TY - JOUR
T1 - The effect of motional averaging on the calculation of NMR-derived structural properties
AU - Daura, Xavier
AU - Antes, Iris
AU - Van Gunsteren, Wilfred F.
AU - Thiel, Walter
AU - Mark, Alan E.
PY - 1999/9/1
Y1 - 1999/9/1
N2 - The effect of motional averaging when relating structural properties inferred from nuclear magnetic resonance (NMR) experiments to molecular dynamics simulations of peptides is considered. In particular, the effect of changing populations of conformations, the extent of sampling, and the sampling frequency on the estimation of nuclear Overhauser effect (NOE) inter-proton distances, vicinal 3J-coupling constants, and chemical shifts are investigated. The analysis is based on 50-ns simulations of a β- heptapeptide in methanol at 298 K, 340 K, 350 K, and 360 K. This peptide undergoes reversible folding and samples a significant proportion of the available conformational space during the simulations, with at 298 K being predominantly folded and at 360 K being predominantly unfolded. The work highlights the fact that when motional averaging is included, NMR data has only limited capacity to distinguish between a single fully folded peptide conformation and various mixtures of folded and unfolded conformations.
AB - The effect of motional averaging when relating structural properties inferred from nuclear magnetic resonance (NMR) experiments to molecular dynamics simulations of peptides is considered. In particular, the effect of changing populations of conformations, the extent of sampling, and the sampling frequency on the estimation of nuclear Overhauser effect (NOE) inter-proton distances, vicinal 3J-coupling constants, and chemical shifts are investigated. The analysis is based on 50-ns simulations of a β- heptapeptide in methanol at 298 K, 340 K, 350 K, and 360 K. This peptide undergoes reversible folding and samples a significant proportion of the available conformational space during the simulations, with at 298 K being predominantly folded and at 360 K being predominantly unfolded. The work highlights the fact that when motional averaging is included, NMR data has only limited capacity to distinguish between a single fully folded peptide conformation and various mixtures of folded and unfolded conformations.
KW - Chemical shift
KW - Computer simulation
KW - J-coupling constant
KW - Molecular dynamics
KW - NMR
KW - NOE distance
KW - Peptides
UR - http://www.scopus.com/inward/record.url?scp=0032800402&partnerID=8YFLogxK
U2 - 10.1002/(SICI)1097-0134(19990901)36:4<542::AID-PROT17>3.0.CO;2-M
DO - 10.1002/(SICI)1097-0134(19990901)36:4<542::AID-PROT17>3.0.CO;2-M
M3 - Article
C2 - 10450095
AN - SCOPUS:0032800402
SN - 0887-3585
VL - 36
SP - 542
EP - 555
JO - Proteins: Structure, Function and Bioinformatics
JF - Proteins: Structure, Function and Bioinformatics
IS - 4
ER -