Accurate Methyl Group Dynamics in Protein Simulations with AMBER Force Fields

TY - JOUR

T1 - Accurate Methyl Group Dynamics in Protein Simulations with AMBER Force Fields

AU - Hoffmann, Falk

AU - Mulder, Frans A. A.

AU - Schaefer, Lars V.

PY - 2018/5/17

Y1 - 2018/5/17

N2 - An approach is presented to directly simulate the dynamics of methyl groups in protein side-chains, as accessible via NMR spin relaxation measurements, by all-atom MD simulations. The method, which does not rely on NMR information or any system-specific adjustable parameters, is based on calculating the time-correlation functions (TCFs) of the C-H bonds in methyl groups and explicitly takes the truncation of the TCFs due to overall tumbling of the molecule into account. Using ubiquitin as a model protein, we show (i) that an accurate description of the methyl dynamics requires reparametrization of the potential energy barriers of methyl group rotation in the AMBER ff99SB∗-ILDN force field (and related parameter sets), which was done with CCSD(T) coupled cluster calculations of isolated dipeptides as reference, and (ii) that the TIP4P/2005 solvation model yields overall tumbling correlation times that are in close agreement with experimental data. The methyl axis squared order parameters Saxis 2 and associated correlation times τ f, obtained within the Lipari-Szabo formalism, are in good agreement with the values derived from NMR deuterium relaxation experiments. Importantly, the relaxation rates and spectral densities derived from MD and NMR agree as well, enabling a direct comparison without assumptions inherent to simplified motional models.

AB - An approach is presented to directly simulate the dynamics of methyl groups in protein side-chains, as accessible via NMR spin relaxation measurements, by all-atom MD simulations. The method, which does not rely on NMR information or any system-specific adjustable parameters, is based on calculating the time-correlation functions (TCFs) of the C-H bonds in methyl groups and explicitly takes the truncation of the TCFs due to overall tumbling of the molecule into account. Using ubiquitin as a model protein, we show (i) that an accurate description of the methyl dynamics requires reparametrization of the potential energy barriers of methyl group rotation in the AMBER ff99SB∗-ILDN force field (and related parameter sets), which was done with CCSD(T) coupled cluster calculations of isolated dipeptides as reference, and (ii) that the TIP4P/2005 solvation model yields overall tumbling correlation times that are in close agreement with experimental data. The methyl axis squared order parameters Saxis 2 and associated correlation times τ f, obtained within the Lipari-Szabo formalism, are in good agreement with the values derived from NMR deuterium relaxation experiments. Importantly, the relaxation rates and spectral densities derived from MD and NMR agree as well, enabling a direct comparison without assumptions inherent to simplified motional models.

KW - SIDE-CHAIN DYNAMICS

KW - NMR RELAXATION DATA

KW - MAGNETIC-RESONANCE RELAXATION

KW - ORDER-PARAMETER ANALYSIS

KW - DEUTERIUM SPIN PROBES

KW - MODEL-FREE APPROACH

KW - MOLECULAR-DYNAMICS

KW - ROTATIONAL DIFFUSION

KW - CONFORMATIONAL ENTROPY

KW - COMPUTER-SIMULATION

UR - http://www.scopus.com/inward/record.url?scp=85046471474&partnerID=8YFLogxK

U2 - 10.1021/acs.jpcb.8b02769

DO - 10.1021/acs.jpcb.8b02769

M3 - Journal article

C2 - 29695158

SN - 1520-6106

VL - 122

SP - 5038

EP - 5048

JO - Journal of Physical Chemistry B

JF - Journal of Physical Chemistry B

IS - 19

ER -