A theoretical analysis on characteristics of protein structures induced by cold denaturation

The Journal of Chemical Physics
Hiraku OshimaMasahiro Kinoshita

Abstract

Yeast frataxin is a protein exhibiting cold denaturation at an exceptionally high temperature (280 K). We show that the microscopic mechanism of cold denaturation, which has recently been suggested by us [Yoshidome and Kinoshita, Phys. Rev. E 79, 030905(R) (2009)], is also applicable to yeast frataxin. The hybrid of the angle-dependent integral equation theory combined with the multipolar water model and the morphometric approach is employed for calculating hydration thermodynamic quantities of the protein with a prescribed structure. In order to investigate the characteristics of the cold-denatured structures of yeast frataxin, we consider the entropy change upon denaturation comprising the loss of the water entropy and the gain in the protein conformational entropy. The minimum and maximum values of the conformational-entropy gain (i.e., the range within which the exact value lies) are estimated via two routes. The range of the water-entropy loss is then determined from the entropy change experimentally obtained [Pastore et al., J. Am. Chem. Soc. 129, 5374 (2007)]. We calculate the water-entropy loss upon the transition from the native structure to a variety of unfolded structures. We then select the unfolded structures for w...Continue Reading

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Citations

Sep 10, 2013·Journal of the American Chemical Society·Mikayel AznauryanBenjamin Schuler
Aug 16, 2011·Physical Chemistry Chemical Physics : PCCP·Hiraku OshimaMasahiro Kinoshita
Sep 28, 2012·Physical Chemistry Chemical Physics : PCCP·Takashi Yoshidome, Masahiro Kinoshita
Feb 16, 2010·The Journal of Chemical Physics·Satoshi YasudaMasahiro Kinoshita
Oct 9, 2012·The Journal of Chemical Physics·Satoshi YasudaMasahiro Kinoshita
Jul 5, 2013·The Journal of Chemical Physics·Hiraku Oshima, Masahiro Kinoshita
Dec 3, 2013·The Journal of Chemical Physics·Hirokazu MishimaMasahiro Kinoshita
Sep 15, 2014·The Journal of Chemical Physics·Satoshi YasudaMasahiro Kinoshita
Nov 29, 2014·The Journal of Chemical Physics·Prathit ChatterjeeNeelanjana Sengupta
May 28, 2013·Biophysical Journal·César A Ramírez-SarmientoVictoria Guixé
Dec 17, 2014·Nature Communications·Changwon YangYoungshang Pak
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Sep 1, 2013·Biophysics Reviews·Masahiro Kinoshita
Feb 26, 2011·Journal of the American Chemical Society·Takashi YoshidomeMasahiro Kinoshita
Dec 9, 2020·Journal of Chemical Theory and Computation·Changwon YangYoungshang Pak

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Methods Mentioned

BETA
protein folding
neutron scattering

Software Mentioned

CHARMM22
Itanium

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