News and Publications

Computer Modeling of Proteins and Nucleic Acids

D.A. Case, M. Crowley, A. Dejaegere,* E. Demchuk, M. Johnson,** T. Macke, D. Sitkoff, J. Smith, J. Srinivasan, M. Trevathan, V. Tsui

* Université Louis Pasteur, Strasbourg, France
** University of Illinois, Chicago, IL

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 spectroscopy, and we are continuing to develop new methods in this area.

PROTEIN AND NUCLEIC ACID STRUCTURE AND DYNAMICS

Our overall goal is to extract the maximum amount of information about biomolecular structure and dynamics from nuclear magnetic resonance experiments. To this end, we are studying the use of direct refinement methods for determining biomolecular structures in solution from nuclear magnetic resonance data, 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, also must be carefully analyzed. Recent investigations included structural studies of the blue-copper protein rusticyanin, DNA oligonucleotide duplexes (both free and bound to potential anticancer drugs), a phospho-transfer protein, and complexes of zinc-finger domains with 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. Models that can be used to more efficiently evaluate electrostatic aspects of solvation and salt dependencies are also being pursued.

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 or models for ribosomal particles. A new 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.

ANALYSIS OF MUTANT HEMOGLOBIN STRUCTURES

We continue to model properties of mutant hemoglobins that might be useful as blood substitutes. Using both continuum electrostatic models and molecular dynamics simulations to study the effects of charge mutations on oxygen binding and subunit dissociation, we have constructed an extensive model for the dependence of hemoglobin oxygen affinity on pH; we considered more than 150 titrating sites. These results offer new insights into the ways in which protons and anions act as allosteric ligands in modulating the functional properties of oxygen-binding proteins. New directions include models of the effects of protein flexibility, specific ion-binding events, and studies of inhibitor binding to factor Xa.

DYNAMICS AND ENERGETICS OF NONNATIVE STATES OF PROTEINS

Analytical 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 second aspect of this work aims at a detailed interpretation of nuclear magnetic resonance results for protein nonnative states through molecular dynamics simulations and the construction of models for molecular motion and disorder.

PUBLICATIONS

Beroza, P., Case, D.A. Calculations of proton binding thermodynamics in proteins. Methods Enzymol., in press.

Case, D.A. Normal mode analysis of biomolecular dynamics. In: Computer Simulations of Biomolecular Systems, Vol. 3. van Gunsteren, W.F., Weiner, P.K., Wilkinson, A.J. (Eds.). ESCOM, Leiden, the Netherlands, 1997, p. 284.

Chen, Y., Case, D.A., Reizer, J., Saier, M.H., Wright, P.E. High resolution structure of Bacillus subtilis IIA^glc. Proteins 31:258, 1998.

Dejaegere, A.P., Case, D.A. Density functional study of ribose and deoxyribose chemical shifts. J. Phys. Chem., in press.

Gippert, G.P., Wright, P.E., Case, D.A. Recursive torsion angle grid search in high dimensions: A systematic approach to NMR structure determination. J. Biomol. NMR, in press.

Kuramochi, H., Noodleman, L., Case, D.A. Density functional study on the electronic structures of model peroxidase compounds I and II. J. Am. Chem. Soc. 119:11442, 1997.

Li, J., Beroza, P., Noodleman, L., Case, D.A. Quantum mechanical modeling of active sites in metalloproteins. In: Molecular Modeling and Dynamics of Biological Molecules Containing Metal Ions. Banci, L., Comba, P. (Eds.). Kluwer, Boston, 1997, p. 279.

Macke, T., Case, D.A. Modeling unusual nucleic acid structures. In: Molecular Modeling of Nucleic Acids. Leontes, N.B., Santa Lucia, J. (Eds.). American Chemical Society, Washington, DC, 1998, p. 379.

Sitkoff, D.F., Case, D.A. Density functional calculations of proton chemical shifts in model peptide systems. J. Am. Chem. Soc. 119:12262, 1997.

Sitkoff, D., Case, D.A. Theories of chemical shift anisotropies in proteins and nucleic acids. Prog. NMR Spectrosc., in press.

Wuttke, D.S., Foster, M.F., Case, D.A., Gottesfeld, J.M., Wright, P.E. Solution structure of the first three fingers of TFIIIA bound to the cognate DNA sequence: Determinants of affinity and sequence specificity. J. Mol. Biol. 273:183, 1997.