M. Thomas Record, Jr.
Publications | Awards | Website |
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Steenbock Professor of Chemical Sciences
John D. Ferry Professor of Chemistry and Biochemistry, Born 1942
B.A. 1964, Yale University
Ph.D. 1967, University of California, San Diego
Room: 4419 BC, 2126 |
 
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1. R. M. Saecker and M. T. Record, Jr. “Protein Surface Salt Bridges and Paths for DNA Wrapping.” Current Opinion in Structural Biology, 12, 311-319 (2002).
2. Ruth M. Saecker, Oleg V. Tsodikov, Kristi L. McQuade, Peter E. Schlax, Jr., Michael W. Capp and M. Thomas Record, Jr. “Kinetic Studies and Structural Models of the Association of E. coli RNA Polymerase with the Lambda PR Promoter: Large Scale Conformational Changes in Forming the Kinetically-Significant Intermediates”. Journal of Molecular Biology , 319, 649-671 (2002).
3. J. A. Holbrook, O. V. Tsodikov, R. M. Saecker and M. T. Record, Jr. “Specific and Nonspecific Interactions of Integration Host Factor with DNA: Thermodynamic Evidence for Disruption of Multiple IHF Surface Salt Bridges Coupled to DNA Binding.” J. Mol. Biol. , 310 (2), 379-401 (2001).
4. O. V. Tsodikov, J. A. Holbrook, I. A. Shkel and M. T. Record, Jr. “Analytical Binding Isotherms Describing Competitive Interactions of a Protein Ligand with Specific and Nonspecific Sites on a DNA Oligomer.” Biophys. J., 81, 1960-1969 (2001).
5. E. S. Courtenay, M. W. Capp, and M. T. Record, Jr. “Thermodynamics of Interactions of Urea and Guanidinium Salts with Protein Surface: Relationship Between Solute effects on Protein Processes and Changes in Water-Accessible Surface.” Protein Science 10, 2485-2497 (2001).
6. E. S. Courtenay, M. W. Capp, C. F. Anderson and M. T. Record, Jr. “Vapor Pressure Osmometry Studies of Osmolyte-Protein Interactions: Implications for the Action of Osmoprotectants in vivo and for the Interpretation of "Osmotic Stress" Experiments in vitro.” Biochemistry , 39 (15), 4455-4471 (2000).
7. E. Courtenay, M. W. Capp, R. M. Saecker and M. T. Record, Jr. “Thermodynamic Analysis of Interactions between Denaturants and Protein Surface Exposed on Unfolding: Interpretation of Urea and Guanidinium Chloride m -Values and their Correlation with Changes in Accessible Surface Area (ASA) Using Preferential Interaction Coefficients and the Local-Bulk Domain Model.” PROTEINS: Structure, Function, and Genetics 41 ( S4 ), 72-85 (2000).
8. D. S. Cayley, H. J. Guttman and M. T. Record, Jr. “Biophysical Characterization of Changes in Amounts and Activity of Escherichia coli Cell and Compartment Water and Turgor Pressure in Response to Osmotic Stress.” Biophys . J. 78(4), 1748-1764 (2000).
9. R. S. Spolar and M. T. Record, Jr., “Coupling of Local Folding to Site-Specific Binding of Proteins to DNA,” Science 263, 777–784 (1994).
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Biophysical studies of protein-nucleic acid interactions in transcription initiation in vitroand in E. coli;computational and experimental studies of polyelectrolyte properties of nucleic acids and their complexes.
The focus of our research is on the thermodynamics (origins of stability and specificity) and the kinetic mechanisms of formation of noncovalent protein-DNA complexes in the control of gene expression, including lac repressor-lac operator, RNA polymerase-promoter, and specific binding effector proteins. For these systems, we seek to relate structure to function by characterizing the driving forces for complexation and the often massive conformational changes in protein and DNA which are driven by binding free energy, including folding of unfolded regions of the protein to form the specific interface,1 hinge bending of protein domains and kinking of DNA,2 global wrapping of DNA on the protein surface, and local opening of the DNA helix.2 We also characterize model systems and processes, including DNA helix formation,4 protein folding,1 and oligocation-DNA interactions.5 In the latter case, we use coulombic polyelectrolyte theory6 and Monte Carlo simulations7 to predict the thermodynamics of binding as a function of salt concentration and DNA length.
In E. coli, the extent of repression of the lac operon is determined by the equilibrium extent of binding of lac repressor protein to its specific operator site. We observe that the thermodynamics of binding contain significant contributions from coupled folding of the protruding DNA binding domain of repressor1,8 and wrapping3 of regions of DNA flanking the operator on the surface of lac repressor. We are currently characterizing the dependences of these coupled conformational changes on sequence and solution conditions in the physiological range. For RNA polymerase-lPR promoter interactions, where specificity is kinetically determined in vivo, we have established the mechanism of formation of a functional complex2,9 and are characterizing the two kinetically-significant intermediates (represented in the sketch below) using rapid-mixing and molecular biological (footprinting, filter binding) methods, in order to identify the contributions of conformational changes in polymerase (hinge binding, coupled folding) and in the promoter DNA10 (wrapping, opening of the helix at the transcription start site) to the kinetics and thermodynamics of the individual mechanistic steps.
Other projects in the laboratory include the characterization of the bacterium E. coli as a chemical and osmotic system,11 and the thermodynamic and molecular characterization of interactions of cytoplasmic and common biochemical solutes with biopolymers12 and of solute effects on biopolymer processes.13
Graduate students from Chemistry, Biochemistry, Biophysics and Bacteriology are conducting this research. The broad range of backgrounds and interests of these students has been a key factor in our research successes and contributes to a stimulating research environment. Many of my students have gone on to academic positions in chemistry and biochemistry departments; many others are engaged in research at chemical, pharmaceutical and biotechnology companies.
References
1. R. S. Spolar and M. T. Record, Jr., "Coupling of Local Folding to Site-Specific Binding of Proteins to DNA," Science 263, 777-784 (1994).
2. M. L. Craig, O. V. Tsodikov, K. L. McQuade, P. E. Schlax, Jr., M. W. Capp, R. M. Saecker, and M. T. Record, Jr. "DNA Footprints of the Two Kinetically-Significant Intermediates in Formation of an RNA Polymerase-Promoter Open Complex: Evidence that Interactions with Start Site and Downstream DNA Induce Sequential Conformational Changes in Polymerase and DNA." J. Mol. Biol. 283, 741-756 (1998).
3. O. V. Tsodikov, R. M. Saecker, S. E. Melcher, M. M. Levandoski, D. E. Frank, M. W. Capp and M. T. Record, Jr. "Wrapping of Flanking Nonoperator DNA in Lac Repressor-Operator Complexes: Implications for DNA Looping." J. Mol. Biol. 294, 639-655 (1999).
4. J. A. Holbrook, M. W. Capp, R. M. Saecker and M. T. Record, Jr. "Enthalpy and Heat Capacity Changes for Formation of an Oligomer DNA Duplex: Interpretation in Terms of Coupled Processes of Formation and Association of Single-Stranded Helices." Biochemistry, 38, 8409-8422 (1999).
5. W. Zhang, H. Ni, M. W. Capp, C. F. Anderson, T. M. Lohman and M. T. Record, Jr. "The Importance of Coulombic End Effects: Experimental Characterization of the Effects of Oligonucleotide Flanking Charges on the Strength and Salt-Dependence of Oligocation (L8+) Binding to Single-Stranded DNA Oligomers." Biophysical J. 76, 1008-1017 (1999).
6. I. Shkel, O. Tsodikov and M. T. Record, Jr. "Complete Asymptotic Solution of Cylindrical and Spherical Poisson-Boltzmann Equations at Experimental Salt Concentrations." J. Phys. Chem. B. 104, 5161-5170 (2000).
7. H. Ni, C. F. Anderson, and M. T. Record, Jr. "Quantifying the Thermodynamic Consequences of Cation (M2+, M+) Accumulation and Anion (X-) Exclusion in Mixed Salt Solutions of Polyanionic DNA Using Monte Carlo and Poisson-Boltzmann Calculations of Ion-Polyion Preferential Interaction Coefficients." J. Phys. Chem. 103, 3489-3504 (1999).
8. D. E. Frank, R. M. Saecker, J. P. Bond, M. W. Capp, O. V. Tsodikov, S. E. Melcher, M. M. Levandoski and M. T. Record, Jr. "Thermodynamics of the Interactions of Lac Repressor with Variants of the Symmetric Lac Operator: Effects of Converting a Consensus Site to a Nonspecific Site." J. Mol. Biol., 267, 1186-1206 (1997).
9. O. V. Tsodikov and M. T. Record Jr. "General Method of Analysis of Kinetic Equations for Multistep Reversible Mechanisms in the Single-Exponential Regime: Application to Kinetics of Open Complex Formation between Es70 RNA Polymerase and lPR Promoter DNA." Biophysical J. 76, 1320-1329 (1999).
10. O. V. Tsodikov, M. L. Craig, R. M. Saecker, M. T. Record, Jr. "Quantitative Analysis of Multiple-Hit Footprinting Studies to Characterize DNA Conformational Changes in Protein-DNA Complexes: Application to DNA Opening by Es70 RNA Polymerase." J. Mol. Biol. 283, 757-769 (1998).
11. D. S. Cayley, H. J. Guttman and M. Thomas Record, Jr. "Biophysical Characterization of Changes in Amounts and Activity of Escherichia coli Cell and Compartment Water and Turgor Pressure in Response to Osmotic Stress. Biophys. J. 78(4), 1748-1764 (2000).
12. E. S. Courtenay, M. W. Capp, C. F. Anderson and M. Thomas Record, Jr. "Vapor Pressure Osmometry Studies of Osmolyte-Protein Interactions: Implications for the Action of Osmoprotectants in vivo and for the Interpretation of "Osmotic Stress" Experiments in vitro." Biochemistry, 39(15), 4455-4471 (2000).
13. E. Courtenay, M. W. Capp., R. M. Saecker and M. T. Record, Jr. "Thermodynamic Analysis of Interactions between Denaturants and Protein Surface Exposed on Unfolding: Interpretation of Urea and Guanidinium Chloride m-Values and their Correlation with Changes in Accessible Surface Area (ASA) Using Preferential Interaction Coefficients and the Local-Bulk Domain Model." PROTEINS: Structure, Function, and Genetics Suppl. 4:72-85 (2000).
Last Updated: Ocotober 9, 2003
1. Biophysical Society Founers Award (2001)
2. UW Vilas Associate Award (1998-2000)
3. NIH Merit Award (1997-2005)
4. Fellow - American Association for the Advancement of Science, 1991
5. WARF - University Houses Professorship, 1990
6. UW Faculty Teaching Award, 1986
7. Phi Beta Kappa Teaching Award, University of Wisconsin, 1976
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