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A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations

Fabrizio Marinelli, Fabio Pietrucci, Alessandro Laio, Stefano Piana, Vijay S. Pande
2009 PLoS Computational Biology  
The model, although constructed from a biased simulation, has a quality similar to those extracted from the analysis of long unbiased molecular dynamics trajectories.  ...  Our work shows that, using biased molecular dynamics trajectories, it is possible to construct a model describing in detail the Trp-cage folding kinetics and thermodynamics in agreement with experimental  ...  A kinetic model of Trp-cage folding Trp-cage is a designed miniprotein that, due to its small size and fast folding rate, has been the object of several theoretical investigations.  ... 
doi:10.1371/journal.pcbi.1000452 pmid:19662155 pmcid:PMC2711228 fatcat:5bekmgc27vf6jjloykrhufbkvi

Sampling the multiple folding mechanisms of Trp-cage in explicit solvent

J. Juraszek, P. G. Bolhuis
2006 Proceedings of the National Academy of Sciences of the United States of America  
Folding events of Trp-cage have been observed in all-atom implicit solvent MD simulations (8, 9, 12) and in a coarse-grained model (15).  ...  We investigate the kinetic pathways of folding and unfolding of the designed miniprotein Trp-cage in explicit solvent.  ...  Vreede for a critical reading of the manuscript.  ... 
doi:10.1073/pnas.0606692103 pmid:17035504 pmcid:PMC1595309 fatcat:xrqaagfaubce5ncturgozgbehe

Insights On Protein Structure And Dynamics From Multiple Biased Molecular Dynamics Simulations

Fabrizio Marinelli, Stefano Piana, Fabio Pietrucci, Nevena Torodova, Irene Yarovsky, Alessandro Laio
2009 Biophysical Journal  
Using this technique it was possible to reversibly fold the Trp cage miniprotein in explicit solvent using only 40 ns of simulation on 8 replicas.  ...  This is caused by replicas having a preference for specific biasing potentials. 3036-Pos Board B83 Force Propagation in Proteins From Molecular Dynamics Simulations Wolfram Stacklies, Frauke Graeter.  ...  Board B81 Insights On Protein Structure And Dynamics From Multiple Biased Molecular Dynamics Simulations Fabrizio Marinelli 1 , Stefano Piana 2 , Fabio Pietrucci 1 , Nevena Torodova 3 , Irene Yarovsky  ... 
doi:10.1016/j.bpj.2008.12.3085 fatcat:ao55s3v5hzbvxkudpop5makj34

Two-state protein folding kinetics through all-atom molecular dynamics based sampling

Peter, G. Bolhuis
2009 Frontiers in Bioscience  
Yang et al. extracted folding kinetics from a REMD simulation (110) .  ...  Nevertheless, there are several methods that aim to simulate the kinetics of folding for all-atom molecular simulation.  ... 
doi:10.2741/3415 pmid:19273237 fatcat:4e2uuccunvbobpcl5p4liv2se4

Characterization of Folding Mechanisms of Trp-Cage and WW-Domain by Network Analysis of Simulations with a Hybrid-Resolution Model

Wei Han, Klaus Schulten
2013 Journal of Physical Chemistry B  
In this study, we apply a hybrid-resolution model, namely PACE, to characterize the free energy surfaces (FESs) of trp-cage and a WW domain variant along with the respective folding mechanisms.  ...  We find that trp-cage folds via a dominant pathway in which hydrophobic collapse occurs before the N-terminal helix forms; full incorporation of Trp6 into the hydrophobic core takes place as the last step  ...  Acknowledgments This work is supported by grant(s) from the National Institutes of Health (9P41GM104601, P41-RR005969, R01-GM067887) and from the National Science Foundation (MCB02-34938).  ... 
doi:10.1021/jp404331d pmid:23915394 pmcid:PMC3811923 fatcat:fogjdnpqxjdqdampgktef4qgfy

The Free Energy Reaction Path Theory of Reliable Protein Folding

Gregg Lois, Jerzy Blawzdziewicz, Corey O'Hern
2009 Biophysical Journal  
Using this technique it was possible to reversibly fold the Trp cage miniprotein in explicit solvent using only 40 ns of simulation on 8 replicas.  ...  This is caused by replicas having a preference for specific biasing potentials. 3036-Pos Board B83 Force Propagation in Proteins From Molecular Dynamics Simulations Wolfram Stacklies, Frauke Graeter.  ...  The villin headpiece folds to a native state after~6 microseconds of molecular dynamics simulation.  ... 
doi:10.1016/j.bpj.2008.12.3088 fatcat:dotffibxirglbf7y455kxejbve

Force Propagation in Proteins From Molecular Dynamics Simulations

Wolfram Stacklies, Frauke Graeter
2009 Biophysical Journal  
Using this technique it was possible to reversibly fold the Trp cage miniprotein in explicit solvent using only 40 ns of simulation on 8 replicas.  ...  This is caused by replicas having a preference for specific biasing potentials. 3036-Pos Board B83 Force Propagation in Proteins From Molecular Dynamics Simulations Wolfram Stacklies, Frauke Graeter.  ...  Board B81 Insights On Protein Structure And Dynamics From Multiple Biased Molecular Dynamics Simulations Fabrizio Marinelli 1 , Stefano Piana 2 , Fabio Pietrucci 1 , Nevena Torodova 3 , Irene Yarovsky  ... 
doi:10.1016/j.bpj.2008.12.3087 fatcat:7wzflljmyrgwnosla35shtrkuy

Simulating The Folding And Assembly Of Viral Ion Channels

Jakob P. Ulmschneider
2009 Biophysical Journal  
Using this technique it was possible to reversibly fold the Trp cage miniprotein in explicit solvent using only 40 ns of simulation on 8 replicas.  ...  This is caused by replicas having a preference for specific biasing potentials. 3036-Pos Board B83 Force Propagation in Proteins From Molecular Dynamics Simulations Wolfram Stacklies, Frauke Graeter.  ...  Board B81 Insights On Protein Structure And Dynamics From Multiple Biased Molecular Dynamics Simulations Fabrizio Marinelli 1 , Stefano Piana 2 , Fabio Pietrucci 1 , Nevena Torodova 3 , Irene Yarovsky  ... 
doi:10.1016/j.bpj.2008.12.3084 fatcat:oaolf7rlbjhndl7jajdfbqinfm

Measuring Intramolecular Diffusion During Protein Folding Using an Ultrarapid Microfluidic Mixer

Steven A. Waldauer, Avinash Kane, Olgica Bakajin, Lisa Lapidus
2009 Biophysical Journal  
Using this technique it was possible to reversibly fold the Trp cage miniprotein in explicit solvent using only 40 ns of simulation on 8 replicas.  ...  This is caused by replicas having a preference for specific biasing potentials. 3036-Pos Board B83 Force Propagation in Proteins From Molecular Dynamics Simulations Wolfram Stacklies, Frauke Graeter.  ...  Board B81 Insights On Protein Structure And Dynamics From Multiple Biased Molecular Dynamics Simulations Fabrizio Marinelli 1 , Stefano Piana 2 , Fabio Pietrucci 1 , Nevena Torodova 3 , Irene Yarovsky  ... 
doi:10.1016/j.bpj.2008.12.3082 fatcat:gedfbznlzbgo7ipcthkw346b5e

Exploring the Folding Landscape of Lambda Repressor with Microfluidic Mixing

Stephen DeCamp, Steven A. Waldauer, Lisa J. Lapidus
2009 Biophysical Journal  
Using this technique it was possible to reversibly fold the Trp cage miniprotein in explicit solvent using only 40 ns of simulation on 8 replicas.  ...  This is caused by replicas having a preference for specific biasing potentials. 3036-Pos Board B83 Force Propagation in Proteins From Molecular Dynamics Simulations Wolfram Stacklies, Frauke Graeter.  ...  Board B81 Insights On Protein Structure And Dynamics From Multiple Biased Molecular Dynamics Simulations Fabrizio Marinelli 1 , Stefano Piana 2 , Fabio Pietrucci 1 , Nevena Torodova 3 , Irene Yarovsky  ... 
doi:10.1016/j.bpj.2008.12.3083 fatcat:5mux7iaktbfepn45ytbs65tqr4

Reordering Hydrogen Bonds In The Protein Backbone In Hamiltonian Exchange MD Enhances Sampling Of Conformational Changes

Jocelyne Vreede, Maarten G. Wolf, Simon W. de Leeuw, Peter G. Bolhuis
2009 Biophysical Journal  
Using this technique it was possible to reversibly fold the Trp cage miniprotein in explicit solvent using only 40 ns of simulation on 8 replicas.  ...  This is caused by replicas having a preference for specific biasing potentials. 3036-Pos Board B83 Force Propagation in Proteins From Molecular Dynamics Simulations Wolfram Stacklies, Frauke Graeter.  ...  Board B81 Insights On Protein Structure And Dynamics From Multiple Biased Molecular Dynamics Simulations Fabrizio Marinelli 1 , Stefano Piana 2 , Fabio Pietrucci 1 , Nevena Torodova 3 , Irene Yarovsky  ... 
doi:10.1016/j.bpj.2008.12.3086 fatcat:3juhhtd3nzar3awmn3aeie7v3a

Molecular Latent Space Simulators

Hythem Sidky, Wei Chen, Andrew L Ferguson
2020 Chemical Science  
Markov state models (MSMs) and equation-free approaches learn low-dimensional kinetic models from MD simulation data by performing...  ...  Small integration time steps limit molecular dynamics (MD) simulations to millisecond time scales.  ...  Trp-cage miniprotein We train our LSS over the 208 ms all-atom simulation of the 20residue TC10b K8A mutant of the Trp-cage mini-protein performed by D. E.  ... 
doi:10.1039/d0sc03635h pmid:34094212 pmcid:PMC8162036 fatcat:52e4wqf2ozdivelh3z73it5qpu

Molecular Latent Space Simulators [article]

Hythem Sidky, Wei Chen, Andrew L. Ferguson
2020 arXiv   pre-print
Markov state models (MSMs) and equation-free approaches learn low-dimensional kinetic models from MD simulation data by performing configurational or dynamical coarse-graining of the state space.  ...  We demonstrate the approach in an application to Trp-cage miniprotein to produce novel ultra-long synthetic folding trajectories that accurately reproduce all-atom molecular structure, thermodynamics,  ...  17, 18 -no analogous approaches exist to recover unbiased dynamical trajectories from biased simulations.  ... 
arXiv:2007.00728v1 fatcat:f4lm64kwnffj7e2tujtmimzmlu

The effects of organic solvents on the folding pathway and associated thermodynamics of proteins: a microscopic view

Yuqi Yu, Jinan Wang, Qiang Shao, Jiye Shi, Weiliang Zhu
2016 Scientific Reports  
Protein folding is subject to the effects of solvation environment. A variety of organic solvents are used as additives for in vitro refolding of denatured proteins.  ...  Examination of the solvent effects on protein folding could be of fundamental importance to understand the molecular interactions in determining protein structure.  ...  The simulations were run at Shanghai Supercomputing Center (SSC) and TianHe 1 supercomputer in Tianjian.  ... 
doi:10.1038/srep19500 pmid:26775871 pmcid:PMC4726029 fatcat:mjimchlnofdwzjxhqmg2xo6bym

Anncolvar: Approximation of Complex Collective Variables by Artificial Neural Networks for Analysis and Biasing of Molecular Simulations

Dalibor Trapl, Izabela Horvacanin, Vaclav Mareska, Furkan Ozcelik, Gozde Unal, Vojtech Spiwok
2019 Frontiers in Molecular Biosciences  
The computational efficiency and the accuracy of anncolvar are demonstrated on selected molecular systems (cyclooctane derivative, Trp-cage miniprotein) and selected collective variables (Isomap, molecular  ...  The state of a molecular system can be described in terms of collective variables.  ...  AUTHOR CONTRIBUTIONS All authors contributed to the code of anncolvar. DT, IH, and VM: tested the code; DT, IH, and VS: carried out simulations, all authors contributed to the manuscript.  ... 
doi:10.3389/fmolb.2019.00025 pmid:31058167 pmcid:PMC6482212 fatcat:wqmvs3jygnaz3a4y7lk4qxqsvi
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