Proteins helix-coil transition

Bond DNA vibrations twisting Hinge motions Helix-coil transitions Protein folding Protein aggregation ... 

Levy, Y., Hanan, E., Solomon, B., and Becker, O. M. (2001). Helix-coil transition of PrP106-126 Molecular dynamic study. Proteins 45, 382-396. 

Thermodynamics of Proteins Calculating the Entropy of a Helix-Coil Transition in a Small Antibacterial Peptide using Statistical Mechanics (J. Mol. Bio. 1999, 294, 785-794. "Thermodynamics of the a-Helix-Coil Transition of Amphipathic Peptides in a Membrane Environment Implications for the Peptide-Membrane Binding Equilibrium")... 

Tphe complexing of virtually all purines with aromatic molecules seems - to have far-reaching biological significance. For example, it is known that caffeine affects the rates of many enzymatic reactions (e.g., 0.01, 0.05, and 0.10M caffeine will inhibit salivary amylase 29, 54, and 72% respectively) (12), and purine can decrease the helix-coil transition temperature of the proteins bovine serum albumin and lysozyme (2). It is not unreasonable to expect the involvement of caffeine-aromatic and purine-aromatic complexes because caffeine derivatives and purine complex with the aromatic amino acids tyrosine, phenylalanine, and tryptophan (2). (In fact tryptophan forms a stable 1 to 1 crystalline complex in 0.5M theophylline glycol.)... 

Like proteins, nucleic acids can undergo denatur-ation. The strands of the double helix of DNA are separated and the double-stranded regions of RNA molecules "melt." Denaturation can be accomplished by addition of acids, bases, and alcohols or by removal of stabilizing counter ions such as Mg2+. The product is a random coil and denaturation can be described as a helix —> coil transition. Denaturation of nucleic acids by heat, like that of proteins, is cooperative (Chapter 7, Section A,3) and can be described by a characteristic melting temperature. 

Some results. Rapid kinetic methods have revealed that enzymes often combine with substrates extremely quickly,60 with values of k] in Eq. 9-14 falling in the range of 106 to 108 M 1 s . Helix-coil transitions of polypeptides have relaxation times of about 10-8 s, but renaturation of a denatured protein may be much slower. The first detectable structural change in the vitamin A-based chromophore of the light-operated proton pump bacteriorhodopsin occurs in - 5 x 10 8 s, while a proton is pumped through the membrane in... 

At this temperature, the entropy change for dissolution of liquid hydrocarbons in water is zero. However, the entropy of protein denaturation is far from zero at this temperature but amounts to 17.6 J - K l per mole of amino acid residues (Privalov, 1979), a value that corresponds to an 8-fold increase of the number of possible configurations and is close to the value expected for the helix-coil transition of polypeptides (Schellman, 1955). This difference shows that an oil drop is an inadequate model for a globular protein. A more suitable model resembles that of a small crystal with a quite definite positive melting entropy (see also Bellow, 1977, 1978). 

M. Vasquez, M. R. Pincus, and H. A. Scheraga, Biopolymers, 26, 351 (1987). Helix-Coil Transition Theory Including Long-Range Electrostatic Interactions Application to Globular Proteins. 

Theoretical approaches to structural biophysics, like the theories of transport and reaction kinetics explored in other chapters of this book, are grounded in physical chemistry concepts. Here we explore a few problems in molecular structural dynamics using those concepts. The first two systems presented, helix-coil transitions and actin polymerization, introduce classic theories. The material in the remainder of the chapter arises from the study of macromolecular interactions and is motivated by current research aimed at uncovering and understanding how large numbers of proteins (hundreds to thousands) interact in cells [7],... 

Both the structures and the dynamics of macromolecules are studied in terms of statistical thermodynamics. In the following section, we introduce the helix-coil transition theory that accounts for formation of the ubiquitous a-helical structure of peptide chains in aqueous solution. To a large extent, current research on protein... 

In summary, we have therefore seen that poly-L-lysine presents a valuable model for a partially helical polypeptide chain, one which is amenable to conformational analysis by optical rotatory dispersion. The method by which residues in a helical conformation may be discerned and counted against a background of disordered regions has been illustrated with this polypeptide under almost ideal conditions. The adequacy of the method is corroborated by copolymers a step closer to proteins in complexity, but some of the limitations that will be encountered in its application to proteins are already foreshadowed. Before this application is discussed, however, two other phenomena relevant to protein structure that are clearly exhibited in synthetic polypeptides, the helix-coil transition and the /3-conformation, will be considered. 

Bastos, M., Pease, J. H., Wemrner, D. E., Murphy, K. P., and Connelly, P. R. (2001) Thermodynamics of the helix-coil transition Binding of S15 and a hybrid sequence, disulfide stabilized peptide to the S-protein. Proteins 42, 523-530. 

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