基于结构的 HIV-1 TAR-RNA 与转录因子核因子-κB（NFkB）之间分子识别的分析。

Structure-based analysis of the molecular recognitions between HIV-1 TAR-RNA and transcription factor nuclear factor-kappaB (NFkB).

机构信息

Department of Biochemistry and Molecular Biology, Section of Molecular Biology, University of Ferrara, Via Fossato di Mortara 74, Ferrara I-44100, Italy.

出版信息

Curr Top Med Chem. 2012;12(8):814-27. doi: 10.2174/156802612800166800.

DOI:10.2174/156802612800166800

PMID:22352910

Abstract

In this paper we applied the "macromolecular docking" procedure to perform molecular modeling with the aim of screening transcription factor sequences for possible interaction to the HIV-1 TAR-RNA, employing the software Hex version 4.2. The molecular modeling data were compared with electrophoretic mobility shift assays (EMSA) and surface plasmon resonance (SPR) based biospecific interaction analysis (BIA) using an optical biosensor. Finally the specific interactions between NF-κB and RNA have been calculated utilizing the AMBER-MM and FMO calculations. The results obtained clearly indicate that (a) NF-kB p50 transcription factor can bind TAR-RNA; (b) this binding efficiency is lower than that displayed by NF-kB factor in respect to DNA sequences; (c) other structured RNAs used as controls do not bind to NF-kB; (d) TAR-RNA is capable to bind pre-formed NF-kB/DNA complexes. Despite the fact that our data do not indicate whether NF-kB/TAR-RNA complexes play a role in the early steps of HIV-1 transcriptional activation, the results presented strongly indicate that interactions between transcription factors recruited at the level of HIV-1 LTR might interact with the TAR-RNA and deserve further studies aimed to determine its role in the HIV-1 life cycle.

摘要

在本文中，我们应用“大分子对接”程序进行分子建模，目的是筛选可能与 HIV-1 TAR-RNA 相互作用的转录因子序列，使用的软件是 Hex 版本 4.2。将分子建模数据与电泳迁移率变动分析（EMSA）和基于表面等离子体共振（SPR）的生物特异性相互作用分析（BIA）进行比较，使用光学生物传感器。最后，利用 AMBER-MM 和 FMO 计算来计算 NF-κB 和 RNA 之间的特异性相互作用。所得结果清楚地表明：(a) NF-κB p50 转录因子可以与 TAR-RNA 结合；(b) 这种结合效率低于 NF-κB 因子与 DNA 序列的结合效率；(c) 用作对照的其他结构 RNA 不与 NF-κB 结合；(d) TAR-RNA 能够与预先形成的 NF-κB/DNA 复合物结合。尽管我们的数据并未表明 NF-κB/TAR-RNA 复合物是否在 HIV-1 转录激活的早期步骤中发挥作用，但所呈现的结果强烈表明，在 HIV-1 LTR 水平募集的转录因子之间的相互作用可能与 TAR-RNA 相互作用，并值得进一步研究，以确定其在 HIV-1 生命周期中的作用。