Predicting NMR relaxation of proteins from molecular dynamics simulations with accurate methyl rotation barriers

Abstract

The internal dynamics of proteins occurring on time scales from picoseconds to nanoseconds can be sensitively probed by nuclear magnetic resonance (NMR) spin relaxation experiments, as well as by molecular dynamics (MD) simulations. This complementarity offers unique opportunities, provided that the two methods are compared at a suitable level. Recently, several groups have used MD simulations to compute the spectral density of backbone and side chain molecular motions, and to predict NMR relaxation rates from these. Unfortunately, in the case of methyl groups in protein side chains, inaccurate energy barriers to methyl rotation were responsible for a systematic discrepancy in the computed relaxation rates, as demonstrated for the AMBER ff99SB*-ILDN force field (and related parameter sets), impairing quantitative agreement between simulations and experiments. However, correspondence could be regained by emending the MD force field with accurate coupled cluster quantum chemical calculations. Spurred by this positive result, we tested whether this approach could be generally applicable, in spite of the fact that different MD force fields employ different water models. Improved methyl group rotation barriers for the CHARMM36 and AMBER ff15ipq protein force fields were derived, such that the NMR relaxation data obtained from the MD simulations now also display very good agreement with experiment. Results herein showcase the performance of present-day MD force fields, and manifest their refined ability to accurately describe internal protein dynamics.

Observation of Sub-Microsecond Protein Methyl-Side Chain Dynamics by Nanoparticle-Assisted NMR Spin Relaxation

“…The main reason is that quantitative experimental information about (sub-)­μs protein dynamics with site-specific resolution remains notably sparse. In the case of methyl-side chains, their quantitative modeling has been more difficult than the backbone, although important progress has been made in recent years. ,− NASR S 2 order parameters will provide new important quantitative benchmarks allowing an independent evaluation of the accuracy of long μs MD trajectories at many different protein sites. Such information should also prove useful for guiding the improvement of current MD force fields.…”

Fitting Side-Chain NMR Relaxation Data Using Molecular Simulations

“…In this case, the only differences between the “data” and the simulations would arise from insufficient sampling. In our second application, we again created synthetic data, in this case, however using the Amber ff15ipq force field (with a modified methyl torsion potential) and the SPC/E b water model. , We performed three 1 μs simulations and used these to generate synthetic NMR relaxation data. This test enables us to examine how the method behaves when there are real differences between the potential used in the simulations we use to fit the data and the one that gives rise to the (synthetic) “experimental data”.…”

“…While this approach does not necessarily provide detailed information about the timescales of these motions, it has the advantage of not being dependent on a specific analytical model which might influence the interpretation of the relaxation data. Recently, an approach was developed to calculate deuterium NMR relaxation rates in methyl-bearing side chains from MD simulations. , Comparison to experiments revealed systematic deviations from simulations with several different force fields, and corrections to the methyl torsion potential were developed based on quantum calculations and shown to increase agreement with experiments. , Despite these improvements and a substantial body of work on studies of side-chain dynamics, ,− the agreement remains imperfect and further improvements would be desirable.…”

SRLS Analysis of 15N–1H NMR Relaxation from the Protein S100A1: Dynamic Structure, Calcium Binding, and Related Changes in Conformational Entropy

“…It is widely accepted that information on structural dynamics is key to understanding protein function. Here, we focus on the internal mobility of proteins as reported by the restricted local motion of small structural moieties such as the amide (N–H) bond. − The leading methods in this context are molecular dynamics (MD) simulations and dynamic models combined with NMR relaxation. − MD provides information at the atom level, with accuracy determined by the quality of the force field. However, it forgoes using valuable information provided by the experimental manifestation of NMR relaxation, typically determines the overall diffusion of the protein with insufficient accuracy, and renders comparison among local sites difficult in view of the wealth of parameters describing them.…”

“…Here, we focus on the internal mobility of proteins as reported by the restricted local motion of small structural moieties such as the amide (N−H) bond. 1−6 The leading methods in this context are molecular dynamics (MD) simulations 7 and dynamic models combined with NMR relaxation. 1−6 MD provides information at the atom level, with accuracy determined by the quality of the force field.…”