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Sathyanarayanan Anita

Bio: Sathyanarayanan Anita is an academic researcher. The author has contributed to research in topics: Gp41. The author has an hindex of 2, co-authored 2 publications receiving 22 citations.
Topics: Gp41

Papers
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Journal ArticleDOI
TL;DR: A non-redundant dataset of 192 heterodimer complex structures from the protein databank is used to identify interface residues and describe their interfaces using amino-acids residue property preference to provide insights to the understanding of protein-protein interactions.
Abstract: Protein heterodimer complexes are often involved in catalysis, regulation, assembly, immunity and inhibition. This involves the formation of stable interfaces between the interacting partners. Hence, it is of interest to describe heterodimer interfaces using known structural complexes. We use a non-redundant dataset of 192 heterodimer complex structures from the protein databank (PDB) to identify interface residues and describe their interfaces using amino-acids residue property preference. Analysis of the dataset shows that the heterodimer interfaces are often abundant in polar residues. The analysis also shows the presence of two classes of interfaces in heterodimer complexes. The first class of interfaces (class A) with more polar residues than core but less than surface is known. These interfaces are more hydrophobic than surfaces, where protein-protein binding is largely hydrophobic. The second class of interfaces (class B) with more polar residues than core and surface is shown. These interfaces are more polar than surfaces, where binding is mainly polar. Thus, these findings provide insights to the understanding of protein-protein interactions.

16 citations

Journal ArticleDOI
TL;DR: Regression analysis shows that blood and brain gp120 and gp41 percent sequence polarity range correlate with mean Shannon entropy, which point to the use of protein modifications to enhance HIV-1 ENV vaccines across multiple clades, blood, and brain.
Abstract: The human immunodeficiency virus type-1 (HIV-1) gp160 (gp120-gp41 complex) trimer envelope (ENV) protein is a potential vaccine candidate for HIV/AIDS. HIV-1 vaccine development has been problematic and charge polarity as well as sequence variation across clades may relate to the difficulties. Further obstacles are caused by sequence variation between blood and brain-derived sequences, since the brain is a separate compartment for HIV-1 infection. We utilize a threedimensional residue measure of solvent exposure, accessible surface area (ASA), which shows that major segments of gp120 and gp41 known structures are solvent exposed across clades. We demonstrate a large percent sequence polarity for solvent exposed residues in gp120 and gp41. The range of sequence polarity varies across clades, blood, and brain from different geographical locations. Regression analysis shows that blood and brain gp120 and gp41 percent sequence polarity range correlate with mean Shannon entropy. These results point to the use of protein modifications to enhance HIV-1 ENV vaccines across multiple clades, blood, and brain. It should be noted that we do not address the issue of protein glycosylation here; however, this is an important issue for vaccine design and development. Abbreviations HIV-1 - human immunodeficiency virus type 1, AIDS - acquired immunodeficiency syndrome, ENV - envelope, gp160 - 160,000d glycoprotein, gp120 - 120,000d glycoprotein, gp41 - 41,000d glycoprotein, LANL - Los Alamos National Laboratories, PDB - Protein Data Bank, HVTN - STEP HIV vaccine trial, AA - amino acids, MSA - multiple sequence alignment, ASA - accessible surface area, SNPs- single nucleotide polymorphisms, HAART - Highly Active Antiretroviral Therapy, CCR5 - C-C chemokine receptor type 5, CNS - central nervous system, HIVE - HIV encephalitis, P - polarity, NP - non-polarity, CTL - cytotoxic T lymphocyte, NIAID - National Institute of Allergy and Infectious Diseases.

8 citations


Cited by
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01 Aug 2000
TL;DR: Assessment of medical technology in the context of commercialization with Bioentrepreneur course, which addresses many issues unique to biomedical products.
Abstract: BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

4,833 citations

Journal ArticleDOI
TL;DR: Interestingly, this analysis has identified five key features of PPI interface features that are discriminatory among the functional classes using Kruskal‐Wallis rank sum test, and these representative features have implications for the prediction of potential function of novel protein complexes.
Abstract: Protein–protein interaction (PPI) establishes the central basis for complex cellular net-works in a biological cell. Association of proteins with other proteins occurs at varying affinities,yet with a high degree of specificity. PPIs lead to diverse functionality such as catalysis, regulation,signaling, immunity, and inhibition, playing a crucial role in functional genomics. The molecularprinciple of such interactions is often elusive in nature. Therefore, a comprehensive analysis ofknown protein complexes from the Protein Data Bank (PDB) is essential for the characterization ofstructural interface features to determine structure–function relationship. Thus, we analyzed a non-redundant dataset of 278 heterodimer protein complexes, categorized into major functionalclasses, for distinguishing features. Interestingly, our analysis has identified five key features(interface area, interface polar residue abundance, hydrogen bonds, solvation free energy gainfrom interface formation, and binding energy) that are discriminatory among the functional classesusing Kruskal-Wallis rank sum test. Significant correlations between these PPI interface featuresamongst functional categories are also documented. Salt bridges correlate with interface area inregulator-inhibitors (r50.75). These representative features have implications for the prediction ofpotential function of novel protein complexes. The results provide molecular insights for betterunderstanding of PPIs and their relation to biological functions.Keywords: protein–protein interaction; heterodimers; surface; interface; protein structure; proteinfunctionIntroduction

32 citations

Journal ArticleDOI
TL;DR: An overview of the experimental methods used to determine protein-protein interactions and the key databases archiving this information is provided and the diverse datasets created/collected by various groups and their key findings inferring distinguishing features are described.
Abstract: Molecular function in cellular processes is governed by protein-protein interactions (PPIs) within biological networks. Selective yet specific association of these protein partners contributes to diverse functionality such as catalysis, regulation, assembly, immunity, and inhibition in a cell. Therefore, understanding the principles of protein-protein association has been of immense interest for several decades. We provide an overview of the experimental methods used to determine PPIs and the key databases archiving this information. Structural and functional information of existing protein complexes confers knowledge on the principles of PPI, based on which a classification scheme for PPIs is then introduced. Obtaining high-quality non-redundant datasets of protein complexes for interaction characterisation is an essential step towards deciphering their underlying binding principles. Analysis of physicochemical features and their documentation has enhanced our understanding of the molecular basis of protein-protein association. We describe the diverse datasets created/collected by various groups and their key findings inferring distinguishing features. The currently available interface databases and prediction servers have also been compiled.

20 citations

Journal ArticleDOI
TL;DR: In this paper, the results of the qualitative phytochemical screening of differentially dried Sargassum polycystum extracts revealed the presence of various secondary metabolites, and the identification of metabolites variations using PCA is considered as very useful procedure as a basis to recommend the most efficient processing (drying) method.

15 citations

Journal ArticleDOI
TL;DR: Structural analysis of αvβ6·uPAR interactions is performed using model data with docking simulations to pinpoint their interface, in accord with earlier reports of the β-propeller region of integrin α-chain interacting with uPAR.

10 citations