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- W1969630768 abstract "For patients suffering from HIV, there exist several therapeutic drugs that can target various aspects of the HIV life cycle; however, treatment aggressiveness is limited by the very potent and potentially dangerous side effects of these drugs. Molecular traffic between the nucleus and the cytoplasm is exclusively regulated by the nuclear pore complex (NPC), which acts as a highly selective channel perforating the nuclear envelope in eukaryotic cells. HIV exploits the nucleocytoplasmic pathway to export its RNA transcripts across the NPC to the cytoplasm. DDX3 is a RNA helicase necessary for HIV replication which is found to interact with a protein, CRM1, which shuttles HIV mRNA out of the nucleus. Recent work has exposed DDX3 as a promising new target of the viral replication cycle that has not yet been thoroughly investigated due to limitations in experimental methodologies. In the present research we have developed a general computational protocol for analyzing protein-protein binding. This method is based on molecular docking followed by molecular dynamics simulation and accompanied by approximate free energy calculation (MM/GBSA), computational alanine scanning, clustering and evolutionary analysis. This research seeks to explore the details of the structural interaction between DDX3 and CRM1 using the proposed hybrid computational approach. Utilizing this approach to study the HIV mRNA export complex, we have highlighted some of the most likely binding modes and interfacial residues between DDX3 and CRM1 both in the absence and presence of RanGTP. This work shows that although DDX3 can bind to free CRM1, addition of RanGTP leads to more concentrated distribution of binding modes and stronger binding between CRM1 and RanGTP." @default.
- W1969630768 created "2016-06-24" @default.
- W1969630768 creator A5077182340 @default.
- W1969630768 date "2014-01-01" @default.
- W1969630768 modified "2023-09-30" @default.
- W1969630768 title "Computational Study of Binding Between DDX3 and Hiv-1 MRNA Nucleocytoplasmic Export Complex" @default.
- W1969630768 doi "https://doi.org/10.1016/j.bpj.2013.11.1813" @default.
- W1969630768 hasPublicationYear "2014" @default.
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