 |
 |
Molecular Biology
Computer Modeling of Proteins and
Nucleic Acids
D.A. Case, S. Brozell, J. Carlsson,
M. Crowley, Q. Cui, P. Dasgupta, F. Dupradeau,* T. Dwyer,** H. Gohlke, D. Groff, D. Mathews, S. Moon,
D. Nguyen, A. Onufriev, R. Torres, R.C. Walker
* Université Jules Verne,
Amiens, France
** 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.
NMR and the 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. As an example, Figure 1 shows a fragment taken from a molecular dynamics simulation
of thioredoxin.
 |
| Fig. 1. Part of the protein thioredoxin shows some of the important
hydrogen-bonding interactions that influence nitrogen and proton chemical shifts. |
Quantum mechanical calculations of chemical shifts on fragments of this size
can provide important information about the connections between protein structure and NMR parameters.
Other types of data, 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. In recent structural studies, we focused on minor groove–binding drugs in complex
with DNA and on complexes of zinc finger proteins with RNA.
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. Figure 2 gives an example
of the reduction in the number of atoms that would be achieved for a small piece of the ribosome consisting
of a stretch of RNA and an associated ribosomal protein.
 |
| Fig. 2. An example of a low-resolution description of a piece of
the central domain of the small subunit of the ribosome shows the decrease in complexity compared
with an all-atom model. |
A computer language, NAB, was developed
to make it easier to construct and simulate molecular models for complex and often low-resolution
problems. The language is being used to study compact and swollen viruses, to analyze curved and
circular DNA, and to simulate ribosomal assembly.
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 aspect 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-β-lactamase,
binase, and cyclic-dependent kinase, in an effort to make more secure connections between the
motions of proteins and the activities of enzymes.
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; recently, we focused on adding aspects of electronic
polarizability, going beyond the usual fixed-charge models, and on methods for handling arbitrary
organic molecules that might be considered potential inhibitors in drug discovery efforts. 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
Case, D.A.
NMR parameters in proteins and nucleic acids. In: Calculation of NMR and EPR Parameters.
Kaupp, M., Bühl, M., Malkin, V.G. (Eds.). Wiley-VCH, New York, 2004, p. 341.
Cui, J., Crich, D., Wink, D., Lam,
M., Rheingold, A.L., Case, D.A., Fu, W., Zhou, Y., Rao, M., Olson, A.J., Johnson, M.E.
Design and synthesis of highly constrained factor Xa inhibitors: amidine-substituted bis(benzoyl)-[1,3]-diazepan-2-ones
and bis(benzylidene)-bis(gem-dimethyl)cycloketones. Bioorg. Med. Chem. 11:3379,
2003.
Feig, M., Onufriev, A., Lee, M.S.,
Im, W., Case, D.A., Brooks, C.L. III. Performance comparison
of generalized Born and Poisson methods in the calculation of electrostatic solvation energies
for protein structures. J. Comput. Chem. 25:265, 2004.
Gohlke, H., Case, D.A.
Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf.
J. Comput. Chem. 25:238, 2004.
Gohlke, H., Kiel, C., Case, D.A.
Insights into protein-protein binding by binding free energy calculation and free energy decomposition
for the Ras-Raf and Ras-RalGDS complexes. J. Mol. Biol. 330:891, 2003.
Gohlke, H., Kuhn, L.A., Case, D.A.
Change in protein flexibility upon complex formation: analysis of Ras-Raf using molecular dynamics
and a molecular framework approach. Proteins 56:322, 2004.
Lovell, T., Liu, T., Case, D.A.,
Noodleman, L. Structural, spectroscopic, and redox consequences
of a central ligand in the FeMoco of nitrogenase: a density functional theoretical study. J. Am.
Chem. Soc. 125:8377, 2003.
Moulnier, L., Case, D.A., Simonson,
T. Reintroducing electrostatics into protein x-ray structure
refinement: bulk solvent treated as a dielectric continuum. Acta Crystallogr. D Biol. Crystallogr.
59(Pt. 12):2094, 2003.
Onufriev, A., Bashford, D., Case,
D.A. Exploring protein native states and large-scale conformational
changes with a modified generalized Born model. Proteins 55:383, 2004. Roberts,
M.F., Cui, Q., Turner, C.J., Case, D.A., Redfield, A.G. High-resolution
field-cycling NMR studies of a DNA octamer as a probe of phosphodiester dynamics and comparison
with computer simulation. Biochemistry 43:3637, 2004.
Roberts, V.A., Case., D.A., Tsui,
V. Predicting interactions of winged-helix transcription
factors with DNA. Proteins 57:172, 2004.
Simonson, T., Carlsson, J., Case,
D.A. Proton binding to proteins: pKa
calculations with explicit and implicit solvent models. J. Am. Chem. Soc. 126:4167, 2004.
Wang, J., Wolf, R.M., Caldwell,
J.W., Kollman, P.A., Case, D.A. Development and testing
of a general Amber force field. J. Comput. Chem. 25:1157, 2004.
|
|
