Anjum Ansari
Associate Professor in Physics
University of Illinois at Chicago

 

Postdoctoral Position Available

 

 

 

Physics Dept. (M/C 273)
845 W. Taylor St.
University of Illinois at Chicago
Chicago, IL 60607
ansari@uic.edu
Office: (312) 996-8735
 Lab: (312) 996-5555
Fax: (312) 996-9016

 
 

Research Area: Experimental Biophysics

 

Conformational changes in proteins and nucleic acids are essential for all biological phenomena and are central to molecular recognition in biological systems. The broad aims of my research program are to make precise measurements of the dynamics of biological macromolecules, to relate the dynamics to the specific function, and to provide a firm experimental foundation aimed at a quantitative understanding of various biological phenomena. I am pursuing two major research directions. One is directed toward an understanding of the energetics and mechanisms by which single-stranded polynucleotides form their secondary and higher order structures. The other is aimed at elucidating the fundamental rules that govern protein-DNA interactions, by probing the dynamics of molecular rearrangements in both the protein and the DNA during complex formation.

 

 

Primary research areas  

·      Hairpin formation in single-stranded polynucleotides

·      Kinetic measurements of higher order structures in RNA molecules.

·      Dynamics of protein-DNA interactions

Publications

 

 

S. V. Kuznetsov and A. Ansari, "Is the Correct Nucleating Loop Formation the Rate-Limiting Step in Hairpin Formation in ss-Polynucleotides?" (manuscript in preparation).

 

S. Sugimura, P. Vivas, S. V. Kuznetsov, P. A. Rice, D. M. Crothers, and A. Ansari, "Study of the Dynamics of Protein-DNA Interactions: Role of DNA "Bendability" in Site-Specific Recognition" (manuscript in preparation).

 

P. Vivas, S. V. Kuznetsov, and A. Ansari, "New Insights into the Transition Pathway from Nonspecific to Specific Complex of DNA with Escherichia coli Integration Host Factor", J. Phys. Chem. B (in press).

 

S. V. Kuznetsov, C. Ren, S. Woodson, and A. Ansari, "Loop Dependence of the Stability and Dynamics of Nucleic Acid Hairpins", Nuc Acids Res. 36, 1098-1112 (2008)

 

S. V. Kuznetsov, S. Sugimura, P. Vivas, D. M. Crothers, and A. Ansari, "Direct Observation of DNA Bending/Unbending Kinetics in Complex with DNA-Bending Protein IHF", Proc. Natl. Acad. Sci. 103, 18515-18520 (2006).  

 

S. V. Kuznetsov, A. G. Kozlov, T. M. Lohman, and A. Ansari, "Microsecond Dynamics of Protein-DNA Interactions: Direct Observation of the Wrapping/Unwrapping Kinetics of Single-Stranded DNA around the E. coli SSB Tetramer", J. Mol. Biol. 359, 55-65 (2006).

 

A. Ansari and S. V. Kuznetsov, "Is Hairpin Formation in Single-Stranded Polynucleotide Diffusion-Controlled?" J. Phys. Chem. B 109, 12982-12989 (2005).

 

A. Ansari and S. V. Kuznetsov, “Hairpin Formation in Polynucleotides: A Simple Folding Problem?” in Biological Nanostructures and Applications of Nanostructures in Biology: Electrical, Mechanical & Optical Properties, Eds. Michael A. Stroscio and Mitra Dutta, Kluwer Academic Publishers, New York, 99-147 (2004).

 

S. V. Kuznetsov, J. Hilario, T. A. Keiderling, and A. Ansari, “Spectroscopic Studies of Structural Changes in Two Beta-Sheet Forming Peptides show an Ensemble of Structures that Unfold Noncooperatively”, Biochemistry 42, 4321-4332 (2003)

 

A. Ansari, Y. Shen, and S. V. Kuznetsov, “Misfolded Traps Decrease the Effective Rate of DNA Hairpin Formation”, Phys. Rev. Lett. 88, 069801-1 (2002)

 

S. V. Kuznetsov, O. M. Sidorkina, J. Laval, and A. Ansari, “Characterization of Thermal Stability of Escherichia Coli Fapy-DNA Glycosylase”, Biochem. Biophys. Res. Comm. 288, 121-128 (2001).

 

A. Ansari, S. V. Kuznetsov, and Y. Shen, “Configurational Diffusion down a Folding Funnel Describes the Dynamics of DNA Hairpins”, Proc. Natl. Acad. Sci. 98, 7771 – 7776 (2001).

 

Y. Shen, S. V. Kuznetsov, and A. Ansari, “Loop Dependence of the Dynamics of DNA Hairpins”, J. Phys. Chem. B. 105, 12202 -12211 (2001).

 

S. V. Kuznetsov, Y. Shen, A. S. Benight, and A. Ansari, “A Semiflexible Polymer Model Applied to Loop Formation in DNA Hairpins”, Biophys. J. 81, 2864-2875 (2001).

 

A. Ansari, “Mean First Passage Time Solution of Smoluchowski Equation: Application to Relaxation Dynamics in Myoglobin”, J. Chem. Phys. 112, 2516-2522 (2000).

 

A. Ansari, “Langevin Modes Analysis of Myoglobin”, J. Chem. Phys. 110, 1774-1780 (1999).

 

J. Hofrichter, E. R. Henry, A. Ansari, C. M. Jones, R. M. Deutsch, and J. Sommer,  “Ligand Binding and Conformational Changes Measured by Time-Resolved Absorption Spectroscopy”, Methods Enzymol. 232, 387-415 (1994).

 

A. Ansari, C. M. Jones, E. R. Henry, J. Hofrichter, and W. A. Eaton, “Dynamics of Myoglobin Conformational Changes”, Biochemistry 33, 5128-5145 (1994).

 

A. Ansari and A. Szabo, “Theory of Photoselection by Intense Light Pulses: The Influence of Reorientational Dynamics and Chemical Kinetics on Absorbance Measurements”, Biophys. J. 64, 838-851 (1993).

 

A. Ansari, C. M. Jones, E. R. Henry, J. Hofrichter, and W. A. Eaton, “Photoselection in Polarized Photolysis Experiments on Heme Proteins”, Biophys. J. 64, 852-868 (1993).

 

A. Ansari, C. M. Jones, E. R. Henry, J. Hofrichter, and W. A. Eaton, “The Role of Solvent Viscosity in the Dynamics of Protein Conformational Changes”, Science 256, 1796-1798 (1992).

 

C. M. Jones, A. Ansari, E. R. Henry, G. W. Christoph, J. Hofrichter, and W. A. Eaton, “Speed of Intersubunit Communication in Hemoglobin”, Biochemistry 31, 6692-6702 (1992).

 

J. Hofrichter, E. R. Henry, A. Szabo, L. P. Murray, A. Ansari, C. M. Jones, M. Coletta, G. Falcioni, M. Brunori, and W. A. Eaton, “Dynamics of the Quaternary Conformational Change in Trout Hemoglobin”, Biochemistry 30, 6583-6598 (1991).

 

P. J. Steinbach, A. Ansari, J. Berendzen, D. Braunstein, K. Chu, B. R. Cowen, D. Ehrenstein, H. Frauenfelder, J. B. Johnson, D. C. Lamb, S. Luck, J. R. Mourant, G. U. Nienhaus, P. Ormos, R. Philipp, A. Xie, and R. D. Young, “Ligand Binding to Heme Proteins: Connection between Dynamics and Function”, Biochemistry 30, 3988-4001 (1991).

 

H. Frauenfelder, N. A. Alberding, A. Ansari, D. Braunstein, B. R. Cowen, M. K. Hong, I. E. T. Iben, J. B. Johnson, S. Luck, M. C. Marden, J. R. Mourant, P. Ormos, L. Reinisch, R. Scholl, A. Schulte, E. Shyamsunder, L. B. Sorenson, P. J. Steinbach, A. Xie, R. D. Young, and K. T. Yue, “Proteins and Pressure”, J. Phys. Chem. 94, 1024-1037 (1990).

 

P. Ormos, A. Ansari, D. Braunstein, B. R. Cowen, H. Frauenfelder, M. K. Hong, I. E. T. Iben, T. B. Sauke, P. J. Steinbach, and R. D. Young, “Inhomogeneous Broadening in Spectral Bands of Carbonmonoxy Myoglobin: the Connection between Spectral and Functional Heterogeneity”, Biophys. J. 57, 191-199 (1990).

 

D. Braunstein, A. Ansari, J. Berendzen, B. R. Cowen, K. D. Egeberg, H. Frauenfelder, M. K. Hong, P. Ormos, T. B. Sauke, R. Scholl, A. Schulte, S. G. Sligar, B. A. Springer, P. J. Steinbach, and R. D. Young, “Ligand Binding to Synthetic Mutant Myoglobin”, Proc. Natl. Acad. Sci. USA 85, 8497-8501 (1988).

 

A. Ansari, J. Berendzen, D. Braunstein, B. R. Cowen, H. Frauenfelder, M. K. Hong, I. E. T. Iben, J. B. Johnson,P. Ormos, T. B. Sauke, R. Scholl, A. Schulte, P. J. Steinbach, J. Vittitow, and R. D. Young, “Rebinding and Relaxation in the Myoglobin Pocket”, Biophys. Chem. 26, 337‑355 (1987).

 

A. Ansari, E. E. DiIorio, D. D. Dlott, H. Frauenfelder, I. E. T. Iben, P. Langer, H. Roder, T. B. Sauke, and E. Shyamsunder, “Ligand Binding to Heme Proteins: Relevance of Low‑Temperature Data” Biochemistry 25, 3139‑3146 (1986).

 

A. Ansari, J. Berendzen, S. F. Bowne, H. Frauenfelder, I. E. T. Iben, T. B. Sauke, E. Shyamsunder, and R.D.Young, “Protein States and Protein Quakes”, Proc. Natl. Acad. Sci. USA 82, 5000‑5004 (1985).