J. Patrick Loria - Publications

Affiliations: 
Molecular Biophysics and Biochemistry Yale University, New Haven, CT 
Area:
General Biophysics, Biochemistry
Website:
https://chem.yale.edu/people/j-patrick-loria

77 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
2020 Beaumont V, Reiss K, Qu Z, Allen B, Batista VS, Loria JP. The allosteric impact of the variable insert loop in Vaccinia H1-related (VHR) phosphatase. Biochemistry. PMID 32348128 DOI: 10.1021/acs.biochem.0c00245  0.68
2020 Reiss K, Batista VS, Loria JP. Allosteric Control of Enzyme Activity: From Ancient Origins to Recent Gene-Editing Technologies. Biochemistry. PMID 32324383 DOI: 10.1021/acs.biochem.0c00275  0.68
2019 Cui DS, Lipchock JM, Brookner D, Loria JP. Uncovering the molecular interactions in the catalytic loop that modulate the conformational dynamics in protein tyrosine phosphatase 1B. Journal of the American Chemical Society. PMID 31339043 DOI: 10.1021/jacs.9b04470  1
2019 Blum RL, Rovny J, Loria JP, Barrett SE. Reaching the sparse-sampling limit for reconstructing a single peak in a 2D NMR spectrum using iterated maps. Journal of Biomolecular Nmr. PMID 31292847 DOI: 10.1007/s10858-019-00262-4  0.36
2019 Rovny J, Blum RL, Loria JP, Barrett SE. Accelerating 2D NMR relaxation dispersion experiments using iterated maps. Journal of Biomolecular Nmr. PMID 31280454 DOI: 10.1007/s10858-019-00263-3  0.36
2018 Negre CFA, Morzan UN, Hendrickson HP, Pal R, Lisi GP, Loria JP, Rivalta I, Ho J, Batista VS. Eigenvector centrality for characterization of protein allosteric pathways. Proceedings of the National Academy of Sciences of the United States of America. PMID 30530700 DOI: 10.1073/pnas.1810452115  0.96
2018 Liptak C, Mahmoud MM, Eckenroth BE, Moreno MV, East K, Alnajjar KS, Huang J, Towle-Weicksel JB, Doublié S, Loria JP, Sweasy JB. I260Q DNA polymerase β highlights precatalytic conformational rearrangements critical for fidelity. Nucleic Acids Research. PMID 30239932 DOI: 10.1093/nar/gky825  0.52
2018 Moise G, Morales Y, Beaumont V, Caradonna T, Loria JP, Johnson SJ, Hengge AC. A YopH PTP1B Chimera shows the importance of WPD-loop sequence to activity, structure, and dynamics in protein tyrosine phosphatases. Biochemistry. PMID 30110154 DOI: 10.1021/acs.biochem.8b00663  0.56
2018 Pantouris G, Ho J, Shah D, Syed MA, Leng L, Bhandari V, Bucala R, Batista VS, Loria JP, Lolis E. Nanosecond Dynamics Regulate the MIF-Induced Activity of CD74. Angewandte Chemie (International Ed. in English). PMID 29669180 DOI: 10.1002/anie.201803191  0.68
2018 Lisi GP, Currier AA, Loria JP. Glutamine Hydrolysis by Imidazole Glycerol Phosphate Synthase Displays Temperature Dependent Allosteric Activation. Frontiers in Molecular Biosciences. 5: 4. PMID 29468164 DOI: 10.3389/fmolb.2018.00004  0.96
2017 Lisi GP, Loria JP. Allostery in enzyme catalysis. Current Opinion in Structural Biology. 47: 123-130. PMID 28865247 DOI: 10.1016/j.sbi.2017.08.002  0.96
2017 Cui DS, Beaumont V, Ginther PS, Lipchock JM, Patrick Loria J. Leveraging reciprocity to identify and characterize unknown allosteric sites in protein tyrosine phosphatases. Journal of Molecular Biology. PMID 28625849 DOI: 10.1016/j.jmb.2017.06.009  0.6
2017 Lisi GP, East KW, Batista VS, Loria JP. Altering the allosteric pathway in IGPS suppresses millisecond motions and catalytic activity. Proceedings of the National Academy of Sciences of the United States of America. PMID 28396388 DOI: 10.1073/pnas.1700448114  0.96
2016 Lipchock JM, Hendrickson HP, Douglas BB, Bird KE, Ginther PS, Rivalta I, Ten NS, Batista VS, Loria JP. Characterization of PTP1B Inhibition by Chlorogenic Acid and Cichoric Acid. Biochemistry. PMID 27959494 DOI: 10.1021/acs.biochem.6b01025  1
2016 Rivalta I, Lisi GP, Snoeberger NS, Manley GA, Loria JP, Batista VS. Allosteric communication disrupted by small molecule binding to the Imidazole glycerol phosphate synthase protein-protein interface. Biochemistry. PMID 27797506 DOI: 10.1021/acs.biochem.6b00859  0.96
2016 Lisi GP, Manley GA, Hendrickson H, Rivalta I, Batista VS, Loria JP. Dissecting Dynamic Allosteric Pathways Using Chemically Related Small-Molecule Activators. Structure (London, England : 1993). PMID 27238967 DOI: 10.1016/j.str.2016.04.010  0.96
2016 Lisi GP, Patrick Loria J. Using NMR spectroscopy to elucidate the role of molecular motions in enzyme function. Progress in Nuclear Magnetic Resonance Spectroscopy. 92: 1-17. PMID 26952190 DOI: 10.1016/j.pnmrs.2015.11.001  0.96
2016 Lisi GP, Loria JP. Solution NMR Spectroscopy for the Study of Enzyme Allostery. Chemical Reviews. PMID 26734986 DOI: 10.1021/acs.chemrev.5b00541  1
2016 Lisi GP, Loria JP. Using NMR spectroscopy to elucidate the role of molecular motions in enzyme function Progress in Nuclear Magnetic Resonance Spectroscopy. 92: 1-17. DOI: 10.1016/j.pnmrs.2015.11.001  1
2015 Moscato B, Swain M, Loria JP. Induced Fit in the Selection of Correct versus Incorrect Nucleotides by DNA Polymerase β. Biochemistry. PMID 26678253 DOI: 10.1021/acs.biochem.5b01213  1
2015 Liptak C, Loria JP. Movement and specificity in a modular DNA binding protein. Structure (London, England : 1993). 23: 973-4. PMID 26039344 DOI: 10.1016/j.str.2015.05.004  1
2015 Khirich G, Loria JP. Complexity of protein energy landscapes studied by solution NMR relaxation dispersion experiments. The Journal of Physical Chemistry. B. 119: 3743-54. PMID 25680027 DOI: 10.1021/acs.jpcb.5b00212  1
2014 Ho J, Newcomer MB, Ragain CM, Gascon JA, Batista ER, Loria JP, Batista VS. MoD-QM/MM Structural Refinement Method: Characterization of Hydrogen Bonding in the Oxytricha nova G-Quadruplex. Journal of Chemical Theory and Computation. 10: 5125-35. PMID 26584390 DOI: 10.1021/ct500571k  0.68
2014 Zhai X, Go MK, O'Donoghue AC, Amyes TL, Pegan SD, Wang Y, Loria JP, Mesecar AD, Richard JP. Enzyme architecture: the effect of replacement and deletion mutations of loop 6 on catalysis by triosephosphate isomerase. Biochemistry. 53: 3486-501. PMID 24825099 DOI: 10.1021/bi500458t  1
2014 Whittier SK, Loria JP. ¹H, ¹⁵N, and ¹³C backbone resonance assignments for the Yersinia protein tyrosine phosphatase YopH. Biomolecular Nmr Assignments. 8: 387-9. PMID 24026965 DOI: 10.1007/s12104-013-9524-0  1
2014 Ho J, Newcomer MB, Ragain CM, Gascon JA, Batista ER, Loria JP, Batista VS. MoD-QM/MM structural refinement method: Characterization of hydrogen bonding in the Oxytricha nova G-quadruplex Journal of Chemical Theory and Computation. 10: 5125-5135. DOI: 10.1021/ct500571k  1
2013 Frey MA, Sethna ZM, Manley GA, Sengupta S, Zilm KW, Loria JP, Barrett SE. Accelerating multidimensional NMR and MRI experiments using iterated maps. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 237: 100-9. PMID 24184710 DOI: 10.1016/j.jmr.2013.09.005  1
2013 Wong M, Khirich G, Loria JP. What's in your buffer? Solute altered millisecond motions detected by solution NMR. Biochemistry. 52: 6548-58. PMID 23991940 DOI: 10.1021/bi400973e  1
2013 Whittier SK, Hengge AC, Loria JP. Conformational motions regulate phosphoryl transfer in related protein tyrosine phosphatases. Science (New York, N.Y.). 341: 899-903. PMID 23970698 DOI: 10.1126/science.1241735  1
2013 Zhai X, Amyes TL, Wierenga RK, Loria JP, Richard JP. Structural mutations that probe the interactions between the catalytic and dianion activation sites of triosephosphate isomerase. Biochemistry. 52: 5928-40. PMID 23909928 DOI: 10.1021/bi401019h  1
2013 Fan C, Rajasekaran D, Syed MA, Leng L, Loria JP, Bhandari V, Bucala R, Lolis EJ. MIF intersubunit disulfide mutant antagonist supports activation of CD74 by endogenous MIF trimer at physiologic concentrations. Proceedings of the National Academy of Sciences of the United States of America. 110: 10994-9. PMID 23776208 DOI: 10.1073/pnas.1221817110  1
2013 Manley G, Rivalta I, Loria JP. Solution NMR and computational methods for understanding protein allostery. The Journal of Physical Chemistry. B. 117: 3063-73. PMID 23445323 DOI: 10.1021/jp312576v  1
2012 Rivalta I, Sultan MM, Lee NS, Manley GA, Loria JP, Batista VS. Allosteric pathways in imidazole glycerol phosphate synthase. Proceedings of the National Academy of Sciences of the United States of America. 109: E1428-36. PMID 22586084 DOI: 10.1073/pnas.1120536109  1
2012 Berlow RB, Swain M, Dalal S, Sweasy JB, Loria JP. Substrate-dependent millisecond domain motions in DNA polymerase β. Journal of Molecular Biology. 419: 171-82. PMID 22446382 DOI: 10.1016/j.jmb.2012.03.013  1
2012 Manley G, Loria JP. NMR insights into protein allostery. Archives of Biochemistry and Biophysics. 519: 223-31. PMID 22198279 DOI: 10.1016/j.abb.2011.10.023  1
2012 Loria JP. Dynamics in enzymes: Solution NMR studies Emagres. 1: 197-204. DOI: 10.1002/9780470034590.emrstm1241  1
2012 Whittier SK, Loria JP. NMR relaxation dispersion studies of large enzymes in solution Rsc Biomolecular Sciences. 151-165.  1
2011 Watt ED, Rivalta I, Whittier SK, Batista VS, Loria JP. Reengineering rate-limiting, millisecond enzyme motions by introduction of an unnatural amino acid. Biophysical Journal. 101: 411-20. PMID 21767494 DOI: 10.1016/j.bpj.2011.05.039  1
2011 Doucet N, Khirich G, Kovrigin EL, Loria JP. Alteration of hydrogen bonding in the vicinity of histidine 48 disrupts millisecond motions in RNase A. Biochemistry. 50: 1723-30. PMID 21250662 DOI: 10.1021/bi1018539  1
2011 Doucet N, Loria JP. Relaxation dispersion studies of enzyme motions Advances in Biomedical Spectroscopy. 3: 185-202. DOI: 10.3233/978-1-60750-695-9-185  1
2010 Lipchock JM, Loria JP. Nanometer propagation of millisecond motions in V-type allostery. Structure (London, England : 1993). 18: 1596-607. PMID 21134639 DOI: 10.1016/j.str.2010.09.020  1
2010 Doucet N, Jayasundera TB, Simonovi? M, Loria JP. The crystal structure of ribonuclease A in complex with thymidine-3'-monophosphate provides further insight into ligand binding. Proteins. 78: 2459-68. PMID 20602460 DOI: 10.1002/prot.22754  1
2009 Williamson JA, Loria JP, Miranker AD. Helix stabilization precedes aqueous and bilayer-catalyzed fiber formation in islet amyloid polypeptide. Journal of Molecular Biology. 393: 383-96. PMID 19647750 DOI: 10.1016/j.jmb.2009.07.077  1
2009 Doucet N, Watt ED, Loria JP. The flexibility of a distant loop modulates active site motion and product release in ribonuclease A. Biochemistry. 48: 7160-8. PMID 19588901 DOI: 10.1021/bi900830g  1
2009 Lipchock J, Loria JP. Millisecond dynamics in the allosteric enzyme imidazole glycerol phosphate synthase (IGPS) from Thermotoga maritima. Journal of Biomolecular Nmr. 45: 73-84. PMID 19565337 DOI: 10.1007/s10858-009-9337-8  1
2009 Wang Y, Berlow RB, Loria JP. Role of loop-loop interactions in coordinating motions and enzymatic function in triosephosphate isomerase. Biochemistry. 48: 4548-56. PMID 19348462 DOI: 10.1021/bi9002887  1
2009 Lipchock JM, Loria JP. Monitoring molecular interactions by NMR. Methods in Molecular Biology (Clifton, N.J.). 490: 115-34. PMID 19157081 DOI: 10.1007/978-1-59745-367-7_5  1
2008 Lipchock JM, Loria JP. 1H, 15N and 13C resonance assignment of imidazole glycerol phosphate (IGP) synthase protein HisF from Thermotoga maritima. Biomolecular Nmr Assignments. 2: 219-21. PMID 19636909 DOI: 10.1007/s12104-008-9125-5  1
2008 Loria JP, Berlow RB, Watt ED. Characterization of enzyme motions by solution NMR relaxation dispersion. Accounts of Chemical Research. 41: 214-21. PMID 18281945 DOI: 10.1021/ar700132n  1
2007 Watt ED, Shimada H, Kovrigin EL, Loria JP. The mechanism of rate-limiting motions in enzyme function. Proceedings of the National Academy of Sciences of the United States of America. 104: 11981-6. PMID 17615241 DOI: 10.1073/pnas.0702551104  1
2007 Jin H, Loria JP, Moore PB. Solution structure of an rRNA substrate bound to the pseudouridylation pocket of a box H/ACA snoRNA. Molecular Cell. 26: 205-15. PMID 17466623 DOI: 10.1016/j.molcel.2007.03.014  0.44
2007 Berlow RB, Igumenova TI, Loria JP. Value of a hydrogen bond in triosephosphate isomerase loop motion. Biochemistry. 46: 6001-10. PMID 17455914 DOI: 10.1021/bi700344v  1
2007 Kempf JG, Jung JY, Ragain C, Sampson NS, Loria JP. Dynamic requirements for a functional protein hinge. Journal of Molecular Biology. 368: 131-49. PMID 17336327 DOI: 10.1016/j.jmb.2007.01.074  1
2007 Doan-Nguyen V, Loria JP. The effects of cosolutes on protein dynamics: the reversal of denaturant-induced protein fluctuations by trimethylamine N-oxide. Protein Science : a Publication of the Protein Society. 16: 20-9. PMID 17123958 DOI: 10.1110/ps.062393707  0.52
2006 Gill ML, Strobel SA, Loria JP. Crystallization and characterization of the thallium form of the Oxytricha nova G-quadruplex. Nucleic Acids Research. 34: 4506-14. PMID 16945956 DOI: 10.1093/nar/gkl616  1
2006 Kovrigin EL, Loria JP. Characterization of the transition state of functional enzyme dynamics. Journal of the American Chemical Society. 128: 7724-5. PMID 16771471 DOI: 10.1021/ja061435a  1
2006 Kovrigin EL, Loria JP. Enzyme dynamics along the reaction coordinate: critical role of a conserved residue. Biochemistry. 45: 2636-47. PMID 16489757 DOI: 10.1021/bi0525066  1
2006 Kovrigin EL, Kempf JG, Grey MJ, Loria JP. Faithful estimation of dynamics parameters from CPMG relaxation dispersion measurements. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 180: 93-104. PMID 16458551 DOI: 10.1016/j.jmr.2006.01.010  1
2005 Gill ML, Strobel SA, Loria JP. 205Tl NMR methods for the characterization of monovalent cation binding to nucleic acids. Journal of the American Chemical Society. 127: 16723-32. PMID 16305263 DOI: 10.1021/ja055358f  1
2005 Beach H, Cole R, Gill ML, Loria JP. Conservation of mus-ms enzyme motions in the apo- and substrate-mimicked state. Journal of the American Chemical Society. 127: 9167-76. PMID 15969595 DOI: 10.1021/ja0514949  1
2005 Ulrich DL, Kojetin D, Bassler BL, Cavanagh J, Loria JP. Solution structure and dynamics of LuxU from Vibrio harveyi, a phosphotransferase protein involved in bacterial quorum sensing. Journal of Molecular Biology. 347: 297-307. PMID 15740742 DOI: 10.1016/j.jmb.2005.01.039  1
2004 Kempf JG, Loria JP. Measurement of intermediate exchange phenomena. Methods in Molecular Biology (Clifton, N.J.). 278: 185-231. PMID 15317998 DOI: 10.1385/1-59259-809-9:185  1
2004 Ulrich DL, Thompson R, Bassler B, Cavanagh J, Loria JP. 1H, 15N, and 13C chemical shift assignments of the Vibrio harveyi histidine phosphotransferase protein LuxU. Journal of Biomolecular Nmr. 29: 551-2. PMID 15243194 DOI: 10.1023/B:JNMR.0000034349.22942.e1  1
2004 Butterwick JA, Loria JP, Astrof NS, Kroenke CD, Cole R, Rance M, Palmer AG. Multiple time scale backbone dynamics of homologous thermophilic and mesophilic ribonuclease HI enzymes. Journal of Molecular Biology. 339: 855-71. PMID 15165855 DOI: 10.1016/j.jmb.2004.03.055  1
2003 Kempf JG, Jung JY, Sampson NS, Loria JP. Off-resonance TROSY (R1 rho - R1) for quantitation of fast exchange processes in large proteins. Journal of the American Chemical Society. 125: 12064-5. PMID 14518971 DOI: 10.1021/ja037101s  1
2003 Cole R, Loria JP. FAST-Modelfree: a program for rapid automated analysis of solution NMR spin-relaxation data. Journal of Biomolecular Nmr. 26: 203-13. PMID 12766418 DOI: 10.1023/A:1023808801134  1
2003 Kovrigin EL, Cole R, Loria JP. Temperature dependence of the backbone dynamics of ribonuclease A in the ground state and bound to the inhibitor 5'-phosphothymidine (3'-5')pyrophosphate adenosine 3'-phosphate. Biochemistry. 42: 5279-91. PMID 12731869 DOI: 10.1021/bi034027h  1
2003 Kempf JG, Loria JP. Protein dynamics from solution NMR: theory and applications. Cell Biochemistry and Biophysics. 37: 187-211. PMID 12625627 DOI: 10.1385/CBB:37:3:187  1
2002 Cole R, Loria JP. Evidence for flexibility in the function of ribonuclease A. Biochemistry. 41: 6072-81. PMID 11994002 DOI: 10.1021/bi025655m  1
2001 Palmer AG, Kroenke CD, Loria JP. Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules. Methods in Enzymology. 339: 204-38. PMID 11462813 DOI: 10.1016/S0076-6879(01)39315-1  1
2000 Millet O, Loria JP, Kroenke CD, Pons M, Palmer AG. The static magnetic field dependence of chemical exchange linebroadening defines the NMR chemical shift time scale Journal of the American Chemical Society. 122: 2867-2877. DOI: 10.1021/ja993511y  1
1999 Loria JP, Rance M, Palmer AG. A TROSY CPMG sequence for characterizing chemical exchange in large proteins. Journal of Biomolecular Nmr. 15: 151-5. PMID 10605088 DOI: 10.1023/A:1008355631073  1
1999 Loria JP, Rance M, Palmer AG. Transverse-relaxation-optimized (TROSY) gradient-enhanced triple-resonance NMR spectroscopy. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 141: 180-4. PMID 10527755 DOI: 10.1006/jmre.1999.1891  1
1999 Rance M, Loria JP, Palmer AG3rd. Sensitivity improvement of transverse relaxation-optimized spectroscopy. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 136: 92-101. PMID 9887294  1
1999 Loria JP, Rance M, Palmer AG. A relaxation-compensated Carr-Purcell-Meiboom-Gill sequence for characterizing chemical exchange by NMR spectroscopy [13] Journal of the American Chemical Society. 121: 2331-2332. DOI: 10.1021/ja983961a  1
1998 Loria JP, Nowak T. Conformational changes in yeast pyruvate kinase studied by 205Tl+ NMR. Biochemistry. 37: 6967-74. PMID 9578583 DOI: 10.1021/bi972454n  1
1998 Kroenke CD, Loria JP, Lee LK, Rance M, Palmer AG. Longitudinal and transverse 1H-15N dipolar/15N chemical shift anisotropy relaxation interference: Unambiguous determination of rotational diffusion tensors and chemical exchange effects in biological macromolecules Journal of the American Chemical Society. 120: 7905-7915. DOI: 10.1021/ja980832l  1
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