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A Monte Carlo simulation study of the influence of internal motions on the molecular conformation deduced from two‐dimensional nmr experiments
Author(s) -
Genest D.
Publication year - 1989
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360281107
Subject(s) - chemistry , two dimensional nuclear magnetic resonance spectroscopy , monte carlo method , nuclear overhauser effect , spins , relaxation (psychology) , proton , nuclear magnetic resonance spectroscopy , molecular dynamics , amplitude , nuclear magnetic resonance , molecular physics , computational chemistry , physics , stereochemistry , nuclear physics , condensed matter physics , psychology , social psychology , statistics , mathematics , quantum mechanics
Monte Carlo methods have been used to simulate internal motions of aromatic protons of an oligonucleotide at the nanosecond time scale. Each proton is allowed to fluctuate about its equilibrium position. The longitudinal cross‐relaxation rates of such a system of spins have been determined by computing the appropriate correlation functions. Then the interproton distances have been deduced according to the procedure generally used in two‐dimensional nmr techniques (nuclear Overhauser effect spectroscopy—NOESY) and compared to the true values. The influence of the amplitude A and of the internal rotational diffusion constant D int characterizing the dynamics of the system has been checked for in‐phase and for uncorrelated motions. It is shown that for the investigated models the distances deduced from NOESY experiments may be under or overestimated, depending strongly on the values of A and D int . Furthermore, the cross‐relaxation rate of a couple of protons is very sensitive to the correlation level of the motions of both protons.