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Enthalpy/entropy contributions to conformational KIEs: theoretical predictions and comparison with experiment.

ABSTRACT: Previous theoretical studies of Mislow's doubly-bridged biphenyl ketone 1 and dihydrodimethylphenanthrene 2 have determined significant entropic contributions to their normal (1) and inverse (2) conformational kinetic isotope effects (CKIEs). To broaden our investigation, we have used density functional methods to characterize the potential energy surfaces and vibrational frequencies for ground and transition structures of additional systems with measured CKIEs, including [2.2]-metaparacyclophane-d (3), 1,1'-binaphthyl (4), 2,2'-dibromo-[1,1'-biphenyl]-4,4'-dicarboxylic acid (5), and the 2-(N,N,N-trimethyl)-2'-(N,N-dimethyl)-diaminobiphenyl cation (6). We have also computed CKIEs in a number of systems whose experimental CKIEs are unknown. These include analogs of 1 in which the C=O groups have been replaced with CH? (7), O (8), and S (9) atoms and ring-expanded variants of 2 containing CH? (10), O (11), S (12), or C=O (13) groups. Vibrational entropy contributes to the CKIEs in all of these systems with the exception of cyclophane 3, whose isotope effect is predicted to be purely enthalpic in origin and whose Bigeleisen-Mayer ZPE term is equivalent to DDH‡. There is variable correspondence between these terms in the other molecules studied, thus identifying additional examples of systems in which the Bigeleisen-Mayer formalism does not correlate with DH/DS dissections.

SUBMITTER: Fong A

PROVIDER: S-EPMC6269852 | biostudies-other | 2013

REPOSITORIES: biostudies-other

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Enthalpy/entropy contributions to conformational KIEs: theoretical predictions and comparison with experiment.

Fong Aaron A Meyer Matthew P MP O'Leary Daniel J DJ

Molecules (Basel, Switzerland) 20130218 2

Previous theoretical studies of Mislow's doubly-bridged biphenyl ketone 1 and dihydrodimethylphenanthrene 2 have determined significant entropic contributions to their normal (1) and inverse (2) conformational kinetic isotope effects (CKIEs). To broaden our investigation, we have used density functional methods to characterize the potential energy surfaces and vibrational frequencies for ground and transition structures of additional systems with measured CKIEs, including [2.2]-metaparacyclophan ...[more]

PMID: 23429344

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Project description:Exploring the protein-folding problem has been a longstanding challenge in molecular biology and biophysics. 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.

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Enthalpy/entropy contributions to conformational KIEs: theoretical predictions and comparison with experiment.

Publications

Enthalpy/entropy contributions to conformational KIEs: theoretical predictions and comparison with experiment.

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