Roopa Thapar

Roopa Thapar

Roopa Thapar

Assistant Professor of Structural Biology

Department of Structural Biology

Jacobs School of Medicine & Biomedical Sciences


Specialty/Research Focus

Cell Cycle; Gene Expression; Genomics and proteomics; Molecular and Cellular Biology; Molecular Basis of Disease; Protein Folding; Protein Function and Structure; RNA; Signal Transduction; Structural Biology; Transcription and Translation

Contact Information
Hauptman-woodward Institute
700 Ellicott Street
Buffalo, NY 14203
Phone: (716) 898-8687
Fax: (716)-898-8660
roopatha@buffalo.edu



Professional Summary:

My primary interest lies in understanding how proteins recognize RNA. Protein/RNA interactions are central to a variety of biological processes such as regulation of gene expression, mRNA processing, mRNA splicing, and translation. Previous studies have shown that complex formation between proteins and RNA is a highly dynamic process that requires conformational rearrangements between both the protein and the RNA. To gain structural insights into the effect of RNA binding on protein structure, dynamics, and stability, we use high resolution NMR spectroscopy combined with biophysical tools such as fluorescence spectroscopy, circular dichroism, and isothermal titration calorimetry. One system currently under study is the stem-loop binding protein (SLBP) which binds histone mRNA hairpin with nanomolar affinity. Complex formation between SLBP and histone mRNA is necessary for correct mRNA processing of histone mRNAs, for histone mRNA transport, and translation. Another project involves characterization of a novel family of eukaryotic exoribonucleases that play important roles in disease.

Education and Training:

  • Postdoctoral Fellow, Structural Biology, University of North Carolina at Chapel Hill (2000)
  • PhD, Biochemistry (Structural Biology), University of Washington, Seattle (1997)

Employment:

  • Research Assistant Professor, Biochemistry, University of North Carolina at Chapel Hill (2000–2009)

Awards and Honors:

  • Lineberger Cancer Center Postdoctoral Fellowship 1997-2000 (1997)
  • Merck Predoctoral Felllowship 1992-1997 (1992)
  • J.N. Tata Scholarship for Higher Education of Indians Abroad (1988)
  • India Foundation Travel Award for Higher Education (1988)

Research Expertise:

  • Biophysics: We use a variety of techniques such as NMR, SPR, ITC, CD, fluorescence, and AUC to characterize the thermodynamics and kinetics of macromolecular interactions
  • Gene Expression: Posttranscriptional control of gene expression
  • Histone mRNA metabolism: Histone mRNAs are the only naturally ocurring mRNAs that are not polyadenylated. We are studying the mechanism by which they are processed, translated, and degraded.
  • Mechanisms of mRNA decay: Our lab is characterizing a novel family of exonucleases called the ERI family that are involved in degradation of structured mRNA targets such as stem-loops and miRNA-mRNA hybrids.
  • Molecular Biology: A variety of molecular biological and cell biological tools are used to characterize protein-RNA interactions in vivo.
  • Nuclear Magnetic Resonance: We use high-resolution multi-dimensional NMR spectroscopy in solution to characterize protein and RNA structure and dynamics
  • RNA-protein interactions: The lab is focused on the interaction of proteins that interact with the histone mRNA stem-loop and the interaction of exonucleases that interact with double-tranded mRNAs.
  • Signal transduction: We have previously characterized the structure and dynamics of Ras and Rho family GTPases by NMR
  • Structural Biology: A variety of structural biology tools are used in the laboratory. Our primary expertise lies in solution NMR of biomolecules, but we also use X-ray crystallography and SAXS.

Grants and Sponsored Research:

  • July 2009–December 2010
    Phosphorylation Dependent Recognition of a Histone mRNA Hairpin by SLBP (ARRA)
    NIH R01 GM076660-S1
    Role: Co-Investigator
  • January 2006–December 2009
    Phosphorylation Dependent Recognition of a Histone mRNA Hairpin by SLBP
    NIH R01 GM076660
    Role: Co-Investigator

Journal Articles:

See all (4 more)

Professional Memberships:

  • Member, RNA Society
  • Member, AAAS
  • Member, ASBMB
  • Member, American Chemical Society

Presentations:

  • "Tracking the assembly of the histone translation initiation complex" Department of Chemistry, SUNY at Brockport (2011)
  • "Structural Insights into Histone Pre-mRNA Processing and Its Regulation by Phosphorylation" Organic Chemistry and Chemical Biology seminar, UB, SUNY at Buffalo (2011)
  • "Structure and dynamics of the phosphorylated Stem-Loop Binding Protein (SLBP)-Histone mRNA complex" Pacifichem Chemical Congress, Honolulu, Hawaii (2010)
  • "ERI mediated Decay: Novel exonucleases in miRNA mediated mRNA decay" 4th annual RNA Stability Meeting, Montreal, Canada (2010)
  • "ERI mediated decay: novel exonucleases in miRNA mediated mRNA decay" RNA-UNY Structure Function Meeting, Albany, NY (2010)
  • "A Phosphorylation-Dependent Conformational Switch Regulates Histone mRNA Recognition and Turnover by Stem Loop Binding Protein" CHESS Users Symposium (Cornell) (2010)

Service Activities:

  • Scientific Governance Council, HWI; Member (2010–2011)
  • Conference Organizer, 11th Upstate NY NMR Meeting; Chair (2009)
  • Journal Reviewer; Biochemistry, ACS Chemical biology, JACS, Journal of Molecular Biology; Ad Hoc Reviewer (2005–2011)
  • Chair, North Carolina ACS Meeting, Biomolecular NMR Session; Chair (2003–2005)
  • Task Force for Faculty Development, UNC Chapel Hill; Member (2003)

School News:

In the Media:


Clinical Specialties:

Clinical Offices:

Insurance Accepted:



Contact Information

Hauptman-woodward Institute
700 Ellicott Street
Buffalo, NY 14203
Phone: (716) 898-8687
Fax: (716)-898-8660
roopatha@buffalo.edu