Molecular Dynamics Simulations Of The Unfolding Processes Of Protein GB1 And GpW

The folding and unfolding of proteins are fundamental biological processes in the cell.Fully understanding of the protein folding and unfolding dynamics at atomic resolution is of great importance in such as facilitating the prediction of protein structure from amino acid sequence and the drug design,the protein design and the study of molecular mechanism of neuron degenerative diseases which are due to protein misfolding and aggregation.Static native structure of proteins can be obtained by X-ray diffraction,nucleic magnetic resonance(NMR),and electron microscopy with atomic resolution,while dynamics of the protein folding and unfolding processes can be studied by biochemical denaturation experiment or single molecule manipulation techniques in usually coarser spatial-temporal scales.On the other hand,atomistic molecular dynamics(MD)simulation is a powerful theoretical approach to study the structure and the folding and unfolding dynamics of proteins.Molecular dynamics simulation allows the observations at the atomistic level which can not be achieved with the experimental methods.At the end of last century,detailed simulation studies were first applied to characterize protein folding/unfolding pathways.The basic ideas behind MD is to apply Newton's laws of motion to every atom of the system using empirical potential energy functions.Usually,due to the limitation of computational power,the study of protein folding/unfolding by the atomistic MD simulation is feasible to only small proteins.However,with the development of the computational technology during the last three decades,molecular dynamics simulations can be applied to larger system and provide more precise results nowadays.Here we apply molecular dynamics simulations to the two-state protein GB1 and downhill folding protein gpW to reveal the relationship of their free energy landscape and dynamics.We compare the unfolding force-extension curves by the steered molecular dynamics simulation and the potential of mean force(PMF)profiles of GB1 and gpW obtained from umbrella sampling simulations.Steered molecular dynamics(SMD)simulation is a computational approach for studying force-induced conformation transitions in biomolecules.The SMD simulations mimic force spectroscopy measurement in single molecule manipulation experiment like AFM.The umbrella sampling simulations use the biased potential to enhance the sampling of the protein conformations around the high energy regions in the conformational space.An obvious force peak in the force-extension curves of GB1 indicates the existence of the transition state.Three SMD simulations with the same parameters of GB1 reveal consistent features of its unfolding processes.Yet no intermediate states can be found in the force-extension curves of gpW,and the maxmimum unfolding force is below 200 pN,which is much smaller than the maxmimum unfolding force of GB1(above 600 pN),demonstrating that gpW is much less mechanically resistant than GB1.Meanwhile six simulations show little similarities,indicating that the unfolding processes of gpW have large variability.The potential of mean force(PMF)of GB1 and gpW obtained by the umbrella sampling simulations shows apparent difference:PMF of GB1 along the coordinate of extension exhibits two kink transition points,while PMF of gpW increases with extension smoothly.PMF of GB1 shows the possible existence of the second transition state at an extension of?4.4 nm,which differs from the previous general finding that GB1 is a two-state model,yet is consistent with the recent experimental finding in our laboratory.PMF of gpW confirms the previous finding of its downhill folding pathway.