News and Publications

Computer Modeling of Proteins and Nucleic Acids

D.A. Case, W. Briggs, M. Crowley, T. Essigke, V. Feher, H. Liu, T. Macke, G. Mer, A. Onufriev, R. Torres, V. Tsui, M. Ullmann, X. Xu

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 a detailed analysis of electrostatics 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 are continuing to develop new methods in this area. Our developments in these areas are incorporated into the Amber molecular modeling package and into other software packages.

PROTEIN AND NUCLEIC ACID STRUCTURE AND DYNAMICS

Our overall goal is to extract the maximum amount of information about biomolecular structure and dynamics from NMR experiments. To this end, we are studying the use of direct refinement methods for using NMR data to determine biomolecular structures in solution, going beyond distance constraints to generate closer connections between calculated and observed spectra. We are also using quantum chemistry approaches to study ways in which chemical shifts and spin-spin coupling constants are related to protein and nucleic acid structure. Qualitatively new types of information, such as chemical-shift anisotropies and direct dipolar couplings in partially oriented samples, are also being used to guide structure refinement. Recent investigations included structural studies of a human leukocyte function--associated antigen, DNA oligonucleotide duplexes (both free and bound to potential anticancer drugs), and complexes of zinc finger domains with DNA. Figure 1 shows results from a joint NMR--molecular dynamics study of hydration of a complex of 3 zinc fingers to DNA.

NUCLEIC ACID MODELING

An ongoing 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-strand DNA complexes, including models for recombination sites. Continuum solvent methods are used to provide a powerful evaluation of the relative energies of different conformers. Examples include comparisons of A and B forms of DNA and RNA and a hairpin-duplex transition in RNA. We found that models that can be used to more efficiently evaluate electrostatic aspects of solvation and salt dependencies are effective in molecular dynamics simulations.

A major effort involves the development of "lower resolution" models for nucleic acids that can be extended to much larger structures such as circular DNA, viruses, or models for 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 the small subunit of the ribosome 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 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 aspect of this work aims at 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 dihydrofolate reductase and in metallo-ß-lactamase in an effort to make more secure connections between the motions of proteins and enzyme activities.

PUBLICATIONS

Bashford, D., Case, D.A. Generalized Born models of macromolecular solvation effects. Annu. Rev. Phys. Chem. 51:129, 2000.

Case, D.A. Calculations of NMR dipolar coupling strengths in model peptides. J. Biomol. NMR 15:95, 1999.

Case, D.A. Interpretation of chemical shifts and coupling constants in macromolecules. Curr. Opin. Struct. Biol. 10:197, 2000.

Case, D.A., Noodleman, L., Li, J. Modern computational approaches to modeling polynuclear transition metal complexes. In: Metal-Ligand Interactions in Chemistry, Physics and Biology. Russo, N., Salahub, D.R. (Eds.). Kluwer, Boston, 2000, p. 19.

Cornilescu, G., Bax, A., Case, D.A. Large variations in one-bond ¹³Ca-¹³C^ß J couplings in polypeptides correlate with backbone conformation. J. Am. Chem. Soc. 122:2168, 2000.

Dejaegere, A.P., Bryce, R.A., Case, D.A. An empirical analysis of proton chemical shifts in nucleic acids. In: Modeling NMR Chemical Shifts. Facelli, J.C., de Dios, A.C. (Eds.). American Chemical Society, Washington, DC, 1999, p. 194.

Legge, G.B., Kriwacki, R.W., Chung, J., Hommel, U., Ramage, P., Case, D.A., Dyson, H.J., Wright, P.E. NMR solution structure of the inserted domain of human leukocyte function associated antigen-1. J. Mol. Biol. 295:1251, 2000.

Onufriev, A., Bashford, D., Case, D.A. Modification of the generalized Born model suitable for macromolecules. J. Phys. Chem. B 104:3712, 2000.

Tsui, V., Case, D.A. Molecular dynamics simulations of nucleic acids using a generalized Born solvation model. J. Am. Chem. Soc. 122:2489, 2000.

Tsui, V., Zhu, L., Huang, T.-H., Wright, P.E., Case, D.A. Assessment of zinc finger orientations by residual dipolar coupling constants. J. Biomol. NMR 16:9, 2000.

VanLoock, M.S., Malhotra, A., Case, D.A., Agrawal, R., Penczek, P., Easterwood, T.R., Frank, J., Harvey, S.C. A functional interpretation of the cryo-electron microscopy map of the 30S ribosomal subunit from Escherichia coli. In: The Ribosome. Garrett, R., Douthwaite, S. (Eds.). ASM Press, Washington, DC, 2000, p. 165.