BMCB-Faculty Research, Florence Tama

Assistant Professor of Biochemistry & Molecular Biophysics
Ph.D., Paul Sabatier University

Computational structural biology; function and dynamics of macromolecular assemblies; multi-scale modeling; methods development to interpret experimental data.

Research Interests

It is now well established that large-scale rearrangements in proteins are important for a variety of protein functions including catalysis and regulation of activity. The recent developments in experimental methods, especially cryo-electron microscopy (EM), have revealed that large-molecular assemblies are also highly dynamic. While experiment can provide a tremendous source of information on these dynamical properties, computational methods must be employed to complement experimental observations.

The primary motivation behind our studies is to explore using computational approaches, at a near-atomic level, functionally important rearrangements in biological systems observed in experiments at high or low-resolution to obtain new insights into the mechanism of these transformations that are presently inaccessible to experiments.

Select Publications

Any link on the below references will take you off of the BMCB site and to an abstract of that particular paper.

Tama, R., and C.L. Brooks III. 2006. Symmetry, form and shape: guiding principles for robustness in macromolecular machines. Annual Review of Biophysics & Biomolecular Structure 35: 115-133.

Konecny, R., J. Trylska, F. Tama, D. Zhang , N.A. Baker, C.L. Brooks III, and J.A. McCammon. 2006. Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids. Biopolymers 82: 106-120.

Mitra, K., C. Scaffitzel, T. Shaikh, F. Tama, S. Jenni, C.L. Brooks III, N. Ban, and J. Frank. 2005. Structure of the E. coli protein-conducting channel bound to a translating ribosome. Nature 438: 318-324.

Tama, F., and C.L. Brooks III. 2005. Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis. Journal of Molecular Biology 345: 299-314.

Tama, F., M. Feig, C.L. Brooks III, and K.A. Taylor. 2005. The requirement for mechanical coupling between head and S2 domains in smooth muscle myosin ATPase regulation and its implications for dimeric motor function. Journal of Molecular Biology 345: 837-854.

Falke, S., F. Tama, C.L. Brooks III, E.P. Gogol, and M.T. Fisher. 2005. The 13 Å structure of a chaperonin GroEL-protein substrate complex by cryo-electron microscopy. Journal of Molecular Biology 348: 219-230.

Tama, F., O. Miyashita, and C.L. Brooks III. 2004. Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis. Journal of Molecular Biology 337: 985-999.

Tama, F., O. Miyashita, and C.L. Brooks III. 2004. Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM. Journal of Structural Biology 147: 315-326.

Trylska, J., R. Konecny, F. Tama, C.L. Brooks III, and J,A McCammon. 2004. Ribosome motions modulate electrostatic properties. Biopolymers 74: 423-431.

Wriggers, W., P. Chacon, J. Kovacs, F. Tama, and S. Birmanns. 2004. Topology representing neural networks reconcile biomolecular shape, structure and dynamics. Neurocomputing 56: 365-379.

Chacon, P., F. Tama, and W. Wriggers. 2003. Mega-dalton biomolecular motion captured from electron microscopy reconstructions. Journal of Molecular Biology 326: 485-492.

Tama, F., M. Valle, J. Frank, and C.L Brooks III. 2003. Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proceedings of the National Academy of Sciences U.S.A. 100: 9319-9323.

Tama, F. 2003. Normal mode analysis with simplified models to investigate the global dynamics of biological systems. Protein and Peptide Letters 10: 119-132.

Tama, F., W. Wriggers, and C.L. Brooks III. 2002. Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory. Journal of Molecular Biology 321: 297-305.

Tama, F. and C.L. Brooks III. 2002. The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus. Journal of Molecular Biology 318: 733-747.

Tama, F., and Y.H. Sanejouand. 2001. Conformational change of proteins arising from normal mode analysis. Protein Engineering 14: 1-6.

Tama, F., F.X. Gadea, O. Marques, and Y.H. Sanejouand. 2000. A building block approach for determining low-frequency normal modes of macromolecules. Proteins 41: 1-7.

Tama, F., O. Miyashita, A. Kitao, and N. Go. 2000. Molecular dynamics simulation shows large volume fluctuation of proteins. European Biophysics Journal 29: 472-480.

BOOK CHAPTER

Tama, F., and C.L Brooks III. 2006. Unveiling molecular mechanisms of biological functions in large macromolecular assemblies using elastic network normal mode analysis. In: Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems (Q. Cui and I. Bahar, Eds.) Mathematical and Computational Biology Series, Vol. 9, CRC Press.

Contact Information

Mailing:
Dr. Florence Tama, Assistant Professor
Department of Biochemistry & Molecular Biophysics
University of Arizona
Biological Sciences West 446
P. O. Box 210088
Tucson, AZ 85721-0088

Telephone:
520-626-4725 (Office)
520-626-9038 (Lab)

Fax:
520-626-9204

Email:
ftama@email.arizona.edu

Please e-mail any comments to:
bmcb@email.arizona.edu