NGEC Principal Investigator
Professor, Biochemistry, University of Washington
Investigator, Howard Hughes Medical Institute
Department of Biochemistry
University of Washington School of Medicine
J Wing Health Sciences Building, Box 357350
Seattle, WA 98195
Tel: (206) 543-1295 Fax: (206) 685-1792
E-mail Dr. Baker
Dr. Baker graduated from Harvard University with a BA and earned his PhD in biochemistry from the University of California, Berkeley, supported by a pre-doctoral fellowship from the National Science Foundation. Dr. Baker completed postdoctoral work in biophysics at the University of California, San Francisco with Dr. David Agard, and also held a postdoctoral fellowship with the Life Sciences Research Foundation.
Dr. Baker is the principal investigator for the NGEC in the area of Computational Design of Novel Homing Endonucleases.
“The NGEC provides a unique opportunity to translate our computational work into having a direct impact on patients with genetic diseases.”For its role in the NGEC, the Baker lab seeks to computationally design homing endonucleases that specifically cleave a desired target site. Dr. Baker and his team will use their computational design methodology – based on an explicit physical model of protein-DNA interfaces – to design novel homing endonuclease variants predicted to cleave specifically within sites in XSCID and other therapeutically important genes. Biochemical and biophysical data about first-generation designs will be used to refine and improve the lab’s computational design methodology.
Computational prediction and design of protein-DNA interfaces using RosettaDesign has made significant recent advances, culminating in the achievement of a designed specificity switch of the I-MsoI LHE by the Baker lab. For the NGEC, the Baker lab will further develop its RosettaDesign methods, and work to apply the new methods to the generation of LHEs for hematopoietic stem cell engineering.
The Baker lab's NGEC work will be accomplished through three specific aims:
Key lab personnel participating in this work include:
Jasmine Gallaher, lab technician in David Baker's lab
The goal of current research in the Baker laboratory is to develop an improved model of intra- and intermolecular interactions and to apply this improved model to the prediction and design of macromolecular structures and interactions. Prediction and design applications can be of great biological interest in their own right, and also provide very stringent and objective tests which drive the improvement of the model and increases in fundamental understanding.
The protein and design calculations are carried out using a computer program called RosettaDesign. RosettaDesign is a lab-developed, continually-refined computer program used for protein folding prediction and protein-protein and protein-DNA interface design.
At the core of RosettaDesign are the physical model of macromolecular interactions and algorithms for finding the lowest energy structure for an amino acid sequence (protein structure prediction) or a protein-protein complex, and for finding the lowest energy amino acid sequence for a protein or protein-protein complex (protein design). Both the physical model and the search algorithms are continually being improved based on feedback from the prediction and design tests.
There are considerable advantages in developing one computer program to treat these quite diverse problems: first, the different applications provide very complementary tests of the underlying physical model (the fundamental physical chemistry is, of course, the same in all cases), and second, many problems of current interest, such as flexible backbone protein design and protein-protein docking with backbone flexibility, involve a combination of the different optimization methods.
The Baker lab has achieved significant advances in many areas, including: the creation and ongoing development of RosettaDesign; the engineering of a homing endonuclease chimera (Chevalier et al, 2002); the design of a novel globular protein fold (Kuhlman et al, 2003); the thermostabilization of an enzyme (Korkegian et al, 2005); and the re-design of homing endonuclease DNA binding and cleavage specificity (Ashworth et al, 2006).
Superimposition of the Top7 computational model and x-ray structure shows the remarkable atomic-level accuracy of the design (1.2Å RMSD). The backbones are respresented as ribbons (computational model : helices - dark blue, strands - red; x-ray structure : helices - light blue, strands - yellow), and selected amino-acid sidechains in the protein core are represented as sticks.
Chevalier, B.S., Kortemme, T., Chadsey, M.S., Baker, D., Monnat, R.J. and Stoddard, B.L. (2002). Design, activity, and structure of a highly specific artificial endonuclease. Mol. Cell. 4:895-905.
Morozov, A., Kortemme, T. and Baker, D. (2003). Evaluation of models of electrostatic interactions in proteins. J. Phys. Chem. 107:2075-2090.
Kuhlman, B., Dantas, G., Ireton, G.C., Varani, G., Stoddard, B.L. and Baker, D. (2003). Design of a novel globular protein fold with atomic-level accuracy. Science 302:1364-8.
Kortemme, T., Morozov, A.V. and Baker, D. (2003). An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J. Mol. Biol. 326:1239-1259.
Scalley-Kim, M., Minard, P., Baker, D. (2003). Low free energy cost of very long loop insertions in proteins. Protein Sci. 12:197-206.
Schueler-Furman, O and Baker D. (2003). Conserved residue clustering and protein structure prediction. Proteins. 52:225-235.
Meiler, J. and Baker, D. (2003) Coupled prediction of protein secondary and tertiary structure. Proc. Natl. Acad. Sci. USA 100:12105-12110.
Morozov, A., Kortemme, T., Tsemekhman, K. and Baker, D. (2004). Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations. Proc. Natl. Acad. Sci. USA 101:6946-6951.
Misura, K.M., Morozov, A.V. and Baker, D. (2004) Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction. J. Mol. Biol. 342:651-664.
Korkegian, A., Black, M.E., Baker, D. and Stoddard, B.L. (2005) Computational thermostabilization of an enzyme. Science 308:357-360.
Havranek, J.J., Duarte, C.M. and Baker D. (2004) A simple physical model for the prediction and design of protein-DNA interactions. J. Mol. Biol. 344:59-70.
Saunders, C.T. and Baker, D. (2005) Recapitulation of protein family divergence using flexible backbone protein design. J. Mol. Biol. 346:631-644. Epub 2005 Jan 8.
Jiang, L., Kuhlman, B., Kortemme, T. and Baker D. (2005) A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins. 58:893-904.
Bradley, P., Misura, K. and Baker, D. (2005). Towards high resolution de novo structure prediction. Science 309: 1868-1871.
Ashworth, J., Havranek, J. J., Duarte, C. M., Sussman, D., Monnat, R. J., Jr., J., Stoddard, B. L., Baker, D. (2006). Computational redesign of endonuclease DNA binding and cleavage specificity. Nature 441: 656-659.
Bradley, P. and Baker, D. (2006). Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation. Proteins. 65(4): 922-999.
Joachimiak, L.A., Kortemme, T.,Stoddard, B.L., Baker, D. (2006). Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface. J Mol Biol. 361(1): 195-208.