scholarly journals PREDICTION OF PROTEIN INTERACTIONS ON HIV-1–HUMAN PPI DATA USING A NOVEL CLOSURE-BASED INTEGRATED APPROACH

2012 ◽  
Keyword(s):  
Protein Interactions ◽  
Integrated Approach ◽  
Hiv 1

Quantitative analysis of the interactions between HIV-1 integrase and retroviral reverse transcriptases

2008 ◽  
Vol 412 (1) ◽  
pp. 163-170 ◽  
Author(s):  
Alon Herschhorn ◽  
Iris Oz-Gleenberg ◽  
Amnon Hizi
Keyword(s):  
Conformational Changes ◽  
Protein Interactions ◽  
Molecular Mechanisms ◽  
Reaction Model ◽  
Protein Protein Interactions ◽  
Common Site ◽  
Leukaemia Virus ◽  
Reverse Transcriptases ◽  
Interaction Kinetics ◽  
Hiv 1

The RT (reverse transcriptase) of HIV-1 interacts with HIV-1 IN (integrase) and inhibits its enzymatic activities. However, the molecular mechanisms underling these interactions are not well understood. In order to study these mechanisms, we have analysed the interactions of HIV-1 IN with HIV-1 RT and with two other related RTs: those of HIV-2 and MLV (murine-leukaemia virus). All three RTs inhibited HIV-1 IN, albeit to a different extent, suggesting a common site of binding that could be slightly modified for each one of the studied RTs. Using surface plasmon resonance technology, which monitors direct protein–protein interactions, we performed kinetic analyses of the binding of HIV-1 IN to these three RTs and observed interesting binding patterns. The interaction of HIV-1 RT with HIV-1 IN was unique and followed a two-state reaction model. According to this model, the initial IN–RT complex formation was followed by a conformational change in the complex that led to an elevation of the total affinity between these two proteins. In contrast, HIV-2 and MLV RTs interacted with IN in a simple bi-molecular manner, without any apparent secondary conformational changes. Interestingly, HIV-1 and HIV-2 RTs were the most efficient inhibitors of HIV-1 IN activity, whereas HIV-1 and MLV RTs showed the highest affinity towards HIV-1 IN. These modes of direct protein interactions, along with the apparent rate constants calculated and the correlations of the interaction kinetics with the capacity of the RTs to inhibit IN activities, are all discussed.

scholarly journals Studies on HIV‐1 RNA‐protein interactions.

2017 ◽  
Vol 31 (S1) ◽  
Author(s):  
Nicole Hadler ◽  
Eryn Stockdale ◽  
Kenneth Wise ◽  
Ina O'Carroll
Keyword(s):  
Protein Interactions ◽  
Hiv 1

Peptides that inhibit HIV-1 integrase by blocking its protein-protein interactions

FEBS Journal ◽  
2012 ◽  
Vol 279 (16) ◽  
pp. 2795-2809 ◽  
Author(s):  
Michal Maes ◽  
Abraham Loyter ◽  
Assaf Friedler
Keyword(s):  
Protein Interactions ◽  
Protein Protein Interactions ◽  
Hiv 1

Extracting Biological Significant Subnetworks from Protein-Protein Interactions Induced by Differentially Expressed Genes of HIV-1 Vpr Variants

2015 ◽  
Vol 4 (4) ◽  
pp. 35-51 ◽  
Author(s):  
Bandana Barman ◽  
Anirban Mukhopadhyay
Keyword(s):  
Differentially Expressed Genes ◽  
Protein Interaction ◽  
Protein Interactions ◽  
Protein Interaction Network ◽  
Interaction Network ◽  
Differentially Expressed ◽  
Wild Type ◽  
Protein Protein Interaction ◽  
Ppi Networks ◽  
Hiv 1

Identification of protein interaction network is very important to find the cell signaling pathway for a particular disease. The authors have found the differentially expressed genes between two sample groups of HIV-1. Samples are wild type HIV-1 Vpr and HIV-1 mutant Vpr. They did statistical t-test and found false discovery rate (FDR) to identify the genes increased in expression (up-regulated) or decreased in expression (down-regulated). In the test, the authors have computed q-values of test to identify minimum FDR which occurs. As a result they found 172 differentially expressed genes between their sample wild type HIV-1 Vpr and HIV-1 mutant Vpr, R80A. They found 68 up-regulated genes and 104 down-regulated genes. From the 172 differentially expressed genes the authors found protein-protein interaction network with string-db and then clustered (subnetworks) the PPI networks with cytoscape3.0. Lastly, the authors studied significance of subnetworks with performing gene ontology and also studied the KEGG pathway of those subnetworks.

scholarly journals A distinct class of plant and animal viral proteins that disrupt mitosis by directly interrupting the mitotic entry switch Wee1-Cdc25-Cdk1

2020 ◽  
Vol 6 (20) ◽  
pp. eaba3418
Author(s):  
Huaibing Jin ◽  
Zhiqiang Du ◽  
Yanjing Zhang ◽  
Judit Antal ◽  
Zongliang Xia ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Viral Proteins ◽  
Plant Viruses ◽  
Amino Acid Residues ◽  
Protein Protein Interactions ◽  
Common Amino Acid ◽  
Mitotic Entry ◽  
Distinct Class ◽  
Barley Yellow Dwarf ◽  
Hiv 1

Many animal viral proteins, e.g., Vpr of HIV-1, disrupt host mitosis by directly interrupting the mitotic entry switch Wee1-Cdc25-Cdk1. However, it is unknown whether plant viruses may use this mechanism in their pathogenesis. Here, we report that the 17K protein, encoded by barley yellow dwarf viruses and related poleroviruses, delays G2/M transition and disrupts mitosis in both host (barley) and nonhost (fission yeast, Arabidopsis thaliana, and tobacco) cells through interrupting the function of Wee1-Cdc25-CDKA/Cdc2 via direct protein-protein interactions and alteration of CDKA/Cdc2 phosphorylation. When ectopically expressed, 17K disrupts the mitosis of cultured human cells, and HIV-1 Vpr inhibits plant cell growth. Furthermore, 17K and Vpr share similar secondary structural feature and common amino acid residues required for interacting with plant CDKA. Thus, our work reveals a distinct class of mitosis regulators that are conserved between plant and animal viruses and play active roles in viral pathogenesis.

HIV‐1 Matrix Protein Interactions with Cellular tRNAs

2020 ◽  
Vol 34 (S1) ◽  
pp. 1-1
Author(s):  
Jason Ejimogu ◽  
Connor Parker ◽  
Mahlet Bauerle ◽  
Cheyenne Palm ◽  
Janae Baptiste Brown ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Matrix Protein ◽  
Hiv 1

scholarly journals Assay Optimization and Screening of RNA-Protein Interactions by AlphaScreen

2007 ◽  
Vol 12 (7) ◽  
pp. 946-955 ◽  
Author(s):  
Nicholas L. Mills ◽  
Anang A. Shelat ◽  
R. Kiplin Guy
Keyword(s):  
Drug Discovery ◽  
Small Molecules ◽  
High Throughput ◽  
Protein Interactions ◽  
Proof Of Concept ◽  
Rna Molecules ◽  
Lead Compounds ◽  
Assay Optimization ◽  
Rna Targets ◽  
Hiv 1

The lack of lead compounds that specifically recognize and manipulate the function of RNA molecules limits our ability to consider RNA targets valid for drug discovery. Herein is reported a high-throughput biochemical screen for inhibitors of RNA-protein interactions based on AlphaScreen technology that incorporates several layers of specificity measurements into the primary screen. This screen was used to analyze approximately 5500 compounds from a collection of bioactive small molecules to detect inhibitors of the HIV-1 Rev-RRE and BIV Tat-TAR interactions. This proof-of-concept screen validates the assay as one that accurately identifies hit molecules and determines the selectivity of those hits. ( Journal of Biomolecular Screening 2007: 946-955)

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