Open AccessNormal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme.
Author(s) -
Bernard R. Brooks,
Martin Karplus
Publication year - 1985
Publication title -
proceedings of the national academy of sciences of the united states of america
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.011
H-Index - 771
eISSN - 1091-6490
pISSN - 0027-8424
DOI - 10.1073/pnas.82.15.4995
Subject(s) - hinge , dihedral angle , eigenvalues and eigenvectors , bending , macromolecule , normal mode , delocalized electron , lysozyme , chemistry , trimer , nucleic acid , energy minimization , adiabatic process , vibration , materials science , crystallography , molecular physics , physics , molecule , computational chemistry , classical mechanics , nuclear magnetic resonance , biochemistry , thermodynamics , quantum mechanics , dimer , hydrogen bond
A method is presented for finding particular normal modes for large molecules such as proteins and nucleic acids. The method is based on an iterative approach that extracts eigenvectors of interest from the full second-derivative matrix. Application of the method to the interdomain (hinge-bending) motion of lysozyme yields a frequency of 3.6 cm-1. This is similar to the value obtained from earlier adiabatic-energy-minimization studies. Analysis of the mode shows that the relaxation associated with the hinge bending is highly delocalized; that is, the dihedral angle and energy changes are distributed over many residues, including some (e.g., Trp-28) that are distant from the cleft and hinge region.