MADHUSUDHAN M.S.

EZH2 promotes neoplastic transformation through VAV interaction-dependent extranuclear mechanisms

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
pubmed: 
28967906
Url: 
http://www.nature.com.ejproxy.a-star.edu.sg/articles/onc2017309
Impact Factor: 
7.519
Date of acceptance: 
2017-07-11

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

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
pubmed: 
27634929
Url: 
http://nar.oxfordjournals.org/content/early/2016/09/14/nar.gkw819.abstract?keytype=ref&ijkey=WsEFoSR4nWzxvyH
Impact Factor: 
6.03
Date of acceptance: 
2016-09-14

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

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
pubmed: 
23766289
Url: 
http://www.ncbi.nlm.nih.gov/pubmed/23766289
Date of acceptance: 
2013-05-15

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

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
pubmed: 
22972763
Impact Factor: 
2.937

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

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
pubmed: 
22618536
Impact Factor: 
5.468

Biological insights from topology independent comparison of protein 3D structures

type: 
Journal Paper
journal: 
Nucleic Acids Res. 2011 Aug;39(14):e94
pubmed: 
21596786
Url: 
http://www.ncbi.nlm.nih.gov/pubmed/21596786
Impact Factor: 
7.836

DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins

type: 
Journal Paper
journal: 
Nucleic Acids Res. 2011 Jul;39:W242-8
pubmed: 
21576233
Url: 
http://www.ncbi.nlm.nih.gov/pubmed/21576233
Impact Factor: 
7.836

CLICK--topology-independent comparison of biomolecular 3D structures

type: 
Journal Paper
journal: 
Nucleic Acids Res. 2011 Jul;39:W24-8
pubmed: 
21602266
Url: 
http://www.ncbi.nlm.nih.gov/pubmed/21602266
Impact Factor: 
7.836

Structure-guided fragment-based in silico drug design of dengue protease inhibitors

type: 
Journal Paper
journal: 
J Comput Aided Mol Des. 2011 Mar;25(3):263-74.
pubmed: 
21344277
Url: 
http://www.ncbi.nlm.nih.gov/pubmed/21344277
Impact Factor: 
3.374

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

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
pubmed: 
21097780
Url: 
http://www.ncbi.nlm.nih.gov/pubmed/21097780
Impact Factor: 
7.836
Date of acceptance: 
2011-01-01
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