2018/06/30 by Hyuntae Na, Daniel ben‐Avraham, Daniel ben-Avraham +1 · 3 citations
Biochemistry, Genetics and Molecular Biology · Chemistry · Materials Science · Mathematics · #Biological system #Biology #Bond length #Cartesian coordinate system #Chemistry #Computer science #Crystallography #Degrees of freedom (physics and chemistry) #Dihedral angle #Eigenvalues and eigenvectors #Enzyme Structure and Function #Gaussian #Geometry #Hydrogen bond #Mathematics #Molecule #Normal mode #Physics #Protein Data Bank #Protein Data Bank (RCSB PDB) #Protein Structure and Dynamics #Protein structure #Quantum mechanics #RNA and protein synthesis mechanisms #Representation (politics) #Vibration #q-bio.BM
paper · pdf · doi:10.1088/1478-3975/aae333
published in Physical Biology 16(1), 016003 (IOP Publishing) · 20 pages plus 7 figures/tables (version to conform with referees remarks)
arxiv created 2018/09/04 · openalex publication_date 2018/09/21 · arxiv updated 2018/12/05 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05
biomolecules with better than 2.8 Å resolution. The listing of the identities and coordinates of the atoms comprising each macromolecule permits an analysis of the slow-time vibrational response of these large systems to minor perturbations. 3D video animations of individual modes of oscillation demonstrate how regions interdigitate to create cohesive collective motions, providing a comprehensive framework for and familiarity with the overall 3D architecture. Furthermore, the isolation and representation of the softest, slowest deformation coordinates provide opportunities for the development of mechanical models of enzyme function. The eigenvector decomposition, therefore, must be accurate, reliable as well as rapid to be generally reported upon. We obtain the eigenmodes of a 1.2 Å 34 kDa PDB entry using either exclusively heavy atoms or partly or fully reduced atomic sets; Cartesian or internal coordinates; interatomic force fields derived either from a full Cartesian potential, a reduced atomic potential or a Gaussian distance-dependent potential; and independently developed software. These varied technologies are similar in that each maintains proper stereochemistry either by use of dihedral degrees of freedom which freezes bond lengths and bond angles, or by use of a full atomic potential that includes realistic bond length and angle restraints. We find that the shapes of the slowest eigenvectors are nearly identical, not merely similar.