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Analysis of Energy Stabilization inside the Hydrophobic Core of Rubredoxin
Author(s) -
Berka Karel,
Hobza Pavel,
Vondrášek Jiří
Publication year - 2009
Publication title -
chemphyschem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.016
H-Index - 140
eISSN - 1439-7641
pISSN - 1439-4235
DOI - 10.1002/cphc.200800401
Subject(s) - rubredoxin , chemistry , van der waals force , globular protein , chemical physics , hydrogen bond , hydrophobic effect , non covalent interactions , electrostatics , crystallography , static electricity , dispersion (optics) , covalent bond , protein structure , computational chemistry , molecule , organic chemistry , physics , biochemistry , quantum mechanics , optics
Dispersion interactions are mainly responsible for holding together the structural arrangement of amino‐acid residues forming the hydrophobic core of the protein rubredoxin (see picture), according to symmetry‐adapted perturbation theory calculations.The hydrophobic core of globular proteins is responsible for major stabilization of the protein tertiary structure. The prevailing amino‐acid residues in the core are of aliphatic or aromatic character, and therefore, the core in a folded protein structure is mostly stabilized by noncovalent interactions of van der Waals origin between the amino‐acid side chains. Herein, we present a theoretical analysis of the interaction energy between the amino acids of the hydrophobic core of the small globular protein rubredoxin (Rd) based on the symmetry‐adapted perturbation theory (SAPT) method. The results show uniform proportions between the second‐order dispersion and first‐order electrostatic energy terms in favor of dispersion interaction, which plays a major role in the stabilization of this important structural element. To demonstrate the contrast between systems stabilized by different mechanisms, we perform a SAPT analysis of the typical hydrogen bonds involved in the formation of protein secondary structure elements in Rd, where dispersion still plays a non‐negligible role but electrostatic energy is the major stabilizing factor.