Conformational transition in signal transduction: metastable states and transition pathways in the activation of a signaling protein.
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[1] R. Bourret. Receiver domain structure and function in response regulator proteins. , 2010, Current opinion in microbiology.
[2] M. Karplus,et al. Molecular dynamics and protein function. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[3] Kirsten Jung,et al. Histidine kinases and response regulators in networks. , 2012, Current opinion in microbiology.
[4] Francesca Fanelli,et al. Wordom: A User-Friendly Program for the Analysis of Molecular Structures, Trajectories, and Free Energy Surfaces , 2010, J. Comput. Chem..
[5] V. Pande,et al. Network models for molecular kinetics and their initial applications to human health , 2010, Cell Research.
[6] D E Wemmer,et al. Two-state allosteric behavior in a single-domain signaling protein. , 2001, Science.
[7] D. Koshland. The Key–Lock Theory and the Induced Fit Theory , 1995 .
[8] C. Schütte,et al. Supplementary Information for “ Constructing the Equilibrium Ensemble of Folding Pathways from Short Off-Equilibrium Simulations ” , 2009 .
[9] Thomas J Lane,et al. MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale. , 2011, Journal of chemical theory and computation.
[10] R. Cukier,et al. Conformational transition of response regulator RR468 in a two-component system signal transduction process. , 2014, The journal of physical chemistry. B.
[11] Kyle A. Beauchamp,et al. Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39). , 2010, Journal of the American Chemical Society.
[12] Vladimir A. Zorich. Elements of the theory , 2011 .
[13] Q. Cui,et al. Reconciling the “old” and “new” views of protein allostery: A molecular simulation study of chemotaxis Y protein (CheY) , 2006, Proteins.
[14] Xuhui Huang,et al. Dynamics of an intrinsically disordered protein reveal metastable conformations that potentially seed aggregation. , 2013, Journal of the American Chemical Society.
[15] G. de Fabritiis,et al. Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations , 2011, Proceedings of the National Academy of Sciences.
[16] C. Brooks,et al. Native states of fast-folding proteins are kinetic traps. , 2013, Journal of the American Chemical Society.
[17] Vincent A. Voelz,et al. Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment. , 2012, Journal of the American Chemical Society.
[18] T. Darden,et al. A smooth particle mesh Ewald method , 1995 .
[19] F. Noé,et al. Transition networks for modeling the kinetics of conformational change in macromolecules. , 2008, Current opinion in structural biology.
[20] S. Vishveshwara,et al. Identification of side-chain clusters in protein structures by a graph spectral method. , 1999, Journal of molecular biology.
[21] Xuhui Huang,et al. Dynamics of pyrophosphate ion release and its coupled trigger loop motion from closed to open state in RNA polymerase II. , 2012, Journal of the American Chemical Society.
[22] S. Takada,et al. Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms , 2008, Proceedings of the National Academy of Sciences.
[23] Pathways for conformational change in nitrogen regulatory protein C from discrete path sampling. , 2008, The journal of physical chemistry. B.
[24] N. Hatzakis,et al. Single molecule insights on conformational selection and induced fit mechanism. , 2014, Biophysical chemistry.
[25] Molecular Dynamic Simulations of the N-Terminal Receiver Domain of NtrC Reveal Intrinsic Conformational Flexibility in the Inactive State , 2006, Journal of biomolecular structure & dynamics.
[26] K Henrick,et al. Electronic Reprint Biological Crystallography Secondary-structure Matching (ssm), a New Tool for Fast Protein Structure Alignment in Three Dimensions Biological Crystallography Secondary-structure Matching (ssm), a New Tool for Fast Protein Structure Alignment in Three Dimensions , 2022 .
[27] Liang Ma,et al. Activation mechanism of a signaling protein at atomic resolution from advanced computations. , 2007, Journal of the American Chemical Society.
[28] G. Ciccotti,et al. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .
[29] F. J. Luque,et al. Protein flexibility and ligand recognition: challenges for molecular modeling. , 2011, Current topics in medicinal chemistry.
[30] Shuanghong Huo,et al. Graph representation of protein free energy landscape. , 2013, The Journal of chemical physics.
[31] Vincent A. Voelz,et al. Atomistic folding simulations of the five-helix bundle protein λ(6−85). , 2011, Journal of the American Chemical Society.
[32] Kyle A. Beauchamp,et al. Markov state model reveals folding and functional dynamics in ultra-long MD trajectories. , 2011, Journal of the American Chemical Society.
[33] D. Kern,et al. The role of dynamics in allosteric regulation. , 2003, Current opinion in structural biology.
[34] S. Vishveshwara,et al. A network representation of protein structures: implications for protein stability. , 2005, Biophysical journal.
[35] G. Bowman,et al. Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites , 2012, Proceedings of the National Academy of Sciences.
[36] R. Nussinov,et al. Induced Fit, Conformational Selection and Independent Dynamic Segments: an Extended View of Binding Events Opinion , 2022 .
[37] Lila M. Gierasch,et al. Sending Signals Dynamically , 2009, Science.
[38] D. Kern,et al. Dynamic personalities of proteins , 2007, Nature.
[39] J Andrew McCammon,et al. Large conformational changes in proteins: signaling and other functions. , 2010, Current opinion in structural biology.
[40] Ann M Stock,et al. A New Perspective on Response Regulator Activation , 2006, Journal of bacteriology.
[41] Ronald M Levy,et al. Insights into the dynamics of HIV-1 protease: a kinetic network model constructed from atomistic simulations. , 2011, Journal of the American Chemical Society.
[42] V. Rubio,et al. The mechanism of signal transduction by two-component systems. , 2010, Current opinion in structural biology.
[43] V. Pande,et al. Error analysis and efficient sampling in Markovian state models for molecular dynamics. , 2005, The Journal of chemical physics.
[44] Alberto Marina,et al. Structural Insight into Partner Specificity and Phosphoryl Transfer in Two-Component Signal Transduction , 2009, Cell.
[45] Wladimir Labeikovsky,et al. Transient Non-native Hydrogen Bonds Promote Activation of a Signaling Protein , 2009, Cell.
[46] A. Berezhkovskii,et al. Reactive flux and folding pathways in network models of coarse-grained protein dynamics. , 2009, The Journal of chemical physics.
[47] Vijay S Pande,et al. Simple few-state models reveal hidden complexity in protein folding , 2012, Proceedings of the National Academy of Sciences.
[48] Frank Noé,et al. Markov models of molecular kinetics: generation and validation. , 2011, The Journal of chemical physics.
[49] Xuhui Huang,et al. Using generalized ensemble simulations and Markov state models to identify conformational states. , 2009, Methods.
[50] Igor B Zhulin,et al. Evolution and phyletic distribution of two-component signal transduction systems. , 2010, Current opinion in microbiology.
[51] Eric Vanden-Eijnden,et al. Transition-path theory and path-finding algorithms for the study of rare events. , 2010, Annual review of physical chemistry.
[52] Benoît Roux,et al. Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories , 2009, Proceedings of the National Academy of Sciences.
[53] P. Deuflhard,et al. Robust Perron cluster analysis in conformation dynamics , 2005 .
[54] Kyle A. Beauchamp,et al. Quantitative comparison of villin headpiece subdomain simulations and triplet–triplet energy transfer experiments , 2011, Proceedings of the National Academy of Sciences.
[55] Vijay S Pande,et al. Protein folded states are kinetic hubs , 2010, Proceedings of the National Academy of Sciences.
[56] Dahlia R. Weiss,et al. Millisecond dynamics of RNA polymerase II translocation at atomic resolution , 2014, Proceedings of the National Academy of Sciences.
[57] Daniel R Roe,et al. PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data. , 2013, Journal of chemical theory and computation.
[58] Rahul Banerjee,et al. Transition paths of Met-enkephalin from Markov state modeling of a molecular dynamics trajectory. , 2014, The journal of physical chemistry. B.
[59] Martin Karplus,et al. Segmented transition pathway of the signaling protein nitrogen regulatory protein C. , 2009, Journal of molecular biology.
[60] P. Hänggi,et al. Reaction-rate theory: fifty years after Kramers , 1990 .
[61] Vijay S Pande,et al. Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach. , 2008, The Journal of chemical physics.