Molecular dynamics correctly models the unusual major conformation of the GAGU RNA internal loop and with NMR reveals an unusual minor conformation

Author:

Spasic Aleksandar,Kennedy Scott D.,Needham Laura,Manoharan Muthiah,Kierzek Ryszard,Turner Douglas H.,Mathews David H.

Abstract

The RNA “GAGU” duplex, (5′GACGAGUGUCA)2, contains the internal loop (5′-GAGU-3′)2 , which has two conformations in solution as determined by NMR spectroscopy. The major conformation has a loop structure consisting of trans-Watson–Crick/Hoogsteen GG pairs, A residues stacked on each other, U residues bulged outside the helix, and all sugars with a C2′-endo conformation. This differs markedly from the internal loops, (5′-GAGC-3′)2, (5′-AAGU-3′)2, and (5′-UAGG-3′)2, which all have cis-Watson–Crick/Watson–Crick AG “imino” pairs flanked by cis-Watson–Crick/Watson–Crick canonical pairs resulting in maximal hydrogen bonding. Here, molecular dynamics was used to test whether the Amber force field (ff99 + bsc0 + OL3) approximates molecular interactions well enough to keep stable the unexpected conformation of the GAGU major duplex structure and the NMR structures of the duplexes containing (5′-GAGC-3′)2, (5′-AAGU-3′)2, and (5′-UAGG-3′)2 internal loops. One-microsecond simulations were repeated four times for each of the duplexes starting in their NMR conformations. With the exception of (5′-UAGG-3′)2, equivalent simulations were also run starting with alternative conformations. Results indicate that the Amber force field keeps the NMR conformations of the duplexes stable for at least 1 µsec. They also demonstrate an unexpected minor conformation for the (5′-GAGU-3′)2 loop that is consistent with newly measured NMR spectra of duplexes with natural and modified nucleotides. Thus, unrestrained simulations led to the determination of the previously unknown minor conformation. The stability of the native (5′-GAGU-3′)2 internal loop as compared to other loops can be explained by changes in hydrogen bonding and stacking as the flanking bases are changed.

Funder

National Institutes of Health

National Institute of General Medical Sciences

National Science Center

Publisher

Cold Spring Harbor Laboratory

Subject

Molecular Biology

Reference71 articles.

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3