WordNet

entropy calculated from the probability that a state could be reached by chance alone
a symmetrical arrangement of the parts of a thing

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〈C〉形態,構造;調和のとれた配置(配列) / 〈U〉(型・性格などべの)一至,適合,適応《+『to』+『名』》
エントロビー(物質の熱力学上の量) / (熱などエネルギーの)拡散,同質化

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出典(authority):フリー百科事典『ウィキペディア（Wikipedia）』「2015/11/23 00:04:52」(JST)

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Conformational entropy is the entropy associated with the number of conformations of a molecule. The concept is most commonly applied to biological macromolecules such as proteins and RNA, but also be used for polysaccharides and other molecules. To calculate the conformational entropy, the possible conformations of the molecule may first be discretized into a finite number of states, usually characterized by unique combinations of certain structural parameters, each of which has been assigned an energy. In proteins, backbone dihedral angles and side chain rotamers are commonly used as parameters, and in RNA the base pairing pattern may be used. These characteristics are used to define the degrees of freedom (in the statistical mechanics sense of a possible "microstate"). The conformational entropy associated with a particular structure or state, such as an alpha-helix, a folded or an unfolded protein structure, is then dependent on the probability or the occupancy of that structure.

The entropy of heterogeneous random coil or denatured proteins is significantly higher than that of the folded native state tertiary structure. In particular, the conformational entropy of the amino acid side chains in a protein is thought to be a major contributor to the energetic stabilization of the denatured state and thus a barrier to protein folding.^[1] However, a recent study has shown that side-chain conformational entropy can stabilize native structures among alternative compact structures.^[2] The conformational entropy of RNA and proteins can be estimated; for example, empirical methods to estimate the loss of conformational entropy in a particular side chain on incorporation into a folded protein can roughly predict the effects of particular point mutations in a protein. Side-chain conformational entropies can be defined as Boltzmann sampling over all possible rotameric states:^[3]

where is the gas constant and is the probability of a residue being in rotamer .^[3]

The limited conformational range of proline residues lowers the conformational entropy of the denatured state and thus increases the energy difference between the denatured and native states. A correlation has been observed between the thermostability of a protein and its proline residue content.^[4]

References

^ Doig AJ, Sternberg MJE. (1995). Side-chain conformational entropy in protein folding. Protein Science 4:2247-51.
^ Zhang J, Liu JS (2006) On Side-Chain Conformational Entropy of Proteins. PLoS Comput Biol 2(12): e168. doi:10.1371/journal.pcbi.0020168
^ ^a ^b Pickett SD, Sternberg MJ. (1993). Empirical scale of side-chain conformational entropy in protein folding. J Mol Biol 231(3):825-39.
^ Watanabe K., Masuda T., Ohashi H., Mihara H. & Suzuki Y. Multiple proline substitutions cumulatively thermostabilize Bacillus cereus ATCC7064 oligo-1,6-glucosidase. Irrefragable proof supporting the proline rule. Eur J Biochem 226,277-83 (1994).

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English Journal

Binding analysis of carbon nanoparticles to human immunoglobulin G: Elucidation of the cytotoxicity of CNPs and perturbation of immunoglobulin conformations.

Zhang S1, Yang H2, Ji X3, Wang Q4.
Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy.Spectrochim Acta A Mol Biomol Spectrosc.2016 Feb 5;154:33-41. doi: 10.1016/j.saa.2015.10.014. Epub 2015 Oct 21.
The chemical compositions, sizes and fluorescent properties of synthesized carbon nanoparticles (CNPs) were characterized. Escherichia coli (E. coli) cells were used as a model to study the cytotoxicity of CNPs, and the results of the cellular uptake of CNPs yielded excellent results: the CNPs demon
PMID 26505286

Ensemble and single-molecule biophysical characterization of D17.4 DNA aptamer-IgE interactions.

Poongavanam MV1, Kisley L2, Kourentzi K3, Landes CF4, Willson RC5.
Biochimica et biophysica acta.Biochim Biophys Acta.2016 Jan;1864(1):154-64. doi: 10.1016/j.bbapap.2015.08.008. Epub 2015 Aug 22.
BACKGROUND: The IgE-binding DNA aptamer 17.4 is known to inhibit the interaction of IgE with the high-affinity IgE Fc receptor FcεRI. While this and other aptamers have been widely used and studied, there has been relatively little investigation of the kinetics and energetics of their interactions
PMID 26307469

Thermodynamics and kinetics of inhibitor binding to human equilibrative nucleoside transporter subtype-1.

Rehan S1, Ashok Y1, Nanekar R1, Jaakola VP2.
Biochemical pharmacology.Biochem Pharmacol.2015 Dec 15;98(4):681-9. doi: 10.1016/j.bcp.2015.09.019. Epub 2015 Sep 30.
Many nucleoside transport inhibitors are in clinical use as anti-cancer, vasodilator and cardioprotective drugs. However, little is known about the binding energetics of these inhibitors to nucleoside transporters (NTs) due to their low endogenous expression levels and difficulties in the biophysica
PMID 26428002

Japanese Journal

Thermodynamic implications of high Q10 of thermoTRP channels in living cells

Ito Etsuro,Ikemoto Yusuke,Yoshioka Tohru
BIOPHYSICS 11(0), 33-38, 2015
… The Gibbs free energy equation shows that a large entropy is required to compensate for this large enthalpy and permit activation of the channels, suggesting a large conformational change of the channels. … These large values of enthalpy and entropy seem to be a match for the values of the unfolding process of globular proteins. …
NAID 130004940809

Allosteric Regulation of the Ligand-Binding Ability of Zinc Porphyrins with Sterically Bulky Shielding Units by Metal Complexation

Ninomiya Yoshikazu,Kozaki Masatoshi,Suzuki Shuichi [他],Okada Keiji
Bulletin of the Chemical Society of Japan 87(11), 1195-1201, 2014
… The allosteric system forms an [Fe(bpy)3]-type complex in the presence of Fe(II) ions and induces a large conformational change in the alkyl side chains and shielding units, in which the anthracene groups would cover both the top and bottom of the porphyrin Zn(II) center. …
NAID 130004677567

Molecular Dynamics of Octyl Urea Crystals Analyzed by Solid-state NMR

Ohashi Ryutaro,Wakabayashi Gou,Mizuno Motohiro,Soeta Takahiro,Hashimoto Masao,Yamamura Kimiaki
Chemistry Letters 41(11), 1433-1435, 2012
… The solid–solid phase transition of octyl urea has a large entropy, that is comparable to its melting entropy. … In this study, octyl urea was examined by solid-state NMR in order to investigate the sources of the large transition entropy. … The NMR results indicate that conformational exchange and molecular motion in the octyl urea are the sources of the large entropy of the solid–solid transition. …
NAID 130004426391