Department of Chemistry and Biochemistry at The University of Northern Iowa

Nalin Goonesekere

Associate Professor - Biochemistry, Bioinformatics, Structural Biology
Department of Chemistry and Biochemistry
University of Northern Iowa
Cedar Falls, IA 50614-0423

Office: 283 McCollum Science Hall
Voice: 319-273-3949
Fax: 319-273-7127
E-mail: nalin.goonesekere@uni.edu

Degrees

  • B.Sc. University of Colombo, Sri Lanka.
  • Ph.D. Princeton University.

Research Interests

The dawn of the 21th century can be characterized as the golden era in biochemistry, as much as the dawn of the 20th century was the golden era for physics. In 2003, we witnessed the complete sequencing of human DNA (genome) and we now have access to many mammalian, plant and microbial genomes. An important scientific challenge for the 21st century is interpreting the vast amounts of DNA sequence data that has become available. A portion of these sequences encode for proteins, which are nature’s ‘nanomachines’. These are the workhorses in a cell, and they have been exquisitely designed to carry out cellular processes with remarkable efficiency and fidelity. Understanding the structure and function of these proteins is critical in converting the DNA sequence information that we now have, into tangible benefits to humankind - whether it be new protein targets for drugs, or perhaps more efficient enzymes for use in biotechnology. Research conducted in our laboratory focuses on the broad problem of interpreting DNA sequence data to obtain biologically meaningful information.

  1. Identification of Disease-causing (virulence) Genes in the Corn Pathogen Fusarium verticillioides. Members of the genus Fusarium are economically important plant pathogens, that cause billions of dollars of damage each year worldwide. Fusarium verticillioides is known to cause destructive diseases in a wide variety of agriculturally important crops including corn, wheat and potato. In corn, it causes the disease knows as stalk rots. In this project, we focus on identifying and characterizing proteins associated with infectivity or virulence. An analysis of the newly-sequenced genome of F. verticillioides has revealed candidate virulence genes. We are now employing recombinant DNA techniques to evaluate these assignments in the laboratory.

  2. Our second area of interest is in using bioinformatics tools developed by us, and others, to predict the function of proteins that are, as yet, not annotated, using just the information from the protein sequence. We have been focusing our attention on a set of protein sequences from the well-known database Pfam. These sequences belong to Pfam families known as ‘Domains of Unknown Function’ (DUF). Since Pfam is used extensively in annotating protein sequence data from genomes such as the human genome, determining the functions of DUFs will directly assist current efforts to decode sequences from genomes.

  3. Development of Tools for Bioinformatics. In the past few years, we have been improving the most popular bioinformatics tool that is currently available, BLAST. We have been using our expertise in structural biology to incorporate protein structure data into BLAST, to significantly enhance its capability in annotating proteins through detection of remote homologs. We have now incorporated a context-specific amino acid substitution matrix into BLAST, to create CSSM-BLAST. CSSM-BLAST excels at detecting remote homologs to proteins of known structure. We are now pursuing our interests in developing a set of second-generation structure-based amino acid substitution matrices.

Selected Publications

Schutt, C.E., Myslik, J.C., Rozycki, M.D., Goonesekere, N.C.W. and Lindberg, U. (1993) The Structure of profilin:actin at 2.55 angstrom resolution, Nature 365 810.

Zeppezauer, E. S. C., Goonesekere, N.C.W., Rozycki, M.D., Myslik, J.C., Dauter, Z., Lindberg, U. and Schutt, C.E. (1994) The structure of profilin at 2.0 angstrom resolution, J Mol Biol 240 459.

Goonesekere, N.C.W., Gunasekera, M.B. and Fernandopulle, N. (1999) Use of DNA typing For Criminal Casework in Sri Lanka. Proceedings of the 10th International Symposium on Human Identification, Promega Corporation, Wisconsin, U.S.A.

Tiedemann, R., Kurt, F., Goonesekere, N.C.W., Gunasekera, M.B., and Ratnasooriya, W.D. (1999) A simulation study on the viability of Sri Lankan elephant populations. Folia Zoologica 48 (supp. 1): 95-104.

Fernandopulle, N., Gunasekera, M.B. and Goonesekere, N.C.W. (2002) Population genetics of eight STR loci from Sri Lanka. Forensic Science International 126 1 93.

Vandebona, H., Goonesekere, N.C.W., Ratnasooriya, W.D., Alahakoon, J. and Gunasekera, M.B. (2002) The establishment of paternity of elephants born in captivity in Pinnawela Elephant Orphanage, Sri Lanka, by DNA fingerprinting. International Zoo Yearbook 39.

Vandebona, H., Goonesekere, N.C.W., Tiedemann, R., Ratnasooriya, W.D., and Gunasekera, M.B. (2002) Sequence variation at two mitochondrial genes in the Asian elephant (Elephas maximus) population in Sri Lanka. Mam Biol 67 4 193.

Mapatuna, Y., Gunasekera, M.B., Ratnasooriya W.D., Goonesekere, N.C.W. & Bates P.J.J. (2002) Unravelling the taxonomic status of the Genus Cynopterus (Chiroptera:Pteropodidae) in Sri Lanka by multivariate morphometrics and mitochondrial DNA sequence analysis, Mam Biol 67: 321.

Goonesekere, N.C.W. and Lee B. (2004) Frequency of gaps observed in a structurally aligned protein pair database suggest a simple gap penalty function, Nucleic Acids Research 32 9 2838.

De Silva, A.P., de Silva, S.S.K., Goonesekere, N.C.W. (2007) Gunaratne, H.Q.N, Lynch, P.L.M, Nesbitt, K.R., Patuwathavithana, S.T., Ramyalal, N.L.D.S. Analog Parallel Processing of Molecular Sensory Information. J Am Chem Soc 129: 3050.

Goonesekere, N.C.W. and Lee B. (2008) Context-specific substitution matrices and their use in the detection of protein homologs. Proteins: Struct Fun and Bioinformatics 71: 910.

Goonesekere, N.C.W., Beaudry, S. and Tasovski, I. (2009) Towards establishing the molecular function of Pfam domain DUF294 by sequence analysis and homology modeling, On J Bioinformatics. 11 (1): 125

Goonesekere, N.C.W. (2009) Evaluating the efficacy of a structure-derived amino acid substitution matrix in detecting protein homologs by BLAST and PSI-BLAST. Adv Appl in Bioinformatics and Chemistry, 2009: 2 71.

Goonesekere, N.C.W., *Shipely, K. and *O'Connor, K. (2010) The challenge of annotating protein sequences: The tale of eight domains of unknown function in Pfam. Comp. Biol. Chem., 2010: 34 210.

Shen, R., Goonesekere, N.C.W. and Chittibabu Guda "Mining functional subgraphs from cancer protein-protein interaction networks", BMC Systems Biology (accepted for publication).

Department of Chemistry and Biochemistry
University of Northern Iowa
1227 West 27th Street
Cedar Falls, IA 50614-0423
Phone: 319-273-2437
FAX: 319-273-7127
E-mail: barbara.reid@uni.edu
Web: http://www.chem.uni.edu

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