Analysis of energy stabilization inside the hydrophobic core of rubredoxin.
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.
Berka
Karel
K
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.
Hobza
Pavel
P
Vondrásek
Jirí
J
D000596:Amino Acids / Q000737:chemistry*; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D011487:Protein Conformation; D012416:Rubredoxins / Q000737:chemistry*
D000596:Amino Acids; D012416:Rubredoxins