Darwin O.V. Alonso, Ph. D.
Research Associate
Computer Systems Administrator
Department of Medicinal Chemsitry, H165
University of Washington
Seattle, 98195-7610
E-Mail:
dalonso@u.washington.edu
Phones:
(206) 616-2780 (office)
(206) 685-3252 (FAX)
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Education and Scientific Experience
2/93-current: I have been a Research Associate and Systems Administrator with Profes-
sor Valerie Daggett since she established this lab at the University of Washington,
Department of Medicinal Chemistry. Our primary focus is molecular dynamics simula-
tion and visualization of proteins.
Current Duties:
Scientific research
(1) Protein Folding; molecular dynamics (MD) simulations
provide details of very fast events that can occur during protein folding and
collapse; however, the entire folding process observed experimentally occurs on
much longer time scales. My primary research efforts have been to gain insights
into protein folding pathways from the MD simulations, while requiring that the
details that we see are consistent with the experimental data.
(2) Identifying sub-states in MD trajectories; automated ways to scan long
molecular dynamics simulations of proteins (>1 GB of coordinate data) for
significant, but possibly nonnative, conformational states.
(3) Structure of the prion protein
(4) Protein sequence/structure relationship.
Systems Administration:
Graphics and computational servers with shared file systems.
Visualization of proteins.
12/91-5/92 Affiliate of University of Alaska, Fairbanks with Professor Larry K.
Duffy at the Department of Biochemistry. I worked on grant proposals for the study
of aggregation of $beta$-amyloid peptides.
9/84-5/91 Ph.D. with Professor Ken A. Dill, Department of Pharmaceutical Chemis-
try, University of California, San Francisco. I developed a mean field statistical
thermodynamics theory treating the dependencies of protein stability on tempera-
ture, solvent, and pH. The theory incorporated the interactions between hydropho-
bic residues, polar residues, water, and different cosolvents. The theory included
contributions of chain conformational entropy.
5/79-3/80 Research Chemist at Cal Ink, Berkeley, California. Analysis of inks and
industrial wastes for heavy metals, rheology of inks, and ink formulation.
9/73-5/77 B.S. Chemistry, Humboldt State University, Arcata, California. Organic
chemistry, electrophilic substitution of phenols, and the $""sup 1$H NMR of steri-
cally hindered aromatic substituents.
6/73-9/73 Summer volunteer research work with Dr. Martin Apple, Cancer Research
Institute, University of California, San Francisco. Separation of tea tannins
with an interest in their anti-cancer properties.
Other: I have extensive experience in construction work including: surveying, lay-
out, electrical planning and implementation. I am handy mechanically.
Personal
Born: May 13, 1953, Ann Arbor, Michigan. Raised: Denver, Colorado; San Juan, Puerto
Rico; and San Francisco and Berkeley, California. High School: Berkeley High School.
Foreign Languages: Spanish and some German.
Publications
S. DeArmond, Y. Qiu, H. Sanchez, P.R. Spilman, A.Ninchak-Casey, D. Alonso and V. Daggett,
PrPC Glycoform Heterogeneity as a Function of Brain Region:
Implications for Selective Targeting of Neurons by Prion Strains.
J. Neuropath. Exp. Neurology, in press,
Alonso, D.O. and Daggett, V. Partial Refolding of Ubiquitin:
Simulations of Hydrophobic Collapse. Protein Science. 7. 860-874. (1998)
Alonso, D.O. and Daggett, V. Molecular Dynamics Simulations of Protein Unfolding and
Limited Refolding: Characterization of Partially Unfolded States of Ubiquitin in
60% Methanol and in Water. J. Mol. Biol., 247, 501-520 (1995).
Kazmirski, S.L., Alonso, D.O., Cohen, F.E., Prusiner, S.B., and Daggett, V.
Theoretical Studies of Sequence Effects the Conformational Properties of the
Prion Protein: Implications for Scrapie Formation. Chemistry and Biology, 2,
305-315 (1995).
Alonso, D.O., Dill, K.A, Stigter, D. The Three States of Globular Proteins: Acid
Denaturation, Biopolymers, 31, 1631-1649 (1991).
Alonso, D.O. and Dill, K.A. Solvent Denaturation and Stabilization of Globular Pro-
teins, D.O., Biochemistry, 30(24), 5974-85 (1991).
Fields, G., Alonso, D.O., Stigter, D., and Dill, K.A. Theory for the Aggregation of
Proteins and Copolymers, J. Phys. Chem., 3974-3981 (1992)
Dill, K.A., Alonso, D.O., and Hutchinson, K. Thermal Stabilities of Globular Pro-
teins, Biochemistry, 28(13): 5439-5449 (1989).
Dill, K.A. and Alonso, D.O. Conformational Entropy and Protein Stability. In Pro-
tein Structure and Protein Engineering, 39, pp. 51-58. Huber, R. and Winnacker,
E.L. eds. Colloquium-Mosbach der Gesellschaft fur Biologische Chemie. Berlin:
Springer-Verlag, 1988.
Stigter, D., Alonso, D.O., and Dill, K.A. Protein Stability: Electrostatics and Com-
pact Denatured States, Proc. Natl. Acad. Sci., 88(10), 4176-80 (1991).
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