RATE OF INTRAMOLECULAR CONTACT FORMATION IN PROTEINS
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RATE OF INTRAMOLECULAR CONTACT FORMATION IN PROTEINS
RATE OF INTRAMOLECULAR CONTACT FORMATION IN PROTEINS
高分子科学(英文版)2007年第2期 页码:197-201
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This research was financially supported by the National Natural Science Foundation of China (No. 20574052)();Program for New Century Excellent Talents in University,and Natural Science Foundation of Zhejiang Province (No. R404047)()
DOI:
中图分类号:O629.73
纸质出版:2007
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[1].RATE OF INTRAMOLECULAR CONTACT FORMATION IN PROTEINS[J].Chinese Journal of Polymer Science,2007(02):197-201.
Lin-xi Zhang, Ting-ting Sun and Xiang-hong Wang Department of Physics, Wenzhou University, et al. RATE OF INTRAMOLECULAR CONTACT FORMATION IN PROTEINS[J]. 2007, (2): 197-201.
[1].RATE OF INTRAMOLECULAR CONTACT FORMATION IN PROTEINS[J].Chinese Journal of Polymer Science,2007(02):197-201.DOI:
Lin-xi Zhang, Ting-ting Sun and Xiang-hong Wang Department of Physics, Wenzhou University, et al. RATE OF INTRAMOLECULAR CONTACT FORMATION IN PROTEINS[J]. 2007, (2): 197-201.DOI:
RATE OF INTRAMOLECULAR CONTACT FORMATION IN PROTEINS
we estimate the rate of contact formation between two residues in the interior of the proteins using the Szabo
Schulten
and Schulten formula with the probability distribution P(r) based on 375 proteins from PDB (Protein Data Bank). The probability distribution for residue pair in proteins is different from the Gaussian distribution
especially for short distance between two residues in proteins. The rate of contact formation in the interior of protein is discussed as a function of distance n (=|j-i|) between two residues
and it decreases monotonically with n and follows the scaling relationship of k∞n-γwithγ= 1.43 for the contact radius a= 0.40 nm andγ= 1.05 for a = 0.50 nm. The diffusion coefficient for the relative diffusion of two residues in the interior of proteins is estimated as D = 6.4×10-6 cm2/s
which is close to the result that is found for monomer diffusion.
Abstract
In this paper
we estimate the rate of contact formation between two residues in the interior of the proteins using the Szabo
Schulten
and Schulten formula with the probability distribution P(r) based on 375 proteins from PDB (Protein Data Bank). The probability distribution for residue pair in proteins is different from the Gaussian distribution
especially for short distance between two residues in proteins. The rate of contact formation in the interior of protein is discussed as a function of distance n (=|j-i|) between two residues
and it decreases monotonically with n and follows the scaling relationship of k∞n-γwithγ= 1.43 for the contact radius a= 0.40 nm andγ= 1.05 for a = 0.50 nm. The diffusion coefficient for the relative diffusion of two residues in the interior of proteins is estimated as D = 6.4×10-6 cm2/s
which is close to the result that is found for monomer diffusion.
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