Polypeptides conformational equilibrium

In one case, a small peptide with enzyme-like capability has been claimed. On the basis of model building and conformation studies, the peptide Glu-Phe-Ala-Ala-Glu-Glu-Phe-Ala-Ser-Phe was synthesized in the hope that the carboxyl groups in the center of the model would act like the carboxyl groups in lysozyme 17). The kinetic data in this article come from assays of cell wall lysis of M. lysodeikticus, chitin hydrolysis, and dextran hydrolysis. All of these assays are turbidimetric. Although details of the assay procedures were not given, the final equilibrium positions are apparently different for the reaction catalyzed by lysozyme and the reaction catalyzed by the decapeptide. Similar peptide models for proteases were made on the basis of empirical rules for predicting polypeptide conformations. These materials had no amidase activity and esterase activity only slightly better than that of histidine 59, 60). 

The influence of the solvent on chiroptical properties of synthetic polymers is dramatically illustrated in the case of poly (propylene oxide). Price and Osgan had already shown, in their first article, that this polymer presents optical activity of opposite sign when dissolved in CHCI3 or in benzene (78). The hypothesis of a conformational transition similar to the helix-coil transition of polypeptides was rejected because the optical activity varies linearly with the content of the two components in the mixture of solvents. Chiellini observed that the ORD curves in several solvents show a maximum around 235 nm, which should not be attributed to a Cotton effect and which was interpreted by a two-term Drude equation. He emphasized the influence of solvation on the position of the conformational equilibrium (383). In turn, Furakawa, as the result of an investigation in 35 different solvents, focused on the polarizability change of methyl and methylene groups in the polymer due to the formation of a contact complex with aromatic solvents (384). 

Polypeptide chains exist in an equilibrium between different conformations as a function of environment (solvent, other solutes, pH) and thermodynamic (temperature, pressure) conditions. If a polypeptide adopts a structurally ordered, stable conformation, one speaks of an equilibrium between a folded state, represented by the structured, densely populated conformer, and an unfolded state, represented by diverse, sparsely populated conformers. Although this equilibrium exists for polypeptide chains of any size, its thermodynamics and kinetics are typically different for oligopeptides and proteins. This can be broadly explained with reference to the different dimensionalities of the free-energy hypersurfaces of these two types of molecules. 

Typical examples are the conversion of the neutral form of an amino acid into its zwitterionic form, the helix-coil transitions in polypeptides and polynucleotides, and other conformational changes in biopolymers. Reactions of higher molecularity in which reactants and products have different dipole moments are subject to the same effect (association of the carboxylic acids to form hydrogen-bonded dimers). Equilibrium involving ions are often more sensitive to the application of an electric field ... 

The spatial macrostructure of the native protein (the equilibrium location of the polypeptide main chain backbone and bulky side groups) is strictly determined. Individual protein molecules having the same sequence of amino acid residues do not differ in their three-dimensional structure, which is the equilibrium one and averaged in time. The activation energy of conformational transitions may be as high as several hundreds of kilojoules per mole. Therefore, the extended fluctuations which are associated with the unfolding of the native macro structure and transitions between conformations occur rather rarely. 

At thermal equilibrium, the helical fraction and all other quantities characterizing the conformation of a helix-forming polypeptide are fluctuating from time to time about certain mean values which are uniquely determined by three basic parameters s, a, and N. The rates of these fluctuations depend on how fast helix units are created or disappear at various positions in the molecular chain. Recently, there has been great interest in estimating the mean relaxation times of these local helix-coil interconversion processes, and several methods have been proposed and tested. In what follows, we outline the theory underlying the dielectric method due to Schwarz (122, 123) as reformulated by Teramoto and Fujita (124). 

A puzzling problem was posed by Levinthal many years ago.329 We usually assume that the peptide chain folds into one of the most stable conformations possible. However, proteins fold very rapidly. Even today, no computer would be able, in our lifetime, to find by systematic examination the thermodynamically most stable conformation.328 It would likewise be impossible for a folding protein to "try out" more than a tiny fraction of all possible conformations. Yet folded and unfolded proteins often appear to be in a thermodynamic equilibrium Experimental results indicate that denatured proteins are frequently in equilibrium with a compact denatured state or "molten globule" in which hydrophobic groups have become clustered and some secondary structures exists.330-336 From this state the polypeptide may rearrange more slowly through other folding intermediates to the final "native conformation."3363 3361 ... 

Evidence from protein fluorescence indicates that the equilibrium conformation of the central regions of the polypeptide backbone, which are amenable to probing by emission from the tryptophan residues, is not changed overall to any major extent in the Pr -< Pfr transformation. The conformational reorganization of the protein, which is induced by the Z - E isomerization (which in turn is presumed to represent the primary photoreaction of the overall Pr -> Pfr transformation), appears to be confined mostly to the domain housing the bilatriene chromophore. 

Interestingly, one can use a Cys-Gly-Gly linker at the N- or C-terminal of the polypeptide chain in the design of disulfide-bridged coiled coils. The advantage of this approach is that the Cys-Gly-Gly linker allows complete flexibility of the polypeptide chains to adopt their most stable conformation, which includes different oligomerization states, while maintaining the polypeptide chains in a parallel manner. 49 In addition, the Cys-Gly-Gly linker eliminates the monomer-dimer equilibrium and the peptide concentration effect on stability, which is observed in two-stranded coiled-coil formation of noncovalent linked polypeptides. 49 861... 

When secondary chemical equilibrium prevail, such as salt in or salt out effects involving changes in the self-association or aggregation state of the polypeptide or protein, or alternatively when additional hydrophobic interaction effects are manifested, or finally if conformational transitions are induced due to the choice of a water structuring or water-destabilizing salt species from the Hofmeister series,91-93 then divergences from this ideal behavior will be evident. 

As is evident from the preceding discussion, the retention behavior of a polypeptide or protein P- expressed in terms of the capacity factor k is governed by thermodynamic considerations. Peak dispersion, on the other hand, arises from time-dependent kinetic phenomena, which are most conveniently expressed in terms of the reduced plate height he, . When no secondary effects, i.e., when no temperature effects, conformational changes, slow chemical equilibrium, pH effects, etc. occur as part of the chromatographic distribution process, then the resolution Rs, that can be achieved between adjacent components separated under these equilibrium or nearequilibrium conditions can be expressed as... 

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