were uniform over the protein molecule and occurred in discrete layers, it (hydration) would result in larger molecular size. However, hydration is not uniform over the molecule and is greater close to charged groups. It increases the molecular volume of protein as where v̅mp is the molar volume in cm3gmol-1, v̅sp is specific volume in cm3g-1, M is the protein molecular weight, ρw the density of water, and δh the extent of hydration in g water (g protein)-1 The Table that follows lists measured and estimated, for different shapes and sizes, diffusion coefficients for the protein lysozyme 14/2/2014 ΔΧ

The previous Table shows that accounting for the shape more accurately, improves the estimate of diffusion coefficient Data from sedimentation in an ultracentrifuge and diffusion can be utilized to estimate the molecular weight of a protein from For a number of proteins, diffusion and sedimentation coefficients at 20o C, the molecular weight, X-ray crystallographic data for shapes, and measured values of f ̅/ f0 are known and listed in the Table to follow The method most commonly used to measure the molecular weight of a protein is gel filtration, nowadays. It involves passing the protein solution through a column of packed porous beads. Molecules smaller than the pore size of the beads enter the beads, and travel longer through the column than other molecules do. The smaller the molecule, the more time it takes to go through the column. By measuring the time required to pass through the column a set of standards of known molecular weight, and establishing a molecular weight vs. residence time calibration curve, the molecular weight of the protein is better determined. This method is easier to apply than the ultracentrifuge and does not need pure samples for its operation 14/2/2014 ΔΧ

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From analysis of a 3-D random walk, the diffusion coefficient is given by Dij = δ2 / 6τ (1) where δ is the displacement and τ is the time between collisions A diffusion velocity, vd , is defined as vd = δ /τ (2) The diffusion velocity can be determined by equating the kinetic energy of the particle or molecule to its thermal energy, according to 1/2 mpvd2 = 3/2 kBT (3) Eqs(1) and (2)  δ = 6Dij /vd (4) Eq.(3)  vd = (3kBT/mp )1/2 (5) The Stokes-Einstein equation is Dij = kBT/ f̅ (6) Substituting from Eqs. (5) and (6) into Eq. (4), results in δ = (12 mpkBT)1/2/ f̅ = (12MkBT/NA )1/2/ f̅ (7) 14/2/2014 ΔΧ

Polypeptides and polynucleic acids (RNA and DNA) differ from globular proteins and are often treated as random coils For a free-draining (solvent moves freely in area occupied by coil) random coil with freely joined N segments (N is the degree of polymerization) of length l each, the root-mean-square end-to-end distance,< Re 2>1/2, is <Re2>1/2= N1/2l If the coil is fully extended, <Re2>1/2= Lc = Nl where Lc is the contour length This applies to natural and synthetic random coil macromolecules in solvents with which the molecule does not interact (theta solvents) Real macromolecules, like those of polypeptides and polynucleic acids are quite different than the free-draining random coil. These differences are (a) The coil has a finite size, hence, an excluded-volume effect needs to be taken into account, (b) The bond angle, θ, and the bond-rotation angle, φ, of the macromolecule are neither fixed nor changing without constraints, and (c) There is molecule-solvent interaction <Re 2>1/2 Rn Rn-1 14/2/2014 ΔΧ

To account for these differences, for polypeptides and polynucleic acids (RNA and DNA), the root-mean-square end-to-end distance,<r2>1/2, is < Re 2>1/2= (CnN)1/2l where Cn is the characteristic ratio, equal to the ratio lK / l, and lK being the Kuhn length which, together with number of Kuhn segments, NK < N, parametrize the stiffness of the coil < Re 2>1/2= NK1/2 lK Lc = NK lK When N  ∞ , Cn  C∞ (finite). Polypeptides without the amino acids glycine or proline have C∞ = 130 and their root-mean-square end-to-end distance is in nm. The large value of C∞ indicates significant interaction of the side chains with water and stiffening of the segments For DNA, lK equals 150 nm and l equals 0.34 nm, which indicates that DNA is a stiff chain. For bacterial DNA with 1.5x106 base pairs, the root-mean-square end-to-end distance is 8.75 μm , much larger than the size of the bacterium For polyamino acids (polypeptides and proteins) and polynucleotides (RNA and DNA), the friction coefficient can be estimated under the assumption that the random coil behaves as a sphere with radius equal to the radius of gyration, Rg 14/2/2014 ΔΧ

The radius of gyration, Rg , is defined in two ways, which can be shown to be equivalent and where rk = Rk – Rk-1 and Rk is the vector from the origin of the coordinate system to the k-th joint of the chain For a free-draining, open-ended, random coil For a circular random coil, which can represent well the configuration of a DNA plasmid found in bacteria 14/2/2014 ΔΧ

Information Flow & Control
A cell is more than a bag filled with water, lipids, amino acids, sugars, enzymes, and nucleic acids. It must control how these components are made and how they interact with each other. To do so the cell possesses the ability of metabolic regulation, i.e., the ability to coordinate a wide variety of chemical reactions taking place within it Key to metabolic regulation is the flow and control of information All living systems obey the same Central Dogma of Biology when it comes to storage, expression and utilization of information. Information is stored on the DNA molecule. This information can be replicated directly to form a second identical molecule. Further segments of the information can be transcribed to yield RNA molecules. Using a variety of RNAs, the information is translated into proteins which perform a structural or enzymatic role in mediating all the metabolic functions in the cell. The information content of the DNA molecule is static; changes occur slowly through infrequent mutations or rearrangements. The type and the amount of RNA species that are present varies with time and culture conditions. Likewise, the proteins that are present change with time on a scale different than the time scale of the RNA change. Some of the proteins bind to DNA to regulate the transcriptional process to form RNAs 14/2/2014 ΔΧ

Information Flow & Control
One important, although relatively minor, deviation from the Central Dogma, is the existence of RNA retroviruses that contain an enzyme called reverse transcriptase which enables reverse transcription from RNA to DNA (example: Human Immunodeficiency Virus causing Acquired ImmunoDeficiency Syndrome; one approach to treatment is to inhibit reverse transcriptase) For information storage and exchange to take place, there must be a language. All life is using a 4-letter alphabet made up of nucleotides A, T, C, and G in DNA. In this language, all words, called codons, are 3- letter long. With 4 letters and only 3-letter words, a language can have a maximum of 64 words. When these words are put into a sequence, one can make a sentence, called gene, which, when properly transcribed and translated, is a protein Each step in the information storage and transfer requires a macromolecular template. The success or failure of the processes of genetically engineering therapeutic proteins depends on the choice of the host organism and the expression system. The most important consideration must be whether posttranslational modifications, e.g., glycosylation, i.e., addition of sugars, or phosphorylation, of the product are necessary 14/2/2014 ΔΧ

consequent inactivation of the protein
Protein Stability Proteins under physiological conditions assume their distinctive tertiary structure, native conformation, of minimum free energy, which is a prerequisite for biological function. The native biologically active form of a protein molecule is held together by a delicate balance of noncovalent forces, hydrophobic, van der Waals, and hydrogen bonds In proteins that contain two or more cystine residues, disulfide bonds, which are covalent, contribute substantially to maintaining the native protein conformation By X-ray structure analysis, it has been confirmed that most water-soluble proteins may be grossly described as a hydrophobic core of nonpolar amino acids, surrounded by a hydrophilic shell of solvated polar amino acids. With exposure to certain denaturants and adverse environmental conditions, the noncovalent forces are weakened and broken apart, leading to unfolding (chaperone proteins are important proteins that assist in proper folding of polypeptide chains) and consequent inactivation of the protein Typically, the native structure exhibits only marginal stability that is easily upset by even subtle environmental changes in pressure, temperature, pH, ionic strength, or a combination thereof. The free energy of denaturation of globular proteins rarely exceeds 15 kcal/mol. The complete or partial unfolding of the protein is usually fully reversible, after removal from the antagonistic agent. This reversible unfolding is the precursor to irreversible protein denaturation by covalent and noncovalent reactions. 14/2/2014 ΔΧ

Covalent Destabilization As with conventional-drug
Protein Stability Covalent Destabilization As with conventional-drug small organic molecules, the chemical reactions involved in protein destabilization are classified as those involving (1) hydrolysis, (2) oxidation, and (3) racemization Disulfide bond cleavage and exchange are also reactions that affect protein stability A striking feature of protein destabilization is that several different reaction mechanisms may proceed simultaneously. Because of the multiple degradation pathways that may take place at elevated temperature, protein stability monitoring data may not conform to the Arrhenius relationship. The chemical reaction mechanisms involved in protein degradation depend on (1) nature of protein, (2) temperature, (3) pH, (4) ionic strength, (5) oxygen vapor pressure, and (6) type and concentration of other solutes 14/2/2014 ΔΧ

Covalent Destabilization - Hydrolysis
Protein Stability Covalent Destabilization - Hydrolysis Primary hydrolytic reactions in protein degradation are peptide bond hydrolysis and deamidation Peptide bond hydrolysis occurs readily under strongly acidic conditions or by combination of milder pH and elevated temperature. Complete acid hydrolysis of protein into its amino acids takes place under extreme conditions, 6M HCl, 24 h, 110oC. Shorter exposures under less acidic conditions, show preferred peptide hydrolysis on aspartic acid residues. Aspartyl-prolyl linkages are especially vulnerable. Loss of oligosaccharide moieties through hydrolysis of glycosidic bonds may also influence protein stability Deamidation is the hydrolysis of the side-chain amide on glutamine and asparagine residues (asparagine residues are more susceptible to deamidation than glutamine residues). Deamidation under physiological conditions proceeds essentially through an imide intermediate. The cyclic imide (succinimide) is rapidly hydrolyzed by water into a mixture of aspartic acid and isoaspartic acid, resulting in the introduction of new negative charge to the protein. The rate of deamidation is affected by the nature of the amino acid residue adjacent to asparagine. The most labile asparagine residues in smaller peptides are followed by glycine residue. Asparagine-serine sequences are next most labile sites of deamidation. In globular proteins, the location of susceptible residue in the folded conformation may be more important in controlling deamidation rate 14/2/2014 ΔΧ

Covalent Destabilization - Oxidation
Protein Stability Covalent Destabilization - Oxidation Can occur with a variety of oxidants for amino acids with aromatic side chains, as well as methionine, cysteine, and cystine residues. Molecular oxygen, hydrogen peroxide, and oxygen radicals are all known oxidants of protein Oxidation of methionine residues to their corresponding sulfoxides is associated with loss of biological activity for many peptide hormones and proteins. The thiol group of cysteine can be oxidized in steps successively to a sulfenic acid, RSOH, a disulfide, RSSH, a sulfinic acid, RSO2H, and finally a sulfonic acid, RSO3H, depending on reaction conditions. Oxidation of thiols occurs readily at basic pH in the presence of transition metal ions such as Cu2+. When oxidized thiol groups are exposed on the protein surface, because of steric effects, intermolecular disulfide bonds may form, leading to protein aggregation Factors that influence the rate of oxidation include temperature, pH, buffer medium, type of catalyst, and oxygen vapor pressure 14/2/2014 ΔΧ

Covalent Destabilization - Racemization
Protein Stability Covalent Destabilization - Racemization of the native L-amino acid to the D-enantiomer generally results from base-catalyzed removal of the a-proton to produce a negatively charged planar carbanion. Return of the proton to the carbanion intermediate through reaction with water produces an enantiomeric mixture Rates of racemization depend on the particular amino acid and are influenced by temperature, pH, ionic strength, and metal ion chelation. Aspartic acid and serine residues are the most prone to racemization. An electron-withdrawing group in the side of the amino acid, as in serine, stabilizes the carbanion intermediate , which in turn accelerates the rate of racemization Intermediate succinimide formation plays a major role in racemization at aspartyl and asparaginyl residues. Racemization of amino acids in proteins can generate nonmetabolizable forms of amino acids (D-enantiomers) or create peptide bonds inaccessible to proteolytic enzymes 14/2/2014 ΔΧ

Covalent Destabilization – Disulfide exchange
Protein Stability Covalent Destabilization – Disulfide exchange Disulfide bonds provide covalent structural stabilization to proteins. Cleavage and subsequent rearrangement of these bonds can alter the tertiary structure, thereby affecting biological activity. Disulfide exchange is catalyzed by thiols, which can arise by initial hydrolytic cleavage of disulfides, or by b-elimination in neutral or alkaline media At pH 6 and 8, thermal inactivation of ribonuclease at 90oC is caused primarily by disulfide exchange. This process was inhibited by thiol scavengers, such as N-ethylmaleimide, p-(chloromercuri)benzoate, and copper ion, and accelerated in the presence of thiols, such as with the addition of cysteine. Rates were generally accelerated under alkaline conditions. Widespread formation of Covalent Insulin Dimers (CIDs) in insulin formulation, as a result of disulfide exchange, has been reported 14/2/2014 ΔΧ

Noncovalent Destabilization
Protein Stability Noncovalent Destabilization Three major categories of irreversible protein inactivation occur as a result of perturbation of the noncovalent forces that maintain the 3-D native state of proteins, (1) aggregation, (2) macroscopic precipitation, and (3) surface adsorption Noncovalent interactions, electrostatic, hydrogen bond, hydrophobic, and protein hydration, may be altered as a result of thermal or pH effects. The irreversible inactivation proceeds following initial reversible unfolding of the native state With an increase in temperature, a protein molecule in solution will undergo a characteristic transition from native to unfolded state at the melting temperature, Tm , defined as the temperature at which 50% of the molecules are unfolded The pH of the solution influences the net charge of the protein, depending on its pI. pH may affect electrostatic interactions, also referred to as salt bridges. At extreme pH values, the net charge of the protein increases with greater charge repulsion, leading to protein unfolding Protein conformation is markedly affected by type and concentration of ionic species in solution. Individual salt effects can be either stabilizing or denaturing. These effects correspond to the Hofmeister lyotropic series: SO4- > HPO42- > Oac- > F- > citrate > Cl- > NO3- > I- > CNS-, ClO4-(CH3)4N+ > NH4+ > K+, Na+ > Mg2+ > Ca2+ > Ba2+ 14/2/2014 ΔΧ

Noncovalent Destabilization
Protein Stability Noncovalent Destabilization Anions and cations to the left of the series are the most stabilizing and reduce the solubility of the hydrophobic groups, salting out) on the protein molecule, by increasing the ionic strength of solution. Anions and cations to the right of the series are destabilizing and are known to denature proteins, causing an increase in solubility or salting in Mechanical forces, such as shearing, shaking, and pressure, may also denature proteins. Shaking may lead to deactivation owing to the increase of the gas/liquid interface. Surface denaturation may occur following adsorption of proteins to container walls and filter materials Noncovalent Destabilization -Aggregation and Precipitation Aggregation is a microscopic process of protein molecule association. Aggregates may be dimers or larger oligomers that remain in solution and may affect biological activity. Irreversible aggregation may follow unfolding as a result of incorrect refolding of the protein. Protein unfolding exposes its hydrophobic interior to the solvent, usually water. Interactions between exposed hydrophobic regions of the protein interior drive aggregation. Although a two-state equilibrium model describes, as a general rule, protein unfolding, several examples of intermediate conformational states have been uncovered and may play a role in aggregate formation and subsequent precipitation 14/2/2014 ΔΧ

Noncovalent Destabilization -Aggregation and Precipitation
Protein Stability Noncovalent Destabilization -Aggregation and Precipitation The conformational intermediaries have considerable secondary structure but lack tertiary structural interactions. Aggregation results from association of exposed hydrophobic regions on the monomeric intermediaries. Protein concentration may influence the rate of formation of intermediaries. Aggregation depends on both, thermal unfolding and pH Precipitation refers to formation of visible particles which, in addition to altering the appearance of a formulation, reduce the potency and performance in infusion devices Shaking a protein solution may lead to aggregation and precipitation as a result of several mechanisms, such as air oxidation, surface denaturation, adsorption to the container walls, or mechanical stress. Proposed mechanism of inactivation by mechanical stress is through orientation of asymmetrical proteins in the shear flow field, which promotes association of aligned molecules Aggregation and precipitation were observed for human interferon-g and human fibroblast interferon. Insulin aggregation and precipitation was an impediment to the development of implantable devices for insulin delivery. Potential causes for insulin aggregation and precipitation are thermal effects, mechanical stress, nature of materials in contact with insulin, and purity of insulin preparation 14/2/2014 ΔΧ

Noncovalent Destabilization – Surface Adsorption
Protein Stability Noncovalent Destabilization – Surface Adsorption Protein adsorption onto the surfaces of container walls, filter, materials of infusion systems, etc., can be critical when the initial protein concentration in solution is low Surface adsorption results from hydrophobic and electrostatic interactions and depends on the conformational state of protein, pH, ionic strength of solution, as well as the nature of the surface. The interaction of the protein molecule with the surface increases with increasing hydrophobicity of both, the surface and the protein molecule. The tendency of protein to undergo conformational change is time- dependent, and protein- and surface-specific Membrane filtration is the only currently acceptable method of sterilizing protein pharmaceuticals and the adsorption of the protein on the membrane is of particular concern. Nitrocellulose and nylon membranes had extremely high protein adsorption, followed by polysulfone, cellulose diacetate, and hydrophilic polyvinylidene fluoride membranes 14/2/2014 ΔΧ

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