Florence Tama
Assistant Professor of Biochemistry and Molecular Biophysics
Ph.D. 2000, Paul Sabatier University

Computational Structural Biology, Function and Dynamics of Macromolecular Assemblies, Multi-Scale Modeling, Methods Development to Interpret Experimental Data

Research group homepage

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.

Recent publications

F. Tama and CL. Brooks III. (2006) Symmetry, form and shape: guiding principles for robustness in macromolecular machines. Annual Review of Biophysics & Biomolecular Structure, in press

R. Konecny, J. Trylska, F. Tama, D. Zhang , NA. Baker, CL. Brooks III and JA. McCammon. (2006) Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids. Biopolymers, in press

K. Mitra, C. Scaffitzel, T. Shaikh, F. Tama, S. Jenni, CL. 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

F. Tama and CL. Brooks III. (2005) Diversity and identity of mechanical  properties of icosahedral viral capsids studied with elastic network normal mode analysis. J. Mol. Biol. 345: 299-314

F. Tama, M. Feig, CL. Brooks, III and KA. 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
J. Mol. Biol 345: 837-854

S. Falke, F. Tama, CL. Brooks III, EP. Gogol and MT. Fisher. (2005) The 13 Å Structure of a Chaperonin GroEL-Protein Substrate complex by Cryo-Electron Microscopy. J. Mol. Biol. 348: 219-230

F. Tama, O. Miyashita and CL. Brooks, III. (2004) Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis. J. Mol. Biol. 337: 985-999

F. Tama, O. Miyashita and CL. Brooks III. (2004) NMFF: Flexible high-resolution annotation of low-resolution experimental data from cryo-EM maps using normal mode analysis. J. Struct. Biol.  147: 315-326

J. Trylska, R. Konecny, F. Tama, CL. Brooks III and JA McCammon. (2004)
Motions of the ribosome modulate electrostatic properties. Biopolymers 74: 423-431

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

P. Chacon, F. Tama and W. Wriggers. (2003) Mega-dalton biomolecular motion captured from electron microscopy reconstructions. J. Mol. Biol. 326: 485-492

F. Tama, M. Valle, J. Frank and CL Brooks III. (2003) Understanding the ratchet-like inter-subunit reorganization of the ribosome. Proc. Natl. Acad. Sci. USA 100: 9319-9323

F. Tama. (2003) Normal mode analysis with simplified models to investigate the global dynamics of biological systems. Prot. Pept. Let. 10: 119-132

F. Tama, W. Wriggers and CL. Brooks III. (2002) Exploring global distortions of biological macromolecules from low-resolution structural information and elastic network theory. J. Mol. Biol.  321: 297-305

F. Tama and CL. Brooks III. (2002) Exploring Large-Scale Conformational Changes in Virus Maturation. J. Mol. Biol. 318: 733-747

F. Tama and Y.H. Sanejouand. (2001) Conformational change of Proteins arising from Normal Mode Analysis. Protein. Eng. 14: 1-6

F. Tama, 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

F. Tama, O. Miyashita, A. Kitao and N. Go. (2000) Molecular dynamics simulation shows large volume fluctuation of proteins. Eur. Biophys. J.  29: 472-480

BOOK CHAPTER

F. Tama and CL Brooks III. (2006) Unveiling molecular mechanisms of biological functions in large macromolecular assemblies using elastic network normal mode analysis. Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems, Mathematical Biology Series, CRC Press

Contact Information

Mailing:
Dr. Florence Tama, Assistant Professor
Department of Biochemistry & Molecular Biophysics
University of Arizona
1041 E. Lowell Street
Biosciences West 446
Tucson AZ 85721-0088

Telephone: 520-626-4725
Fax: 520-626-9204

ftama@u.arizona.edu

Biological Sciences West
1041 East Lowell Street
P.O. Box 210088 · Tucson, AZ 85721-0088
Tel: (520) 621-5110
FAX (520) 626-9204

Life Sciences South
1007 East Lowell Street
P.O. Box 210106 · Tucson, AZ 85721-0106
FAX (520) 621-3709