|
Kevin W.
Plaxco
Professor of Chemistry and
Biochemistry
Address:
Department
of Chemistry and Biochemistry (805)
893-5558
University
of California, Santa Barbara (805)
893-4120 (fax)
Santa
Barbara, CA 93106 kwp@chem.ucsb.edu
Professional Experience:
Professor ’07-
Associate
Professor (with Tenure) ’04-‘07
Assistant
Professor; Department of Chemistry and Intercollegiate Program in ’98-’04
Biomolecular
Science and Engineering, University of California, Santa Barbara
Postdoctoral
Fellow, University of Washington ’97-’98
Mentor:
David Baker
Postdoctoral
Fellow, University of Oxford ’94-’96
Mentors:
Christopher M. Dobson and Iain D. Campbell
Education:
Caltech Ph.D. Molecular
Biology ’87-’93
Mentor:
William A. Goddard, III
U.C. Riverside B.Sc. Chemistry
and Biochemistry ’83-’87
Mentor:
Thomas H. Morton
Published Articles, Reviews and
Book Chapters:
Pre-1996
1.
Mason, F.R., Leong, F-C., Plaxco, K.W. and Morton, T.H. (1985) “Two n
covalent modification of proteins: Selective labeling of Schiff base forming
sites and selective blockade of the sense of smell in vivo.” J. Am. Chem. Soc., 107, 6075-6084
2.
Plaxco, K.W., Mathiowetz, A.A. and Goddard, W.A. (1989) “Predictions of
structural elements for the binding of hin recombinase with the hix site of DNA.” Proc. Nat. Acad. Sci. USA, 86,
9841-9845
3.
Plaxco, K.W. and Goddard, W.A. III (1994) “Contributions of the thymine
methyl group to the specific recognition of poly- and mono-nucleotides: An analysis
of the relative free energy of solvation of thymine and uracil.” Biochemistry, 33, 3050-3054
1996
4.
Plaxco, K.W., Spitzfaden, C., Campbell, I.D. and Dobson, C.M. (1996)
“Rapid folding of a proline rich, all beta-sheet fibronectin type III domain.” Proc.
Natl. Acad. Sci. USA, 93, 10703-10706
5.
Plaxco, K.W. and Dobson, C.M. (1996) “Time-resolved biophysical methods
in the study of protein folding.” Curr.
Opin. Struc. Biol., 6, 630-636
1997
6.
Plaxco, K.W., Spitzfaden, C., Campbell, I.D. and Dobson, C.M. (1997)
“Comparison of the folding kinetics and thermodynamics of two homologous
fibronectin type III modules.” J. Mol.
Biol. 270, 763-770
7.
Plaxco K.W. and Gross, M. (1997) “The importance of being unfolded.” Nature, 386, 657-659
8.
Plaxco, K.W., Morton, C.J., Grimshaw, S., Jones, J.A., Pitkeathly, M.,
Campbell, I.D. and Dobson, C.M. (1997) “The effects of guanidine hydrochloride
on the ‘random coil’ conformations and NMR chemical shifts of the peptide
series GGXGG.” J. Biomolec. NMR, 10, 221-230
9.
Gross, M. and Plaxco, K.W. (1997) “Protein engineering: reading,
writing and re-designing.” Nature, 367, 419-420
10.
O'Brien, R., Wynn, R.,
Driscoll, P.C., Davis, B., Plaxco, K.W., Sturtevant, J.M. and Ladbury, J.E.
(1997) “The adaptability of Escherichia coli thioredoxin to non-conservative
amino acid substitutions.” Prot. Sci., 6, 1325-133
1998
11.
Plaxco, K.W., Guijarro,
J.I., Morton, C.J., Pitkeathly, M., Campbell, I.D. and Dobson, C.M. (1998) “The
folding kinetics and thermodynamics of the FynSH3 domain.” Biochemistry, 37, 2529-2537
12.
Guijarro, J.I., Morton,
C.J., Plaxco, K.W., Campbell, I.D. and Dobson, C.M. (1998) “Folding kinetics of
the SH3 domain of PI3 by real-time NMR and optical techniques.” J. Mol. Biol., 275, 657-667
13.
Plaxco, K.W., Riddle, D.S.,
Grantcharova, V. and Baker, D. (1998) “Simplified proteins: Minimalist
solutions of the ‘protein folding problem’.” Curr. Op. Struct. Biol, 8, 80-85
14.
Plaxco, K.W., Simons, K.T.
and Baker, D. (1998) “Contact order, transition state placement and the
refolding rates of single domain proteins.” J.
Mol. Biol., 277, 985-994
15.
Plaxco, K.W. (1998) “Protein
chemistry comes of age. Again.” Trends in Biotech., 16, 278
16. Plaxco, K.W. and Baker, D. (1998) “Limited internal friction in the rate limiting conformational change of a two-state protein folding reaction.” Proc. Natl. Acad. Sci. USA, 95, 13591-13596
17.
Plaxco, K.W. and Dobson,
C.M. (1998) “Monitoring protein folding using time-resolved biophysical
techniques.” in Protein Dynamics, Function and Design, O. Jardetzky and
J. Lefevre, eds., Plenum Press, New York, pp 331-332
1999
18.
Plaxco, K.W., Millett, I.S.,
Segel, D.J., Doniach, S. and Baker, D. (1999) “Polypeptide chain collapse can
occur concomitantly with the rate limiting step in protein folding.” Nat. Struct. Biol., 6, 554-557
19.
Viani, M.B., Schaffer, T.E.,
Paloczi, G.T., Pietrasanta, L., Smith, B.L, Thompson, J.B., Reif, M., Gaub,
H.E., Plaxco, K.W., Cleland, A., Hansma, H.G. and Hansma, P.K. (1999) “Fast
imaging and fast force spectroscopy of single biopolymers with anew atomic
force microscope designed for small cantilevers.” Rev. Sci. Inst., 70,
4300-4303
2000
20.
Plaxco, K.W., Larson, S.,
Ruczinski, I., Riddle, D.S., Thayer, E.C., Buchwitz, B., Davidson, A.R. and
Baker, D. (2000) “Evolutionary conservation in protein folding kinetics.” J. Mol. Biol., 298, 303-312
21.
Plaxco, K.W., Simons, K.T.,
Ruczinski, I. and Baker, D. (2000) “Sequence, stability, topology and length;
the determinants of two-state protein folding kinetics.” Biochemistry, 39,
11177–11183
22.
Gillespie, B. and Plaxco,
K.W. (2000) “Non-glassy kinetics in the folding of a simple, single domain
protein.” Proc. Natl. Acad. Sci. USA, 97, 12014-12019
2001
23.
Plaxco, K.W. and Gross, M.
(2001) “Unfolded, yes, but random? Never!” Nat.
Struct. Biol., 8, 659-670
2002
24.
Millet, I.S., Townsley, L.,
Chiti, F., Doniach, S. and Plaxco, K.W. (2002) “Equilibrium collapse and the
kinetic ‘foldability’ of proteins.” Biochemistry, 41, 321-325
25.
Makarov, D.E., Keller, C.A.,
Plaxco, K.W. and Metiu, H. (2002) “How the folding rate constant of
simple-single domain proteins depends on number of native contacts.” Proc. Natl. Acad. Sci. USA, 99, 3535-3539
26.
Larson, S., Ruczinski, I.,
Davidson, A.R., Baker, D. and Plaxco, K.W. (2002) “Residues
participating in the protein folding nucleus do not exhibit preferential evolutionary
conservation.” J. Mol. Biol., 316, 225-233
27.
Fan, C., Plaxco, K.W. and
Heeger, A.J. (2002) “High-efficiency fluorescence quenching of conjugated
polymers by proteins.” J. Am. Chem. Soc., 124, 5642-5643
28.
Thompson, J.B., Hansma,
H.H., Hansma, P.K. and Plaxco, K.W. (2002) “The backbone conformational entropy
of protein folding: experimental measures from atomic force microscopy.” J. Mol. Bio., 322, 645-652
29.
Millett, I.S., Doniach, S.
and Plaxco, K.W. (2002) “Towards a taxonomy of the denatured state: small angle
scattering studies of unfolded proteins.” Adv.
Prot. Chem., 62, 241-262
30.
Fan, C., Gillespie, B.,
Wang, G., Heeger, A.J. and Plaxco, K.W. (2002) “Spectroscopy and
electrochemistry of the pyridine-chytochrome c complex and the pyridine-induced
‘alkaline-like’ conformation.” J. Phys. Chem. B, 106, 11375-11383
2003
31.
Makarov, D.E. and Plaxco,
K.W. (2003) “The topomer search model: a quantitative, first-principles
description of two-state protein folding kinetics.” Prot. Sci., 12, 17-26
32.
Jewett, A., Pande, V.S. and
Plaxco, K.W. (2003) “Cooperativity, smooth energy landscapes and the origins of
topology-dependent protein folding rates.” J.
Mol. Bio., 326, 247-253
33.
Fan, C., Hirasa,
T., Plaxco, K.W. and Heeger, A.J. (2003) “Photoluminescence quenching of water-soluble
conjugated polymers by viologen derivatives: effect of hydrophobicity.” Langmiur, 19, 3554-3556
34.
Fan, C., Wang, S., Hong,
J.M., Bazan, G.C., Plaxco, K.W. and Heeger, A.J. (2003) “Beyond superquenching:
hyper-efficient energy transfer from conjugated polymers to gold nanoparticles.” Proc.
Natl. Acad. Sci. USA, 100, 6297-6301
35.
Calloni, G., Taddei, N., Plaxco, K.W., Ramponi, G., Stefani, M. and
Chiti, F. (2003) “Comparison of the folding processes of distantly related proteins.
Importance of hydrophobic content in folding.” J.
Mol. Bio., 330, 577-591.
36.
Gillespie, B., Vu, D., Shah,
P.S., Marshall, S., Dyer, R.B., Mayo, S.L., and Plaxco, K.W. (2003) “NMR and
Temperature Jump measurements of de novo designed proteins demonstrate rapid folding in the absence of explicit
selection for kinetics.” J. Mol. Bio., 330, 813-819
37.
Fan, C., Plaxco, K.W. and
Heeger, A.J. (2003) “Electrochemical interrogation of conformational changes as
a reagentless method for the sequence-specific detection of DNA.” Proc. Natl. Acad. Sci. USA, 100, 9134-9137
38.
Ivankov, D.N., Alm, E.,
Plaxco, K.W., Baker, D. and Finkelstein, A.V. (2003) “Contact order revisited:
the influence of protein size on folding rates.” Prot. Sci., 12, 2057-2062
39.
Xu, J., Ramian, G.J., Galan,
J.F., Savvidis, P.G., Scopatz, A.M., Birge, R.R. Allen, S.J. and Plaxco, K.W.
(2003) “Terahertz circular dichroism spectroscopy: a potential approach to
unbiased, in situ life detection.” Astrobiology, 3,
489-504
2004
40.
Gillespie, B. and Plaxco,
K.W. (2004) “Using protein folding rates to test protein folding theories.” Ann. Rev. Biochem. Biophys., 73, 837-859
41.
Kohn, J.E., Millett, I.S.,
Jacob, J., Zagrovic, B., Dillon, T., Cingel, N., Seifert, S.,
Thiyagarajan, P., Sosnick. T.R., Ruczinski, I., Hasan, M.Z., Pande, V.S.
Doniach, S. and Plaxco, K.W (2004) “Do the dimensions of chemically unfolded
proteins differ significantly from the expectations of a random-coil model?” Proc. Natl. Acad. Sci. USA, 101, 12491-12496
42.
Gillespie, B. and Plaxco,
K.W. (2004) “Can theory predict two-state protein folding rates? An
experimental perspective.” In: Forces, Growth and Form in Soft Condensed
Matter: At the Interface between Physics and Biology, Skjeltorp, A.T. and Velushkin, A.V., Eds, Kluwer Academic
Publishers BV, Dordrecht, Netherlands, pp
93-111
43.
Xu, J., Ramian, G.J., Galan,
J.F., Savvidis, P.G., Scopatz, A.M., Birge, R.R., Allen, S.J. and Plaxco, K.
(2004) “Terahertz circular dichroism spectroscopy of biomolecules.” In: Chemical and Biological Standoff Detection. J.O. Jensen and J-M. Theriault, Eds. Proceedings of the
SPIE, Vol. 5268, pp 19-26
2005
44.
Raleigh, D.S. and Plaxco,
K.W. (2005) “Plasticity and heterogeneity in the folding nucleus; what are f-values really telling us?” Prot. Pep. Sci., 12, 117-122
45.
de los Rios, M.A. and
Plaxco, K.W. (2005) “Apparent Debye-Huckel electrostatic effects in the folding
of a simple, single domain protein.” Biochemistry, 44, 1243-1250
46. Maxwell, K.L., Wildes, D., Zarrine-Afsar, A., de los Rios, M.A., Brown, A.G., Friel, C.T, Hedberg, L., Horng, J-C., Bona, D., Miller, E.J., Vallée-Bélisle, A., Main, E.R.G., Bemporad, F., Qiu, L., Teilum, K., Vu, N.-D., Edwards, A.M., Ruczinski, I., Poulsen, F.M., Kragelund, B.B., Michnick, S.W., Chiti, F., Bai, Y., Hagen, S.J., Serrano, L., Oliveberg, M., Raleigh, D.P., Wittung-Stafshede, P., Radford, S.E., Jackson, S.E., Sosnick, T.R., Marqusee, S., Davidson, A.R., Plaxco, K.W. (2005) “Protein folding: defining a ‘standard’ set of experimental conditions and a preliminary kinetic data set of two-state proteins.” Prot. Sci., 14, 602-616
47.
Fan, C., Plaxco, K.W. and
Heeger, A.J. (2005) “Ligand-modulated electron- or energy-transfer as a
biosensor signaling mechanism.” Trends
Biotech., 23,186-192
48.
Kohn, J.E. and Plaxco, K.W.
(2005) “Engineering of a signal-transduction mechanism for protein-based
biosensors.” Proc. Natl. Acad. Sci. USA, 102, 10841-10845
49.
McCarney, E.R., Kohn, J.E.
and Plaxco, K.W. (2005) “Is there or isn’t there? The case for (and against) residual structure in chemically
denatured proteins.” Crit. Rev. Bioch.
Mol. Biol., 40, 181-189
50.
Xiao, Y., Lubin, A.A.,
Heeger, A.J. and Plaxco, K.W. (2005) “Label-free electronic detection of
thrombin in blood serum using an aptamer based sensor.” Angw. Chem. Int. Ed., 44,
2-5
51.
McCarney, E.R., Werner,
J.H., Ruczinski, I., Makarov, Goodwin, P.M. and Plaxco, K.W. (2005) “Random
coil dimensions in a highly denatured protein; A single molecule study.” J. Mol. Biol., 352,
672-682
52.
de los Rios, M.A., Danashi,
M. and Plaxco, K.W. (2005) “Experimental investigation of the frequency and
substitution dependence of negative f-values in two-state proteins.” Biochemistry, 44, 12160 -12167
53.
Xiao, Y., Piorek, B.D.,
Plaxco, K.W. and Heeger, A.J. (2005) “A reagentless, signal-on design for
electronic aptamer-based sensors via target-induced strand displacement.” J. Am. Chem. Soc., 127, 17990-17991
2006
54.
Xu, J., Plaxco, K.W. and
Allen, S.J. (2006) “Absorption spectra of liquid water and aqueous buffers
between 0.3 - 3.72 terahertz.” J. Chem.
Phys. 124, 036101
55. de los Rios, M.A.,
Muralidhara, B.K., Wildes, D., Marqusee, S., Wittung-Stafshed, P., Plaxco, K.W.
and Ruczinski, I. (2006) “On the precision of experimentally determined folding
rates and f-values.” Prot.
Sci., 15, 553-563
56.
Lai, R.Y, Lee, S-H., Soh,
H., Plaxco, K.W. and Heeger, A.J. (2006) “Differential labeling of
closely-spaced biosensor electrodes via electrochemical lithography.” Langmiur, 22,
1932-1936
57.
Lai, R.Y., Lagally, E.T.,
Lee, S.-H., Soh, T.H., Plaxco, K.W. and Heeger, A.J. (2006) “Rapid,
sequence-specific detection of unpurified PCR amplicons via a reusable, electrochemical sensor.” Proc.
Natl. Acad. Sci. USA, 103,
4017-4021
58.
Baker, B.R., Lai, R.Y.,
Wood, M.S., Doctor, E.H., Heeger, A.J. and Plaxco, K.W. (2006) “An electronic,
aptamer-based small molecule sensor for the rapid, reagentless detection of
cocaine in adulterated samples and biological fluids.” J. Am. Chem. Soc. 128, 3138-3139
59.
Xu, J., Plaxco, K.W. and Allen, S.J. (2006) “0.3 – 3.72 Terahertz
absorption spectroscopy of a protein in liquid water.” Prot.
Sci, 15, 1175-1181
60.
Faisca, P.F.N. and Plaxco,
K.W. (2006) “Cooperativity and the origins of rapid, single-exponential
kinetics in protein folding.” Prot. Sci., 15, 1608-1618
61.
Lubin, A.A, Lai, R.Y.,
Heeger, A.J. and Plaxco, K.W. (2006) “On the sequence specificity, selectivity
and reusability of E-DNA, a reagentless, electronic DNA sensor.” Anal. Chem., 78,
5671-5677
62.
Ruczinski, I., Sosnick, T.R.
and Plaxco, K.W. (2006) “Methods for the accurate estimation of confidence
intervals on experimental f values.” Prot.
Sci., 15, 2257-2264
63.
Xiao, Y, Lubin, A.A., Baker,
B.R., Plaxco, K.W. and Heeger, A.J. (2006) “Single-step
electronic detection of femtomolar DNA by target-induced strand displacement in
an electrode-bound duplex.” Proc.
Natl. Acad. Sci. USA, 103, 16677-16680
64.
Oh, K.J, Cash, K.J. and
Plaxco, K.W. (2006) “Excimer-based
peptide beacons; a convenient experimental approach for monitoring
polypeptide-protein and polypeptide-oligonucleotide interactions.” J. Am. Chem. Soc., 128,
14018-14019
65.
Seferos, D.S., Lai, R.Y.,
Plaxco, K.W. and Bazan, G.C. (2006) “a,w-Dithiol
oligo(phenylenevinylene)s for the preparation of high-quality conjugated SAMs
and nanoparticle functionalized electrodes.” Adv. Funct. Mat., 16, 2387–2392
66.
Lai, R.Y, Seferos, D.S.,
Heeger, A.J., Bazan, G.C. and Plaxco, K.W. (2006) “Comparison
of the signaling and stability of electrochemical DNA sensors fabricated from
6- or 11-carbon self-assembled monolayers.” Langmuir, 22, 10790-10800
67.
Xu, J., Plaxco, K.W. and
Allen, S.J. (2006) “The collective dynamics of lysozyme in water: terahertz
absorption spectroscopy and comparison with theory.” J. Phys. Chem,, 110, 24255-24259
2007
68.
Lai, R.Y., Plaxco, K.W. and
Heeger, A.J. (2007) “Rapid, aptamer-based electrochemical detection of
platelet-derived growth factor at picomolar concentrations directly in blood
serum.” Anal. Chem., 79, 229-233
69.
Xu, J., Plaxco, K.W., Allen,
S.J., Bjarnason, J.E. and Brown, E.R. (2007) “0.15 – 3.72 terahertz
absorption of aqueous salts and saline solutions.” J. Chem. Phys., 90, 031908
70.
Xiao, Y., Rowe, A.A. and
Plaxco, K.W. (2007) “Electrochemical detection of parts per billion lead via an
electrode-bound DNAzyme assembly.” J. Am.
Chem. Soc., 129, 262 – 263
71.
Plaxco, K.W. (2007) “A
biologist’s perspective on Astrobiology.” Guest essay in Universe, 8th Ed by Freedman, R.A and Kaufmann, W.J., W.H. Freeman & Company, New York,
NY, pp. 28-17
72.
Werner, J.H., McCarney,
E.R., Keller, R.A., Plaxco, K.W. and Goodwin, P.M. (2007) “Increasing the
resolution of single pair energy transfer measurements.” Anal. Chem., 79, 3509-3513
73.
Oh, K.J., Cash, K.J.,
Hugenberg, V. and Plaxco, K.W. (2007) “Peptide
beacons: A new design for polypeptide-based optical biosensors.” Bioconj. Chem., 18,
607-609
74.
Ricci, F., Lai, R.Y.,
Heeger, A.J., Plaxco, K.W. and Sumner, J.J. (2007) “Effect of molecular
crowding on the response of an electrochemical DNA sensor.” Langmuir, 23,
6827-6834
75.
Wang,
Z., Plaxco, K.W., and Makarov, D.E. (2007) “Influence of local, residual
structure on the scaling behavior and dimensions of unfolded proteins.” Biophys. J., 86,321-328
76.
Ricci, F., Lai, R.Y. and
Plaxco, K.W. (2007) “Linear, redox modified DNA probes as electrochemical DNA
sensors.” Chem. Comm., 3768-3770
77.
Xiao, Y., Qu, X., Plaxco,
K.W. and Heeger, A.J. (2007) “Label-free electrochemical detection of DNA in
blood serum via target-induced resolution of an electrode-bound DNA
pseudoknot.” J. Am. Chem. Soc., 129, 11896 - 11897
78.
Xiao, Y., Lai, R.Y., and Plaxco, K.W. (2007) “Preparation of
electrode-immobilized, redox-modified oligonucleotides for electrochemical DNA
and aptamer-based sensing.” Nature Prot., 2, 2875 - 2880
79.
Oh, K. J., Cash, K.J.,
Lubin, A.A. and Plaxco, K.W. (2007) “Chimeric peptide beacons: a direct
polypeptide analog of DNA molecular beacons.” Chem. Comm., 4869 - 4871
2008
80.
Xu, J., Plaxco, K.W. and Allen, S.J. (2008) “THz spectroscopy of
proteins in water: direct absorption and circular dichroism.” Int. J. High Speed Elec. Sys., 17, 709-718
81.
Lubin, A.A., Fan, C., Schafer, M., Clelland, C.T., Bancroft, C.,
Heeger, A.J. and Plaxco, K.W. (2008) “Rapid, electronic detection of DNA and
non-natural DNA analogs for molecular marking applications.” For. Sci. Comm., 10 (1)
82.
Pavlovic, E., Lai, R.Y., Wu,
T.T., Ferguson, B.S., Sun, R., Plaxco, K.W. and Soh, H.T. (2008) “Specific,
electrochemical detection of multiple DNA sequences in an integrated
microfluidic system.” Anal. Chem., 24, 1102 –
1107
83.
Pavel, I., McCarney, E.,
Elkhaled, A., Morrill, A., Plaxco, K. and Moskivits, M. (2008) “Label-free SERS
detection of small proteins modified to act as bifunctional linkers.” J. Phys. Chem., 112, pp
4880 - 4883
84.
White, R.J., Phares, N.,
Lubin, A.A. Xiao, Y. and Plaxco, K.W. (2008) “Optimization of electrochemical aptamer-based
sensors by controlling surface probe densities and surface attachment
chemistry.” Langmuir, 24, 10513–10518
85.
Ricci, F. and
Plaxco, K.W. (2008) “E-DNA: a convenient, label-free method for the
electrochemical detection of hybridization.” Microchim. Acta, 163,
149-155
2009
86.
Ruczinski, I. and Plaxco,
K.W. (2009) “Some recommendations for the practitioner to improve the precision
of experimentally determined protein folding rates and f values.” Proteins, Struc. Func. Genet., 74, 461-474
87.
Plaxco, K.W. and Gross, M.
(2008) “Protein complexes: The evolution of symmetry.” Curr. Biol., 19, R25-26
88.
Cash, K.J., Heeger, A.J.,
Plaxco, K.W. and Xiao, Y. (2008) “Optimization of a reusable, DNA pseudoknot-based
electrochemical sensor for sequence-specific DNA detection in blood serum.” Anal. Chem., 81, 656-661
89.
Plaxco, K.W. (2008) “At the
heart of the matter: Chemistry and the origins of life.” Chem. World, In press.
90.
Xiao, Y. and Plaxco, K.W.
(2008) “Electrochemical aptamer
sensors.” in: Functional nucleic acids for sensing and other analytical
applications, Y. Lu and Y. Li, Eds. Kluwer/Springer. In press.
91.
Phares, N., White, R.J. and
Plaxco, K.W. (2008) “Improving the stability and sensing of electrochemical
biosensors by employing trithiol-anchoring groups in a six-carbon
self-assembled monolayer.” Anal. Chem., In press.
92.
Ricci, F., Bonham, A.J.,
Reich, N.O. and Plaxco, K.W. (2008) “A reagentless, electrochemical approach
for the specific detection of double- and single-stranded DNA binding
proteins.” Anal. Chem., In press.
93.
Lubin, A.A., Vander Stoep Hunt, B. and
Plaxco, K.W. (2008) “The effects of
probe length, probe geometry and redox-tag placement on the performance of the
electrochemical E-DNA sensor .” Anal.
Chem., In press.
94.
Oh, K.J., Cash, K.J. and
Plaxco, K.W. (2008) “Beyond Molecular Beacons: optical sensors based on the binding-induced
folding of proteins and polypeptides.” Chem.
Europ. J., In press.
95.
Swenson, J.S., Xiao, Y.,
Ferguson, B.S., Lai, R.Y., Heeger, A.J., Plaxco, K.W. and Soh, T. (2008)
“Continuous, real-time monitoring of cocaine in undiluted, unmodified blood
serum via a microfluidic, aptamer-based sensor.” J. Am. Chem. Soc., In press.
96.
Xiao, Y., Uzawa, T., White, R.J., DeMartini, D. and
Plaxco, K.W. (2009) “On the signaling of electrochemical, aptamer-based
sensors: collision- and folding-based mechanisms.” Electroanalysis, Submitted.
97.
Ricci, F., Zari, N., Caprio,
F., Recine, S., Amine, A., Moscone, D., Palleschi, G. and Plaxco, K.W. (2009)
“Surface chemistry effects on the performance of an electrochemical DNA
sensor.” Bioelectrochemistry, Submitted.
Books:
1.
Plaxco, K.W. and Gross, M. (2006) Astrobiology; A Brief Introduction Johns Hopkins University Press.
2.
Plaxco, K.W. and Gross, M. (2009) Astrobiology; A Brief
Introduction, 2nd Edition Johns Hopkins University Press, In
press.
Patents:
1.
Plaxco, K.W. and Kayyem, J.F. “Biosensors utilizing ligand-induced
conformation changes.” US Patent 6432723 Awarded 8/13/2003
2.
Fan, C., Heeger, A.J. and Plaxco, K.W. “Electronic-DNA sensors and DNA
authentication.” Pending,
submitted 2003
3.
Xiao, Y., Lubin, A., Plaxco, K.W. “A signal-on architecture for
electronic, oligonucleotide-based sensors via target-induced strand
displacement.” Pending, submitted 2005
4.
Kash, K.J., Ricci, F. and Plaxco, K.W. “Devices and methods for
electrochemical detection of molecules.” Pending, submitted 2009
Invited
Seminar Presentations:
1998
1.
“The Determinants of Protein Folding Kinetics.” Department of Chemistry
and Biochemistry, UCSC, Santa Cruz, CA 05/22/98
2.
“The Determinants of Protein Folding Kinetics.” Department of
Pharmaceutical Chemistry, UCSF, San Francisco, CA 05/23/98
1999
3.
“The Determinants of Protein Folding Kinetics.” Department of
Biochemistry, Tulane University, New Orleans, LA, 3/10/99
4.
“The Determinants of Protein Folding Kinetics.” Department of
Chemistry, University of Arkansas, Fayettville, AK, 3/11/99
5.
“The Determinants of Protein Folding Kinetics.” Department of
Chemistry, Stanford University, Stanford, CA, 5/10/99
6.
“The Determinants of Protein Folding Kinetics.” Oxford Centre for
Molecular Sciences, Oxford University, Oxford, England, 10/1/99
2000
7.
“Protein Folding Kinetics.” Buroughs Welcome Quantitative Challenges
Symposium, San Diego, CA, 1/6/00
8.
“The Determinants of Protein Folding Kinetics.” Department of Physics
and Astronomy, Cal State Northridge, Northridge, CA, 1/15/00
9.
“Proteins as materials.” Material Outreach Program, UCSB, 2/29/00
10.
“The Determinants of Protein
Folding Kinetics.” Biosciences Division, Los Alamos National Laboratory, Los
Alamos, NM, 3/13/00
11.
“Protein folding made
simple(r).” Institute for Theoretical Physics, UCSB, 11/08/00
12.
“Theory and experiment meet
in the folding of the simplest proteins.” First Experimentalist’s Seminar in
Blue Gene Seminar Series, IBM, Yorktown, New York, 07/23/00
13.
“Theory and experiment meet…” Department of Biophysics, Johns
Hopkins University, Baltimore, MD, 11/28/00
2001
14.
“Folding-based sensors and
materials”, Material Outreach Program, UCSB, 2/1/1
15.
“Theory and experiment meet
…” IBM Blue Gene folding workshop, San Diego, CA, 3/30/1
16.
“Theory and experiment
meet…” International Center for Theoretical Physics, Trieste, Italy, 6/19/1
17.
“Protein folding made
simple(r).” Department of Biochemistry, University di Firenze, Florence, Italy,
6/26/1
18.
“Theory and experiment
meet...” Department of Molecular, Cell and Developmental Biology, UCSB, 10/11/1
2002
19.
“From theory to experiment
to application in protein folding kinetics.” Materials Outreach Program, UCSB,
2/6/2
20.
“Theory, experiment and the
folding of the simplest proteins.” Department of Biochemistry, Texas South West
Medical Center, Dallas, TX, 3/5/2
21.
“Theory, experiment and the
folding of the simplest proteins.” Department of Chemistry, University of
Texas, Austin, TX, 3/7/2
22.
“Theory, experiment and the
folding of the simplest proteins.” Inaugural seminar in new, Biochemistry and
Bioengineering joint series, Departments of Bioengineering and Biochemistry,
Washington University Saint Louis, St. Louis, MO, 13/3/2
23.
“Theory, experiment and the
folding of the simplest proteins.” American Physical Society Fall Meeting,
Indianapolis, IN, 3/21/2
24.
“Theory, experiment and the
folding of the simplest proteins.” Department of Chemistry, UC Irvine, Irvine,
CA, 4/14/2
25.
“Protein folding made
simple(r).” Department of Chemistry, Pomona Colleges, Claremont CA, 4/16/2
26.
“Protein folding made
simple(r).” Department of Chemistry, Cal State Long Beach, Long Beach CA,
4/17/2
27.
“My protein folds faster
than yours; a simple theory of protein folding kinetics.” Institute for
Theoretical Physics, UCSB, 6/13/2
28.
“Protein folding: theory and
application.” So. Cal. Nanotriangle Meeting, Marina Del Ray, CA, 7/9/2
29.
“My protein folds faster
than yours: testing theories of relative folding rates.” Departments of
Chemistry and Molecular Biology and Biochemistry, UC Berkeley 9/24/2
30.
“My protein folds faster
than yours…” Institute for Protein Research, Russian Academy of Sciences,
Puschino, Russia, 10/2/2
31.
“My protein folds faster than
yours…” Polish Academy of Sciences and University of Warsaw, Warsaw, Poland,
10/4/2
32.
“The theory and application
of a nanoscale self-assembly process (A.K.A. Protein folding).” Centrum fur
NanoScience Workshop, Munich, Germany, 10/7/2
33.
“My protein folds faster
than yours…” Department of Chemistry, University of Frankfurt, Frankfurt,
Germany, 10/9/2
34.
“My protein folds faster
than yours…” Department of Chemical Biology, The Scripps Research Institute, La
Jolla, CA, 10/24/2
35.
“My protein folds faster
than yours…” Molecular Biology Institute, UCLA, Los Angeles, CA, 11/14/2
36.
“My protein folds faster
than yours…” Department of Biochemistry, University of Chicago, Chicago IL,
11/20/2
37.
“My protein folds faster
than yours…” PENCE Seminar, University of Toronto, Toronto, ON Canada 11/21/2
38.
“Terahertz circular
dichroism as an unbiased, in situ life detection technology.” American Geophysical Society Fall Meeting, San
Francisco, CA, 12/07/2
2003
39.
“My protein folds faster
than yours...” Department of Chemistry, UConn, Storrs, CT 2/26/3
40.
“My protein folds faster
than yours…” Department of Chemistry, UPenn, Philadelphia, PA 2/27/3
41.
“Why is protein folding so
slow?” Hopkins Folding Meeting, Berkeley Springs, W.V. 3/23/3
42.
“Protein folding from theory
to experiment to application.” (Instructor)
NATO ASI Workshop on Topological Effects in Soft Condensed Matter, Geilo,
Norway 3/28/3
43.
“The topomer search model of
protein folding.” American Physiology Society, San Diego, CA 4/13/3
44.
“My protein folds faster
than yours...” Department of Chemistry and Biochemistry, UCSB, Santa Barbara,
CA 4/21/3
45.
“My protein folds faster
than yours…” Department of Physics, UCLA, Los Angeles, CA 5/9/3
46.
“Why is protein folding so
slow?” CECAM Protein Folding Workshop, Ecole Normale
Superieure de Lyon, Lyon, France 9/10/3
47.
“My protein folds faster
than yours...” Department of Crystallography, Birkbeck College, University of
London, London UK 9/8/3
48.
“My protein folds faster
than yours...” Department of Chemistry, Cambridge University, Cambridge, UK
9/15/3
49.
“My protein folds faster than yours…” Department of Physics,
Leeds University, Leeds UK 9/18/3
50.
“My protein folds faster
than yours...” Department of Chemistry, Cal State LA, 10/7/3
50.
“My protein folds faster
than yours...” Interdepartmental Structural Biology Seminar, University of
Florida, 10/20/3
51.
“My protein folds faster than yours…” Department of
Chemistry, Cal Poly San Louis Obisbo, 11/6/3
52.
“My protein folds faster
than yours...” Interdepartmental Biophysics Seminar, Department of Applied and
Engineering Physics, Cornell University, Ithaca, NY 11/19/3
53.
“My protein folds faster
than yours…” Department of Chemistry, SUNY Stony Brooke, Stony Brooke, NY
11/21/3
54.
“My protein folds faster
than yours...” Department of Chemistry, University of Delaware, 11/24/3
2004
55.
“Better living through
biosensors.” CNSI Brown Bag Lunch Seminar, UCSB, 1/8/4
56.
“Spectroscopy, scattering
and simulations; putting constraints on residual denatured state structure.”
Computational Aspects of Biomolecular NMR Gordon Research Conference, Ventura
CA 1/22/4
57.
“Metals in folding.” Session
chair/introduction, Metals in Biology Gordon Research Conference, Ventura CA
1/20/4
58.
“Better Living through
Biosensors.” California NanoSystems Institute Seminar Series, UCLA 2/3/4
59.
“My protein folds faster
than yours…” Department of Chemistry, USC 2/9/4
60.
“My protein folds faster
than yours…” Basic Science Division, Fred Hutchinson Cancer Research Center,
Seattle, WA 2/17/4
61.
“Cooperativity and the
predictability of protein folding rates.” ACS Meeting, Anaheim, CA 4/1/4
62.
“The direct, electronic
detection of DNA” Panel discussion as part of “Advance Sensor Technologies”
outreach program US-Asia Technology Management Center, Stanford University
4/8/4
63.
“Better living through
biosensors.” Physical Chemistry Seminar, Department of Chemistry and
Biochemistry, UCSB 4/12/4
64.
“My protein folds faster
than yours…” Department of Chemistry and Biochemistry, UCSC 4/28/4
65.
“My protein folds faster
than yours…” Institute for Pure and Applied Mathematics, UCLA 5/6/4
66.
“Reconciling the behavior of
simple toy models with that of real proteins.” Workshop on Structure and
Function of Biomolecules, Bedlewo, Poland 5/14/4
67.
“Better living through biosensors.” Bioengineering Graduate
Program, UCSF 5/27/4
68.
“My protein folds faster
than yours…” Chemical Physics Seminar, Caltech 6/2/4
69.
“Does your protein fold fast
enough?” Amgen Award Lecture, Society for Industrial Microbiology Annual
Meeting, Anaheim, California 7/27/4
70.
“On the predictability of
protein folding rates.” FEBS Summer Conference “Folding in the Cell,” Vermont
8/4/4
71.
“My protein folds faster
than yours…” Leloir Institute, University of Buenos Aires, Buenos Aires
Argentina 9/4/4
72.
“Does your protein fold fast
enough?” Amgen, Inc. Thousand Oaks, CA 9/9/4
73.
“Better living through biosensors.” Department of Chemistry,
Georgia State University, Atlanta, GA 10/22/4
74.
“My protein folds faster
than yours…” Department of Biochemistry, UNC, Chapel Hill, NC 10/26/4
75.
My protein folds faster than
yours…” Department of Biochemistry, Rice University, Houston, TX 11/15/4
76.
“Better living through
biosensors.” DakoCytomation, Inc., Camarillo, CA 11/30/4
77.
“Why is protein folding so
slow?” Department of Chemistry and Biochemistry, UCSD, San Diego, CA 12/2/4
78.
“Better living through
Biosensors” Center for Theoretical Biophysics, UCSD, San Diego, CA 12/3/4
79.
“A biologist’s true
confession: proteins are polymers after all.” Workshop
of the Center of Protein Folding Machinery, Stanford University, Stanford, CA
12/4/4
2005
80.
“Better living through
biosensors.” Department of Biomolecular Engineering, UCSC, Santa Cruz
3/1/5
81.
“Unraveling the denatured
state.” TSRC Workshop on Protein Dynamics, Telluride, CO 2/8/5
82.
“Better Living Through
Biosensors.” International Summer School on Biomaterials, UCSB, 10/9/5
83.
“My protein folds faster
than yours: an experimentalist’s view of protein-folding theory.” Genencore,
Inc., San Francisco, CA 8/19/5
84.
“Better living through biosensors.” CALPACS Fall Luncheon,
Buelton, CA 1/10/5
85.
“A biologist’s true confession: proteins are polymers after
all.” U. Iowa, Ames, IA 17/10/5
86.
“Better living through
biosensors.” Chemistry Department Colloquium, Stanford University, 27/10/5
87.
“Better living through
biosensors.” Materials Department Colloquium, UCSB, 17/11/5
2006
88.
“Looking for the landscape.” Session Chair, Protein Folding
Gordon Research Conference, Ventura, CA 12/1/6
89.
“Better living through
biosensors” Lawrence Livermore National Laboratory, 1/24/6
90.
“From playing with toys to
predicting protein folding rates.” Keystone Symposium: Frontiers in Structural
Biology, Keystone, CO 3/2/6
91.
“Better living through
biosensors.” Somalogic, Inc. Boulder CO 3/9/6
92.
“My protein folds faster
than yours; theory and experiment in protein folding.” Keynote Address,
Southern Symposium on Computational Chemistry, Jackson, MI 4/8/6
93.
“Better living through
biosensors.” Bio-Engineering/Chemistry joint seminar, Rice University, Houston,
TX 4/20/6
94.
“How I hope to save the
world (and make a million bucks) through folding.” Keynote Address, Texas
Folders Meeting, Camp Allen, TX 4/21/6
95.
“Terahertz absorption spectroscopy:
a direct experimental probe of global and sub-global collective modes.”
Steenbock Symposium, U. Wisconsin, Madison WI 5/18/6
96.
“Biosensors and
nano-medicine; the future is looking very, very
small.” Introductory Address, 12th German-American Frontiers of
Science Symposium. Potsdam, Germany 21/6/6
97.
“My protein
folds faster than yours: an experimentalist’s view of protein folding theory.”
Max Plank Institute, Postdam, Germany 23/6/6
98.
“Folding-based biosensors.” Asia-Pacific Workshop on
Biological Physics, Singapore, 5/7/6
99.
“Better living through
biosensors.” Escola Tècnica Superior d’Enginyeria,
Universitat Rovira i Virgili, Tarragona) 9/15/6
100.
“The nature of chemically- and physiologically-unfolded states.” CECAM
Protein Folding Workshop, Lyon, France 9/20/6
101.
“My protein folds faster.” PSTAT seminar, Department of Statistics and
Applied Probability, UCSB 10/4/6
102.
“Better living through Biosensors.” Department of Chemistry, University
of Utah, Salt Lake City 10/16/6
103.
“Better living through Biosensors.” External speaker, Biophysics/Physics biannual joint seminar,
Johns Hopkins University, Baltimore, MD. 11/13/6
104.
“Predetermination, randomness and the nature of the unfolded state.”
Rice Computational Biology Workshop, Houston, TX 12/16/6
2007
105.
“Better living through Biosensors.” Mech. E. Colloquium, UCSB 1/8/7
106.
“Better living through Biosensors.” Santa Barbara Science &
Engineering Council, 1/11/7
107.
“Folding-based
Biosensors.” Gordon Research
Conference on Electrochemistry, Ventura, CA 1/20/7
108.
“Better living through biosensors.” Department of Biochemistry, U.
Wisconsin, Madison 1/23/7
109.
“Folding-based electronic biosensors.” CNSI Brown Bag Lunch Seminar,
CNSI, UCSB 2/8/7
110.
“Folding-based biosensors for pathogen and small molecule detection.”
USAMRIID, Fort Detrick, MD, 2/18/7
111.
“Better living through biosensors.” Department of Bioengineering,
Washington University St. Louis, MI 2/23/7
112.
“Better living through Biosensors.” Chemistry Division, Los Alamos
Natl. Lab., Los Alamos, NM 6/13/7
113.
“Unwraveling the unfolded state.” Protein Society Annual Meeting,
Boston, MA 7/22/7
114.
“Better living through biosensors.” Chemical Engineering, UC Berkeley, Berkeley CA 8/29/7
115.
“Better living through biosensors.” Department of Physics,
Ohio State University, Columbus, OH 9/25/7
116.
“Better living through biosensors.” Plenary lecture, Third
International Workshop on Biosensors for Food Safety and Environmental
Monitoring, Fez, Morocco 10/20/7
117.
“Biosensors for affordable molecular diagnostics and
environmental monitoring.” Kwame Nkrumah University of Science and Technology,
Kumasi, Ghana 11/14/7
118.
“Biosensors for affordable molecular diagnostics and
environmental monitoring.” Noguchi Memorial Institute for Medical Research,
University of Ghana, Legon, Ghana 11/28/7
2008
119.
“Better living through biosensors.” Department of Chemistry, Georgia
State University, Atlanta, GA, 2/18/8
120.
“Better living through biosensors.” Center for the Study of
Systems Biology, Georgia Tech, Atlanta, GA 2/19/8
121.
“Is the ‘God’ hypothesis a unique theory of apparent
‘miracles’?” Veritas Forum, UCSB, 2/20/8
122.
“Signal transduction across the biology/technology
interface.” Symposium Organizer, Materials Research Society March meeting, San
Francisco, CA 3/24-27/8
123.
“Better living through biosensors.” Department of
Chemistry, U of I Urbana-Champaign, 4/24/8
124.
“Better living through biosensors.” Department of
Chemistry, UNLV, Las Vegas, NV 5/16/8
125.
“Better living through biosensors.” Dipartimento di Scienze e
Tecnologie Chimiche; Università di Roma Tor Vergata 6/14/8
126.
“Reagenteless, electrochemical aptasensors for real-time threat
detection.” Edgewood Chemical and Biological Center, Aberdeen Proving Ground,
MD 7/29/8
127.
“Reagenteless, electrochemical aptasensors for real-time threat
detection.” Army Research Laboratory, Adelphi, MD 7/30/8
128.
“Terahertz spectroscopy: a new experimental probe of
biomolecular dynamics.” ACS Fall Meeting, Philadelphia, PA 8/17/8
129.
“Better living through biosensors.” Department of Chemistry, Cal State
Northridge, Northridge CA 10/9/8
130.
“Better living through biosensors.” Department of Chemistry, Penn
State, University Park, PA 11/19/8
131.
“Better living through biosensors.” Department of Biochemistry,
University of Arizona, Tucson, AZ 11/21/8
2009
Former PhD students, thesis titles and defense dates:
1.
Miguel A. de los Rios
“Snapshots of the Folding Transition State.” 5/9/5
2.
Evan McCarney “Single
Molecule Studies of the Unfolded State.” 6/4/5
3.
Jonathan E. Kohn “The
Physics and Applications of Unfolded Proteins.” 12/10/5
4.
Jing Xu (co-advisor with S.
James Allen) “Terahertz Collective Dynamics of Biopolymers.” 7/25/6
5.
Kenneth J. Oh “Peptide
Beacons: a General, Polypeptide-based Sensing Platform.” 9/21/7
Sabbatical
visitors:
1.
Prof. Dr. rer. nat. Winfried Boos, Microbiology, University
of Konstanz; Spring 2003
2.
Prof. Ingo
Ruczinski, Department of Biostatistics, Johns Hopkins University; Winter 2006
3.
Prof. Xiaogang
Qu, Chinese Academy of Sciences; Winter 2007
4.
Prof. Dimitri
Makarov, Department of Chemistry, U.T. Austin; Summer and Winter 2008
Consultant, Clinical Microsensors, Inc. (1999-2002)
Instructor, NATO Workshop on Soft Condensed Matter Physics, Geilo, Norway (March ’03)
International Advisory Committee, Newton School in Physics, Cambridge, UK (Winter ’04)
Advisory Committee, Polish Academy of Sciences-European Physical Society Workshop Structure and Function in Biomolecules, Bedlewo, Poland (May ’04)
Editorial Member, Faculty of 1000 (2002-2005)
Editorial Advisory Board Protein Science (2005-)
Session organizer, Materials Research Society Spring Symposium (March ’08)
Ad hoc panelist
(multiple panels) on MSF-B (Macromolecular
Structure and Function B) and ISD (Instrument and Systems Design) NIH study
sections
Reviewer/site visitor/panelist for NIH, UCBioSTAR, SSRL, NSF, ACS, ASF, DOE
Regular reviewer for: Science,
Nature, PNAS, Nat. Struc. Bio., JMB, Biochemistry, JACS, JCP, Phys. Rev. Let.,
Proteins, Prot. Sci., Langmuir, Collection of Czechoslovak Chemical
Communications, Nuc. Acid Res., Bioinorg. Chem., Anal. Chem.
Chem 147: Astrobiology and the origins of life
Chem 142: Biochemistry