News and Publications

Computer Modeling of Proteins and Nucleic Acids

* University of San Diego, San Diego, California

Computer simulations offer an exciting approach to the study of many aspects of biochemical interactions. 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 genomic sequence databases.

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

Structure and Dynamics of Proteins and Nucleic Acids

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 minor-groove-binding drugs complexed with DNA and on the protein glutaredoxin 2.

Modeling of Nucleic Acids

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 research 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-ß-lactamase, binase, and cyclic-dependent kinase, in an effort to make more secure connections between the motions of proteins and enzyme activities.

All of these modeling activities are based on molecular mechanics force fields, which provide estimates of energies as a function of conformation. We continue to work on improvements in force fields; recent efforts focused on adding aspects of electronic polarizability, going beyond the usual fixed-charge models. As an example, Figure 1 shows new and old models for the charge distribution in N-methylacetamide, a model for the peptide group in proteins. In addition to allowing the charge distribution to depend on conformation (through the polarization terms), we added "extra points" at places corresponding to classical lone-pair positions. These extra charge points allow the angular dependence of hydrogen bonding to be more faithfully captured. Overall, the new models should provide a better picture of the noncovalent interactions between peptide groups and their surroundings, leading ultimately to more faithful simulations.

Publications

Allawi, H.T., Kaiser, M.W., Onufriev, A.V., Ma, W.-P., Brogaard, A.E., Case, D.A., Neri, B.P., Lyamichev, V.I. Modeling of flap endonuclease interactions with DNA substrate. J. Mol. Biol. 328:537, 2003.

Cheng, R.-J., Chen, P.-Y., Lovell, T., Liu, T., Noodleman, L., Case, D.A. Symmetry and bonding in metalloporphyrins: a modern implementation for the bonding analyses of five- and six-coordinate high-spin iron(III) porphyrin complexes through density functional calculation and NMR spectroscopy. J. Am. Chem. Soc. 125:6774, 2003.

Chou, J.J., Case, D.A., Bax, A. Insights into the mobility of methyl-bearing side chains in proteins from ³J_CC and ³J_CN couplings. J. Am. Chem. Soc. 125:8959, 2003.

Fee, J.A., Catagnetto, J.M., Case, D.A., Noodleman, L., Stout, C.D., Torres, R.A. The circumsphere as a tool to assess distortion in [4Fe-4S] atom clusters. J. Biol. Inorg. Chem. 8:519, 2003.

Gouda, H., Kuntz, I.D., Case, D.A., Kollman, P.A. Free energy calculations for theophylline binding to an RNA aptamer: comparison of MM-PBSA and thermodynamic integration methods. Biopolymers 68:16, 2003.

Kollman, P.A., Case, D.A. Drug-target binding forces: advances in force field approaches. In: Drug Discovery. Wiley & Sons, New York, 2003, p. 169. Burger's Medicinal Chemistry and Drug Discovery, 6th ed., Vol. 1. Abraham, D.J. (Ed.).

Liu, H., Qu, C., Johnson, J.E., Case, D.A. Pseudo-atomic models of swollen CCMV from cryo-electron microscopy data. J. Struct. Biol. 142:356, 2003.

Lovell, T., Case, D.A., Noodleman, L. FeMo cofactor of nitrogenase: energetics and local interactions in the protein environment. J. Biol. Inorg. Chem. 7:735, 2002.

Lovell, T., Torres, R.A., Han, W.-G., Liu, T., Case, D.A., Noodleman, L. Metal substitution in the active site of nitrogenase MFe₇S₉ (M = Mo⁴⁺, V³⁺, Fe³⁺). Inorg. Chem. 41:5744, 2002.

Onufriev, A., Case, D.A., Bashford, D. Effective Born radii in the generalized Born approximation: the importance of being perfect. J. Comput. Chem. 23:1297, 2002.

Onufriev, A., Case, D.A., Bashford, D. Structural details, pathways, and energetics of unfolding of apomyoglobin. J. Mol. Biol. 325:555, 2003.

Ponder, J.W., Case, D.A. Force fields for protein simulations. Adv. Prot. Chem. 66:27, 2003.

Torres, R.A., Lovell, T., Noodleman, L., Case, D.A. Density functional and reduction potential calculations of Fe₄S₄ clusters. J. Am. Chem. Soc. 125:1923, 2003.

Tsui, V., Macke, T., Case, D.A. A novel method for finding tRNA genes. RNA 9:507, 2003.

Waugh, A., Gendron, P., Altman, R., Brown, J.W., Case, D., Guatheret, D., Harvey, S.C., Leontis, N., Westbrook, J., Westhof, E., Zuker, M., Major, F. RNAML: a standard syntax for exchanging RNA information. RNA 8:707, 2002.

Xu, X.P., Case. D.A. Probing multiple effects on ¹⁵N, ¹³Ca, ¹³Cb and ¹³C´ chemical shifts in peptides using density functional theory. Biopolymers 65:408, 2002.