Abstract
AbstractWe have extended our analytically derived PDB-NMA formulation, ATMAN [1], to include protein dimers using mixed internal and Cartesian coordinates. A test case on a 1.3Å resolution model of a small homodimer, ActVA-ORF6, consisting of two 112-residue subunits identically folded in a compact 50Å sphere, reproduces the distinct experimental Debye-Waller motility asymmetry for the two chains, demonstrating that structure sensitively selects vibrational signatures. The vibrational analysis of this PDB entry, together with biochemical and crystallographic data, demonstrates the cooperative nature of the dimeric interaction of the two subunits and suggests a mechanical model for subunit interconversion during the catalytic cycle.
Publisher
Cold Spring Harbor Laboratory
Reference24 articles.
1. “Atomic torsional modal analysis for high-resolution proteins,”;Phys. Rev. E,2015
2. “The normal modes of a protein: Native bovine pancreatic trypsin inhibitor,”;Int. J. Quantum Chem,1983
3. “Normal mode analysis of g-actin,”;J. Mol. Biol,1993
4. Collective Variable Description of Native Protein Dynamics
5. “Conventional nma as a better standard for evaluating elastic network models,”;Proteins: Structure, Function, and Bioinformatics,2015