Alexander L. Tournier

Translational hydration water dynamics drives the protein glass transition.

Experimental and computer simulation studies have revealed the presence of a glass-like transition in the internal dynamics of hydrated proteins at approximately 200 K involving an increase of the amplitude of anharmonic dynamics. This increase in flexibility has been correlated with the onset of protein activity. Here, we determine the driving force behind the protein transition by performing molecular dynamics simulations of myoglobin surrounded by a shell of water. A dual heat bath method is used with which, in any given simulation, the protein and solvent are held at different temperatures, and sets of simulations are performed varying the temperature of the components. The results show that the protein transition is driven by a dynamical transition in the hydration water that induces increased fluctuations primarily in side chains in the external regions of the protein. The water transition involves activation of translational diffusion and occurs even in simulations where the protein atoms are held fixed.

Time-resolved computational protein biochemistry: Solvent effects on interactions, conformational transitions and equilibrium fluctuations

Solvent plays an important role in modulating internal motions of proteins. Here we present a computational method for including solvent effects on charge-charge interactions and on pathways between functional protein conformations, and examine solvent effects on equilibrium internal fluctuations in proteins. A computationally efficient charge reparametrisation method is presented that satisfactorily reproduces the electrostatic interactions present in a full continuum Poisson-Boltzmann representation. The application of charge reparametrisation in the calculation of a large-scale conformational transition pathway in a protein, annexin V, is illustrated. We also examine solvent effects on fast (picosecond timescale) internal protein dynamics. Nosé-Hoover dual heatbath molecular dynamics simulations are performed. These simulations allow the solvent region to be fixed at one temperature and the protein at another. The results of the Nosé-Hoover simulations on hydrated myoglobin confirm that the solvent temperature strongly influences the protein fluctuations. We consider to what extent the solvent can be considered to determine the high temperature protein dynamics.

Solvent caging of internal motions in myoglobin at low temperaturesThis paper was originally presented as a poster at the Faraday Discussion 122 meeting.

Experimental and simulation studies have reported the presence of a transition in the internal dynamics of proteins at 220 K. This transition has been correlated with the onset of activity in several proteins. The role of the solvent in the dynamical transition has been the subject of increased attention. Here simulation techniques are used to distinguish dynamical features inherent to the protein energy landscape from those induced by the surrounding solvent. The present results indicate that the protein dynamical transition primarily affects the side-chains on the outer layers of the protein. Moreover, the results indicate that the solvent restrains protein motions at low temperatures.

Conformational Transitions in Proteins and Membranes

An understanding of protein and biological membrane function requires the realization that these objects are dynamic. This present survey treats simulationbased methods for investigating internal motions in soluble and membrane proteins and for probing the dynamics of membranes themselves.