Investigations aimed at a complete understanding of the structure and function of genes and gene products in all life forms are rapidly progressing due to the availability of genome sequences. Structural proteomics initiatives all around the world are implementing technologies that will permit to determine three dimensional protein structures at high throughput automated fashion. The understanding of basic molecular and cellular processes at atomic level through structural proteomics approach allows for rational design of therapeutic drugs and treatments. These studies are usually based on X-ray crystallography, an exceptionally powerful tool to study the structures of proteins, nucleic acids, and their complexes. It enables the determination of the precise arrangement of all atoms and the shape and property of all surfaces in single molecules as well as in huge molecular complexes.
The structure determination process includes target selection; cloning the coding sequence; protein expression and purification; biophysical characterization; identifying and optimizing crystallization conditions and incorporating suitable heavy atoms; collecting multiple or single wavelength anomalous dispersion (MAD or SAD) data at a synchrotron beamline; solving the phase problem; tracing the electron density map and building the model; refining the structure and finally, drawing functional inferences from the solved structure by combining with biochemical, biophysical and bioinformatics experiments.
During the year 2008, Research & Industry Incubation Center (RIIC), Dayanandasagar Institutions (DSI) established a Structural Proteomics Group which comprises collaborative interdisciplinary group of scientists applies high throughput protein structure analysis approaches to address current, future challenges and opportunities in human health, and more generally to problems in the basic life sciences and technology development. The group is mainly carry out and foster structural proteomics research of proteins related to biotechnological interest, human health, DNA binding proteins and DNA-protein complexes, multi-domain proteins. The group promotes international collaboration and enhances research competitiveness in structural proteomics areas.
Current Projects
- Structure and Function Analysis of Enzymes of Industrial Interest
- Tools development for Synchrotron Based Proteomics Technologies
- Knowledge based Structural Prediction of Protein Complexes and Modeling.
- Structure based Computer-aided Drug Design.
Publications, Reviews and Book Chapters (Year 2000 onwards)
- Structural Proteomics Technologies: Its impact on biotechnology and the life sciences. Biotechnology & Genetic Engineering Reviews (ISSN: 0264-8725). Invited Review article. In preparation.
- Automated technologies and novel techniques to accelerate protein crystallography for structural genomics. PROTEOMICS Reviews, 2008, 8: 612-625.
- Nano-Biotechnology: Structure and dynamics of Nanoscale Biosystems. J. Research Industry, 2008, 1.
- Crystal Structure of Mn2+ bound E. coli L-arabinose Isomerase: Its implications in Protein Catalytic Mechanism and Thermo-Stability. J Young Investigators 2007; 17(3).
- Crystallization and Preliminary X-ray Crystallographic Analysis of the Archaeal Tryptophan Regulator, TrpY. Department of Energy Journal of Undergraduate Research, Biology Abstracts, 2007, 7.
- .High throughput approach to protein structure analysis. Genet Eng (N.Y): Principles and Methods. 2007; 28:105-128. Review. (ISBN: 978-0-387-33840-8: Book Chapter).
- Crystal structure of E.coli L-arabinose isomerase (ECAI), the putative target of biological tagatose production. J Mol Biol 2006; 360(2):297-309.
- Crystal structure of Homo sapiens PTD012 reveals a novel Zinc-containing fold. Protein Science 2006; 15(4):914-920.
- Recent Advances in Protein Structure Analysis. In Recent Res Devel Biochem., 7(2006): 47-71. Review. (ISBN:81-308-0076-4 : Book Chapter).
- .X-ray structure of engineered human Aortic Preferentially Expressed Protein-1 (APEG-1). BMC Struct Biol 2005; 5(1):21.
- Metalloproteomics : High Throughput Structural and Functional Annotation of Proteins in Structural Genomics. Structure 2005; 13:1473-1486.
- The ybeY protein from E.coli is a metalloprotein. Acta Crystallogr F Struct Biol Cryst Commun 2005; F61:959-963.
- X-ray structure of human gankyrin, the product of a gene linked to hepatocellular carcinoma. Proteins: Struct Funct & Bioinformatics 2004; 55:214-217.
- X-ray structure of Fumarylacetoacetate Hydrolase family member Homo sapiens FLJ36880. Biol Chem 2004; 385:935-942.
- Crystal structure of circularly permuted DsbAQ100T99: Preserved global fold and local structural adjustments. Acta Crystallogr D Biol Crystallogr 2004; D60:304-309.
- Crystal structure of Homo sapiens protein hp14.5. Proteins: Struct Funct & Bioinformatics 2004; 54:797-800.
- .Secure web book to store structural genomics research data. J Struct Funct Genomics 2003; 4(2-3):121-127.
- Crystal structure of a bifunctional aldolase-dehydrogenase: sequestering a reactive and volatile intermediate. Proc Natl Acad Sci USA 2003; 100(12):6992-6997.
- Crystallization and preliminary X-ray analysis of dmpFG-encoded 4-hydroxy-2-ketovalerate aldolase-aldehyde dehydrogenase (acylating) from Pseudomonas strain CF600. Acta Crystallogr D Biol Crystallogr 2001; D57:582-585.
- Crystal structures of the recombinant histones HMfA and HMfB from the hyperthermophilic archaeon Methanothermus fervidus. J Mol Biol 2000; 303:35-47.
Selected Contributions to Meetings
| 2008 |
“Structural Proteomics: Protein Folds and Function”. Presented at the international conference, “Structural Proteomics Day” held at CD Sagar Auditorim, Dayananda Sagar Institutions, Bangalore, India. |
| 2008 |
“Journey to the Doctoral Program”. Presented at the national conference, “Innovations 2008: Masters and Doctoral Symposium”, held at CD Sagar Auditorim, Dayanandasagar Institutions, Bangalore, India. |
| 2008 |
“Synchrotron X-Ray Diffraction Data Collection: Towards the Development of the Remote Access to the Synchrotron Facility”. Presented at the European Molecular Biology Laboratory (EMBO) World Lecture Course, “Recent Developments in Macromolecular Crystallography”, held at National Chemical Laboratory, Pune, India. |
| 2008 |
“Gene to protein structure at Protein Structure Factory”. Presented at the Poster presented at the IISc Centenary Symposium on, “Future Directions in NMR”, held at Faculty Hall, Indian Institute of Science, Bangalore, India. |
| 2008 |
“Structure and function analysis of E.coli L-Arabinose Isomerase through structural genomics approach”. Presented at the national conference, “Genomics, Proteomics and Systems Biology”, held at J.N. Tata Auditorium, Indian Institute of Science, Bangalore, India. |
| 2008 |
“Nano-Biotechnology: ZnO nanosystems for biosensors”. Presented at the international conference, & exhibition on, “Total Engineering, Analysis and Manufacturing Technologies”, held at J.N. Tata Auditorium, Indian Institute of Science, Bangalore, India. |
| 2008 |
“Biomolecular Structure and Function at MX Beamline“. Presented at the Joint NSLS-CFN Users' Meeting Workshop on, “Applications of Synchrotron-Based Microprobe and Imaging Techniques to Studies of Human Disease” and “Nanofluidics”, held at Brookhaven National Laboratory, New York, USA. |
| 2007 |
Case Proteomics Center Beamlines for Protein Crystallography”. Podium Presentation in Advances in Protein Crystallography, South San Francisco, CA, USA. |
| 2007 |
“Case Proteomics Center Beamlines for Structural Proteomics”, Presentation at School of Medicine, Case Western Reserve University, Cleveland, OH, USA |
| 2006 |
“Structural Genomics at BESSY and NSLS : Protein Structures - Folds and Function”, Humboldt Foundation Sponsored Research in Sciences, German-American Crosscurrents and Exchanges in the 21st Century, Alexander von Humboldt Association of America, Ohio State University, Columbus, OH, USA |
| 2004 |
A Day on “High throughput methods in structural biology” and two days meeting on “Structural Proteomics and Protein-Protein Interactions” Netherlands Cancer Institute, Centre for Biomedical Genetics held at Amsterdam, NETHERLANDS. |
| 2003 |
“Structural Genomics: Crystal Structure Analysis of Human Proteins”, International Center for Academic Exchange (IBZ), Berlin, GERMANY |
| 2002 |
“Design of Web Book to Handle Meta-Crystallographic Data”, Hot Topics in Structural Genomics Section, International Structural Genomics Organization (ISGO), International conference on Structural Genomics, Berlin, GERMANY |
| 2002 |
“BCLIMS: BESSY Crystallography Laboratory Information Management System”, Lightning Talk of Python for Science and Industry, European Zope Conference, Charleroi, BELGIUM |
| 2001 |
“Structure of a bi-functional enzyme involved in substrate channeling”, Late Breaking Macromolecular Structures Section, American Crystallographic Association Annual Meeting, Los Angeles, CA, USA. |
| 1999 |
“Crystallization and preliminary diffraction studies of the circularly permuted cpDsbaq100t99 variant”. Presented at the 3rd International conference on, “Molecular Structural Biology (ICMSB)”, Vienna, AUSTRIA. |
| 1999 |
“Eukaryal nucleosome and high resolution crystal structures of archaeal histones”. Presented at the 26th Meeting of the Federation of European Biochemical Societies (FEBS), Nice, FRANCE. |
| 1995 |
Participated in the Mahabaleshwar Seminar on Modern Biology: “Protein-Nucleic Acid Interactions” organized by Tata Institute of Fundamental Research, Bombay conducted at Radio Astronomy Centre, Ooty, India. |
| 1994 |
Participated in the, “discussion meeting on macromolecular crystallography”, organized by Jawaharlal Nehru Center for advanced Scientific Research and Molecular Biophysics, Indian Institute of Science, Bangalore, India. |
| 1994 |
Participated in the Satellite Meeting on “Molecular Mechanisms of Enzyme Action”, Department of Biochemistry, Indian Institute of Science, Bangalore, India. |
Faculty Profile: |
