[NMR paper] Assessment of the Use of NMR Chemical Shifts as Replica-Averaged Structural Restraints in Molecular Dynamics Simulations to Characterize the Dynamics of Proteins.
Assessment of the Use of NMR Chemical Shifts as Replica-Averaged Structural Restraints in Molecular Dynamics Simulations to Characterize the Dynamics of Proteins.
Related ArticlesAssessment of the Use of NMR Chemical Shifts as Replica-Averaged Structural Restraints in Molecular Dynamics Simulations to Characterize the Dynamics of Proteins.
J Phys Chem B. 2013 Feb 1;
Authors: Camilloni C, Cavalli A, Vendruscolo M
Abstract
It has been recently proposed that NMR chemical shifts can be used as replica-averaged structural restraints in molecular dynamics simulations to determine the conformational fluctuations of proteins. In this work, we assess the accuracy of this approach by considering its application to the case of ribonuclease A. We found that the agreement between experimental and calculated chemical shifts improves on average when the chemical shifts are used as replica-averaged restraints with respect to the cases in which X-ray structures or ensembles of structures obtained by standard molecular dynamics simulations are considered. These results indicate that the use of chemical shifts as structural restraints enables a bias of the conformational sampling to be introduced in a system-specific manner to reproduce accurately the conformational fluctuations of proteins.
PMID: 23327201 [PubMed - as supplied by publisher]
Interpreting Protein Structural Dynamics from NMR Chemical Shifts
Interpreting Protein Structural Dynamics from NMR Chemical Shifts
Paul Robustelli, Kate A. Stafford and Arthur G. Palmer
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja300265w/aop/images/medium/ja-2012-00265w_0003.gif
Journal of the American Chemical Society
DOI: 10.1021/ja300265w
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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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Structural characterization of recombinant human myoglobin isoforms by (1)H and (129)Xe NMR and molecular dynamics simulations.
Structural characterization of recombinant human myoglobin isoforms by (1)H and (129)Xe NMR and molecular dynamics simulations.
Structural characterization of recombinant human myoglobin isoforms by (1)H and (129)Xe NMR and molecular dynamics simulations.
Biochim Biophys Acta. 2011 Jul 13;
Authors: Gussoni M, Scorciapino MA, Vezzoli A, Anedda R, Greco F, Ceccarelli M, Casu M
Myoglobin (Mb), the main cytosolic oxygen storage/deliver protein, is also known to interact with different small ligands exerting other fundamental physiological roles. In...
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Structure and Dynamics of the A?21–30 Peptide from the Interplay of NMR Experiments and Molecular Simulations
Structure and Dynamics of the A?21–30 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
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http://feeds.feedburner.com/~r/acs/jacsat/~4/bEQEah_ik60
[NMR paper] NMR-detected hydrogen exchange and molecular dynamics simulations provide structural
NMR-detected hydrogen exchange and molecular dynamics simulations provide structural insight into fibril formation of prion protein fragment 106-126.
Related Articles NMR-detected hydrogen exchange and molecular dynamics simulations provide structural insight into fibril formation of prion protein fragment 106-126.
Proc Natl Acad Sci U S A. 2003 Dec 9;100(25):14790-5
Authors: Kuwata K, Matumoto T, Cheng H, Nagayama K, James TL, Roder H
PrP106-126, a peptide corresponding to residues 107-127 of the human prion protein, induces neuronal cell...
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11-24-2010 09:16 PM
Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations
Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations of Proteins.
Related Articles Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations of Proteins.
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...
Assessment of the Use of NMR Chemical Shifts as Replica-Averaged Structural Restraints in Molecular Dynamics Simulations to Characterize the Dynamics of Proteins.
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