We proposed a practical way for mapping the results of coarse-grained molecular simulations to the observables in hydrogen change experiments. By combining an atomic-interaction based coarse-grained model with an all-atom structure reconstruction algorithm, we reproduced the experimental hydrogen exchange data with reasonable accuracy using molecular dynamics simulations. We also showed that the coarse-grained model can be further improved by imposing experimental restraints from hydrogen exchange data via an iterative optimization strategy. These results suggest that it is feasible to develop an integrative molecular simulation scheme by incorporating the hydrogen exchange data into the coarse-grained molecular dynamics simulations and therefore help to overcome the accuracy bottleneck of coarse-grained models.
机构:
School of Physics,National Laboratory of Solid State Microstructure,and Collaborative Innovation Center of Advanced Microstructures,Nanjing UniversitySchool of Physics,National Laboratory of Solid State Microstructure,and Collaborative Innovation Center of Advanced Microstructures,Nanjing University
祝文涛
李文飞
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School of Physics,National Laboratory of Solid State Microstructure,and Collaborative Innovation Center of Advanced Microstructures,Nanjing UniversitySchool of Physics,National Laboratory of Solid State Microstructure,and Collaborative Innovation Center of Advanced Microstructures,Nanjing University
机构:
Univ Penn, Johnson Res Fdn, Dept Biochem & Biophys, Perelman Sch Med, Philadelphia, PA 19104 USAUniv Penn, Johnson Res Fdn, Dept Biochem & Biophys, Perelman Sch Med, Philadelphia, PA 19104 USA
Skinner, John J.
Lim, Woon K.
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Pusan Natl Univ, Coll Nat Sci, Dept Mol Biol, Pusan 609735, South KoreaUniv Penn, Johnson Res Fdn, Dept Biochem & Biophys, Perelman Sch Med, Philadelphia, PA 19104 USA
Lim, Woon K.
Bedard, Sabrina
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Univ Penn, Johnson Res Fdn, Dept Biochem & Biophys, Perelman Sch Med, Philadelphia, PA 19104 USAUniv Penn, Johnson Res Fdn, Dept Biochem & Biophys, Perelman Sch Med, Philadelphia, PA 19104 USA
Bedard, Sabrina
Black, Ben E.
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Univ Penn, Johnson Res Fdn, Dept Biochem & Biophys, Perelman Sch Med, Philadelphia, PA 19104 USAUniv Penn, Johnson Res Fdn, Dept Biochem & Biophys, Perelman Sch Med, Philadelphia, PA 19104 USA
Black, Ben E.
Englander, S. Walter
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Univ Penn, Johnson Res Fdn, Dept Biochem & Biophys, Perelman Sch Med, Philadelphia, PA 19104 USAUniv Penn, Johnson Res Fdn, Dept Biochem & Biophys, Perelman Sch Med, Philadelphia, PA 19104 USA
机构:
Indian Inst Sci, NMR Res Ctr, Bangalore 560012, Karnataka, India
Indian Inst Sci, Dept Biochem, Bangalore 560012, Karnataka, IndiaIndian Inst Sci, NMR Res Ctr, Bangalore 560012, Karnataka, India
Thakur, Anushikha
Chandra, Kousik
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Indian Inst Sci, NMR Res Ctr, Bangalore 560012, Karnataka, IndiaIndian Inst Sci, NMR Res Ctr, Bangalore 560012, Karnataka, India