Citation:
Lin-xi Zhanga, Ting-ting Sunb, Xiang-hong Wanga. RATE OF INTRAMOLECULAR CONTACT FORMATION IN PROTEINS[J]. Chinese Journal of Polymer Science,
2007, 25(2): 197-201.
RATE OF INTRAMOLECULAR CONTACT FORMATION IN PROTEINS
摘要:
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 with = 1.43 for the contact radius a = 0.40 nm and = 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 = 6.4 106 cm2/s, which is close to the result that is found for monomer diffusion.
English
RATE OF INTRAMOLECULAR CONTACT FORMATION IN PROTEINS
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 with = 1.43 for the contact radius a = 0.40 nm and = 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 = 6.4 106 cm2/s, which is close to the result that is found for monomer diffusion.
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