Protein Dynamics

Proteins and other biomolecules are often thought of in terms of the exquisitely detailed atomic pictures revealed by x-ray crystal structures. However, x-ray crystallography only provides a representation of the average structure, or a snapshot of a single configuration. In reality, proteins are constantly fluctuating between conformers that may represent large displacements from the atomic positions shown in the crystalline form. These motions impact fundamental biochemical processes such as allostery, interactions with binding partners, susceptibilities to proteolytic cleavage, and hydrogen exchange kinetics. A molecular-level description of biology therefore requires an understanding of protein dynamics

The dynamics of biological macromolecules span an enormous range of time scales, ranging from femtoseconds (10^-15 sec) to seconds. The characterization of these motions represents a formidable experimental challenge. Furthermore, the role of these dynamics in biological function is not yet well understood. My primary interests are in measuring the spectra of biomolecular motions, understanding the structural nature of these motions, and relating the dynamics to biological function. The laboratory employs ultrafast laser spectroscopies for measuring the femtosecond through nanosecond time scale dynamics which underlie the slower motions. Studies are performed on samples modified with biochemical techniques which produce well-defined changes in molecular structure. Specific problems of interest include non-native conformational states of metalloproteins (including imaging of conformational diversity in vivo), the dynamics of photoactive yellow protein, and the molecular dynamics of RNA aptamers. We will also develop a quantitative understanding of the role of femtosecond-nanosecond dynamics in the entropy changes which occur during ligand binding, folding, and other conformational transitions.

Selected Publications

“Protein dynamics and the immunological evolution of molecular recognition,” R. Jimenez, J. Yin, T. Joo, and F.E. Romesberg (2003), submitted.

“Flexibility and molecular recognition in the immune system,” R. Jimenez, G. Salazar, K.K. Baldridge, and F.E. Romesberg (2003) Proc. Natl. Acad. Sci. USA, 100, 92-97.

“Excited state dynamics and heterogeneity of folded and unfolded states of cytochrome c” R. Jimenez and F.E. Romesberg (2002) J. Phys. Chem. B., 106, 9172-9180.

“Protein dynamics and cytochrome c: Correlations between ligand vibrations and redox activity,” J.K. Chin, R. Jimenez, and F.E. Romesberg (2002) J. Am. Chem. Soc., 124, 1846-1847.

“Flexibility of an antibody binding site measured with photon echo spectroscopy,” R. Jimenez, D.A. Case, and F.E. Romesberg (2001) J. Phys. Chem. B., 106, 1090-1103.

“Three pulse echo experiments on LH1 and LH2 complexes of Rhodobacter sphaeroides: A nonlinear spectroscopic probe of energy transfer,” R. Jimenez, F. van Mourik, J.Y. Yu, and G.R. Fleming (1997) J. Phys. Chem. B., 101, 7350-7359.

“Femtosecond solvation dynamics of water,” R. Jimenez, G.R. Fleming, P.V. Kumar, and M. Maroncelli (1994) Nature, 369, 471-473.