PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles

Da-Wei Li; Rafael Brüschweiler

doi:10.1007/s10858-012-9668-8

journal article Sep 13, 2012

PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles

Da-Wei Li

Rafael Brüschweiler

Journal of Biomolecular NMR Vol. 54 No. 3 pp. 257-265 · Springer Science and Business Media LLC

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References

56

[1]

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements

Kyle A. Beauchamp, Yu-Shan Lin, Rhiju Das et al.

Journal of Chemical Theory and Computation 2012 10.1021/ct2007814

[2]

GROMACS: A message-passing parallel molecular dynamics implementation

H.J.C. Berendsen, D. van der Spoel, R. van Drunen

Computer Physics Communications 1995 10.1016/0010-4655(95)00042-e

[3]

A Simple Method To Predict Protein Flexibility Using Secondary Chemical Shifts

Mark V. Berjanskii, David S. Wishart

Journal of the American Chemical Society 2005 10.1021/ja054842f

[4]

The Protein Data Bank

H. M. Berman

Nucleic Acids Research 2000 10.1093/nar/28.1.235

[5]

Brüschweiler R, Case DA (1994) Adding harmonic motion to the Karplus relation for spin–spin coupling. J Am Chem Soc 116:11199–11200 10.1021/ja00103a062

[6]

Importance of the CMAP Correction to the CHARMM22 Protein Force Field: Dynamics of Hen Lysozyme

Matthias Buck, Sabine Bouguet-Bonnet, Richard W. Pastor et al.

Biophysical Journal 2006 10.1529/biophysj.105.078154

[7]

Protein structure determination from NMR chemical shifts

Andrea Cavalli, Xavier Salvatella, Christopher M. Dobson et al.

Proceedings of the National Academy of Sciences 2007 10.1073/pnas.0610313104

[8]

A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations

Yong Duan, Chun Wu, Shibasish Chowdhury et al.

Journal of Computational Chemistry 2003 10.1002/jcc.10349

[9]

Haigh CW, Mallion RB (1972) New tables of ring current shielding in proton magnetic-resonance. Org Magn Res 4:203–228 10.1002/mrc.1270040203

[10]

Ring current theories in nuclear magnetic resonance

C.W. Haigh, R.B. Mallion

Progress in Nuclear Magnetic Resonance Spectroscop... 1979 10.1016/0079-6565(79)80010-2

[11]

SHIFTX2: significantly improved protein chemical shift prediction

Beomsoo Han, Yifeng Liu, Simon W. Ginzinger et al.

Journal of Biomolecular NMR 2011 10.1007/s10858-011-9478-4

[12]

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

Berk Hess, Carsten Kutzner, David van der Spoel et al.

Journal of Chemical Theory and Computation 2008 10.1021/ct700301q

[13]

Comparison of multiple Amber force fields and development of improved protein backbone parameters

Viktor Hornak, Robert Abel, Asim Okur et al.

Proteins: Structure, Function, and Bioinformatics 2006 10.1002/prot.21123

[14]

Comparison of simple potential functions for simulating liquid water

William L. Jorgensen, Jayaraman Chandrasekhar, Jeffry D. Madura et al.

The Journal of Chemical Physics 1983 10.1063/1.445869

[15]

Long-timescale molecular dynamics simulations of protein structure and function

John L Klepeis, Kresten Lindorff-Larsen, Ron O Dror et al.

Current Opinion in Structural Biology 2009 10.1016/j.sbi.2009.03.004

[16]

Fast and Accurate Predictions of Protein NMR Chemical Shifts from Interatomic Distances

Kai J. Kohlhoff, Paul Robustelli, Andrea Cavalli et al.

Journal of the American Chemical Society 2009 10.1021/ja903772t

[17]

Korzhnev DM, Religa TL, Banachewicz W, Fersht AR, Kay LE (2010) A transient and low-populated protein-folding intermediate at atomic resolution. Science 329:1312–1316 10.1126/science.1191723

[18]

Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data

Oliver F. Lange, David van der Spoel, Bert L. de Groot

Biophysical Journal 2010 10.1016/j.bpj.2010.04.062

[19]

Lehtivarjo J, Hassinen T, Korhonen SP, Perakyla M, Laatikainen R (2009) 4D prediction of protein H-1 chemical shifts. J Biomol NMR 45:413–426 10.1007/s10858-009-9384-1

[20]

Lehtivarjo J, Tuppurainen K, Hassinen T, Laatikainen R, Perakyla M (2012) Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction. J Biomol NMR 52:257–267 10.1007/s10858-012-9609-6

[21]

NMR‐Based Protein Potentials

Da‐Wei Li, Rafael Brüschweiler

Angewandte Chemie International Edition 2010 10.1002/anie.201001898

[22]

Li DW, Brüschweiler R (2010b) Certification of molecular dynamics trajectories with NMR chemical shifts. J Phys Chem Lett 1:246–248 10.1021/jz9001345

[23]

Iterative Optimization of Molecular Mechanics Force Fields from NMR Data of Full-Length Proteins

Da-Wei Li, Rafael Brüschweiler

Journal of Chemical Theory and Computation 2011 10.1021/ct200094b

[24]

GROMACS 3.0: a package for molecular simulation and trajectory analysis

Erik Lindahl, Berk Hess, David van der Spoel

Journal of Molecular Modeling 2001 10.1007/s008940100045

[25]

Interpreting Dynamically-Averaged Scalar Couplings in Proteins

Kresten Lindorff-Larsen, Robert B. Best, Michele Vendruscolo

Journal of Biomolecular NMR 2005 10.1007/s10858-005-8873-0

[26]

Improved side‐chain torsion potentials for the Amber ff99SB protein force field

Kresten Lindorff‐Larsen, Stefano Piana, Kim Palmo et al.

Proteins: Structure, Function, and Bioinformatics 2010 10.1002/prot.22711

[27]

Long D, Li DW, Walter KFA, Griesinger C, Brüschweiler R (2011) Toward a predictive understanding of slow methyl group dynamics in proteins. Biophys J 101:910–915 10.1016/j.bpj.2011.06.053

[28]

Exploring Multiple Timescale Motions in Protein GB3 Using Accelerated Molecular Dynamics and NMR Spectroscopy

Phineus R. L. Markwick, Guillaume Bouvignies, Martin Blackledge

Journal of the American Chemical Society 2007 10.1021/ja0687668

[29]

Markwick PR, Showalter SA, Bouvignies G, Brüschweiler R, Blackledge M (2009) Structural dynamics of protein backbone phi angles: extended molecular dynamics simulations versus experimental (3) J scalar couplings. J Biomol NMR 45:17–21 10.1007/s10858-009-9341-z

[30]

Markwick PRL, Cervantes CF, Abel BL, Komives EA, Blackledge M, McCammon JA (2010) Enhanced conformational space sampling improves the prediction of chemical shifts in proteins. J Am Chem Soc 132:1220–1221 10.1021/ja9093692

[31]

McConnell HM (1957) Theory of nuclear magnetic shielding in molecules. I. Long-range dipolar shielding of protons. J Chem Phys 27:226–229 10.1063/1.1743676

[32]

Meiler J, Prompers JJ, Peti W, Griesinger C, Brüschweiler R (2001) Model-free approach to the dynamic interpretation of residual dipolar couplings in globular proteins. J Am Chem Soc 123:6098–6107 10.1021/ja010002z

[33]

Moon S, Case DA (2007) A new model for chemical shifts of amide hydrogens in proteins. J Biomol NMR 38:139–150 10.1007/s10858-007-9156-8

[34]

Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts

Stephen Neal, Alex M. Nip, Haiyan Zhang et al.

Journal of Biomolecular NMR 2003 10.1023/a:1023812930288

[35]

A new analysis of proton chemical shifts in proteins

Klara Osapay, David A. Case

Journal of the American Chemical Society 1991 10.1021/ja00025a002

[36]

Robustelli P, Stafford KA, Palmer AG (2012) Interpreting protein structural dynamics from NMR chemical shifts. J Am Chem Soc 134:6365–6374 10.1021/ja300265w

[37]

Blind Testing of Routine, Fully Automated Determination of Protein Structures from NMR Data

Antonio Rosato, James M. Aramini, Cheryl Arrowsmith et al.

Structure 10.1016/j.str.2012.01.002

[38]

Ruschak AM, Religa TL, Breuer S, Witt S, Kay LE (2010) The proteasome antechamber maintains substrates in an unfolded state. Nature 467:868–871 10.1038/nature09444

[39]

Sahakyan AB, Vranken WF, Cavalli A, Vendruscolo M (2011) Structure-based prediction of methyl chemical shifts in proteins. J Biomol NMR 50:331–346 10.1007/s10858-011-9524-2

[40]

Shen Y, Bax A (2007) Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology. J Biomol NMR 38:289–302 10.1007/s10858-007-9166-6

[41]

SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network

Yang Shen, Ad Bax

Journal of Biomolecular NMR 2010 10.1007/s10858-010-9433-9

[42]

Consistent blind protein structure generation from NMR chemical shift data

Yang Shen, Oliver Lange, Frank Delaglio et al.

Proceedings of the National Academy of Sciences 2008 10.1073/pnas.0800256105

[43]

De novo protein structure generation from incomplete chemical shift assignments

Yang Shen, Robert Vernon, David Baker et al.

Journal of Biomolecular NMR 2009 10.1007/s10858-008-9288-5

[44]

Showalter SA, Brüschweiler R (2007) Validation of molecular dynamics simulations of biomolecules using NMR spin relaxation as benchmarks: application to the AMBER99SB force field. J Chem Theory Comput 3:961–975 10.1021/ct7000045

[45]

Showalter SA, Johnson E, Rance M, Brüschweiler R (2007) Toward quantitative interpretation of methyl side-chain dynamics from NMR by molecular dynamics simulations. J Am Chem Soc 129:14146–14147 10.1021/ja075976r

[46]

Structural analysis of protein dynamics by MD simulations and NMR spin‐relaxation

Nikola Trbovic, Byungchan Kim, Richard A. Friesner et al.

Proteins: Structure, Function, and Bioinformatics 2008 10.1002/prot.21750

[47]

BioMagResBank

E. L. Ulrich, H. Akutsu, J. F. Doreleijers et al.

Nucleic Acids Research 2008 10.1093/nar/gkm957

[48]

GROMACS: Fast, flexible, and free

David van der Spoel, Erik Lindahl, Berk Hess et al.

Journal of Computational Chemistry 2005 10.1002/jcc.20291

[49]

Vila JA, Arnautova YA, Martin OA, Scheraga HA (2009) Quantum-mechanics-derived C-13(alpha) chemical shift server (CheShift) for protein structure validation. Proc Natl Acad Sci USA 106:16972–16977 10.1073/pnas.0908833106

[50]

Limits on Variations in Protein Backbone Dynamics from Precise Measurements of Scalar Couplings

Beat Vögeli, Jinfa Ying, Alexander Grishaev et al.

Journal of the American Chemical Society 2007 10.1021/ja070324o

Showing 50 of 56 references

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Details

Published: Sep 13, 2012
Vol/Issue: 54(3)
Pages: 257-265
License: View

Authors

D

Da-Wei Li

Department of Chemistry and Biochemistry and ‡Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States

R

Rafael Brüschweiler

Department of Physics, Mathematics and Informatics

Cite This Article

Da-Wei Li, Rafael Brüschweiler (2012). PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles. Journal of Biomolecular NMR, 54(3), 257-265. https://doi.org/10.1007/s10858-012-9668-8

PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles

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