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Coordinated functions of WSS1, PSY2, and TOF1 in the DNA damage response

B.M. O’Neill, D. Hanway, E.A. Winzeler, F.E. Romesberg, Nucleic Acids Res. (2004) 32:6519–6530.
pubpic2004oneillThe stabilization and processing of stalled replication forks is required to maintain genome integrity in all organisms. Based on both physical and genetic interactions detected between WSS1, PSY2, and TOF1, we suggest that Wss1 and Psy2 similarly function to stabilize or process stalled or collapsed replication forks.

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Optimization of interstrand hydrophobic packing interactions within unnatural base pairs

S. Matsuda, F.E. Romesberg, J. Am. Chem. Soc. (2004) 126:14419–14427.
pubpic2004matsudaWe report the synthesis and stability of unnatural base pairs formed between simple phenyl rings modified at different positions with methyl groups. Several are virtually as stable as a natural base pair in the same sequence context, showing that neither hydrogen-bonding nor large aromatic surface area are required for base pair stability within duplex DNA and that interstrand interactions between small aromatic rings may be optimized for both stability and selectivity.

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Isotope effects and quantum tunneling in enzyme-catalyzed hydrogen transfer. Part I. The experimental basis

F.E. Romesberg, R.L. Schowen, Adv. Phys. Org. Chem. (2004) 39:27–77.
pubpic2004schowenWe review the role of quantum tunneling as a mechanism of the enymatic transfer of hydrogenic entities (protons, hydrogen atoms, and hydride ions), including the background of the subject, the conceptual apparatus that underlies the isotopic studies, the phenomenology of the experimental observations, and a qualitative sketch of the interpretative, mechanistic models that have emerged.

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Preliminary characterization of light harvesting in E. coli DNA photolyase

A.A. Henry, R. Jimenez, D. Hanway, F.E. Romesberg, Chembiochem (2004) 5:1088-1094.
pubpic2004bhenryE. coli DNA photolyase is a monomeric light-harvesting enzyme that utilizes a methenyltetrahydrofolate (MTHF) antenna cofactor to harvest light energy for the repair of thymine dimers in DNA. Here, we investigate the origins of how the enzyme tunes the photophysical properties of the antenna cofactor appropriately for biological function.

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A high-resolution probe of protein folding

L.B. Sagle, J. Zimmermann, P.E. Dawson, F.E. Romesberg, J. Am. Chem. Soc. (Comm.) (2004) 126:3384-3385.
pubpic2004sagleTo generate residue-specific information on the equilibrium folding of cyt c, we have semisynthesized the protein with specifically deuterated residues. Plotted as a function of added guanidine hydrochloride denaturant, the absorption intensities of the protein C-D bonds reveal that cyt c undergoes a conformational change at the protein-based heme ligand, Met80, which is then followed by a more global unfolding at 2.3 M GdnHCL.

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Protein dynamics and the immunological evolution of molecular recognition

R. Jimenez, G. Salazar, J. Yin, T. Joo, F.E. Romesberg, Proc. Natl. Acad. Sci. USA (2004) 101:3803–3808.
pubpic2004jimenez3PEPS and steady-state spectroscopy in combination with binding and structural data, are used to examine the immunological evolution of protein flexibility in an anti-fluorescein antibody. We show that antibody dynamics are systematically manipulated during affinity maturation, and suggest that the evolution of protein flexibility may be a central component of the immune response.