Related ArticlesHelix motion in protein C12A-p8(MTCP1): comparison of molecular dynamics simulations and multifield NMR relaxation data.
J Comput Chem. 2002 Dec;23(16):1577-86
Authors: Barthe P, Roumestand C, Déméné H, Chiche L
The human p8(MTCP1) protein is constituted by an original disulfide bridged alpha-hairpin motif, and a third hydrophilic helix that appeared mobile and independent in NMR analysis. To get atomic scale description of the possible motions involved, a 12-ns molecular dynamics simulation of the C12A-p8(MTCP1) mutated protein and 10 400-ps simulations were performed in explicit water at 298 K. Analyses of the essential dynamics subspace and of the time-evolution of secondary structures indicate large displacements and internal motions of the third helix. Simulated order parameters, S,(2) are consistent to those obtained from (15)N-NMR relaxation data recorded at five different magnetic fields (proton resonance frequencies: 400, 500, 600, 700, and 800 MHz). The simulations show a fairly rigid alpha-hairpin motif with only very small local conformational changes, although the loop between helices undergoes significant correlated motions. The displacements and internal motions of the third helix can be essentially accounted for by alpha-helical to 3(10)-helical transitions near its N-terminus and by a hinge-bending motion near glycine 52. The loss of the alpha-helical conformation for a large part of the third helix during about 25% of the simulation time supports the possible occurrence of a slow motion as suggested by previous analyses of the (3)J(NH-H(alpha)) coupling constant values and of the proton-deuterium NH exchange kinetics.
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction
Abstract While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein 1H chemical shifts in which molecular motions, the...
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Structure and Dynamics of the A?2130 Peptide from the Interplay of NMR Experiments and Molecular Simulations
Structure and Dynamics of the A?2130 Peptide from the Interplay of NMR Experiments and Molecular Simulations
Nicolas L. Fawzi, Aaron H. Phillips, Jory Z. Ruscio, Michaeleen Doucleff, David E. Wemmer and Teresa Head-Gordon
Journal of the American Chemical Society
DOI: 10.1021/ja204315n
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/bEQEah_ik60
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[NMR paper] Probing conformational disorder in neurotensin by two-dimensional solid-state NMR and comparison to molecular dynamics simulations.
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Biophys J. 2005 Sep;89(3):2113-20
Authors: Heise H, Luca S, de Groot BL, Grubmüller H, Baldus M
An approach is introduced to characterize conformational ensembles of intrinsically unstructured peptides on the atomic level using two-dimensional solid-state NMR data and...
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[NMR paper] Molecular dynamics simulations of protein G challenge NMR-derived correlated backbone
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Angew Chem Int Ed Engl. 2005 May 30;44(22):3394-9
Authors: Lange OF, Grubmüller H, de Groot BL
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Eur Biophys J. 2002 Dec;31(7):504-20
Authors: Antes I, Thiel W, van Gunsteren WF
Photoactive yellow protein (PYP) is a...
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Biochem Cell Biol. 1998;76(2-3):164-70
Authors: van der Spoel D
The conformations that amino acids can adopt in the random coil state are of fundamental interest in the context of protein folding research and studies of protein-peptide interactions. To date, no...
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J Biomol Struct Dyn. 1992 Apr;9(5):935-49
Authors: Braatz JA, Paulsen MD, Ornstein RL
Mainly due to computational limitations, past protein molecular dynamics simulations have rarely been extended to 300 psec; we are not aware of any published results beyond 350 psec. The present...
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Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations
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Structure. 2010 Aug 11;18(8):923-933
Authors: Robustelli P, Kohlhoff K, Cavalli A, Vendruscolo M
We introduce a procedure to determine the structures of proteins by incorporating NMR chemical shifts as structural restraints in molecular dynamics simulations. In this approach, the chemical shifts are expressed as differentiable...
Helix motion in protein C12A-p8(MTCP1): comparison of molecular dynamics simulations
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