J. Patrick Loria

Professor: Depts of Chemistry and Molecular Biophysics and Biochemistry

B.S. The George Washington University, 1990; Ph.D. University of Notre Dame, 1997; NIH Postdoctoral Fellowship, Columbia University, 1998-2000; joined Yale faculty 2001; Camille & Henry Dreyfus New Faculty Fellow; NSF CAREER 2003; Alfred P. Sloan Fellow 2004.

Selected References

2024

87. "A salt bridge of the C-termnal carboxyl group regulates PHPT1 substrate affinity and catalytic activity" Zavala, E., Dansereau, S., Burke, M.J., Lipchock, J.M., Maschietto, F., Batista, V.S., Loria, J.P. Protein Science. In Press , (2023)

2023

86. "Temperature increase mimics allosteric signaling in imidazole glycerol phosphate synthase" Maschietto, F., Morzan, U., Gheeraert, A., Chaudhuri, A., Tofleanu, F., Kyro, G.W., Nekrasov, P., Loria, J.P., Rvialta, I., and Batista, V.S. Nature Communications. 14 , 2239 (2023)

2022

85. "Insights into the importance of WPD-loop sequence for activity and structure in protein tyrosine phosphatases" Shen, R., Crean, R.M., Olsen, K.J., Corbella, M., Calixto, A.R., Richan, T., Brandao, T.A.S., Berry, R.D., Tolman, A., Loria, J.P., Johnson, S.J., Kamerlin, S.C.L., and Hengge, A.C. Chemical Sciences. 13 ,13524-13540 (2022)

84. "Unified total synthesis of limonoid alkaloids: Strategies for the de novo synthesis of highly substituted pyridine scaffolds" Schuppe, A.W., Liu, Y., Gonzalez-Hurtado, E., Zhao, Y., Jiang, X., Ibarraran, S., Huang, D., Wang, E., Lee, J., Loria, J.P., Dixit, V.D., Li, X., and Newhouse, T.R. Chem. 8 ,2856-2887 (2022)

83. "A simple method to determine changes in the affinity between HisF and HisH in the imidazole glycerol phosphate synthase heterodimer" Almeida, V.M., Loria, J.P., and Marana, S.R. PLOS ONE https://doi.org/10.1371/journal.pone.0267536 , (2022)

82. "MptpA kinetics enhanced by allosteric control of an active conformation" Maschietto, F., Zavala, E., Allen, B., Loria, J.P., Batista, V. J. Mol. Biol 434 , (2022) https://doi.org/10.1016/j.jmb/2022.167540

2021

81. "Significant loop motions in the SsoPTP protein tyrosine phosphatase allow for dual general acid functionality" Pinkston, J., Jo, J., Olsen, K., Comer, D., Glaittli, C., Loria, J.P., Johnson, S., and Hengge, A. Biochemistry 60 ,2888-2901 (2021)

80. "Phosphorylation of a human microprotein promotes dissociation of biomolecular condensates" Na, Z., Luo, Y., Cui, D., Khitun, A., Smelyansky, S., J.P. Loria, and Slavoff, S. J. Am. Chem. Soc . 143 ,12675-12678 (2021)

79. "The role of a high centrality residue in protein dynamics and thermal stability" V. Almeida, A. Chaudhuri, M. Cardoso, B. Matsuyama, G. Ferreira, G. Trossini, S. Farah, R. Salinas, J.P. Loria, and S. Marano J. Structural Biology. 213 ,107773 (2021)

2020

78. "The allosteric impact of the variable insert loop in Vaccinia H1-related (VHR) phosphatase" V. Beaumont, K. Reiss, Z. Qu, B. Allen, V.Batista, and J.P. Loria. Biochemistry 59 ,1896-1908 (2020)

77. "Allosteric control of enzyme activity: From ancient origins to recent gene-editing technologies" K. Reiss, V. Batista, and J.P. Loria Biochemistry. 59 ,1711-12 (2020)

76. "A deubiquitylase with an unusually high-affinity ubiquitin-binding domain from the scrub typhus pathogen Orientia tsutsugamushi" J. Berk, C. Lim, J. Ronau, A. Chaudhuri, H. Chen, J. Beckman, J.P. Loria, Y. Xiong, and M. Hochstrasser. Nature Comm. 11 , 1-17 (2020)

2019

75. "Uncovering the molecular interactions in the catalytic loop that modulates the conformational dynamics in protein tyrosine phosphatase 1B" D. Cui, J. Lipchock, D. Brookner, and Loria, J.P. J.Am. Chem. Soc.R 141 ,pp.12634-12647 (2019).

74. "Accelerating 2D NMR relaxation dispersion experiments using iterated maps" Rovny, J., Blum, R.L., Loria, J.P., Barrett, S.E. J. Biomol NMR 73 ,pp.561-576 (2019).

73. "Reaching the sparse-sampling limit for reconstructing a single peak in a 2D NMR spectrum using iterated maps" Blum, R.L., Rovny, J., Loria, J.P., Barrett, S.E. J. Biomol NMR 73 ,pp.545-560 (2019).

2018

72. "Eigenvector centrality for characterization of protein allosteric pathways" Negre, C.F.A, Morzan, U.N., Hendrickson, H.P., Pal, R., Lisi, G.P., Loria, J.P., Rivalta, I., Ho, J., Batista, V.S. PNAS 115 ,pp. E12202-E12208 (2018).

71. "I260Q DNA polymerase beta highlights precatalytic conformational rearrangements critical for fidelity" Cary Liptak, Mariam Mahmoud, Brian Eckenroth, Marcus Moreno, Kyle East, Khadijeh Alnajjar, Ji Huang, Jamie Towle-Weicksel, Sylvie Doublie, J. Patrick Loria, and Joann Sweasy Nucleic Acid Research 46, pp. 10740-10756 (2018).

70. "A YopH PTP1B chimera shows the importance of WPD-loop sequence to activity, structure, and dynamics in protein tyrosine phosphatases" Gwendolyn Moise, Yalemi Morales, Victor Beaumont, Tim Caradonna, J. Patrick Loria, Sean Johnson, and Alvan Hengge Biochemistry 57, pp. 5315-5326 (2018).

69. "Nanosecond dynamics regulate the MIF-induced activity of CD74" Georgios Pantouris, Junming Ho, Dilip Shah, Mansoor Ali Syed, Lin Leng, Vineet Bhandari, Richard Bucula, Victor Bastista, J. Patrick Loria, and Elias Lolis Angewandte Chemie 57 ,pp. 7116-19 (2018).

2017

68. "Glutamine hydrolysis by imidazole glycerol phosphate synthase displays temperature dependent allosteric activation" George Lisi, Allen Currier, and J. Patrick Loria Frontiers in Molecular Biosciences 5 ,Article 4, pp. 1-12 (2017).Supported by NIH GM 106121

67. "Allostery in enzyme catalysis" George Lisi and J. Patrick Loria Current Opinion in Structural Biology 47,123-130 (2017).Supported by NIH GM 106121

66. "Leveraging reciprocity to identify and characterize unknown allosteric sites in protein tyrosine phosphatases" Danica S. Cui, Victor Beaumont, Patrick S. Ginther, James M Lipchock, and J. Patrick Loria J. Mol. Biol. 429, 2360-2372 (2017).Supported by NSF MCB 1615415 and GM 112781

65. "Altering the allosteric pathway in IGPS suppresses millisecond motions and catalytic activity" George Lisi, Kyle East, Victor Batista, and J. Patrick Loria PNAS. 114,E3414-E3423 (2017).

64. "Exploring protein structure and dynamics through a project-oriented biochemistry laboratory module" James Lipchock, Patrick Ginther, Bonnie Douglas, Kelly Bird, and J. Patrick Loria Biochem. & Mol. Biol. Ed. DOI: 10.1002/bmb/21056 (2017).

2016

63. "Characterization of PTP1B inhbition by chlorogenic and cichoric acid" James Lipchock, Heidi Hendrickson, Bonnie Douglas, Kelly Bird, Patrick Ginther, Ivan Rivalta, Nicholas Ten, Victor Batista, and J. Patrick Loria Biochemistry 56,96-106 (2016).Supported by NSF MCB 1615415

62. "Allosteric communication disrupted by a small molecule binding to the imidazaole glycerol phosphate synthase protein-protein interface" Ivan Rivalta, George P. Lisi, Ning-Shiuan Snoeberger, G.A. Manley, J.P. Loria, and V.S. Batista Biochemistry 55,6484-6494 (2016).

61. "Dissecting dynamic allosteric pathways using chemically related small molecule activators" G.P. Lisi, G.A. Manley, H. Hendrickson, I. Rivalta, V.S. Batista , and J.P. Loria Structure 24, 1155-1166 (2016).

60. "Induced fit in the selection of correct versus incorrect nucleotides by DNA polymerase beta",B. Moscato, M. Swain , and J.P. Loria Biochemistry 55,382-395 (2016).

59. "Solution NMR spectroscopy for the study of enzyme allostery",G.P. Lisi and J.P. Loria Chem. Rev. 116, 6323-6369 (2016).

58. "Using NMR spectroscopy to elucidate the role of molecular motions in enzyme function",G.P. Lisi and J.P. Loria Prog. NMR Spectroscopy 92-93,1-17 (2016).

2015

57. "The complexity of protein energy landscapes studied by solution NMR relaxation dispersion experiments",G. Khirich, J.P. Loria J. Phys. Chem. B 119,3743-3754 (2015).

56. "Movement and specificity in a modular DNA binding protein",C. Liptak, J.P. Loria Structure 23,973-4 (2015).

2014

55. "MoD-QM/MM structural refinement method: Characterization of hydrogen bonding in the Oxytricha nova G-Quadruplex",J. Ho, M.B. Newcomer, C.M. Ragain, J.A. Gascon, E.R. Batista, J.P. Loria, V.S. Batista J. Chem Theory Comput. 10,5125-5135 (2014).

54. "Enzyme architecture: the effect of replacement and deletion mutations of loop 6 on catalysis by triosephosphate isomerase",X. Zhai, M.K. Go, A.C. Donoghue, T.L. Amyes, S.D. Pegan, Y. Wang, J.P. Loria, A.D. Mesecar, and J.P. Richard Biochemistry 53,3486-3501 (2014).

2013

53. "Conformational motions regulate phosphoryl transfer in related protein tyrosine phosphatases",Sean Whittier, Alvan Hengge, and J.P. Loria Science 341,899-903 (2013). http://www.sciencemag.org/cgi/content/short/341/6148/899

52. "What's in your buffer? Solute altered millisecond motions detected by solution NMR",M.Wong, G. Khirich, and J.P. Loria Biochemistry 52, 6548-6558 (2013).

51. "Structural mutations that probe the interactions between the catalytic and dianion activation sites in triosephosphate isomerase",X. Zhai, T.L. Amyes, R.K. Wierenga, J.P. Loria, and J.P. Richard Biochemistry 52,5928-5939 (2013).

50. “Accelerating multidimensional NMR and MRI experiments using iterated maps”, M.A. Frey, Z.M. Sethna, G.A. Manley, S. Sengupta, K.W. Zilm, J.P. Loria, and S.E. Barrett, J. Magn. Reson, 237, 100-109 (2013).

49. "1H,15N, and 13C resonance assignments for the Yersinia protein tyrosine phosphatase, YopH", Sean Whittier and J.P. Loria Biomol. NMR Assignments Epub ahead of print, Sept, 12 (2013).

48. "MIF intersubunit disulfide mutant antagonist supports activation of CD74 by endogenous MIF trimer at physiological concentrations",Chengpeng Fan, Deepa Rajasekaran, Mansoor Ali Syed, Lin Leng, J.P. Loria, Vineet Bhandari, Richard Bucala, and Elias Lolis Proc. Natl. Acad. Sci. USA 110, 10994-10999 (2013).

47. "Solution NMR and computational methods for understanding protein allostery",Gregory Manley, Ivan Rivalta, and J.P. Loria Featured Article J.Phys.Chem. B 117, 3063-3073 (2013).

2012

46. "Allosteric pathways in the imidazole glycerol phosphate synthase",Ivan Rivalta, Mohammed M. Sultan, Ning-Shiuan Lee, Gregory Manley, J.P. Loria, and Victor Batista Proc. Natl. Acad. Sci. USA 109,E1428-E1436 (2012).

45. "Substrate-dependent millisecond domain motions in DNA Polymerase Beta",Rebecca Berlow, Monalisa Swain, Shibani Dalal, Joann Sweasy, and J.P. Loria J. Mol. Biol. 419,171-182 (2012).

44. "Dynamics in enzymes:solution NMR studies,"J.P. Loria in Encyclopedia of Magnetic Resonance DOI:10.1002/9780470034590.emrstm1241, (2012).

43. "NMR relaxation dispersion studies of large enzymes in solution,"Sean K. Whittier and J.P. Loria Royal Society of Chemistry: Recent Developments in Biomolecular NMR RSC series No. 25 ,Ed. M. Clore & J. Potts, RSC Publishing, Cambridge, 151-162 (2012).

42. "NMR insights into protein allostery,"Gregory Manley and J.P. Loria Arch. Biochem. Biophys. 519, 223 (2012).

2011

41. "Reengineering rate-limiting millisecond enzyme motion by introduction of an unnatural amino acid," Eric D. Watt, Ivan Rivalta, Sean Whittier, Victor Batista and J.P. Loria Biophysical Journal 101, 411 (2011).

40. "Relaxation Dispersion Studies of Enzyme Motions," Nicolas Doucet and J.P. Loria in Advances in Biomedical Spectroscopy: Biomolecular NMR Spectroscopy IOS Press, Vol 3,185 (2011).

39. "The alteration of hydrogen bonding in the vicinity of histidine 48 disrupts millisecond motions in RNase A", Nicolas Doucet, Gennady Khirich, Evgenii Kovrigin, and J.P. Loria Biochemistry 50,1723-1730(2011).

2010

38. "Nanometer propagation of millisecond motions in V-type allostery", James Lipchock and J.P. Loria Structure 18,1596-1607 (2010).

37. "The crystal structure of ribonuclease A in complex with thymidine-3'-monophosphate provides further insight into ligand binding", Nicolas Doucet, Thusitha Jayasundera, Miljan Simonovic and J.P. Loria Prot:Structure, Function, and Bioinformatics 78,2459-2468 (2010).

2009

36. "Helix stabilization precedes aqueous and bilayer catalyzed fiber formation in islet amyloid polypeptide", Jessica A. Williamson, J.P. Loria and A.D. Miranker J. Mol. Biol.. 393,383-396 (2009).

35. "The flexibility of a distant loop modulates active-site motion and product release in ribonuclease A", Nicolas Doucet, Eric Watt and J.P. Loria Biochemistry. 48,7160-7168 (2009).

34. "Millisecond dynamics in the allosteric enzyme imidazole glycerol phosphate synthase (IGPS) from Thermotoga maritima", James Lipchock and J.P. Loria J. Biomol NMR. 45,73-84 (2009).

33. "The role of loop-loop interactions in coordinating motions and enzymatic function in triosephosphate isomerase" Wang, Y., Berlow, R., and J.P. Loria Biochemistry. 48,4548-4556 (2009).

32. "Molecular Interactions by NMR," James Lipchock and J.P. Loria in Methods Mol Biol:Protein Structure, Stability, and Interactions Humana Press (2009).

2008

31. "Characterization of enzyme motions by solution NMR relaxation dispersion," J.P. Loria, Rebecca B. Berlow, and Eric D. Watt Acc. Chem. Res. 41,214-221 (2008).

30. "1H, 15N and 13C resonance assignment of imidazole glycerol phosphate (IGP) synthase protein HisF from Thermotoga maritima," James Lipchock and J.P. Loria Biomol. NMR Ass. 2,219-221 (2008).

2007

29. "The Mechanism of Rate-limiting Motions in Enzyme Function," Eric D. Watt, Hiroko Shimada, Evgenii L. Kovrigin, and J.P. Loria PNAS 104, 11981-11986 (2007).

28. "The value of a hydrogen bond in triosephosphate isomerase loop motion," R. Berlow, T. Igumenova, and J.P. Loria Biochemistry 46, 6001-6010 (2007).

27. "Solution structure of an rRNA substrate bound to the pseudouridylation pocket of a box H/ACA snoRNA," Hong Jin, J.P. Loria, and Peter B. Moore Mol. Cell 26, 205-215 (2007).

26. "Dynamic requirements for a functional protein hinge," Kempf, J.G., Jung, J., Ragain, C., Sampson, N., and J.P. Loria J. Mol. Bio. 368, 131-149 (2007).

25. "The effects of cosolutes on protein dynamics: The reversal of denaturant-induced protein fluctuations by trimethylamine N-oxide," Vicky Doan-Nguyen and J.P. Loria Protein Science 16,20-29 (2007).

2006

24. "Crystallization and characterization of the thallium-form of the Oxytricha nova G-quadruplex," Michelle Gill, Scott Strobel and J.P. Loria Nuc. Acid Res. 34, 4506-4514 (2006).

23. "Characterization of the transition state of functional enzyme dynamics," Evgenii L. Kovrigin and J.P. Loria J. Am. Chem. Soc. 128,7724-7725 (2006).

22. "Enzyme dynamics along the reaction coordinate: critical role of a conserved residue," Evgenii L. Kovrigin and J.P. Loria Biochemistry 45,2636-2647 (2006).

21. "Faithful estimation of dynamics parameters from CPMG relaxation dispersion measurements," Evgenii L. Kovrigin, James G. Kempf, Michael J. Grey, and J.P. Loria J. Magn. Reson. 180,93-104 (2006).

2005

20. "205Tl NMR methods for the characterization of monovalent cation binding to nucleic acids," Michelle Gill, Scott Strobel, and J.P. Loria J. Am. Chem. Soc. 127, 16723-16732 (2005).

19. "Conservation of us-ms enzyme motions in the apo- and substrate mimicked state," Heather Beach, Roger Cole, Michelle Gill, and J.P. Loria J. Am. Chem. Soc. 127, 9167-9176 (2005).

18. "Solution structure and dynamics of LuxU from Vibrio harveyi a phosphotransferase protein involved in bacterial quorum sensing," Dagny L. Ulrich, Douglas Kojetin, Bonnie Bassler, John Cavanagh, and J.P. Loria J. Mol. Bio. 347, 297-307 (2005).

2004

17. "1H, 15N, and 13C chemical shift assignments of the Vibrio harveyi histidine phosphotransferase protein LuxU," Dagny L. Ulrich, Richele Thompson, Bonnie Bassler, John Cavanagh, and J.P. Loria J. Biomol. NMR 29, 551-552 (2004).

16. "Multiple time-scale dynamics of homologous thermophilic and mesophilic ribonuclease HI enzymes," Joel A. Butterwick, J.P. Loria, Nathan S. Astrof, Christopher D. Kroenke, Roger Cole, Mark Rance, and Arthur G. Palmer J.Mol. Biol. 339, 855-871 (2004).

15. "Measurement of intermediate exchange phenomena," James G. Kempf & J.P. Loria in Methods Mol Biol:Protein NMR Techniques Humana Press Ed. 2, 185-231 (2004).

2003

14. "Off-resonance TROSY (R1rho - R1) for quantitation of fast exchange processes in large proteins," James G. Kempf, Ju-yeon Jung, N.S. Sampson, and J.P. Loria, J. Am. Chem. Soc 125, 12064-5 (2003).

13. "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," Evgenii Kovrigin, Roger Cole and J.P. Loria, Biochemistry 42, 5279-5291 (2003).

12. "FAST-Modelfree: a program for rapid automated analysis of solution NMR spin-relaxation data," Roger Cole and J.P. Loria, Journal of Biomolecular NMR 26, 203-213 (2003).

2002

11. "Protein dynamics from solution NMR: Theory and applications," James G. Kempf and J.P. Loria, Cell Biochemistry & Biophysics 39, 187-212 (2002).

10. "Evidence for flexibility in the function of Ribonuclease A," Roger Cole and J.P. Loria, Biochemistry 41, 6072-6081 (2002).

2001

9. "NMR methods for quantifying microsecond-millisecond motions in biological macromolecules," A.G. Palmer, C.D. Kroenke, and J.P. Loria, Methods. Enzymol. 339, 204-238 (2001).

2000

8. "The static magnetic field dependence of chemical exchange linebroadening defines the NMR chemical shift time scale," O. Millet, J.P. Loria, C.D. Kroenke, M. Pons, and A.G. Palmer, J. Am. Chem. Soc. 122, 2867-2877 (2000).

1999

7. "Transverse-relaxation-optimized (TROSY) gradient-enhanced triple-resonance NMR spectroscopy," J.P. Loria, M. Rance, and A.G. Palmer, J. Magn. Reson. 141, 180-184 (1999).

6. "A TROSY CPMG sequence for characterizing chemical exchange in large proteins," J.P. Loria, M. Rance, and A.G. Palmer, J. Biomol. NMR. 15. 151-155 (1999).

5. "Relaxation-compensated Carr-Purcell-Meiboom-Gill experiments for characterizing kinetic processes by NMR spectroscopy," J.P. Loria, M. Rance, and A.G. Palmer, J. Am. Chem. Soc. 121, 2331-2332 (1999).

4. "Sensitivity improvement in transverse relaxation optimized spectroscopy (TROSY)," M. Rance, J.P. Loria, and A.G. Palmer, J. Magn. Reson. 136, 82-102 (1999).

1998

3. "Longitudinal and transverse 1H-15N chemical shift anisotropy relaxation interference: Unambiguous determination of rotational diffusion tensors and chemical exchange effects in biological macromolecules," C.D. Kroenke, J.P. Loria, L.K. Lee, M. Rance, and A.G. Palmer, J. Am. Chem. Soc. 120, 7905-7915 (1998).

2. "Conformational changes in yeast pyruvate kinase studied by 205Tl+ NMR," J.P. Loria and T. Nowak, Biochemistry 37, 6967-6974 (1998).

1995

1. "Glycerolphosphocholine, a component of both Ascaris suum and Caenorhabditis elegans," J.L. Arevalo, H.J. Saz, T. Nowak, and J.P. Larry(Loria) J.Parasitol 81, 335-340 (1995).