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Title: Effects of heme on the thermal stability of mesophilic and thermophilic cytochromes c: Comparison between experimental and theoretical results.
Authors: Oda, Koji
Kodama, Ryota
Yoshidome, Takashi
Yamanaka, Masaru
Sambongi, Yoshihiro
Kinoshita, Masahiro  kyouindb  KAKEN_id
Author's alias: 木下, 正弘
Keywords: biochemistry
biothermics
entropy
integral equations
molecular biophysics
molecular configurations
proteins
thermal stability
Issue Date: 14-Jan-2011
Publisher: American Institute of Physics
Journal title: The Journal of chemical physics
Volume: 134
Issue: 2
Thesis number: 025101
Abstract: We have recently proposed a measure of the thermal stability of a protein: the water-entropy gain at 25 °C upon folding normalized by the number of residues, which is calculated using a hybrid of the angle-dependent integral equation theory combined with the multipolar water model and the morphometric approach. A protein with a larger value of the measure is thermally more stable. Here we extend the study to analyses on the effects of heme on the thermal stability of four cytochromes c (PA c(551), PH c(552), HT c(552), and AA c(555)) whose denaturation temperatures are considerably different from one another despite that they share significantly high sequence homology and similar three-dimensional folds. The major conclusions are as follows. For all the four cytochromes c, the thermal stability is largely enhanced by the heme binding in terms of the water entropy. For the holo states, the measure is the largest for AA c(555). However, AA c(555) has the lowest packing efficiency of heme and the apo polypeptide with hololike structure, which is unfavorable for the water entropy. The highest stability of AA c(555) is ascribed primarily to the highest efficiency of side-chain packing of the apo polypeptide itself. We argue for all the four cytochromes c that due to covalent heme linkages, the number of accessible conformations of the denatured state is decreased by the steric hindrance of heme, and the conformational-entropy loss upon folding becomes smaller, leading to an enhancement of the thermal stability. As for the apo state modeled as the native structure whose heme is removed, AA c(555) has a much larger value of the measure than the other three. Overall, the theoretical results are quite consistent with the experimental observations (e.g., at 25 °C the α-helix content of the apo state of AA c(555) is almost equal to that of the holo state while almost all helices are collapsed in the apo states of PA c(551), PH c(552), and HT c(552)).
Rights: © 2011 American Institute of Physics
URI: http://hdl.handle.net/2433/134794
DOI(Published Version): 10.1063/1.3519814
PubMed ID: 21241149
Appears in Collections:Journal Articles

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