Search Results - "Fenn, Timothy"

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  1. 1

    Comparative Enzymology in the Alkaline Phosphatase Superfamily to Determine the Catalytic Role of an Active-Site Metal Ion by Zalatan, Jesse G., Fenn, Timothy D., Herschlag, Daniel

    Published in Journal of molecular biology (31-12-2008)
    “…Mechanistic models for biochemical systems are frequently proposed from structural data. Site-directed mutagenesis can be used to test the importance of…”
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  2. 2

    Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase by Fafarman, Aaron T, Sigala, Paul A, Schwans, Jason P, Fenn, Timothy D, Herschlag, Daniel, Boxer, Steven G

    “…Understanding the electrostatic forces and features within highly heterogeneous, anisotropic, and chemically complex enzyme active sites and their connection…”
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  3. 3

    Noncanonical E2 recruitment by the autophagy E1 revealed by Atg7–Atg3 and Atg7–Atg10 structures by Kaiser, Stephen E, Mao, Kai, Taherbhoy, Asad M, Yu, Shanshan, Olszewski, Jennifer L, Duda, David M, Kurinov, Igor, Deng, Alan, Fenn, Timothy D, Klionsky, Daniel J, Schulman, Brenda A

    Published in Nature structural & molecular biology (01-12-2012)
    “…An early step in the autophagy process is the conjugation of the ubiquitin-like proteins (UBLs) Atg8 and Atg12 to their targets. Structural and functional…”
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  4. 4

    Rab and Arl GTPase Family Members Cooperate in the Localization of the Golgin GCC185 by Burguete, Alondra Schweizer, Fenn, Timothy D., Brunger, Axel T., Pfeffer, Suzanne R.

    Published in Cell (25-01-2008)
    “…GCC185 is a large coiled-coil protein at the trans Golgi network that is required for receipt of transport vesicles inbound from late endosomes and for…”
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  5. 5
  6. 6

    Processive ATP-driven Substrate Disassembly by the N-Ethylmaleimide-sensitive Factor (NSF) Molecular Machine by Cipriano, Daniel J., Jung, Jaemyeong, Vivona, Sandro, Fenn, Timothy D., Brunger, Axel T., Bryant, Zev

    Published in The Journal of biological chemistry (09-08-2013)
    “…SNARE proteins promote membrane fusion by forming a four-stranded parallel helical bundle that brings the membranes into close proximity. Post-fusion, the…”
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  7. 7

    Structural and Functional Comparisons of Nucleotide Pyrophosphatase/Phosphodiesterase and Alkaline Phosphatase:  Implications for Mechanism and Evolution by Zalatan, Jesse G, Fenn, Timothy D, Brunger, Axel T, Herschlag, Daniel

    Published in Biochemistry (Easton) (15-08-2006)
    “…The rapid expansion of the amount of genomic and structural data has provided many examples of enzymes with evolutionarily related active sites that catalyze…”
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  8. 8

    Disassembly of All SNARE Complexes by N-Ethylmaleimide-sensitive Factor (NSF) Is Initiated by a Conserved 1:1 Interaction between α-Soluble NSF Attachment Protein (SNAP) and SNARE Complex by Vivona, Sandro, Cipriano, Daniel J., O'Leary, Seán, Li, Ye Henry, Fenn, Timothy D., Brunger, Axel T.

    Published in The Journal of biological chemistry (23-08-2013)
    “…Vesicle trafficking in eukaryotic cells is facilitated by SNARE-mediated membrane fusion. The ATPase NSF (N-ethylmaleimide-sensitive factor) and the adaptor…”
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  9. 9

    Distinct immune stimulatory effects of anti-human VISTA antibodies are determined by Fc-receptor interaction by Mostböck, Sven, Wu, Helen Haixia, Fenn, Timothy, Riegler, Bettina, Strahlhofer, Susanne, Huang, Yining, Hansen, Gale, Kroe-Barrett, Rachel, Tirapu, Iñigo, Vogt, Anne B.

    Published in Frontiers in immunology (28-07-2022)
    “…VISTA (PD-1H) is an immune regulatory molecule considered part of the next wave of immuno-oncology targets. VISTA is an immunoglobulin (Ig) superfamily cell…”
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  10. 10

    Dissecting the paradoxical effects of hydrogen bond mutations in the ketosteroid isomerase oxyanion hole by Kraut, Daniel A, Sigala, Paul A, Fenn, Timothy D, Herschlag, Daniel

    “…The catalytic importance of enzyme active-site interactions is frequently assessed by mutating specific residues and measuring the resulting rate reductions…”
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  11. 11

    Dead-End Elimination with a Polarizable Force Field Repacks PCNA Structures by LuCore, Stephen D., Litman, Jacob M., Powers, Kyle T., Gao, Shibo, Lynn, Ava M., Tollefson, William T.A., Fenn, Timothy D., Washington, M. Todd, Schnieders, Michael J.

    Published in Biophysical journal (18-08-2015)
    “…A balance of van der Waals, electrostatic, and hydrophobic forces drive the folding and packing of protein side chains. Although such interactions between…”
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  12. 12

    High-Resolution Analysis of Zn2+ Coordination in the Alkaline Phosphatase Superfamily by EXAFS and X-ray Crystallography by Bobyr, Elena, Lassila, Jonathan K., Wiersma-Koch, Helen I., Fenn, Timothy D., Lee, Jason J., Nikolic-Hughes, Ivana, Hodgson, Keith O., Rees, Douglas C., Hedman, Britt, Herschlag, Daniel

    Published in Journal of molecular biology (01-01-2012)
    “…Comparisons among evolutionarily related enzymes offer opportunities to reveal how structural differences produce different catalytic activities. Two…”
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  13. 13

    Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site by Sigala, Paul A, Fafarman, Aaron T, Schwans, Jason P, Fried, Stephen D, Fenn, Timothy D, Caaveiro, Jose M M, Pybus, Brandon, Ringe, Dagmar, Petsko, Gregory A, Boxer, Steven G, Herschlag, Daniel

    “…Hydrogen bond networks are key elements of protein structure and function but have been challenging to study within the complex protein environment. We have…”
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  14. 14

    Polarizable Atomic Multipole X-Ray Refinement: Particle Mesh Ewald Electrostatics for Macromolecular Crystals by Schnieders, Michael J, Fenn, Timothy D, Pande, Vijay S

    Published in Journal of chemical theory and computation (12-04-2011)
    “…Refinement of macromolecular models from X-ray crystallography experiments benefits from prior chemical knowledge at all resolutions. As the quality of the…”
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  15. 15

    High-resolution analysis of Zn(2+) coordination in the alkaline phosphatase superfamily by EXAFS and x-ray crystallography by Bobyr, Elena, Lassila, Jonathan K, Wiersma-Koch, Helen I, Fenn, Timothy D, Lee, Jason J, Nikolic-Hughes, Ivana, Hodgson, Keith O, Rees, Douglas C, Hedman, Britt, Herschlag, Daniel

    Published in Journal of molecular biology (06-01-2012)
    “…Comparisons among evolutionarily related enzymes offer opportunities to reveal how structural differences produce different catalytic activities. Two…”
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  16. 16

    Reintroducing Electrostatics into Macromolecular Crystallographic Refinement: Application to Neutron Crystallography and DNA Hydration by Fenn, Timothy D., Schnieders, Michael J., Mustyakimov, Marat, Wu, Chuanjie, Langan, Paul, Pande, Vijay S., Brunger, Axel T.

    Published in Structure (London) (13-04-2011)
    “…Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity…”
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  17. 17

    Xylose Isomerase in Substrate and Inhibitor Michaelis States:  Atomic Resolution Studies of a Metal-Mediated Hydride Shift by Fenn, Timothy D, Ringe, Dagmar, Petsko, Gregory A

    Published in Biochemistry (Easton) (01-06-2004)
    “…Xylose isomerase (E.C. 5.3.1.5) catalyzes the interconversion of aldose and ketose sugars and has an absolute requirement for two divalent cations at its…”
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  18. 18

    Polarizable Atomic Multipole X-Ray Refinement: Hydration Geometry and Application to Macromolecules by Fenn, Timothy D., Schnieders, Michael J., Brunger, Axel T., Pande, Vijay S.

    Published in Biophysical journal (16-06-2010)
    “…We recently developed a polarizable atomic multipole refinement method assisted by the AMOEBA force field for macromolecular crystallography. Compared to…”
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  19. 19

    Polarizable atomic multipole X-ray refinement: application to peptide crystals by Schnieders, Michael J., Fenn, Timothy D., Pande, Vijay S., Brunger, Axel T.

    “…Recent advances in computational chemistry have produced force fields based on a polarizable atomic multipole description of biomolecular electrostatics. In…”
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  20. 20

    Arginine Coordination in Enzymatic Phosphoryl Transfer: Evaluation of the Effect of Arg166 Mutations in Escherichia coli Alkaline Phosphatase by O’Brien, Patrick J, Lassila, Jonathan Kyle, Fenn, Timothy D, Zalatan, Jesse G, Herschlag, Daniel

    Published in Biochemistry (Easton) (22-07-2008)
    “…Arginine residues are commonly found in the active sites of enzymes catalyzing phosphoryl transfer reactions. Numerous site-directed mutagenesis experiments…”
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