Search Results - "Fenn, Timothy"
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Comparative Enzymology in the Alkaline Phosphatase Superfamily to Determine the Catalytic Role of an Active-Site Metal Ion
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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Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase
Published in Proceedings of the National Academy of Sciences - PNAS (07-02-2012)“…Understanding the electrostatic forces and features within highly heterogeneous, anisotropic, and chemically complex enzyme active sites and their connection…”
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Noncanonical E2 recruitment by the autophagy E1 revealed by Atg7–Atg3 and Atg7–Atg10 structures
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
Rab and Arl GTPase Family Members Cooperate in the Localization of the Golgin GCC185
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
Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment
Published in The Journal of chemical physics (07-07-2024)“…Force Field X (FFX) is an open-source software package for atomic resolution modeling of genetic variants and organic crystals that leverages advanced…”
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Processive ATP-driven Substrate Disassembly by the N-Ethylmaleimide-sensitive Factor (NSF) Molecular Machine
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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Structural and Functional Comparisons of Nucleotide Pyrophosphatase/Phosphodiesterase and Alkaline Phosphatase: Implications for Mechanism and Evolution
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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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
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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Distinct immune stimulatory effects of anti-human VISTA antibodies are determined by Fc-receptor interaction
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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Dissecting the paradoxical effects of hydrogen bond mutations in the ketosteroid isomerase oxyanion hole
Published in Proceedings of the National Academy of Sciences - PNAS (02-02-2010)“…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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Dead-End Elimination with a Polarizable Force Field Repacks PCNA Structures
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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High-Resolution Analysis of Zn2+ Coordination in the Alkaline Phosphatase Superfamily by EXAFS and X-ray Crystallography
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
Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site
Published in Proceedings of the National Academy of Sciences - PNAS (09-07-2013)“…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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Polarizable Atomic Multipole X-Ray Refinement: Particle Mesh Ewald Electrostatics for Macromolecular Crystals
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
High-resolution analysis of Zn(2+) coordination in the alkaline phosphatase superfamily by EXAFS and x-ray crystallography
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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Reintroducing Electrostatics into Macromolecular Crystallographic Refinement: Application to Neutron Crystallography and DNA Hydration
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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Xylose Isomerase in Substrate and Inhibitor Michaelis States: Atomic Resolution Studies of a Metal-Mediated Hydride Shift
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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Polarizable Atomic Multipole X-Ray Refinement: Hydration Geometry and Application to Macromolecules
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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Polarizable atomic multipole X-ray refinement: application to peptide crystals
Published in Acta crystallographica. Section D, Biological crystallography. (01-09-2009)“…Recent advances in computational chemistry have produced force fields based on a polarizable atomic multipole description of biomolecular electrostatics. In…”
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Arginine Coordination in Enzymatic Phosphoryl Transfer: Evaluation of the Effect of Arg166 Mutations in Escherichia coli Alkaline Phosphatase
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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