John Sumida has over 10 years of experience using biophysical techniques like CD, DSC, fluorescence spectroscopy, and chromatography to characterize proteins. He established a biophysical core facility and has experience managing research labs, supervising staff, and mentoring students. His research has characterized flexibility in tropomyosin important for muscle regulation using techniques like limited proteolysis and fluorescence.

1. John Sumida, Ph.D. Chemistry Biophysics/Spectroscopy/ Protein Chemistry
E-mail: sumida@bbri.org or jpsumida@comcast.net Cell: 617-877-3002
Summary: I have 10+ years of experience in biophysical characterization of proteins and their
biochemistry using a variety of techniques: CD, DSC, TR-FRET, steady state
fluorescence, UV/vis spectroscopy, recombinant protein expression, protein purification,
FPLC, N-terminal amino acid analysis, , MALDI, chemical cross-linking, and
fluorescent labeling of proteins.
Accomplishments:
• Established a new Biophysical Core and Cost Facility at the University of Washington.
• Characterized a new dynamic region in the middle of tropomyosin that is important in muscle
regulation and may have more general implications in muscle related diseases.
• Presented a platform presentation at the 2008 Biophysical Meeting, entitled “Conserved
Destabilization of Tropomyosin at Asp 137: Functional Significance of Flexibility.”
• Poster award for best poster at the 2008 Myofilament Meeting
• Quantitative determination of N-terminal sequences from a mixture of proteolytic fragments.
• Promotion to Research Associate in 2007.
• First author JBC paper: “Conserved Asp-137 Imparts Flexibility to Tropomyosin and Affects
Function”
• First author J. Phys Chem paper: "Contrasting Photoinduced Electron Transfer Properties of Two
Closely Related Rigidly-Linked Porphyrin-Quinone Dyads,"
• First characterization of the photophysical properties of a buckminster fullerene: "Preparation and
Photophysical Studies of Porphyrin-C60 Dyads,"
Professional Work Experience
University of Washington Bioanalytical Pharmacy Core, (2010-current)
Biophysical Core Facility Manager.
Responsibilities:
1. act as point of contact for industry and academic scientists interested in performing biophysical
measurements within the core.
2. Supervise two facility staff scientists.
3. establish accounting procedures that enable use of the facility by both industry and academic users
4. manage a budget, generate quarterly reports, hire staff
5. create and manage a website for the facility
6. consult with users about various biophysical approaches available within the core and assist them in
developing analytical methods suitable for their objectives. The Biophysical Core provides instrumental
expertise in DSC, ITC, SPR, and AUC. For more information see the link to the website:
http://depts.washington.edu/cidb4bio/index.shtml
7. provide training and workshops to graduate students, post-docs and visiting scientists
8. handle all the day to day instrument scheduling, maintenance, and procurement for the lab.
9. Facilitate a monthly biophysics user group meeting open to both industry and academic scientists.

2. Boston University, (2009-current)
Position: Research Assistant
Molecular dynamics simulations of tropomyosin using CHARMM, calculation of dynamic and static
persistence lengths of a series of tropomyosin fragments to quantitate flexibility.
Boston Biomedical Research Institute, (2002-2009).
Position: Research Associate.
The research objective at BBRI was to address a central and persistent problem in our understanding of how the
muscle thin filament is physically able to modulate the regulatory states of the muscle system. The following
techniques were used to identify a new flexible region in Tm which affects its conformational dynamics, and
regulatory function:
• Limited proteolysis,
• CD,
• DSC,
• UV/vis spectroscopy,
• cosedimentation analyses and
• ATPase kinetics
• Time resolved fluorescence (time domain)
This work is published in JBC (see below).
This position at BBRI also involves the review of outside scientific work being considered for publication. Peer
review was provided for:
• Journal of Molecular Biology,
• Journal of Biological Chemistry,
• Proteins
The position at BBRI involves a significant amount of supervision and management of the laboratory’s day to
day function. These duties include
• supervision of technical assistants
• training of colleagues and visiting scientists
• mentorship of student interns on their research projects
• instructor in institute biophysics
Universities Space Research Assoc. /NASA Marshall Space Flight Center, (1999-2002).
Position: Staff Scientist (contractor). The research task at Marshall was to detect and characterize protein
nucleation in solution. The following techniques were used to correlate solution distances with the nearest
neighbor crystallographic distance:

3. • Fluorescence
• CD

4. Education
1993 - 1999, Ph.D. Chemistry, Arizona State University, Tempe, AZ
1990 - 1992, B.S. Biochemistry, Seattle University, Seattle, WA
1982 - 1988, B.A. Anthropology, Brown University, Providence, RI
Professional Associations:
Biophysical Society Member since 2001
AAAS Member since 2005
Biophysical Expertise
DSC • domain specific unfolding, Fluorescence • steady-state and time-resolved, (both
• determination of thermodynamic constants, frequency and time domain)
∆H, ∆G, ∆S, ∆Cp • TR-FRET intermolecular distances
• ∆∆G measurements to assess mutational and dynamics
effects on thermodynamics and structure • Stern Volmer quenching to assess
• Pressure perturbation calorimetry to site accessibility.
determine partial volume of unfolding and • Rotational anisotropy to detect
thermal expansion coeffiecient conformational changes
AUC • Sedimentation velocity using • Binding constants
o Interference • Synchronously scanned emission
o Absorption spectroscopy for the analysis of
o Fluorescence heterogeneous solutions
UV/vis • concentration determination,
CD • helix unfolding • determination of labeling
• near uv analysis for tertiary interactions efficiency,
• kinetic enzymatic analyses
SPR • Kinetics and equilibrium mode
affinity measurements using a
Biacrore T100
Standard Biochemical techniques
SDS-PAGE, N-terminal sequence analysis, Chemical modification of proteins, Proteolysis, MALDI-ToF Mass
Spec, cosedimentation analyses, bacterial expression and purification of recombinant proteins, FPLC
chromatography, IEX, SEC, HIC,
• recombinant protein expression
in bacterial cells
• protein purification
•
ion exchange, • coursework in AUC
•
hydrophobic interaction, mixed • synthetic boundary
mode (hydroxyapatite) measurements
• size exclusion chromatography
Chromatography • dynamic light scattering

5. Important Publications [citations]
1. “Conserved Asp-137 Imparts Flexibility to Tropomyosin and Affects Function.” Sumida, J.P., Wu, E., Lehrer,
S.S., J. Biol. Chem., 283, 6728-6734 (2008)
2. “Preparation and preliminary characterization of crystallizing fluorescent derivatives of chicken egg white
lysozyme,” J. P. Sumida, E. L. Forsythe, M. L. Pusey, J. Crystal Growth, 232, 308–316 (2001).
3. Pusey, Marc L; Sumida, John P. "Fluorescence of protein crystal nucleation" Proceedings of SPIE vol.4098,
Optical Devices and Diagnostics in Materials Science, ed. Andrews, David L.; Asakura, Toshimitsu; Jutamulia,
Suganda; Kirk, Wiley P.; Lagally, Max G.; Ravindra B.; Trolinger, James D. September 2000.
4. "Contrasting Photoinduced Electron Transfer Properties of Two Closely Related Rigidly-Linked Porphyrin-
Quinone Dyads," J. P. Sumida, P. A. Liddell, A. N. Macpherson, G. R. Seely, A. L. Moore, T. A. Moore and D.
Gust, J. Phys. Chem. A, 102, 5512-5519 (1998)
5. “Increasing the yield of photoinduced charge separation through parallel electron transfer pathways,” Maniga, N.I.,
Sumida, J.P., Stone, S., Moore, A.L., Moore, A.S., Gust, D., J. Porphyrins and Pthalocyanines, 3, 32-34, (1999)
6. "Photoinduced Charge Separation and Charge Recombination to a Triplet State in a Carotene-Porphyrin-Fullerene
Triad," P. A. Liddell, D. Kuciauskas, J. P. Sumida, B. Nash, D. Nguyen, A. L. Moore, T. A. Moore and D. Gust, J.
Am. Chem. Soc., 119, 1400-1405 (1997).
7. "Preparation and Photophysical Studies of Porphyrin-C60 Dyads," P. A. Liddell, J. P. Sumida, A. N. Macpherson,
L. Noss, G. R. Seely, K. N. Clark, A. L. Moore, T. A. Moore and D. Gust, Photochem. Photobiol. 60, 537 - 541
(1994).
8. “Solvent dependence of photoinduced electron transfer in porphyrin dyads,” DeGraziano J.M., Macpherson A.N.,
Liddell P.A., Noss L., Sumida J.P., Seely G.R., Lewis J.E., Moore A.L., Moore T.A., Gust D., New J. Chem., 20,
839-851, (1996)
Poster Presentations
47th annual Biophysical Society Meeting: poster presentation
J. P. Sumida, N. Kirkland, and M. Pusey. Molecular response of chicken egg white lysozyme to buffer, salt
concentration and pH.
49th annual Biophysical Society Meeting: poster presentation
J.P Sumida, K Langsetmo, S.S. Lehrer. Conserved Asp137 destabilizes tropomyosin: CD, DSC and pressure
perturbation measurements
50th annual Biophysical Society Meeting: poster presentation
J.P. Sumida, D. Hayes, K. Langsetmo, A. Hopping, S.S. Lehrer. Tropomyosin: Asp137→Leu Mutation Causes a
Loss of Actin Binding.
51st annual Biophysical Society Meeting: poster presentation
E.R. Wu, J.P. Sumida, S.S. Lehrer. Conserved Asp137 Locally Destabilizes Tropomyosin
Oral Presentations
53rd annual Biophysical Society Meeting: poster presentation
J.P. Sumida, E.R. Wu, S.S. Lehrer. Conserved Destabilization of Tropomyosin at Asp 137: Functional
Significance of Flexibility.
2008 Myofilament Meeting, (award talk).
John Sumida, Eleanor Wu, David Hayes, Knut Langsetmo, Sherwin Lehrer. Tropomyosin: native instability and
functional flexibility