> Don Bashford, Ph.D.
Associate Member, Molecular Biotechnology
Contact Information
Don Bashford, Ph.D.
Hartwell
Center for Bioinformatics & Biotechnology
Molecular Biotechnology
Division
St. Jude Children's Research
Hospital
332 N. Lauderdale
Memphis, TN 38105-2794
Email: don(dot)bashford@stjude(dot)org
Phone: (901) 495-3970
Fax: (901) 495-2945
Education
Department of Physics, Tufts Medford, MA
1980-1985 Ph.D. Physics, 1985. Thesis advisor: David Weaver.
Dissertation: “A Diffusion-Collision Model for the Folding
of Small Alpha-Helical Proteins.”
Purdue University W. Lafayette, IN
1972-1976 B.S. Agricultural Engineering, 1976.
Research Interests
We are developing and applying macroscopic dielectric models of the macromolecule--solvent system. The protein is treated as a low dielectric medium immersed in a high dielectric solvent, and the electric potential is determined by the Poisson--Boltzmann equation, which is solved by finite-difference methods. The details of the atomic structure are incorporated into the placement of charges and dielectric boundaries. We call the model, MEAD (Macroscopic Electrostatics with Atomic Detail). MEAD is also the name of our computer program suite, which is is free software that you are welcome to download . The use of the MEAD programs is documented in a README file in the download; and a brief description of the MEAD suite's overall design is given in Bashford, 1997.
A related program is Paul Beroza's mcti (or xmcti), which uses a Monte Carlo method to calculated average protonations of sites, give the intrinsic pKa of each site, and the matrix of site-site interactions. You can find it here.
The calculation of pKa values is a key test of electrostatic calculations, as well as an important application. We have extended our previous methods of calculating the pKa of ionizable sidechains in proteins by including conformational flexibility of the sidechains (You and Bashford, 1995b ). The method has been shown to improve the accuracy of our pKa predictions for lysozyme. Further improvements to and applications of this methodology are underway.
We have continued our investigations of the protonation states of functional groups in the light-driven, retinal-containing proton pump, bacteriorhodopsin. Molecular modeling and dynamics simulations were used to build refined models of the ground state structure and models of intermediate states in the photocycle based on two different hypotheses of retinal conformational changes. Our calculations lead to pKa shifts that could promote subsequent proton transfer in the case of one hypotheses, but not the other ( Engels et al. 1995a ).
In collaboration with Professor Robert Van Etten of Purdue University we are calculating pKa values of histidine residues in the wild-type and site-directed mutants of low-molecular-weight protein tyrosine phosphatases. The Van Etten lab has obtained high-resolution X-ray structures of several proteins of this class and found the histidines to have unusually high pKa values. They have also made a number mutants, measured their pKa values, and are working to determine the structures of some of the mutants. Measured and calculated pKa values are presented and compared in Tishmack et el., 1997 . More recently, we have made calculations of the highly perturbed protonation states and pKa values in the active site of a a number of different PTPases, in both the free-enzyme, and Michaelis-complex form (paper to appear in J. Phys. Chem.) Together with MEAD, above, you can reproduce the results using the data provided here.
Water strongly modifies inter- and intra- molecular interactions that are important for stability and binding in biological molecules. In particular, water weakens hydrogen bonds and alters the conformational preferences of protein backbone units. We have studied the suitability of MEAD for calculating this effect by comparing MEAD calculations with a number of analogous molecular dynamics calculations of solvation free energies. Good general agreement between the two types of calculations was found ( Ösapay et al. 1996 ). We are also applying a combination of MEAD and molecular dynamics to the study of the conformational preferences of turn-forming peptides.
In collaboration with L. Noodleman and D. Case we have combined density functional theory (DFT) methods of quantum chemistry with the MEAD by using MEAD to calculate the reaction fields due to the solvent or the solvent/protein environment, and DFT to calculate the electronic structure of the solutes. We have applied this method to the calculation of solvation free energies, geometry changes upon solvation, and pKa values of small molecules ( Chen et al. 1994 ; Richardson et al. 1996 ), and to the redox potentials of iron--sulfur cluster model compounds analogous to protein active sites ( Mouesca et al., 1994 ; Fisher et al., 1996 ); Li et al., 1996 . We have now extended this technique to clusters in protein active sites (manuscript submitted). For this purpose, a three-dielectric version of the MEAD programs has been developed.
Self Assembling Peptide Nanotubes
We are continuing our studies (Engels et al. 1995b) of the diffusion of water and ions through peptide nanotubes of the type developed in the laboratory of M. Reza Ghadiri. The calculations show that water in the nanotubes has a layered structure with deviations that allow water molecules to pass one another, in contrast to the single-file structure of water in the gramicidin pore, which has slower transport properties. We have developed a ``hopping model'' of the diffusion process that reproduces the diffusion rates calculated by molecular dynamics and are working on studies of ion diffusion and the effects of altering tube size and composition on transport properties.
Selected Recent Publications
- Onufriev, A., Smondyrev, A. and Bashford, D. "Proton affinity changes driving unidirectional proton transport in the bacteriorhodopsin photocycle" J. Mol. Biol. 332:1183--1193, 2003
- Dilipkumar Asthagiri, Valerie Dillet, Tiqing Liu, Louis Noodleman, Robert L. Van Etten and Donald Bashford "Density Functional Study of the Mechanism of a Tyrosine Phosphatase: I. Intermediate Formation"
- Alexey Onufriev, David A. Case and Donald Bashford "Effective Born Radii in the Generalized Born Approximation: The Importance of Being Perfect" J. Comp. Chem. 23:1297--1304, 2002
