B.S. Physics (1995) University of Florence
M.Sc. Physics (1996) Int'l School for Advanced Studies
Ph.D. Physics (1998) Int'l School for Advanced Studies
Physical Chemistry; Theoretical Biophysics; Statistical Mechanics; Protein Folding; Computational Molecular Biology; Molecular Modeling
Email: cecilia@rice.edu
Phone: (713) 348-3485
Office: Anderson Biological Lab, 304
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Cecilia Clementi
Wiess Career Development Chair, Associate Professor of Chemistry and Associate Professor of Chemical and Biomolcular Engineering
Interdisciplinary training on theoretical physics, physical chemistry and biochemistry, molecular biology and biophysics.
PhD in Theoretical Physics (Statistical Mechanics), postdoctoral experience as a LJIS fellow (La Jolla Interfaces in Science - Burroughs Wellcome program) working on a project across the Physics department and the Chemistry and Biochemistry departments.
Current research and educational activities lie at the interface of Physical Chemistry, Theoretical Physics, Computer Science and Molecular Biology.
Research Statement
"Anyone who has ever struggled to fold a roadmap should have an extra measure of respect for protein molecules, which fold up all on their own and practically put themselves away in the glove box" - (by Brian Hayes, from a paper published on American Scientist, 1998)
Virtually all biological activities are regulated by proteins. Proteins -hundreds of thousands of different ones- are the biochemical molecules that make up cells and organs.
Chemically, a protein is a linear polymer, a sequence of amino acids joined together with peptide bonds, but the biological function (or functions) of a specific protein is strongly related to a particular 3-dimensional structure (or, sometimes, set of structures), the so-called "native-state" of the protein. As a consequence, a failure in the achievement of the native state of a protein may lead to serious problems in the accomplishment of its biological function: many diseases are related to the misfolding of proteins. The key to understanding how proteins work (or don't work) lies in learning how amino acid sequences fold into particular shapes, and characterizing the thermodynamics and kinetics of the protein folding mechanism. Nowadays this is one of the most important unanswered question in the life sciences. Nevertheless, the study of the protein folding is just the first step towards the understanding the way living systems work and behave. Quite often a biological function requires the participation and interaction of many proteins. At the same way as the folding of a single protein is important for the activity of that protein, at a larger scale, the coming together and interaction of several proteins is crucial for the fulfillment of a biological task. For the very nature of these problems, the most interesting and significant advances are achieved at the interface of Physics, Chemistry and Biology.
My research activity is centered on the application of statistical mechanics techniques, molecular modeling and simulations to the study of protein systems, with a particular interest in protein folding and dynamics.
Our group has several active collaborations with experimental groups, to test in the wet-lab the efficiency of the methods we develop and our theoretical predictions. We are creating new techniques for the optimal combination of theory, experiments and simulations that we believe can significantly improve the characterization of free energy landscapes associated with protein systems. Our models and techniques are good starting points for numerous applications to well defined bio-medical problems.
We collaborate with computer scientists (Kavraki group at Rice) to combine the realistic physical/chemical modeling of protein molecules with the development and implementation of new algorithms, in order to effectively deal with the computational complexity associated with the exploration and sampling of a protein configurational space.
Please visit our group web page to find more information on the ongoing research projects: http://leonardo.rice.edu/~cecilia/research
Selected Publications
S. Matysiak, C. Clementi "Characterization of Protein-Folding Landscapes by Coarse-Grained Models Incorporating Experimental Data." Coarse-graining in Condensed Phase and Biomolecular Systems (2008): 157-170.
C. Clementi "Coarse-Grained Models of Protein Folding." Curr. Opin. Struct. Biol., 18 (2008): 10-15.
S. Matysiak C. Clementi "Mapping Folding Energy Landscapes with Theory and Experiment." Arc. Biochem. Biophys., 469 (2008): 29-33.
S. Matysiak, C. Clementi, M. Praprotnik, K. Kremer, L. delle Site "Modeling diffusive dynamics in adaptive resolution simulation of liquid water." J. Chem. Phys., 128 (2008): 024503.
A. Shehu, L. E. Kavraki, C. Clementi "Unfolding the Fold of Cyclic Systeine-rich Peptides." Protein Sci., 17 (2008): 482-493.
Plaku, E., Stamati, H., Clementi, C. & Kavraki, L.E. "Fast and Reliable Analysis of Molecular Motion Using Proximity Relations and Dimensionality Reduction." Proteins, 67 (2007): 897-907.
Heath, A.P., Kavraki, L.E. & Clementi, C. "From Coarse-Grain to All-Atom: Toward Multiscale Analysis of Protein Landscapes." Proteins, 68 (2007): 646-661.
Shehu, A., Kavraki, L.E. & Clementi, C. "On the Characterization of Protein Native State Ensembles." Biophysical Journal, 92 (2007): 1503-1511.
Mossa, A. & Clementi, C. "Supersymmetric Langevin equation to explore free energy landscapes." Phys. Rev. E, 75 (2007): 046707.
P. Das, M. Moll, H. Stamati, L. E. Kavraki, and C. Clementi "Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction." Proc. Natl. Acad. Sci. USA, 103 (2006): 9885-9890.
Presentations
"Optimal Combination of Theory and Experiment for the Characterization of Protein Folding Landscapes." International meeting on “Theory and simulation of biomolecular nano-machines”, Kobe, Japan. (Dec 12-16 2006)
"Multiscale modeling of water molecules." 62nd SouthWest Regional Meeting of the American Chemical Society, Houston, TX. (October 19-22, 2006)
"Symposium on "Protein Folding"." 62nd SouthWest Regional Meeting of the American Chemical Society, Houston, TX. (October 19-22, 2006)
"Optimal Combination of Theory and Experiment for the Characterization of Protein Folding Landscapes." 20th Annual Symposium of The Protein Society, San Diego, CA. (August 5-8, 2006)
"A Novel Approach toward a Complete Characterization of Protein Flexibility." “Trends in Enzymology” meeting, Como, Italy. (June 7-10, 2006)
Theses
Silvina Matysiak, Ph.D. "A Multi-scale Approach for Macromolecular Systems." (2008).(Thesis or Dissertation Director)
Awards
NSF CAREER AWARD, National Science Foundation. (2004-2009).
Norman Hackerman - Welch Young Investigator, The Welch Foundation. (2001-2003).
La Jolla Interfaces in Science (LJIS) fellowship, Burroughs Wellcome Fund. (1998-2001).
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