Macromolecular Interaction Energies from a Theoretical Databank of Transferable Aspherical Pseudoatoms

Paulina M. Dominiak ,  Anatoliy Volkov ,  Xue Li ,  Marc Messerschmidt ,  Philip Coppens 

State University of New York at Buffalo, Department of Chemistry (UB), Natural Sciences Complex, Buffalo 14260-3000, United States


A comprehensive version of the SUNY-Buffalo theoretical databank (SBDB) of aspherical atoms will be presented and its first application to protein/ligand interaction energies will be discussed [1].
The databank consists of all atom-types encountered in peptides, proteins and some other biologically relevant molecules. Each atom-type results from averaging over a family of chemically unique pseudoatoms, taking into account both first and second neighbors. A new atom type is spawned when one of the parameters for a member of the family deviate more than one standard deviation of the sample. The algorithm for atom-type definition assures that close transferability is obeyed, and will be presented.
It was shown that the databank gives an excellent reproduction of the electron density in a number of amino acids when compared with those calculated with conventional ab initio methods at the B3LYP/6-31G** level, while requiring only a small fraction of the computational time [2]. The databank reproduces electrostatic interaction energies of glycine dimers with an accuracy ~3 kJ per mole [3].
In the present study the SBDB is applied to the interactions between the PDZ domain of the scaffolding protein syntenin and a number of peptides, for which accurate structures are available [4, 5]. It shows the importance of the P0 and P-2 residues of the peptide in establishing the interaction, whereas the P-1 residue plays a smaller role, as recognized earlier [6]. Unexpectedly, the charged P-3 residue contributes significantly also. Furthermore preliminary results of energy calculations relevant to the inhibition of the neuraminidase enzyme from the influenza virus will be presented.
The SBDB has obvious applications in the refinement of macromolecular crystal structures.

[1] P. M. Dominiak, A. Volkov, Xue Li, M. Messerschmidt, P. Coppens, Acta Cryst. D 2006, to be published.
[2] A. Volkov, Xue Li, T. Koritsanszky, P. Coppens, J. Phys. Chem. A 2004, 108, 4283-4300.
[3] A. Volkov, T. Koritsanszky, P. Coppens, Chem. Phys. Lett., 2004 391, 170-175.

[4] B. S. Kang, D.R. Cooper, Y. Devedjiev, U. Derewenda, Z. S. Derewenda, Structure 2003, 11, 845-853.
[5] B. S. Kang, Y. Devedjiev, U. Derewenda, Z. S. Derewenda, J. Mol. Biol. 2004, 338, 483-493.
[6] J. Grembecka, T. Cierpicki, Y. Devedjiev, U. Derewenda, B.S. Kang, J. H. Bushweller, Z. S. Derewenda, Biochemistry 2006, 45, 3674-3683.

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Presentation: poster at 18th Conference on Physical Organic Chemistry, Posters, by Paulina M. Dominiak
See On-line Journal of 18th Conference on Physical Organic Chemistry

Submitted: 2006-05-31 18:03
Revised:   2009-06-07 00:44
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