Evidence of functional protein dynamics from X-ray crystallographic ensembles.
It is widely recognized that representing a protein as a single static conformation is inadequate to describe the dynamics essential to the performance of its biological function. We contrast the amino acid displacements below and above the protein dynamical transition temperature, T(D)∼215K, of hen egg white lysozyme using X-ray crystallography ensembles that are analyzed by molecular dynamics simulations as a function of temperature. We show that measuring structural variations across an ensemble of X-ray derived models captures the activation of conformational states that are of functional importance just above T(D), and they remain virtually identical to structural motions measured at 300K. Our results highlight the ability to observe functional structural variations across an ensemble of X-ray crystallographic data, and that residue fluctuations measured in MD simulations at room temperature are in quantitative agreement with the experimental observable.
Kohn
Jonathan E
JE
Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America.
Afonine
Pavel V
PV
Ruscio
Jory Z
JZ
Adams
Paul D
PD
Head-Gordon
Teresa
T
D000818:Animals; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009113:Muramidase / Q000737:chemistry*; D011487:Protein Conformation
C421864:hen egg lysozyme; D009113:Muramidase