MADHUSUDHAN M.S.

EZH2 promotes neoplastic transformation through VAV interaction-dependent extranuclear mechanisms

Published date : 02 Oct 2017

Recently, we reported that the histone methyltransferase, EZH2, controls leukocyte migration through interaction with the cytoskeleton remodeling effector, VAV, and direct methylation of the cytoskeletal regulatory protein, Talin. However, it is unclear whether this extranuclear, epigenetic-independent function of EZH2 has a profound impact on the initiation of cellular transformation and metastasis. Here, we show that EZH2 increases Talin1 methylation and cleavage, thereby enhancing adhesion turnover and promoting accelerated tumorigenesis.

type
Journal Paper
journal
Oncogene 2017, Pg 1-17, doi:10.1038/onc.2017.309
Impact Factor
7.519

Topology independent comparison of RNA 3D structures using the CLICK algorithm

Published date : 14 Sep 2016

RNA molecules are attractive therapeutic targets because non-coding RNA molecules have increasingly been found to play key regulatory roles in the cell. Comparing and classifying RNA 3D structures yields unique insights into RNA evolution and function. With the rapid increase in the number of atomic-resolution RNA structures, it is crucial to have effective tools to classify RNA structures and to investigate them for structural similarities at different resolutions.

type
Journal Paper
journal
Nuclei Acids Research 2016, doi: 10.1093/nar/gkw819
Impact Factor
6.03

Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pKa of ionizable residues in proteins

Published date : 12 Jun 2013

Residue depth accurately measures burial and parameterizes local protein environment. Depth is the distance of any atom/residue to the closest bulk water. We consider the non-bulk waters to occupy cavities, whose volumes are determined using a Voronoi procedure. Our estimation of cavity sizes is statistically superior to estimates made by CASTp and VOIDOO, and on par with McVol over a data set of 40 cavities. Our calculated cavity volumes correlated best with the experimentally determined destabilization of 34 mutants from five proteins.

type
Journal Paper
journal
Nucleic Acids Research 2013, Vol. 41, Pg 314-321, doi:10.1093/nar/gkt503

Transplantation of a hydrogen bonding network from West Nile virus protease onto Dengue-2 protease improves catalytic efficiency and sheds light on substrate specificity.

Published date : 12 Sep 2012

The two-component serine protease of flaviviruses such as Dengue virus (DENV) and West Nile virus (WNV) are attractive targets for inhibitor/therapeutic design. Peptide aldehyde inhibitors that bind to the covalently tethered two-component WNV protease (WNVpro) with 50% inhibitory concentration (IC50) at sub-micromolar concentrations,bind the equivalent DENV-2 protease

type
Journal Paper
journal
Protein Engineering, Design & Selection, 2012,, Vol. 25, No. 12, Pg 843-850, doi: 10.1093/protein/gzs049. Epub 2012 Sep 12
Impact Factor
2.937

SALIGN: a web server for alignment of multiple protein sequences and structures

Published date : 21 May 2012

ABSTRACT
Summary: Accurate alignment of protein sequences and/or structures is crucial for many biological analyses, including
functional annotation of proteins, classifying protein sequences into families, and comparative protein structure modeling. Described
here is a web interface to SALIGN, the versatile protein multiple sequence/structure alignment module of MODELLER. The web
server automatically determines the best alignment procedure based on the inputs, while allowing the user to override default parameter

type
Journal Paper
journal
Bioinformatics. 2012 Aug 1;28(15):2072-3. doi: 10.1093/bioinformatics/bts302
Impact Factor
5.468

ModBase, a database of annotated comparative protein structure models, and associated resources

Published date : 30 Jan 2011

ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and model assessment (http://salilab.org/modeller/). ModBase currently contains 10,355,444 reliable models for domains in 2,421,920 unique protein sequences.

type
Journal Paper
journal
Nuclei Acids Research 2011, Jan:39 (Database issue) D465-74, doi: 10.1093/nar/gkq1091
Impact Factor
7.836