Walter F. Stafford, III

Walter F. Stafford, III


Press on!
“Nothing in the world can take the place of persistence.
Talent will not; nothing is more common than unsuccessful men with talent.
Genius will not; unrewarded genius is almost a proverb.
Education will not; the world is full of educated derelicts.
Persistence and determination alone are omnipotent.
-Calvin Coolidge

Senior Scientist,
Director, Analytical Ultracentrifugation Research Laboratory, and
Director of Computer Science, Boston Biomedical Research Institute and
Associate, Department of Neurology, Harvard Medical School.
B.A., Lake Forest College, Chemistry, 1966
Ph.D., University of Connecticut, Biophysics, 1973


Protein physical chemistry. Interacting systems. Biothermodynamics. Hydrodynamics. Investigation of protein-protein interactions (PPI) and protein-nucleic acid interactions with particular emphasis on contractile proteins, DNA binding proteins, and antigen-antibody interactions using Analytical Ultracentrifugation, Circular Dichroism, and other biophysical techniques.


All living processes are mediated by interactions between different proteins or between proteins and other molecules or ions. For example, the expression of genes is regulated by binding of regulator proteins called transcription factors to DNA. The immune response is mediated by the interaction of the immunoglobin (antibody) protein with an antigen molecule. Many metabolic processes are regulated by the binding of small molecules to enzymes. Muscle contraction is mediated by interaction of calcium ions with regulatory proteins that in turn interact with the contractile proteins to initiate the production of contractile work. Understanding the nature of these interactions is central to understanding the chemical and physical processes that constitute life.

My main interests are in the application of physical methods to the study of dynamically reversible protein-protein interactions (PPI) and protein-nucleic acid interactions that are relevant to physiological function in normal and diseased states. Many interactions peculiar to disease states can be targets for drug therapy. I have been involved in a project called The National Cooperative Drug Discovery Group funded by the National Cancer Institute, in which we are engineering single chain antibodies to breast cancer cells. These antibody molecules are being used as vehicles for the targeted delivery of therapeutic agents to kill breast cancer cells.

The engineered antibody proteins are produced by using techniques of molecular biology to produce antibody molecules with the desired reactivity and properties. A very important step in designing protein molecules is the assessment of their properties in solution and their strength of binding to unique molecules found on the surface of breast cancer cells. The physical methods of analytical ultracentrifugation are being applied to the analysis of the strength of binding of the antibody molecules after changes are engineered into them. New highly sensitive techniques for the analytical ultracentrifuge have been developed in my lab at BBRI and are being applied to these and other problems.


Liu, H., W. F. Stafford and M. Bouvier (2005). “The endoplasmic reticulum lumenal domain of the adenovirus type 2 E3-19K protein binds to peptide-filled and peptide-deficient HLA-A*1101 molecules.” J Virol 79(21): 13317-25.
Knight, P. J., K. Thirumurugan, Y. Xu, F. Wang, A. P. Kalverda, W. F. Stafford, 3rd, J. R. Sellers and M. Peckham (2005). “The predicted coiled-coil domain of myosin 10 forms a novel elongated domain that lengthens the head.” J Biol Chem 280(41): 34702-8.
Mukhopadhyay, S., K. Langsetmo, W. F. Stafford, 3rd, G. D. Henry, J. D. Baleja and S. Sarkar (2005). “Identification of a region of fast skeletal troponin T required for stabilization of the coiled-coil formation with troponin I.” J Biol Chem 280(1): 538-47.
Stafford, W. F., M. L. Walker, J. A. Trinick and L. M. Coluccio (2005). “Mammalian class I myosin, Myo1b, is monomeric and cross-links actin filaments as determined by hydrodynamic studies and electron microscopy.” Biophys J 88(1): 384-91.
Gelinas AD, Toth J, Bethoney KA, Stafford WF and CJ Harrison. (2004) Mutational analysis of the energetics of the GrpE.DnaK binding interface: equilibrium association constants by sedimentation velocity analytical ultracentrifugation. J Mol Biol, 339(2), 447-58.
Eva-Maria Frickel, Patrick Frei, Marlene Bouvier, Walter F. Stafford, Ari Helenius, Rudi Glockshuber and Lars Ellgaard,(2004) “ERp57 is a multifunctional thiol-disulfide oxidoreductase”, J. Biol. Chem. Feb 10
Stafford, W. F. and P. J. Sherwood (2004). “Analysis of heterologous interacting systems by sedimentation velocity: Curve fitting algorithms for estimation of sedimentation coefficients, equilibrium and rate constants.” Biophysical Chemistry,108,231-243.
Stafford, W. F. and E. H. Braswell (2004). “Sedimentation Velocity, Multi-speed Method for Analyzing Polydisperse Solutions.” Biophysical Chemistry,108,273-279.
Sontag, C. A., W. F. Stafford, and J. J. Correia (2004). “A Comparison of Weight Average and Direct Boundary Fitting of Sedimentation Velocity Data for Indefinite Polymerizing Systems.” Biophysical Chemistry, 108, 215-230
Wang F, Thirumurugan K, Stafford WF, Hammer JA 3rd, Knight PJ, Sellers JR. (2003) “Regulated conformation of Myosin V.” J Biol Chem. Nov 22 [Epub ahead of print]
D. G. Myszka, Y. N. Abdiche, F. Arisaka, O. Byron, E. Eisenstein, P. Hensley, J. A. Thomson, C. R. Lombardo, F. Schwarz, W. Stafford, and M. L. Doyle (2003) “The ABRF-MIRG’02 Study: Assembly State, Thermodynamic, and Kinetic Analysis of an Enzyme/Inhibitor Interaction.” Journal of Biomolecular Techniques 14:247-269.
Stafford, W.F. (2003) “Analytical Ultracentrifugation. Sedimentation Velocity Analysis” Current Protocols in Protein Science. 20.7.1-20.7.11, John Wiley & Sons.
Gelinas, A. D., J. Toth, K. A. Bethoney, K. Langsetmo, W. F. Stafford, and C.J. Harrison (2003). “Thermodynamic linkage in the GrpE nucleotide exchange factor, a molecular thermosensor.” Biochemistry 47(30): 9050-9.
Nyitrai, M., W. F. Stafford, et al. (2003). “Ionic interactions play a role in the regulatory mechanism of scallop heavy meromyosin.” Biophys J 85(2): 1053-62.
Terrak, M., Wu, G., Stafford, W.F., Lu, R.C. and Dominguez, R. (2003) “Two distinct myosin light chain structures are induced by specific variations within the bound IQ motifs – functional implications.” EMBO J., 22, 1-10.
Mingnan Chen, Walter F. Stafford, Gundo Diedrich,| Amir Khan, and Marlene Bouvier (2002) “A Characterization of the Lumenal Region of Human Tapasin Reveals the Presence of Two Structural Domains.” Biochemistry, 41, 14539-14545.
Tetsuya Mori, Sergei V. Saveliev, Yao Xu, Walter F. Stafford, Michael M. Cox, Ross B. Inman, Carl H. Johnson (2002) “Circadian Clock Protein KaiC forms ATP-dependent Hexameric Rings and Binds DNA” Proc.Nat.Acad.Sci. 99, 17203-17208.
Gelinas, A.D., K. Langsetmo, J. Toth, K.A. Bethony, W.F. Stafford, C.J. Harrison (2002) “A structure based interpretation of E. coli GrpE Thermodynamic properties.” J. Mol. Biol. 323,131-142.
Waller, G., W. Stafford, H. Tsuruta, and P. Matsudaira (2002). “Calmodulin acts as a calcium-dependent latch on scruin domains.” Biophys. J 82(1): 1861-.
Langsetmo, K., W. Stafford and T. Tao (2002). “Interactions between the coiled coil regions of the small and targeting subunits of smooth muscle myosin light chain phosphatase.” Biophys. J 82(1): 1736-.
W.F. Stafford, M.P. Jacobsen, J. Woodhead, R. Craig, E. 0’Neall-Hennessey and A.G. Szent-Gy�rgyi,(2001), “Calcium-dependent Structural Changes in Scallop Heavy Meromyosin.”, J. Mol. Biol. 307, 137-147.
Li, Z., W. F. Stafford, and M. Bouvier (2001).” The metal ion binding properties of calreticulin modulate its conformational flexibility and thermal stability.” Biochemistry 40(37):11193-201.
Langsetmo, K., W. F. Stafford, K. Mabuchi, and T. Tao (2001). “Recombinant small subunit of smooth muscle myosin light chain phosphatase. Molecular properties and interactions with the targeting subunit”. J Biol Chem 276(36): 34318-322.
Stafford, W. F. (2000). “Analysis of reversibly interacting macromolecular systems by time derivative sedimentation velocity.” Methods Enzymol 323, 302-325.
Bouvier, M. and W. F. Stafford (2000). “Probing the three-dimensional structure of human calreticulin.” Biochemistry 39(48): 14950-9.
Doyle, M.L., Brigham-Burke, M., Brooks, I.S., Blackburn, M.N., Smith, T.M., Sokoloski, T., Newman, R., Reff, M., Stafford, W.F., Sweet, R.M., Truneh, A., Hensley, P., and O’Shannessy, D.J. ,(2000) “Measurement of Protein Interaction Bioenergetics: Application to Structural Variants of Anti-sCD4 Antibody.”, Methods in Enzymology.323, 207-230.
Laue, T. M. and W. F. Stafford (1999). “Modern applications of analytical ultracentrifugation.” Annu Rev Biophys Biomol Struct 28: 75-100.
Leinweber, B., Tang, J. X., Stafford, W. F., and Chalovich, J. M.(1999). Calponin interaction with alpha-actinin-actin: Evidence for a structural role for calponin, Biophysical Journal, 77, 3208-3217 .
Margossian, S. S., Anderson, P. A. W., Chantler, P. D., Deziel, M., Umeda, P. K., Patel, H., Stafford, W. F., Norton, P., Malhotra, A., Yang, F., Caulfield, J. B., and Slayter, H. S.(1999)” Calcium regulation in the human myocardium affected by dilated cardiomyopathy: A structural basis for impaired Ca2+- sensitivity.” Molecular and Cellular Biochemistry, 194, 301-313.
Rivas, G., W. F. Stafford, and A.P. Minton (1999). “Characterization of Heterologous Protein-Protein Interaction via Analytical Ultracentrifugation.” Methods: A Companion to Methods in Enzymology. 19,194-212.
Stafford, W. F. (1998). “Time Difference Sedimentation Velocity Analysis of Rapidly Reversible Interacting Systems: determination of equilibrium constants by non-linear curve fitting procedures.� Bioph. J. 74: 301.
Kordowska, J., Stafford, W.F., Wang, C.-L.A. “Ca+2 and Zn+2 Induce Different Conformational Changes in Calcyclin” (1998) Eur. J. Biochem., 253,.57-66.
Ikebe, M., Kambara, T., Stafford, W.F., Sata, M., Katayma and Ikebe, R. (1998), “A Hinge at the Central Helix of the Regulatory Light Chain of Myosin is Critical for Phosporylation Dependent Regulation of Smooth Muscle Myosin Motor Activity”. J. Biol. Chem. 273(28): 17702-17707.
Raso, V. McGrath, Brown, M. Liu, S., and Stafford, W.F. (1997) “Antibodies Capable of Releasing Diphtheria Toxin in Response to the pH Found in Endosomes.” J. Biol. Chem. 272, 27618-27622.
Parker, M.H. , Stafford, W.F., and Prevelige, P.E., Jr. (1997) “Bacteriophage P22 Scaffolding Protein forms Oligomers in Solution.” J Mol Biol. 268(3): 655-665.
MacPhee, C. E., Chan, R. Y. S., Sawyer, W. H., Stafford, W. F., & Howlett, G. J. (1997).” Interaction of lipoprotein lipase with homogeneous lipid emulsions.” J Lipid Res. 1997 Aug 1; 38, 1649-1659.
Mullins, R.D., Stafford, W.F. & Pollard, T.D.(1997) “Structure, Subunit Topology, and Actin-binding Activity of the Arp2/3 Complex from Acanthamoeba.” J. Cell. Biol. 136, 331-343.
Stafford, W.F. “Sedimentation velocity spins a new weave for an old fabric.” (1997) Current Opinion in Biotechnology 8, 14-24.
Sata, M, Stafford, W.F., Mabuchi, K., and Ikebe, M.(1997) “The Motor Domain and the Regulatory Domain of Myosin Soley Dictate Enzymatic Activity and Phosphorylation-Dependent Regulation, Respectively.” Proc. Natl. Acad. Sci USA 94, 91-96.
Phan, B. C., P. Cheung, W. F. Stafford and E. Reisler. (1996). “Complexes Of Myosin Subfragment-1 With Adenosine Diphosphate and Phosphate Analogs – Probes Of Active Site and Protein Conformation.” Biophysical Chemistry. 59, 341-349.
Liu, S. and W. F. Stafford. (1995). “An Optical Thermometer for Direct Measurement of Cell Temperature in the Beckman Instruments XL-A Analytical Ultracentrifuge.” Anal. Biochem. 224, 119-202.
Stafford, W. F. and S. Liu. (1995). “Methods for increasing the sensitivity of sedimentation velocity analysis: A signal averaging Rayleigh optical system for the Beckman Instruments Optima XL-A analytical ultracentrifuge.” Prog. Biomed. Optics. 2386, 130-135.
Stafford, W. F., S. Liu and P. E. Prevelige. (1995). “New High Sensitivity Sedimentation Methods: Application to the Analysis of the Assembly of Bateriophage P22.” Techniques in Protein Chemistry VI. Ed. J. W. Crabb. San Diego, Academic Press. 427-432.
Stafford, W. F., K. Mabuchi, K. Takahashi and T. Tao. (1995). “Physical Characterization of Calponin.” J. Biol. Chem. 270, 10576-10579.
Stafford, W. F. and T. M. Schuster. (1995). “Hydrodynamic Transport Methods”. Introduction to Biophysical Methods for Protein and Nucleic Acid Research. Ed. J. A. Glaser and M. P. Deutscher. Orlando, Academic Press, Inc.
Tai, M. S., J. E. McCartney, G. P. Adams, D. Jin, R. M. Hudziak, H. Oppermann, A. A. Laminet, M. A. Bookman, E. J. Wolf, S. Liu, W. F. Stafford, I. Fand, L. L. Houston, L. M. Weiner and J. S. Huston. (1995). “Targeting C-ErbB-2 Expressing Tumors Using Single-Chain Fv Monomers and Dimers.” Cancer Research. 55, S5983-S5989.
Yphantis, D.A., J.W. Lary, W.F. Stafford, S. Liu, P.H. Olsen, D.B. Hayes, T.P. Moody, T.M. Ridgeway, D.A. Lyons, & T.M. Laue (1994) “On line Data Acquisition for the Rayleigh Interference Optical System of the Analytical Ultracentrifuge.” Modern Analytical Ultracentrifugation: Acquisition and Interpretation of Data for Biological Synthetic Polymer System. Boston, Birkhauser-Boston. pp. 209-226.
Stafford, W.F. (1994) “Sedimentation Boundary Analysis of Interacting Systems: Use of the Apparent Sedimentation Coefficient Distribution Function.” Modern Analytical Ultracentrifugation: Acquisition and Interpretation of Data for Biological and Synthetic Polymer Systems. Boston, Birkhauser-Boston. pp. 119-137.
Stafford, W.F. (1994) “Boundary Analysis in Sedimentation Velocity Experiments.” Methods in Enzymology. Numerical Computer Methods, Part B, Orlando, Academic Press. pp. 478-501.
Adams, G.P., J.E. McCartney, M.S. Tai, H. Oppermann, J.S. Huston, W.F. Stafford, M.A. Bookman, I. Fand, L.L. Houston, L.M. Weiner & W.F. Stafford (1993) “Highly Specific in vivo Tumor Targeting by Monovalent and Divalent Forms of 741F8 anti-c-erbB-2 Single-chain Fv.” Cancer Res. 53, 4026-4034.
Fairman, R., Beran-Steed, R.K., Anthony-Cahill, S.J., Lear, J.D., Stafford, W.F., III, DeGrado, W.F., Benfield, P.A. & Brenner, S.L. (1993) Multiple Oligomeric States Regulate the DNA Binding of Helix-Loop-Helix Peptides. Proc. Natl. Acad. Sci. USA 90, 10429-10433.
Stafford, W.F. (1992) “Boundary Analysis in Sedimentation Transport Experiments – A Procedure for Obtaining Sedimentation Coefficient Distributions Using the Time Derivative of the Concentration Profile.” Analytical Biochem. 203, 295.
Brenner, S.L., Zlotnick, A. & Stafford W.F. (1990) “RecA Protein Self-assembly. II. Analytical Equilibrium Ultracentrifugation Studies of the Entropy-driven Self-association of RecA.” J. Mol. Biol. 216, 949.
Stafford, W.F., Jancso, A. & Graceffa, P. (1990) “Caldesmon from Rabbit Liver – Molecular Weight and Length by Analytical Ultracentrifugation.” Arch. Biochem. Biophys 281., 66.
O’Shea, E.K., Rutkowski, R., Stafford, W.F. & Kim, P.S. (1989) Preferential Heterodimer Formation by Isolated Leucine Zippers from Fos and Jun. Science 245, 646.
Sinard, J.H., Stafford, W.F. & Pollard, T.D. (1989) “The Mechanism of Assembly of Acanthamoeba Myosin-II Minifilaments: Minifilaments Assemble by Three Successive Dimerization Steps.” J. Cell Biol.. 109, 1537.