Entropy enthalpy compensation is seen for a wide variety of ligand interactions. Are they relevant to protein folding problem?
In discussing computational chemistry coupling Gibbs energy, and this change is drastically with the configuration of the protein. Speaking enthalpic-entropic compensation refers to drastic changes of entropy and enthalpy for the Gibbs energy changes are smooth. So I think that interactions with the ligand are very relevant
I am not sure I understand your question, but to answer what I think you're asking, protein folding generally involves both a large entropic cost, and a large enthalpic gain. These two contributions to the free energy almost cancel, resulting in a small negative folding free energy in a given temperature range, usually just enough to provide the conformational stability needed for function. These topics are discussed in a clear manner in this book http://www.google.no/books?id=Vbb01Eo8VBAC
The slope of entropy enthalpy change which has dimension of 1/T* , where T* is some pseudo temperature remains constant for a wide variety of thermodynamic systems. There are two questions of very general nature :
(a)Whether this pseudo temperature carries any signature of a given class of protein ligand pair
(b) Whether this compensation can be considered as a new thermodynamic principle
(c) Whether for a metabolic network , in a coupled system of reactions ,whether enthalpy of reaction is compensated by entropy of other reactions.
In a more general context can we extrapolate the entropy enthalpy compensation as a guiding principle of simulation , particularly in situations where multiple optima is possible (like the rugged landscape problem of protein folding , and Crick's theory of dreams).
Intramolecular hydrogen (H)-bonds play an extremely important role in stabilizing protein structures. To form these intramolecular H-bonds, nascent unfolded polypeptide chains need to escape from hydrogen bonding with surrounding polar water molecules under the solution conditions that require entropy-enthalpy compensations, according to the Gibbs free energy equation and the change in enthalpy. Here, by analyzing the spatial layout of the side-chains of amino acid residues in experimentally determined protein structures, we reveal a protein-folding mechanism based on the entropy-enthalpy compensations that initially driven by laterally hydrophobic collapse among the side-chains of adjacent residues in the sequences of unfolded protein chains. This hydrophobic collapse promotes the formation of the H-bonds within the polypeptide backbone structures through the entropy-enthalpy compensation mechanism, enabling secondary structures and tertiary structures to fold reproducibly following explicit physical folding codes and forces. The temperature dependence of protein folding is thus attributed to the environment dependence of the conformational Gibbs free energy equation. The folding codes and forces in the amino acid sequence that dictate the formation of β-strands and α-helices can be deciphered with great accuracy through evaluation of the hydrophobic interactions among neighboring side-chains of an unfolded polypeptide from a β-strand-like thermodynamic metastable state. The folding of protein quaternary structures is found to be guided by the entropy-enthalpy compensations in between the docking sites of protein subunits according to the Gibbs free energy equation that is verified by bioinformatics analyses of a dozen structures of dimers. Protein folding is therefore guided by multistage entropy-enthalpy compensations of the system of polypeptide chains and water molecules under the solution conditions. The details are illustrated in this paper https://www.mdpi.com/1422-0067/22/17/9653
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