Molecular dynamics simulation shows large volume fluctuations of proteins.
In this paper we present a new approach to study the volume fluctuations of proteins. From a 1 ns molecular dynamics simulation, the volume fluctuation of human lysozyme has been calculated. We used two different ways for the calculation. In the first one, the volume fluctuation is extracted directly from the trajectory. For the second one, a newly developed formalism based on principal component analysis is used. The r.m.s. volume fluctuations obtained from the two analyses agree well with each other. The isothermal intrinsic compressibility was found to be larger than the one reported by experiment. The difference is discussed and suggested to exist in the assumed uncertainty of the compressibility of hydrated water to deduce the isothermal intrinsic compressibility from the experimental value. Spectral analysis shows that low-frequency dynamics dominate the total volume fluctuation. The same aspect is found in the study using principal component analysis. This low-frequency region is related to large and slow motions of proteins. Therefore a long time dynamics simulation is necessary to describe the volume fluctuations of proteins.
Tama
F
F
Department of Chemistry, Graduate School of Science, Kyoto University, Japan.
Miyashita
O
O
Kitao
A
A
Go
N
N
D003198:Computer Simulation; D006801:Humans; D008958:Models, Molecular; D008962:Models, Theoretical; D009113:Muramidase / Q000737:chemistry*; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012984:Software; D014867:Water
D011506:Proteins; D014867:Water; D009113:Muramidase