Dr. Srikrishna Subramanian

Biography

Significant recognition: Awards, fellowships, international funding of distinction, technologies transferred/licensed etc.: Associate Editor – BMC Bioinformatics (March 2010 – present) Adjunct Professor – Sanford|Burnham Institute for Medical Research, La Jolla, California, USA (Jan 2010 – present) Invited attendee at SciFoo 2007 an annual, interdisciplinary, invite-only scientific unconference organized by Nature Publishing Group, Google and O'Reilly Media held on Aug 3 - 5, 2007 at the Googleplex in Mountain View, CA Invited speaker at Keystone Symposium, Structural Genomics and its Applications to Chemistry, Biology and Medicine, at the Sheraton Steamboat Resort in Steamboat Springs, Colorado. Jan 6 - 11, 2008 Invited speaker at the Enabling Technologies for Structural Biology Workshop, at the Natcher Conference Center, National Institutes of Health, Bethesda, Maryland. Mar 04 – 06, 2009 Co-organizer of a series of international workshops on “Innovative approaches for characterizing protein structures” and “Exploring Structure-Function Relationships using Community-Input-Based Collaborative Environments” with Prof. John Wooley (http://proteinstructurefunction.calit2.net) at the Cailt2 center, UCSD. Co-organizer of an international workshop on “New communication channels for Biology” with Prof. John Wooley (http://ccbw.calit2.net) at the Cailt2 center, UCSD, which focused on emerging approaches within e-science. Selected list of Publications and Patents: Publications: Krishna, S.S.§ and Aravind, L. The bridge-region of the Ku superfamily is an atypical zinc ribbon domain. Journal of structural biology (2010). Krishna, S.S., Aravind L, Bakolitsa C, Caruthers J, Carlton D, Miller MD, Abdubek P, Astakhova T, Axelrod HL, Chiu H-J et al: Crystal structure of SSO2064, the first representative of Pfam family PF01796, reveals a novel two-domain zinc ribbon - OB-fold architecture with a potential acyl-CoA binding role. Acta Cryst. F66 (2010). Jaroszewski L., Li Z, Krishna S.S., Bakolitsa C., Wooley J., Deacon A.M., Wilson I.A., Godzik A.: Exploration of uncharted regions of the protein universe. PLoS biology 2009, 7(9):e1000205. Krishna, S.S., Tautz, L., Xu, Q., McMullan, D., Miller, M.D., Abdubek, P., Ambing, E., Astakhova, T., Axelrod, H.L., Carlton, D. et al. (2007) Crystal structure of NMA1982 from Neisseria meningitidis at 1.5 A resolution provides a structural scaffold for nonclassical, eukaryotic-like phosphatases. Proteins, 69, 415-421. Zhi, D., Krishna, S.S., Cao, H., Pevzner, P. and Godzik, A. (2006) Representing and comparing protein structures as paths in three-dimensional space. BMC bioinformatics, 7, 460. Krishna, S.S., Sadreyev, R.I. and Grishin, N.V. (2006) A tale of two ferredoxins: sequence similarity and structural differences. BMC structural biology, 6, 8. Cheek, S., Krishna, S.S. and Grishin, N.V. (2006) Structural classification of small, disulfide-rich protein domains. Journal of molecular biology, 359, 215-237. Majumdar, I., Krishna, S.S. and Grishin, N.V. (2005) PALSSE: a program to delineate linear secondary structural elements from protein structures. BMC bioinformatics, 6, 202. Krishna, S.S. and Grishin, N.V. (2005) Structural drift: a possible path to protein fold change. Bioinformatics (Oxford, England), 21, 1308-1310. Das, D., Krishna, S.S., McMullan, D., Miller, M.D., Xu, Q., Abdubek, P., Acosta, C., Astakhova, T., Axelrod, H.L., Burra, P. et al. (2009) Crystal structure of the Fic (Filamentation induced by cAMP) family protein SO4266 (gi|24375750) from Shewanella oneidensis MR-1 at 1.6 A resolution. Proteins, 75, 264-271. Zubieta, C., Krishna, S.S., McMullan, D., Miller, M.D., Abdubek, P., Agarwalla, S., Ambing, E., Astakhova, T., Axelrod, H.L., Carlton, D. et al. (2007) Crystal structure of homoserine O-succinyltransferase from Bacillus cereus at 2.4 A resolution. Proteins, 68, 999-1005. Zubieta, C., Krishna, S.S., Kapoor, M., Kozbial, P., McMullan, D., Axelrod, H.L., Miller, M.D., Abdubek, P., Ambing, E., Astakhova, T. et al. (2007) Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif. Proteins, 69, 223-233. Shi, S., Zhong, Y., Majumdar, I., Krishna, S.S. and Grishin, N.V. (2007) Searching for three dimensional secondary structural patterns in proteins with ProSMoS. Bioinformatics (Oxford, England). Krishna, S.S. ‡, Tautz, L., Xu, Q., McMullan, D., Miller, M.D., Abdubek, P., Ambing, E., Astakhova, T., Axelrod, H.L., Carlton, D. et al. (2007) Crystal structure of NMA1982 from Neisseria meningitidis at 1.5 A resolution provides a structural scaffold for nonclassical, eukaryotic-like phosphatases. Proteins, 69, 415-421. Zhi, D., Krishna, S.S., Cao, H., Pevzner, P. and Godzik, A. (2006) Representing and comparing protein structures as paths in three-dimensional space. BMC bioinformatics, 7, 460. Krishna, S.S., Sadreyev, R.I. and Grishin, N.V. (2006) A tale of two ferredoxins: sequence similarity and structural differences. BMC structural biology, 6, 8. Cheek, S., Krishna, S.S. and Grishin, N.V. (2006) Structural classification of small, disulfide-rich protein domains. Journal of molecular biology, 359, 215-237. Majumdar, I., Krishna, S.S. and Grishin, N.V. (2005) PALSSE: a program to delineate linear secondary structural elements from protein structures. BMC bioinformatics, 6, 202. Krishna, S.S. and Grishin, N.V. (2005) Structural drift: a possible path to protein fold change. Bioinformatics (Oxford, England), 21, 1308-1310. Krishna, S.S. and Grishin, N.V. (2004) Structurally analogous proteins do exist! Structure, 12, 1125-1127. Krishna, S.S.§ and Grishin, N.V. (2004) The finger domain of the human deubiquitinating enzyme HAUSP is a zinc ribbon. Cell cycle (Georgetown, Tex, 3, 1046-1049. Cheek, S., Qi, Y., Krishna, S.S., Kinch, L.N. and Grishin, N.V. (2004) SCOPmap: automated assignment of protein structures to evolutionary superfamilies. BMC bioinformatics, 5, 197. Krishna, S.S. §, Majumdar, I. and Grishin, N.V. (2003) Structural classification of zinc fingers: survey and summary. Nucleic acids research, 31, 532-550. Kinch, L.N., Wrabl, J.O., Krishna, S.S., Majumdar, I., Sadreyev, R.I., Qi, Y., Pei, J., Cheng, H. and Grishin, N.V. (2003) CASP5 assessment of fold recognition target predictions. Proteins, 53 Suppl 6, 395-409. Krishna, S.S., Zhou, T., Daugherty, M., Osterman, A. and Zhang, H. (2001) Structural basis for the catalysis and substrate specificity of homoserine kinase. Biochemistry, 40, 10810-10818. Krishna, S.S., Sastri, M., Savithri, H.S. and Murthy, M.R. (2001) Structural studies on the empty capsids of Physalis mottle virus. Journal of molecular biology, 307, 1035-1047. Krishna, S.S., Hiremath, C.N., Munshi, S.K., Prahadeeswaran, D., Sastri, M., Savithri, H.S. and Murthy, M.R. (1999) Three-dimensional structure of physalis mottle virus: implications for the viral assembly. Journal of molecular biology, 289, 919-934. Patents: Annotation and Publication Framework by Adam Godzik, Srikrishna Subramanian and Dana Weekes (Filed Aug 2007, Pub. No. US 2009/0049046 A1)

Research Interest

Current research Interests My broad research interests are in bioinformatics and structural biology with special emphasis on molecular evolution. My primary research interests are in the development of new computational approaches for studying protein sequence and structures, evolutionary analysis and classification of protein families/folds, theoretical modeling of proteins and deciphering the functions of novel proteins by insightful in silico analysis. My future research plans are aimed at classifying all protein domains according to their evolutionary history and deducing the molecular function of proteins from knowledge of their sequence and structure.