Anisotropic atomic motions in high-resolution protein crystallography molecular dynamics simulations.
Molecular dynamics (MD) simulations using empirical force fields are popular for the study of proteins. In this work, we compare anisotropic atomic fluctuations in nanosecond-timescale MD simulations with those observed in an ultra-high-resolution crystal structure of crambin. In order to make our comparisons, we have developed a compact graphical technique for assessing agreement between spatial atomic distributions determined by MD simulations and observed anisotropic temperature factors.
Burden
Conrad J
CJ
Centre for Bioinformation Science, Mathematical Sciences Institute, Australian National University, Canberra, ACT, Australia. Conrad.Burden@anu.edu.au
Oakley
Aaron J
AJ
D000465:Algorithms; D016880:Anisotropy; D001703:Biophysics / Q000379:methods*; D001937:Brassica / Q000378:metabolism; D003198:Computer Simulation; D003460:Crystallization; D018360:Crystallography, X-Ray / Q000379:methods*; D003627:Data Interpretation, Statistical; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D036103:Nanotechnology / Q000379:methods; D010940:Plant Proteins / Q000737:chemistry; D013696:Temperature
D010940:Plant Proteins; C024934:crambin protein, Crambe abyssinica