A molecular dynamic study of HIV-1 Tat protein as a potential therapeutic target.
DOI:
https://doi.org/10.22024/UniKent/03/ajpp.1318Abstract
Background: Research and development remain ongoing to continue improving the current landscape of HIV treatment. Important stages of the HIV life cycle such as transcription have still yet to be targeted by therapies, and one important transcriptional regulator is the ‘Trans-Activator of Transcription’, or ‘Tat’ protein. Despite widespread acknowledgement of Tat’s role in HIV replication, current information on Tat remains limited; at present the only molecular models of the protein available are of a portion of the binding site with TAR-RNA, and a model of Tat from HIV subtype B which is a less clinically relevant subtype. This project aims to produce a model or Tat subtype C both solo and docked with TAR-RNA, as well as characterising the properties, interactions, and behaviour of Tat and TAR RNA to inform future drug development.
Methods: Three molecular dynamic runs of Tat solo and two docked with RNA (one constrained, one unconstrained) were simulated using NAMD and run at Canterbury Christ Church University using accelerated GPU calculations and a 2-femtosecond integration timestep for a minimum of 500ns. VMD, PyMOL, and qtGrace software were used to run, visualise, and analyse the data produced using RMSD, hydrogen-bonding, RMSF, electrostatic mapping and PCA K-means clustering analysis.
Results: RMSD of solo Tat runs was found to be consistently higher than that of Tat when docked with RNA, both constrained and unconstrained. Hydrogen bond analysis supported this, with detailed analysis showing Arg55 – Asp67 H-bonding at 72.72% occupancy in Tat docked with constrained RNA compared to the highest occupancy of Tyr32 – Tyr26 at 24.90% for Tat solo. K-means clustering from PCA analysis again supported this, showing a large spread of data for solo Tat versus a more consistent and concentrated plot of data for Tat docked with RNA. Structural analysis allowed for visualisation, and combined with RMSF overlay showed the stretched and unstable conformation of solo Tat versus compact conformation when docked with RNA. Electrostatic mapping of these more compact structures revealed positively charged regions encompassing the core and binding functional domains, as well as a negatively charged tail which protrudes from the core structure and moves freely.
Conclusions: Solo Tat runs demonstrated the flexibility and relative unpredictability of the protein, suggesting that future drug development for Tat in unbound conformations may prove difficult. However, when docked with RNA, the more compact and stable structure may be better suited to drug design. The core and binding functional domains of Tat appear relatively strongly positively charged, and hydrogen bonding and RMSD data shows that these regions are far less subject to change. Novel models of full Tat subtype C, and Tat with TAR RNA have been produced from this project for distribution and further investigation into Tat. Repeat analysis with longer RNA strands to avoid constraining the RNA are recommended in future, as well as comparison between different HIV subtypes. Consideration of Tat interaction with other known transcription factors such as pTEFb may also prove useful, and deep docking to identify candidate drug molecules based on these findings is recommended.
Downloads
Published
How to Cite
Issue
Section
License
© The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
AJPP requests that, as the creator(s)/author(s) of the manuscript you are submitting, that you assign certain rights to the manuscript to the AJPP in exchange for undertaking to publish the article in electronic form and, in general, to pursue its dissemination throughout the world. The rights the AJPP requests are:
- The right to publish the article in electronic form or in any other form it may choose that is in keeping with its role as a scholarly journal with the goal of disseminating the work as widely as possible;
- The right to be the sole publisher of the article for a period of 12 months;
- The right to make the article available to the public within a period of not more than 24 months, as determined by relevant journal staff of the AJPP;
- The right to grant republication rights to itself or others in print, electronic, or any other form, with any revenues accrued to be shared equally between the author(s) and the journal;
- The right to administer permission to use portions of the article as requested by others, seeking recompense when the AJPP sees it as warranted;
- The right to seek or take advantage of opportunities to have the article included in a database aimed at increasing awareness of it;
- As the author(s), the AJPP wishes you to retain the right to republish the article, with acknowledgement of the AJPP as the original publisher, in whole or in part, in any other pbulication of your own, including any anthology that you might edit with up to three others;
- As the author(s), the AJPP wishes you to retain the right to place the article on your personal Web page or respository of your university or institution. The AJPP askes that you include this notice: A fully edited, peer-reviewed version of this article was first published by the Advanced Journal of Professional Practice, <Year>, <Volume>, <Issue>, <Page Numbers>.
- You retain the right to unrestricted use of your paper for yourself or for your own teaching purposes.
BY AGREEING TO THE FOREGOING, YOU CONFIRM THAT THE MANUSCRIPT YOU ARE SUBMITTING HAS NOT BEEN PUBLISHED ELSEWHERE IN WHOLE OR IN PART, AND THAT NO AGREEMENT TO PUBLISH IS OUTSTANDING.
SHOULD THE ARTICLE CONTAIN MATERIAL WHICH REQUIRES WRITTEN PERMISSION FOR INCLUSION, YOU AGREE THAT IT IS YOUR OBLIGATION IN LAW TO IDENTIFY SUCH MATERIAL TO THE EDITOR OF THE AJPP AND TO OBTAIN SUCH PERMISSION. THE AJPP WILL NOT PAY ANY PERMISSION FEES. SHOULD THE AJPP BE OF THE OPINION THAT SUCH PERMISSION IS NECESSARY, IT WILL REQUIRE YOU TO PURSUE SUCH PERMISSSION PRIOR TO PUBLICATION.
AS AUTHOR(S), YOU WARRANT THAT THE ARTICLE BEING SUBMITTED IS ORIGINAL TO YOU.
Provided the foregoing terms are satisfactory, and that you are in agreement with them, please indicate your acceptance by checking the appropriate box and proceed with your submission.
