Protein Simulations: 66 (Advances in Protein Chemistry)
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Conference paper. This is a preview of subscription content, log in to check access. Alder, T. Wainwright, Phase transition for a hard sphere system. Levitt, The birth of computational structural biology. McCammon, B. Gelin, M. Karplus, Dynamics of folded proteins. Nature , — CrossRef Google Scholar. Ryckaert, G. Ciccotti, H. Berendsen, Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n -alkanes. Jorgensen, J. Chandrasekhar, J. Madura, R. Impey, M. Klein, Comparison of simple potential functions for simulating liquid water.
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Reyes, P. Kollman, Biomolecular simulations: Recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. Hockney, J. Eastwood, Computer simulation using particles Google Scholar.
York, L. Larson, C. Snow, M. Shirts, V.
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Pande, Folding home and genome home: Using distributed computing to tackle previously intractable problems in computational biology. Genomics Google Scholar. Bowers, E. Chow, H. Xu, R. Dror, M. Eastwood, B. Gregersen, J. Klepeis, I. Kolossvary, M. Moraes, F. Sacerdoti et al.
Shaw, M. Deneroff, R. Dror, J.
Kuskin, R. Larson, J. Salmon, C. Young, B. Batson, K. Bowers, J. Chao et al. Daggett, Long timescale simulations. Figure 11 shows the result at K. Figure 9.
Figure From Figures 4 , 9 — 11 , we compare the effects of the temperature on each system in the AMD simulations. We can see very clearly that K has the smallest RMSD values with the highest percentage in the four temperatures. In other words, the proportion of structure of native or close to native state is the highest by AMD simulation at K.
We can also see that the 2KFE system has the native state structure at K, and no folding state is found in the top three cluster at three high temperatures. To summarize, we can conclude that the efficiency of AMD simulations at different temperatures is higher than that of MD simulations, and different systems show different temperature sensitivities; however, K is generally the most favorable temperature for protein folding.
In addition, temperature has the most significant effect on the system of 2KFE. Next, Figures S4—S6 in the Supporting Information illustrates the detailed development about the fractional native helix content during the last 20 ns of the AMD simulation and MD simulation at different temperature , , K for eight proteins, respectively. It is clear that the overall fractional native helix contents in AMD simulation are higher than that in MD simulation, which is in excellent agreement with the above analysis.
We can clearly see that in the AMD simulation the values of the RMSD of the most populated states of all systems at all temperatures is smaller than that in MD simulation, except for the system of 2I9M at K temperature. The result indicates that the AMD simulation is highly efficient for studying the folding of proteins. It should be noted here that the results based on a single AMD simulation trajectory may not be sufficient to support the conclusion that AMD simulations accelerate protein folding.
So, we perform another set of independent AMD simulation of the eight proteins starting from the linear initial structure at K. Figure 12 shows the plots of the two trajectories for eight different systems, and the evolution of RMSD value over time is analyzed. It is observed from the figure that although the details of the folding paths and steps for each individual trajectory are not exactly the same, for both trajectories, the proteins fold into the corrected native structures by AMD simulation. The red curve denotes the trajectory discussed in the current paper and the black curve denotes another trajectory with the same starting structure but different random seed for momentum.
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Second, it does not require the knowledge of the free energy surface in advance and does not need to define the reaction coordinates in advance. The results of the AMD and MD simulations of the eight systems at K are analyzed and compared using the following six aspects: the RMSD, the native contacts, the cluster analysis, the process of the protein folding, the R g and the free energy landscape. The final RMSD values are 0. The native contacts analysis shows that the fraction of the native contacts of these eight proteins in AMD simulation are clearly higher than those in the MD simulation, indicating that the structures generated from AMD simulations are more consistent with the native states.
Cluster analysis shows that the conformations in the native state cluster have the highest occupancy for AMD simulations at K. Then, the folding pathways are further discussed and analyzed for the eight proteins using AMD simulations at K. Although these proteins have different folding pathways, they all finally fold into their native structures. Free energy landscape analysis shows that the structures in the lowest free energy state in AMD simulation at K are the native structures.
Investigating Protein-Protein and Protein-Ligand Interactions by Molecular Dynamics Simulations
R g s values fluctuate around their corresponding native values suggesting that these folding simulations are generally completed. The above described results show that AMD simulations can correctly fold the proteins into native structures, but the same protein folding fail when the traditional MD simulations are carried out for the same times as the AMD simulation at K. It was also found that K is the most suitable temperature for the folding of all proteins. In this report, AMD is used to fold helical protein in explicit water.
Protein Simulations, Volume 66 - 1st Edition
We examine the applicability of AMD simulation in folding by testing a series of proteins and find that it has the advantages of fast speed and small calculation. The efficiency and accuracy of the AMD simulation method compared with the traditional MD simulation method are verified. Generally, the AMD simulation results obtained here are very encouraging for the further use of this method in the studies the protein folding. Our studies on the folding of these eight proteins will provide useful guidance for other protein folding investigations.
LD designed this study and revised the manuscript. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Andersen, O.