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Timothy D. Fenn, Ph.D. - Publications

Affiliations: 
Brandeis University, Waltham, MA, United States 
Area:
relationship of protein three-dimensional structure to chemical function
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31 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 Avdic A, Tollefson MR, Tatro N, LuCore SD, Litman JM, Fenn TD, Schnieders MJ. Polarizable Amoeba Force Field Metadynamics with Minimization Predicts Missing Protein Loops Biophysical Journal. 112: 55a. DOI: 10.1016/J.Bpj.2016.11.332  0.353
2015 LuCore SD, Litman JM, Powers KT, Gao S, Lynn AM, Tollefson WT, Fenn TD, Washington MT, Schnieders MJ. Dead-End Elimination with a Polarizable Force Field Repacks PCNA Structures. Biophysical Journal. 109: 816-26. PMID 26287633 DOI: 10.1016/J.Bpj.2015.06.062  0.328
2013 Andrews LD, Fenn TD, Herschlag D. Ground state destabilization by anionic nucleophiles contributes to the activity of phosphoryl transfer enzymes. Plos Biology. 11: e1001599. PMID 23843744 DOI: 10.1371/Journal.Pbio.1001599  0.364
2013 Vivona S, Cipriano DJ, O'Leary S, Li YH, Fenn TD, Brunger AT. 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. The Journal of Biological Chemistry. 288: 24984-91. PMID 23836889 DOI: 10.1074/Jbc.M113.489807  0.308
2013 Sigala PA, Fafarman AT, Schwans JP, Fried SD, Fenn TD, Caaveiro JM, Pybus B, Ringe D, Petsko GA, Boxer SG, Herschlag D. Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site. Proceedings of the National Academy of Sciences of the United States of America. 110: E2552-61. PMID 23798390 DOI: 10.1073/Pnas.1302191110  0.524
2013 Cipriano DJ, Jung J, Vivona S, Fenn TD, Brunger AT, Bryant Z. Processive ATP-driven substrate disassembly by the N-ethylmaleimide-sensitive factor (NSF) molecular machine. The Journal of Biological Chemistry. 288: 23436-45. PMID 23775070 DOI: 10.1074/Jbc.M113.476705  0.339
2012 Kaiser SE, Mao K, Taherbhoy AM, Yu S, Olszewski JL, Duda DM, Kurinov I, Deng A, Fenn TD, Klionsky DJ, Schulman BA. Noncanonical E2 recruitment by the autophagy E1 revealed by Atg7-Atg3 and Atg7-Atg10 structures. Nature Structural & Molecular Biology. 19: 1242-9. PMID 23142976 DOI: 10.1038/Nsmb.2415  0.31
2012 Fafarman AT, Sigala PA, Schwans JP, Fenn TD, Herschlag D, Boxer SG. Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase. Proceedings of the National Academy of Sciences of the United States of America. 109: E299-308. PMID 22308339 DOI: 10.1073/Pnas.1111566109  0.365
2012 Bobyr E, Lassila JK, Wiersma-Koch HI, Fenn TD, Lee JJ, Nikolic-Hughes I, Hodgson KO, Rees DC, Hedman B, Herschlag D. High-resolution analysis of Zn(2+) coordination in the alkaline phosphatase superfamily by EXAFS and x-ray crystallography. Journal of Molecular Biology. 415: 102-17. PMID 22056344 DOI: 10.1016/J.Jmb.2011.10.040  0.42
2012 Fenn T, Schnieders M, Pande V. Bayesian Modeling of Crystallographic Disorder Biophysical Journal. 102: 225a. DOI: 10.1016/J.Bpj.2011.11.1235  0.323
2011 Schnieders MJ, Fenn TD, Pande VS. Polarizable Atomic Multipole X-Ray Refinement: Particle Mesh Ewald Electrostatics for Macromolecular Crystals. Journal of Chemical Theory and Computation. 7: 1141-1156. PMID 26606362 DOI: 10.1021/Ct100506D  0.331
2011 Fenn TD, Schnieders MJ, Mustyakimov M, Wu C, Langan P, Pande VS, Brunger AT. Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration. Structure (London, England : 1993). 19: 523-33. PMID 21481775 DOI: 10.1016/J.Str.2011.01.015  0.316
2010 Fenn TD, Schnieders MJ, Brunger AT, Pande VS. Polarizable atomic multipole x-ray refinement: hydration geometry and application to macromolecules. Biophysical Journal. 98: 2984-92. PMID 20550911 DOI: 10.1016/J.Bpj.2010.02.057  0.346
2010 Kraut DA, Sigala PA, Fenn TD, Herschlag D. Dissecting the paradoxical effects of hydrogen bond mutations in the ketosteroid isomerase oxyanion hole. Proceedings of the National Academy of Sciences of the United States of America. 107: 1960-5. PMID 20080683 DOI: 10.1073/Pnas.0911168107  0.334
2010 Schnieders MJ, Fenn TD, Pande VS, Brunger AT. X-Ray Crystallography Refinement as Ewald Intended: From Drug Design to Ribosome Crystals Biophysical Journal. 98: 177a. DOI: 10.1016/J.Bpj.2009.12.946  0.319
2010 Fenn T, Schnieders M, Pande V, Brunger A. Is Theory Leading Neutron Diffraction in Macromolecular Solvent Networks? Biophysical Journal. 98: 760a. DOI: 10.1016/J.Bpj.2009.12.4172  0.311
2010 Jung J, Fenn TD, Chu S, Brunger AT. Single Molecule Study of Disassembly of SNARE Complex by NSF/α−SNAP Biophysical Journal. 98: 670a. DOI: 10.1016/J.Bpj.2009.12.3680  0.316
2009 Schnieders MJ, Fenn TD, Pande VS, Brunger AT. Polarizable atomic multipole X-ray refinement: application to peptide crystals. Acta Crystallographica. Section D, Biological Crystallography. 65: 952-65. PMID 19690373 DOI: 10.1107/S0907444909022707  0.316
2008 Zuniga JE, Schmidt JJ, Fenn T, Burnett JC, Araç D, Gussio R, Stafford RG, Badie SS, Bavari S, Brunger AT. A potent peptidomimetic inhibitor of botulinum neurotoxin serotype A has a very different conformation than SNAP-25 substrate. Structure (London, England : 1993). 16: 1588-97. PMID 18940613 DOI: 10.1016/J.Str.2008.07.011  0.405
2008 Zalatan JG, Fenn TD, Herschlag D. Comparative enzymology in the alkaline phosphatase superfamily to determine the catalytic role of an active-site metal ion. Journal of Molecular Biology. 384: 1174-89. PMID 18851975 DOI: 10.1016/J.Jmb.2008.09.059  0.379
2008 O'Brien PJ, Lassila JK, Fenn TD, Zalatan JG, Herschlag D. Arginine coordination in enzymatic phosphoryl transfer: evaluation of the effect of Arg166 mutations in Escherichia coli alkaline phosphatase. Biochemistry. 47: 7663-72. PMID 18627128 DOI: 10.1021/Bi800545N  0.455
2007 Henzler-Wildman KA, Thai V, Lei M, Ott M, Wolf-Watz M, Fenn T, Pozharski E, Wilson MA, Petsko GA, Karplus M, Hübner CG, Kern D. Intrinsic motions along an enzymatic reaction trajectory. Nature. 450: 838-44. PMID 18026086 DOI: 10.1038/Nature06410  0.414
2007 Loening AM, Fenn TD, Gambhir SS. Crystal structures of the luciferase and green fluorescent protein from Renilla reniformis. Journal of Molecular Biology. 374: 1017-28. PMID 17980388 DOI: 10.1016/J.Jmb.2007.09.078  0.416
2006 Zalatan JG, Fenn TD, Brunger AT, Herschlag D. Structural and functional comparisons of nucleotide pyrophosphatase/phosphodiesterase and alkaline phosphatase: implications for mechanism and evolution. Biochemistry. 45: 9788-803. PMID 16893180 DOI: 10.1021/Bi060847T  0.436
2006 Loening AM, Fenn TD, Wu AM, Gambhir SS. Consensus guided mutagenesis of Renilla luciferase yields enhanced stability and light output. Protein Engineering, Design & Selection : Peds. 19: 391-400. PMID 16857694 DOI: 10.1093/Protein/Gzl023  0.346
2005 Fenn TD, Holyoak T, Stamper GF, Ringe D. Effect of a Y265F mutant on the transamination-based cycloserine inactivation of alanine racemase. Biochemistry. 44: 5317-27. PMID 15807525 DOI: 10.1021/Bi047842L  0.624
2004 Fenn TD, Ringe D, Petsko GA. Xylose isomerase in substrate and inhibitor michaelis states: atomic resolution studies of a metal-mediated hydride shift. Biochemistry. 43: 6464-74. PMID 15157080 DOI: 10.2210/Pdb1S5N/Pdb  0.58
2003 Holyoak T, Fenn TD, Wilson MA, Moulin AG, Ringe D, Petsko GA. Malonate: a versatile cryoprotectant and stabilizing solution for salt-grown macromolecular crystals. Acta Crystallographica. Section D, Biological Crystallography. 59: 2356-8. PMID 14646118 DOI: 10.1107/S0907444903021784  0.66
2003 Holyoak T, Wilson MA, Fenn TD, Kettner CA, Petsko GA, Fuller RS, Ringe D. 2.4 A resolution crystal structure of the prototypical hormone-processing protease Kex2 in complex with an Ala-Lys-Arg boronic acid inhibitor. Biochemistry. 42: 6709-18. PMID 12779325 DOI: 10.1021/Bi034434T  0.699
2003 Fenn TD, Stamper GF, Morollo AA, Ringe D. A side reaction of alanine racemase: transamination of cycloserine. Biochemistry. 42: 5775-83. PMID 12741835 DOI: 10.1021/Bi027022D  0.685
2003 Fenn TD, Ringe D, Petsko GA. POVScript+: A program for model and data visualization using persistence of vision ray-tracing Journal of Applied Crystallography. 36: 944-947. DOI: 10.1107/S0021889803006721  0.499
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