News and Publications

Computer Modeling of Proteins and Nucleic Acids

D.A. Case, S. Brozell, M. Crowley, P. Dasgupta, T. Dwyer,* H. Gohlke, F. Himo, H. Liu, T. Liu, G. Mer, T. Meyer, A. Onufriev, R. Torres, G.M. Ullmann, X.P. Xu* University of San Diego, San Diego, CA

Computer simulations offer an exciting approach to the study of many aspects of biochemical interactions. In our group, we focus primarily on molecular dynamics simulations (in which Newton's equations of motions are solved numerically) to model the solution behavior of biomacromolecules. Recent applications include detailed analyses of electrostatic interactions in short peptides (folded and unfolded), proteins, and oligonucleotides in solution.

In addition, molecular dynamics methods are useful in refining solution structures of proteins by using constraints derived from nuclear magnetic resonance (NMR) spectroscopy, and we continue to explore new methods in this area. Our developments are incorporated into the Amber molecular modeling package, designed for large-scale biomolecular simulations, and into other software, including Nucleic Acid Builder, for developing 3-dimensional models of unusual nucleic acid structures; SHIFTS, for analyzing chemical shifts in proteins and nucleic acids; and RNAMotif, for finding structural motifs in databases of genomic sequences.

Additional studies on active sites of nitrogenase and other metalloenzymes are described in the report of L. Noodleman, Department of Molecular Biology.

PROTEIN AND NUCLEIC ACID STRUCTURE AND DYNAMICS

Our overall goal is to extract the maximum amount of information on biomolecular structure and dynamics from NMR experiments. To this end, we are studying the use of direct refinement methods for determining biomolecular structures in solution, going beyond distance constraints to generate closer connections between calculated and observed spectra. We are also using quantum chemistry to study chemical shifts and spin-spin coupling constants. New types of information, such as chemical shift anisotropies, direct dipolar couplings in partially oriented samples, and analysis of cross-correlated relaxation, are also being used to guide structure refinement. Recent structural studies focused on transcription factors and minor groove-binding drugs complexed with DNA.

As an example, Figure 1 shows a member of a family of structures (determined by NMR) of a cyclic polyamide ligand bound to the minor groove of duplex DNA. The ligand, which can be designed to recognize specific base-pair sequences, is shown as light spheres and the DNA atoms as dark spheres. This structure is the first high-resolution NMR structure of such a complex, and it has interesting differences from crystal structures of similar complexes. Structural information of this sort can be used to help improve the design of sequence-specific DNA ligands.

NUCLEIC ACID MODELING

Another project centers on the development of novel computer methods to construct models of "unusual" nucleic acids that go beyond traditional helical motifs. We are using these methods to study circular DNA, small RNA fragments, and 3- and 4-stranded DNA complexes, including models for recombination sites. We continue to develop efficient computer implementations of continuum solvent methods to allow simplified simulations that do not require a detailed description of the solvent (water) molecules; this approach also provides a useful way to study salt effects.

This research is part of a larger effort to develop "low resolution" models for nucleic acids that can be extended to much larger structures such as circular DNA, viruses, or models of ribosomal particles. A computer language, NAB, has been developed to make it easier to construct initial molecular models for complex and often low-resolution problems. The language is being used to construct models for compact and swollen viruses and for the analysis of curved and circular DNA.

DYNAMICS AND ENERGETICS OF NATIVE AND NONNATIVE STATES OF PROTEINS

Analysis methods similar to those described for nucleic acids are also being used to estimate thermodynamic properties of "molten globules" and unfolded states of proteins. These studies are an extension of our earlier work on the folding of peptide fragments of proteins. A key feature is the development of computational methods that can be used to model pH and salt dependence of complex conformational transitions, such as unfolding events.

A second goal of this work is a detailed interpretation of NMR results for protein nonnative states through molecular dynamics simulations and the construction of models for molecular motion and disorder. In a parallel effort, we are studying correlated fluctuations about native conformations in a variety of proteins, including dihydrofolate reductase, metallo-b -lactamase, binase, and cyclic-dependent kinase, in an effort to make more secure connections between proteins motions and enzyme activities.

PUBLICATIONS

Batcho, P.F., Case, D.A., Schlick, T. Optimized particle-mesh Ewald/multiple-time step integration for molecular dynamics simulations. J. Chem. Phys. 115:4003, 2001.

Botuyan, M.V., Mer, G., Yi, G.-S., Koth, C.M., Case, D.A., Edwards, A.M., Chazin, W.J., Arrowsmith, C.H. Solution structure and dynamics of yeast elongin C in complex with a von Hippel-Lindau peptide. J. Mol. Biol. 312:177, 2001.

Case, D.A. Molecular dynamics and NMR spin relaxation in proteins. Acc. Chem. Res. 35:325, 2002.

Case, D.A., Herschbach, D. Statistical theory of angular momentum polarization in chemical reactions. Mol. Phys. 100:109, 2002.

Jimenez, R., Case, D.A., Romesberg, F. Flexibility of an antibody binding site measured with photon echo spectroscopy. J. Phys. Chem. B 106:1090, 2002.

Lovell, T., Case, D.A., Noodleman, L. FeMo cofactor of nitrogenase: energetic and local interactions in the protein environment. J. Biol. Inorg. Chem., in press.

Lovell, T., Li, J., Case, D.A., Noodleman, L. Binding modes for the first coupled electron and proton addition to FeMoco of nitrogenase. J. Am. Chem. Soc. 124:4546, 2002.

Lovell, T., Li, J., Liu, T., Case, D.A., Noodleman, L. FeMo cofactor of nitrogenase: a density functional study of states M^N, M^OX, M^R, and M^I. J. Am. Chem. Soc. 123:12392, 2001.

Macke, T.J., Ecker, D.J., Gutell, R.R., Gautheret, D., Case, D.A., Sampath, R. RNAMotif: a new RNA secondary structure definition and discovery algorithm. Nucleic Acids Res. 29:4724, 2001.

Onufriev, A., Case, D.A., Bashford, D. Effective Born radii in the generalized Born approximation: the importance of being perfect. J. Comput. Chem., in press.

Sosa, C.P., Hewitt, T., Lee, M.R., Case, D.A. Vectorization of the generalized Born model for molecular dynamics on shared-memory computers. J. Mol. Struct. Theochem 549:193, 2001.

Tsui, V., Case, D.A. Theory and applications of the generalized Born solvation model in macromolecular simulations. Biopolymers 56:275, 2001.

Tsui, V., Case, D.A. Calculations of the absolute free energies of binding between RNA and metal ions using molecular dynamics simulations and continuum electrostatics. J. Phys. Chem. B 105:11314, 2001.

Ullmann, G.M., Noodleman, L., Case, D.A. Density functional calculation of the pK_a values of the histidines coordinating one iron in the bovine Rieske iron-sulfur protein. J. Biol. Inorg. Chem. 7:623, 2002.

Waugh, A., Gendron, P., Altman, R., Brown, J.W., Case, D., Gautheret, D., Harvey, S.C., Leontis, N., Westbrook, J., Westhof, E., Zuker, M., Major, F. RNAML: a standard syntax for exchanging RNA information. RNA, in press.

Xia, B., Tsui, V., Case, D.A., Dyson, H.J., Wright, P.E. Comparison of protein solution structures refined by molecular dynamics simulations in vacuum, with a generalized Born model, and with explicit water. J. Biomol. NMR 33:317, 2002.

Xu, X.P., Case, D.A. Automated prediction of ¹⁵N, ¹³Ca , ¹³Cb , and ¹³C´ chemical shifts in proteins using a density functional database. J. Biomol. NMR 21:321, 2001.