The proposed research aims to develop new biocrystallographic methodologies to extract maximal information from atomic-resolution diffraction data from protein crystals. Such data are now becoming available at a rapidly increasing rate, and from such data, crystallography can reveal, in quantitative detail, not only the three-dimensional geometric atomic structure of protein crystals, but also their three dimensional electrostatic atomic structure, their acid-base hydrogen structure, and the dynamical structure of their modes of anisotropic mean-square atomic displacement due to disorder and/or thermal vibration. The proposed work will employ and develop ultrahigh-resolution, ultralow-cryotemperature crystallographic techniques in order to map and analyze at atomic, or even sub-atomic, resolution the aspherical atomic valence electron density distributions, the molecular electrostatic potential distributions, and the structural dynamical modes in protein crystals. The crystallographic charge density and electrostatic potential analyses will employ an established experimental databank of transferable, amino acid and oligopeptide, electron density parameters; and a complementary theoretical databank based on high-level quantum chemical calculations will be built, tested, and compared with the experimental databank. Experimental charge density distributions will be used to derive experimental net atomic charges, electrical dipole and higher multiple moments, and electrostatic interaction energies, for atoms and functional groups of atoms and protein molecules interacting with one another and with the molecules in their solvation shells in crystallography. In addition, crystallographic analyses of mean-square atomic displacements will fit structural dynamical models of flexibly-joined rigid-body segments or domains to model the external and internal modes of protein molecular motions in crystallography. Test cases for the development of these new biocrystallographic methodologies will be analyses of the roles of structured electrostatics and structured dynamical modes in the phenomena of insulin hexamer allosterism and ribonuclease. Both problems will be analyzed by both X-ray and neutron diffraction.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM056829-05
Application #
6613633
Study Section
Molecular and Cellular Biophysics Study Section (BBCA)
Program Officer
Flicker, Paula F
Project Start
1999-05-01
Project End
2007-05-31
Budget Start
2003-06-01
Budget End
2004-05-31
Support Year
5
Fiscal Year
2003
Total Cost
$273,472
Indirect Cost
Name
Hauptman-Woodward Medical Research Institute
Department
Type
DUNS #
074025479
City
Buffalo
State
NY
Country
United States
Zip Code
14203
Dominiak, Paulina M; Volkov, Anatoliy; Dominiak, Adam P et al. (2009) Combining crystallographic information and an aspherical-atom data bank in the evaluation of the electrostatic interaction energy in an enzyme-substrate complex: influenza neuraminidase inhibition. Acta Crystallogr D Biol Crystallogr 65:485-99
Volkov, Anatoliy; Messerschmidt, Marc; Coppens, Philip (2007) Improving the scattering-factor formalism in protein refinement: application of the University at Buffalo Aspherical-Atom Databank to polypeptide structures. Acta Crystallogr D Biol Crystallogr 63:160-70
Li, Xue; Volkov, Anatoliy V; Szalewicz, Krzysztof et al. (2006) Interaction energies between glycopeptide antibiotics and substrates in complexes determined by X-ray crystallography: application of a theoretical databank of aspherical atoms and a symmetry-adapted perturbation theory-based set of interatomic potentials Acta Crystallogr D Biol Crystallogr 62:639-47
Smith, G David; Pangborn, Walter A; Blessing, Robert H (2005) The structure of T6 bovine insulin. Acta Crystallogr D Biol Crystallogr 61:1476-82
Volkov, Anatoliy; Coppens, Philip (2004) Calculation of electrostatic interaction energies in molecular dimers from atomic multipole moments obtained by different methods of electron density partitioning. J Comput Chem 25:921-34
Coppens, Philip; Volkov, Anatoliy (2004) The interplay between experiment and theory in charge-density analysis. Acta Crystallogr A 60:357-64
Smith, G David; Pangborn, Walter A; Blessing, Robert H (2003) The structure of T6 human insulin at 1.0 A resolution. Acta Crystallogr D Biol Crystallogr 59:474-82
Smith, G David; Blessing, Robert H (2003) Lessons from an aged, dried crystal of T(6) human insulin. Acta Crystallogr D Biol Crystallogr 59:1384-94
Koritsanszky, Tibor; Volkov, Anatoliy; Coppens, Philip (2002) Aspherical-atom scattering factors from molecular wave functions. 1. Transferability and conformation dependence of atomic electron densities of peptides within the multipole formalism. Acta Crystallogr A 58:464-72
Koritsanszky, T S; Coppens, P (2001) Chemical applications of X-ray charge-density analysis. Chem Rev 101:1583-627

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