Welcome to the Bashford group homepage in the Department of Molecular Biology of The Scripps Research Institute. We work in several areas of theoretical molecular biophysics, as described below. Donald Bashford's mailing address is,

Department of Molecular Biology, TCP-15
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, California 92037
U.S.A.

Phone: 858 784 9612
FAX: 858 784 8896
E-mail: bashford@scripps.edu

Local Links

Current Group Members

Former Group Members (incomplete list)

A photo of the group from 1999.

RESEARCH INTERESTS

Electrostatics

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. (If the above download link doesn't work for you, please try anonymous FTP from ftp.scripps.edu, directory pub/bashford using an FTP program rather than a web browser.) 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.

Recent Publications

  1. Engels, M., Gerwert, K. Bashford, D. Computational studies on bacteriorhodopsin: Conformation and proton transfer energetics. Biophys. Chem. 56:95, 1995a.
  2. Chen, J.-L., Noodleman, L, Case, D.A., Bashford, D. Incorporating solvation effects into density functional electronic structure calculations. J. Phys. Chem 98:11059, 1994.
  3. Mouesca, J.-M., Chen, J.-L., Noodleman, L, Bashford, D., Case, D.A. Density functional/Poisson--Boltzmann calculations of redox potentials for iron--sulfur clusters. J. Amer. Chem. Soc. 116:11898, 1994.
  4. Engels, M., Bashford, D., Ghadiri, M.R. Structure and dynamics of self-assembling peptide nanotubes and the channel-mediated water organization and self-diffusion. a molecular mechanics study. J. Amer. Chem. Soc., 117:9151, 1995b.
  5. You, T., Bashford, D. An analytical algorithm for the rapid determination of the solvent accessibility of points in a three-dimensional lattice around a solute molecule. J. Comp. Chem. 16:743, 1995a.
  6. You, T., Bashford, D. Conformation and hydrogen ion titration of proteins: A continuum electrostatic model with conformational flexibility Biophys. J. 69:1721, 1995b.
  7. Ösapay, K., Young, W. S., Bashford, D., Brooks, III, C. L., Case, D. A. Dielectric continuum models for hydration effects on peptide conformational transitions J. Phys. Chem., 100:2698, 1996.
  8. Richardson, William H., Peng C.-Y., Bashford, D., Noodleman, L., Case, D. A. Incorporating solvation effects into density functional theory: Calculation of Absolute Acidities. Int. J. Quant. Chem. 61:207, 1996.
  9. Fisher, C. L., Chen, J.-L., Li, J., Bashford, D., Noodleman, L. Density-functional and electrostatic calculations for a model of a manganese superoxide dismutase active site in aqueous solution. J. Phys. Chem. 100:13498, 1996.
  10. Li, J., Fisher, C. L., Bashford, D., Noodleman, L. Calculation of redox Potentials and p$K_a$ values of hydrated transition metal cations by a combined density functional and continuum dielectric theory. Inorganic Chemistry 35:4694, 1996.
  11. Tishmack, P. A., Bashford, D., Harms, E., Van Etten, R. L. Use of 1H NMR spectroscopy and computer simulations to analyze histidine pKa changes in a protein tyrosine phosphatase: Experimental and theoretical determination of electrostatic properties in a small protein. Biochemistry 36:11984, 1997.
  12. Bashford, D. An object-oriented programming suite for electrostatic effects in biological molecules. In Yutaka Ishikawa, Rodney~R. Oldehoeft, John V.~W. Reynders, and Marydell Tholburn, editors, Scientific Computing in Object-Oriented Parallel Environments, volume 1343 of Lecture Notes in Computer Science, pages 233-240, Berlin, 1997. ISCOPE97, Springer.

Page updated (sort of) 20 June 2000

Valid HTML 4.0!