Vamsi Boyapati

Education :

• Ph.D. Biochemistry, Louisiana State University, Baton Rouge, LA-USA (2011) Advisor: Dr. Fareed Aboul-Ela
• M.Sc. Biochemistry, Acharya Nagarjuna University, India (2005)
• B.Sc. Osmania University, India (2003)

Research Focus Areas

• Structural biology and drug design. The determination of the atomic structure of proteins and RNA, the study of their interaction with small molecule drugs and metabolites and the use of this information to design lead molecules for the discovery of new therapeutic drugs.
• Ph.D. focus: Designed and put-together an Ribonucleic acid (RNA) targeted small molecule library with the aid of computational tools. Implemented Nuclear magnetic resonance (NMR) spectroscopy experiments to screen the library small molecules against RNA drug targets in a high-throughput setup.
• Investigated the mechanistic contributions of SAM-I riboswitch RNA with its effector metabolite S-adenosyl methionine in gene regulation mechanism in bacteria. Multi dimensional NMR, inline probing and other biophysical experiments along with computational and molecular dynamic simulations were used to delineate the structural features of the SAM-I riboswitch.
• Current research: As a post doctoral researcher, currently investigating protein protein interactions between Ras GTPase-activating-like protein (IQGAP) in association with GTPase proteins. The IQGAPS are multi domain scaffold proteins. Each domain interacts with a host of other proteins to control cell division, cell adhesion, cancer metastasis, cytoskeleton rearrangement. The interaction of GAP related domain (GRD) of the IQGAP with GTPase is believed to sequester or open the other domains of IQGAP protein to control the above cellular processes. High resolution structural information is necessary to understand the functional role of the IQGAP proteins. Crystals of the IQGAP-GRD in complex with GTPase are made to collect high resolution X-ray diffraction data. The diffraction data is used to build models of physiological relevance.

Affiliations

• The RNA Society
• American Chemical Society
• Academic Drug Discovery Consortium
• New Orleans Protein Folding Intergroup

Peer reviewed publications

 Bodoor, K. Vamsi Boyapati, et al., Design and implementation of an ribonucleic acid (RNA) directed fragment library. J Med Chem, 2009. 52(12): p. 3753-61.

Wei Huang, Joohyun Kim, Shantenu Jha, Fareed Aboul-ela, Vamsi Boyapati, Dynamics differences of SAM-I riboswitch aptamer between SAM bound and  without SAM: insight into conformational rearrangement. FASEB J. 23: 842.1

Vamsi K Boyapati, Jessica Spedale, Wei Huang, Fareed Aboul-Ela Basis for ligand discrimination between ON and OFF state riboswitch conformations: the  case of the SAM-I riboswitch. RNA, 2012. 18(6): p.1230-1243.

Conference Papers and posters

ACS Regional Meeting, Houston, Tx-USA (Oct 2006): Poster Title: “Design of  small molecule RNA binding compound library: An In silico approach”. By Vamsi  Boyapati, Vikram Gopu, and Fareed Aboul-ela.

RNA Society Annual Meeting, Wisconsin, MD-USA (May 2007): Poster Title: “Design of an RNA-Directed Small Molecule “Fragment” Library” by Fareed Aboul-ela, Vamsi Boyapati and Vikram Gopu.

ACS National Meeting, New Orleans LA-USA (April 2008): Poster Title: “Computational Study of Conformational Switching of S-box Riboswitch” by Wei Huang, Fareed Aboul-ela, Shantenu Jha and Vamsi Boyapati.  

CHI Conference on Structure-Based Drug Design, Boston, MA-USA (June 2008): Poster Title: “Design of an RNA-Directed Small Molecule “Fragment” Library” by Fareed Aboul-ela, Vamsi Boyapati and Vikram Gopu.

Zing Nucleic Acids Conference, Cancun-Mexico (Feb 2009): Poster Title: “Design of an RNA-Directed Small Molecule “Fragment” Library” by Fareed Aboul-ela, Vamsi Boyapati and Vikram Gopu.

RNA Society Annual Meeting Seattle, WA-USA (June 2010): Poster Title: “The ON Conformation of the SAM-I Riboswitch and Design of Novel Riboswitch Binding Small Molecules” by Vamsi Boyapati, Wei Huang and Fareed Aboul-ela.

Zing Nucleic Acids Conference, Cancun-Mexico (November 2010): Poster Title: “Bridging the Gap between “ON” State and “OFF” State of the SAM-I Riboswitch” by Wei Huang, Vamsi Boyapati, Sunayana Mitra, Jooyun Kim, Shantenu Jha, Fareed Aboul-ela.

RNA Society Annual Meeting Ann Arbor, MI-USA (June 2012): Poster Title: “Microsecond Timescale Molecular Dynamics Simulation of Ligand-Induced Strand Migration in an S-Adenosyl Methionine Riboswitch” by Wei Huang, Vamsi Boyapati, Fareed Aboul-Ela, Shantenu Jha, Jooyun Kim.

New Orleans Protein Folding Intergroup (New Orleans, Louisiana- USA), March 2013 : “Study of Complex RNA Function Modulated by Small Molecules: The Development of RNA Directed Small Molecule Library and Probing the S-Adenosyl Methionine Discrimination between ON and OFF Conformational States of the SAM-I riboswitch” by Vamsi Boyapati.