Effect of subdomain interactions on methyl group dynamics in the hydrophobic core of villin headpiece protein.
Thermostable villin headpiece protein (HP67) consists of the N-terminal subdomain (residues 10-41) and the autonomously folding C-terminal subdomain (residues 42-76) which pack against each other to form a structure with a unified hydrophobic core. The X-ray structures of the isolated C-terminal subdomain (HP36) and its counterpart in HP67 are very similar for the hydrophobic core residues. However, fine rearrangements of the free energy landscape are expected to occur because of the interactions between the two subdomains. We detect and characterize these changes by comparing the µs-ms time scale dynamics of the methyl-bearing side chains in isolated HP36 and in HP67. Specifically, we probe three hydrophobic side chains at the interface of the two subdomains (L42, V50, and L75) as well as at two residues far from the interface (L61 and L69). Solid-state deuteron NMR techniques are combined with computational modeling for the detailed characterization of motional modes in terms of their kinetic and thermodynamic parameters. The effect of interdomain interactions on side chain dynamics is seen for all residues but L75. Thus, changes in dynamics because of subdomain interactions are not confined to the site of perturbation. One of the main results is a two- to threefold increase in the value of the activation energies for the rotameric mode of motions in HP67 compared with HP36. Detailed analysis of configurational entropies and heat capacities complement the kinetic view of the degree of the disorder in the folded state.
Department of Chemistry, University of Alaska Anchorage, Anchorage, Alaska.
Liliya
L
Vugmeyster
Tien
T
Do
Dmitry
D
Ostrovsky
Riqianq
R
Fu
D000818:Animals; D002645:Chickens; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D019277:Entropy; D057927:Hydrophobic and Hydrophilic Interactions; D007700:Kinetics; D008840:Microfilament Proteins / Q000737:chemistry*; D008958:Models, Molecular; D016900:Neurofilament Proteins / Q000737:chemistry*; D019906:Nuclear Magnetic Resonance, Biomolecular; D010446:Peptide Fragments / Q000737:chemistry*; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D013816:Thermodynamics
D008840:Microfilament Proteins; D016900:Neurofilament Proteins; D010446:Peptide Fragments; C026615:villin; C115223:villin headpiece subdomain peptide
hydrophobic core; protein dynamics; solid-state NMR; villin headpiece