J 2016

Assessing the Current State of Amber Force Field Modifications for DNA

GALINDO-MURILLO, Rodrigo, James C. ROBERTSON, Marie ZGARBOVÁ, Jiří ŠPONER, Michal OTYEPKA et. al.

Basic information

Original name

Assessing the Current State of Amber Force Field Modifications for DNA

Authors

GALINDO-MURILLO, Rodrigo, James C. ROBERTSON, Marie ZGARBOVÁ, Jiří ŠPONER, Michal OTYEPKA, Petr JUREČKA and Thomas E. CHEATHAM

Edition

Journal of Chemical Theory and Computation, Washington DC, American Chemical Society, 2016, 1549-9618

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10403 Physical chemistry

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

Impact factor

Impact factor: 5.245

Organization unit

Central European Institute of Technology

DOI

UT WoS

000381320200061

Keywords in English

MOLECULAR-DYNAMICS SIMULATIONS; PARTICLE MESH EWALD; PAIR OPENING KINETICS; IMINO PROTON-EXCHANGE; B-DNA; NUCLEIC-ACIDS; BIOMOLECULAR SIMULATIONS; SYNTHETIC DNA; RNA; DODECAMER

Tags

Změněno: 7/10/2016 15:40, Mgr. Eva Špillingová

Abstract

V originále

The utility of molecular dynamics (MD) simulations to model biomolecular structure, dynamics, and interactions has witnessed enormous advances in recent years due to the availability of optimized MD software and access to significant computational power, including GPU multicore computing engines and other specialized hardware. This has led researchers to routinely extend conformational sampling times to the microsecond level and beyond. The extended sampling time has allowed the community not only to converge conformational ensembles through complete sampling but also to discover deficiencies and overcome problems with the force fields. Accuracy of the force fields is a key component, along with sampling, toward being able to generate accurate and stable structures of biopolymers. The Amber force field for nucleic acids has been used extensively since the 1990s, and multiple artifacts have been discovered, corrected, and reassessed by different research groups. We present a direct comparison of two of the most recent and state-of-the-art Amber force field modifications, bsc1 and OL15, that focus on accurate modeling of double-stranded DNA. After extensive MD simulations with five test cases and two different water models, we conclude that both modifications are a remarkable improvement over the previous bsc0 force field. Both force field modifications show better agreement when compared to experimental structures. To ensure convergence, the Drew-Dickerson dodecamer (DDD) system was simulated using 100 independent MD simulations, each extended to at least 10 mu s, and the independent MD simulations were concatenated into a single 1 ms long trajectory for each combination of force field and water model. This is significantly beyond the time scale needed to converge the conformational ensemble of the internal portions of a DNA helix absent internal base pair opening. Considering all of the simulations discussed in the current work, the MD simulations performed to assess and validate the current force fields and water models aggregate over 14 ms of simulation time. The results suggest that both the bsc1 and OL15 force fields render average structures that deviate significantly less than 1 angstrom from the average experimental structures. This can be compared to similar but less exhaustive simulations with the CHARMM 36 force field that aggregate to the similar to 90 mu s time scale and also perform well but do not produce structures as close to the DDD NMR average structures (with root-mean-square deviations of 1.3 angstrom) as the newer Amber force fields. On the basis of these analyses, any future research involving double-stranded DNA simulations using the Amber force fields should employ the bsc1 or OL15 modification.