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Mapping protein-protein interactions through experiment and theory

Jeffrey Mandell

Appointment Period: 1997-1999, Grant Years: [12,13,14]

Jeffrey MandellThe aim of my research is to develop rapid methods for determining the interacting regions of two proteins. Determining where two proteins bind to each other is the first step in elucidating the structure-function relationship of a protein-protein interaction. My work is interdisciplinary, and utilizes two complementary and rapid approaches for mapping protein-protein interactions. The first method is to experimentally monitor the regions of decreased solvent accessibility that occur upon protein complexation, work that was conducted with Dr. E. Komives. The other method is a computational technique that I developed with Dr. L. Ten Eyck. In the experimental approach, we use hydrogen/deuterium exchange coupled to mass spectrometry to determine the regions of decreased solvent accessibility that occur upon protein complexation. While this information is highly reliable and quickly determined, it is fairly low resolution and only identifies the binding site to within a window of 5-10 amino acids.

In the computational approach, we developed a novel algorithm that is capable of predicting how two proteins exactly fit together (given their structures solved separately) but returns this answer in a list of many possibilities, most of which are "false positives." I am currently interfacing these two techniques by using the experimentally-determined solvent exclusion data as a potential in my computational docking. In this manner, the computational algorithm is biased towards the experimental data, and the goal is to move the correct answers to the top of the list. During my research, I applied these techniques to predict the unknown structure of the thrombin-thrombomodulin interaction.

PUBLICATIONS (resulting from this training, and some recent ones)

Mandell JG, Falick AM, Komives EA. (1998) Measurement of amide hydrogen exchange by MALDI-TOF mass spectrometry. Anal Chem. 70:3987-95.

Mandell JG, Falick AM, Komives EA. (1998) Identification of protein-protein inte rfaces by decreased amide proton solvent accessibility. Proc Natl Acad Sci USA. 95:14705-10.

Mandell JG, Baerga-Ortiz A, Akashi S, Takio K, Komives EA. (2001) Solvent accessibility of the thrombin-thrombomodulin interface. J Mol Biol. 306:575-89.

Hughes CA, Mandell JG, Anand GS, Stock AM, Komives EA. (2001) Phosphorylation causes subtle changes in solvent accessibility at the interdomain interface of methylesterase CheB. J Mol Biol. 307:967-76.

Mandell JG, Roberts VA, Pique ME, Kotlovyi V, Mitchell JC, Nelson E, Tsigelny I, Ten Eyck LF. (2001) Protein docking using continuum electrostatics and geometric fit. Protein Eng. 14:105-13.

Baerga-Ortiz A, Hughes CA, Mandell JG, Komives EA. (2002) Epitope mapping of a monoclonal antibody against human thrombin by H/D-exchange mass spectrometry reveals selection of a diverse sequence in a highly conserved protein. Protein Sci. 11:1300-8.

Anand GS, Law D, Mandell JG, Snead AN, Tsigelny I, Taylor SS, Ten Eyck LF, Komives EA. (2003) Identification of the protein kinase A regulatory RIalpha-catalytic subunit interface by amide H/2H exchange and protein docking. Proc Natl Acad Sci USA 100:13264-9.

Baerga-Ortiz A, Bergqvist S, Mandell JG, Komives EA. (2004) Two different proteins that compete for binding to thrombin have opposite kinetic and thermodynamic profiles. Protein Sci. 13:166-76.

Mandell JG, Goodrich KJ, Bahler J, Cech TR. (2005) Expression of a RecQ helicase homolog affects progression through crisis in fission yeast lacking telomerase. J Biol Chem. 280:5249-57.

Mandell JG, Bahler J, Volpe TA, Martienssen RA, Cech TR. (2005) Global expression changes resulting from loss of telomeric DNA in fission yeast. Genome Biol. 6:R1.

Mandell JG, Baerga-Ortiz A, Falick AM, Komives EA. (2005) Measurement of solvent accessibility at protein-protein interfaces. Methods Mol Biol. 305:65-80.

Mandell JG, Barbas CF 3rd. (2006) Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases. Nucleic Acids Res. 34:W516-23.