title: Analysis of energy stabilization inside the hydrophobic core of rubredoxin.
abstract: 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.
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nam. 2, 16610 Prague 6, Czech Republic.
authors.forename: Karel
authors.initials: K
authors.lastname: Berka
authors.forename: Pavel
authors.initials: P
authors.lastname: Hobza
authors.forename: Jirí
authors.initials: J
authors.lastname: Vondrásek
mesh_terms: D000596:Amino Acids / Q000737:chemistry*; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D011487:Protein Conformation; D012416:Rubredoxins / Q000737:chemistry*
chemical_list: D000596:Amino Acids; D012416:Rubredoxins