Nuclear magnetic resonance (NMR) relaxation experiments shine light onto the dynamics of molecular systems in the picosecond to millisecond timescales. As these methods cannot provide an atomically resolved view of the motion of atoms, functional groups, or domains giving rise to such signals, relaxation techniques have been combined with molecular dynamics (MD) simulations to obtain mechanistic descriptions and gain insights into the functional role of side chain or domain motion. In this work,...
[NMR paper] Structure Determination of Challenging Protein-Peptide Complexes Combining NMR Chemical Shift Data and Molecular Dynamics Simulations
Structure Determination of Challenging Protein-Peptide Complexes Combining NMR Chemical Shift Data and Molecular Dynamics Simulations
Intrinsically disordered regions of proteins often mediate important protein-protein interactions. However, the folding-upon-binding nature of many polypeptide-protein interactions limits the ability of modeling tools to predict the three-dimensional structures of such complexes. To address this problem, we have taken a tandem approach combining NMR chemical shift data and molecular simulations to determine the structures of peptide-protein complexes. Here,...
[NMR paper] Effect of Saturated Very Long-Chain Fatty Acids on the Organization of Lipid Membranes: A Study Combining (2)H NMR Spectroscopy and Molecular Dynamics Simulations.
Effect of Saturated Very Long-Chain Fatty Acids on the Organization of Lipid Membranes: A Study Combining (2)H NMR Spectroscopy and Molecular Dynamics Simulations.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles Effect of Saturated Very Long-Chain Fatty Acids on the Organization of Lipid Membranes: A Study Combining (2)H NMR Spectroscopy and Molecular Dynamics Simulations.
J Phys Chem B. 2016 07 21;120(28):6951-60
Authors: Paz Ramos A, Lagüe P, Lamoureux G, Lafleur M
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04-19-2018 01:52 PM
NMR Relaxation and Molecular Dynamics Simulations of Side Chain Dynamics in Proteins
NMR Relaxation and Molecular Dynamics Simulations of Side Chain Dynamics in Proteins
Publication date: 2 February 2018
Source:Biophysical Journal, Volume 114, Issue 3, Supplement 1</br>
Author(s): Falk Hoffmann, Mengjun Xue, Frans Mulder, Lars Schäfer</br>
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02-07-2018 03:41 PM
Molecular simulations for dynamic nuclear polarization in liquids: a case study of TEMPOL in acetone and DMSO
From The DNP-NMR Blog:
Molecular simulations for dynamic nuclear polarization in liquids: a case study of TEMPOL in acetone and DMSO
Kucuk, S.E., et al., Molecular simulations for dynamic nuclear polarization in liquids: a case study of TEMPOL in acetone and DMSO. Phys Chem Chem Phys, 2015. 17(9): p. 6618-28.
http://www.ncbi.nlm.nih.gov/pubmed/25665728
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05-11-2015 09:06 PM
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
[NMR paper] Solution structure and dynamics of integral membrane proteins by NMR: a case study in
Solution structure and dynamics of integral membrane proteins by NMR: a case study involving the enzyme PagP.
Related Articles Solution structure and dynamics of integral membrane proteins by NMR: a case study involving the enzyme PagP.
Methods Enzymol. 2005;394:335-50
Authors: Hwang PM, Kay LE
Solution NMR spectroscopy is rapidly becoming an important technique for the study of membrane protein structure and dynamics. NMR experiments on large perdeuterated proteins typically exploit the favorable relaxation properties of backbone amide...
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11-24-2010 11:14 PM
[NMR paper] Helix motion in protein C12A-p8(MTCP1): comparison of molecular dynamics simulations
Helix motion in protein C12A-p8(MTCP1): comparison of molecular dynamics simulations and multifield NMR relaxation data.
Related Articles Helix 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...
Unraveling motion in proteins by combining NMR relaxometry and molecular dynamics simulations: A case study on ubiquitin
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