New crystallographic methods will be developed to experimentally map and analyze electronic charge density and electrostatic potential distributions in proteins. Test cases for the development will be a series of allosteric insulin structures, already well-characterized by high-resolution X-ray diffraction. Experimentally, we shall employ the powerful technologies of macromolecular cryocrystallography with synchrotron X-ray sources and area detectors to measure diffraction data to atomic resolution. Computationally, we shall develop procedures to introduce experimental electron density parameters transferable to protein crystals at atomic resolution from a database of results from analyses of amino acid and oligopeptide crystals at sub-atomic resolution. The new methods to be developed will be able to provide answers to questions about the electrostatic, as distinct from geometric, atomic structure of proteins that present-day protein crystallographic methods cannot answer. Such questions include ambiguous states of ionization/protonation due to pK values being different in different molecular environments, ambiguous states of water-counterion structure at protein surfaces, and ambiguous protein- water hydrogen bonding donor-acceptor relationships. Also of great importance, the new methods will provide an experimental basis for calibrating the now theoretically derived electrostatic parameters used in molecular modelling and simulation calculations widely employed in many areas of structural biology. With respect to problems of insulin structural biochemistry, in particular, we expect our work will help resolve important questions of ill-defined electrostatic interactions in, for example, insulin-hexamer (GluB13)6 clusters, which according to various biophysical and biochemical evidence are probably key pieces in the mechanism of T6 T3R3 R6 insulin allosterism.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
1R01GM056829-01A1
Application #
2746751
Study Section
Molecular and Cellular Biophysics Study Section (BBCA)
Project Start
1999-05-01
Project End
2003-04-30
Budget Start
1999-05-01
Budget End
2000-04-30
Support Year
1
Fiscal Year
1999
Total Cost
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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