Abstract
A robust protocol for the treatment of NMR protein structures is presented that makes them amenable to long time scale molecular dynamics (MD) simulations that are stable. The protocol embeds an NMR structure in a native low energy region of the recently developed ff99SB_??(g24;CS) molecular mechanics force field. Extended MD trajectories that start from these structures show good consistency with proton-proton nuclear Overhauser effect data, and they reproduce NMR chemical shift data better than the original NMR structures as is demonstrated for four protein systems. Moreover, for all proteins studied here the simulations spontaneously approach the X-ray crystal structures, thereby improving the effective resolution of the initial structural models.
Time-averaged order parameter restraints in molecular dynamics simulations
Time-averaged order parameter restraints in molecular dynamics simulations
Abstract
A method is described that allows experimental \(S^2\) order parameters to be enforced as a time-averaged quantity in molecular dynamics simulations. The two parameters that characterize time-averaged restraining, the memory relaxation time and the weight of the restraining potential energy term in the potential energy function used in the simulation, are systematically investigated...
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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02-11-2012 10:31 AM
Microsecond Time-Scale Conformational Exchange in Proteins: Using Long Molecular Dynamics Trajectory To Simulate NMR Relaxation Dispersion Data
Microsecond Time-Scale Conformational Exchange in Proteins: Using Long Molecular Dynamics Trajectory To Simulate NMR Relaxation Dispersion Data
Yi Xue, Joshua M. Ward, Tairan Yuwen, Ivan S. Podkorytov and Nikolai R. Skrynnikov
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja206442c/aop/images/medium/ja-2011-06442c_0001.gif
Journal of the American Chemical Society
DOI: 10.1021/ja206442c
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/NvRRKHU2H3k
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01-28-2012 05:27 AM
[KPWU blog] NMR protocol (recipe)?make stretch gel for protein RDC measurement
NMR protocol (recipe)?make stretch gel for protein RDC measurement
I bought the starter kit (NE-373-B-6/4.2) at NewEraNMR for RDC experiment on Varian NMR (with 700 MHz grade) and I decided to stretch the gel a lot, so 6mm-wide gel chamber and “6mm-4.2mm gel funnel” are included. The NMR tube seems to be more fragile than Wilmad products I often used, so I also ordered http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=587&subd=kpwu&ref=&feed=1
Go to KPWU blog to read complete post.
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10-20-2011 09:45 AM
[NMR paper] Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of
Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation.
Related Articles Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation.
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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11-24-2010 08:58 PM
[NMR paper] Measurement of slow (micros-ms) time scale dynamics in protein side chains by (15)N r
Measurement of slow (micros-ms) time scale dynamics in protein side chains by (15)N relaxation dispersion NMR spectroscopy: application to Asn and Gln residues in a cavity mutant of T4 lysozyme.
Related Articles Measurement of slow (micros-ms) time scale dynamics in protein side chains by (15)N relaxation dispersion NMR spectroscopy: application to Asn and Gln residues in a cavity mutant of T4 lysozyme.
J Am Chem Soc. 2001 Feb 7;123(5):967-75
Authors: Mulder FA, Skrynnikov NR, Hon B, Dahlquist FW, Kay LE
A new NMR experiment is presented for...
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11-19-2010 08:32 PM
[NMR paper] Sampling of protein dynamics in nanosecond time scale by 15N NMR relaxation and self-
Sampling of protein dynamics in nanosecond time scale by 15N NMR relaxation and self-diffusion measurements.
Related Articles Sampling of protein dynamics in nanosecond time scale by 15N NMR relaxation and self-diffusion measurements.
J Biomol Struct Dyn. 1999 Aug;17(1):157-74
Authors: Orekhov VY, Korzhnev DM, Pervushin KV, Hoffmann E, Arseniev AS
This paper presents a procedure for detection of intermediate nanosecond internal dynamics in globular proteins. The procedure uses 1H-15N relaxation measurements at several spectrometer frequencies...
Protocol To Make Protein NMR Structures Amenable to Stable Long Time Scale Molecular Dynamics Simulations.
Linear Mode
