摘要:
IntroductionVarious experimental techniques such as neutron scattering, Mössbauer spectroscopy, and X-ray scattering have shown the presence of a temperature-dependent transition in protein dynamics at around 180–220 K.1–16This dynamical transition has also been reproduced using Molecular Dynamics (MD) simulation techniques.17–205,14,22The transition is thought to be associated with a transition in the dynamics of protein from harmonic to anharmonic, and is often referred to as the protein glass transition.16,23A number of experiments have indicated that when a protein is solvated the dynamical transition is strongly coupled to the surrounding solvent.1,5,7,24–27The observed dependence of the dynamical transition behavior on the solvent composition leads to the question of the role of solvent in the dynamical transition.7,18Simulations have demonstrated that proteinsin vacuoundergo the dynamical transition.17,18,21However, whether solvent drives the dynamical transition in a hydrated protein is still open to question. Here we probe solvent effects by using dual heatbath methods to set the protein and its solvent at different temperatures. This approach enables the distinction of features inherent to the protein energy landscape from features due to properties of the solvent. Dual heatbath methods differ from standard simulation techniques in which the system has a constant and uniform temperature, in that different parts are set at different temperatures.Fig. 1presents a schematic diagram of how such simulations are performed. The method involves using Nosé–Hoover–Chain (NHC) thermostats to set the temperatures of the different parts.28,29A similar approach, using the Nosé–Hoover thermostat, has previously been used by Vitkupet al.and confirmed the importance of solvent effects on internal fluctuations.30The present results extend this work and examine in greater detail the effect of the solvent on the dynamical transition in proteins.Schematic of dual-heatbath methods.Our results indicate the protein side-chain atoms to be more mobile than the backbone atoms and that the protein layers closest to the solvent are the most affected by the dynamical transition, whereas the protein core is seen not to show any transition in fast dynamics along the observed temperature range. The results of the dual heatbath simulations show that cold solvent effectively cages protein motions.
ISSN:1460-2733
DOI:10.1039/b209839c
出版商:RSC
年代:2002
数据来源: RSC