About

Professor J. Patrick Loria is a faculty member at Yale University, with a research focus on enzyme dynamics, substrate specificity, and protein interactions. His lab investigates the structural and functional mechanisms of enzymes such as protein tyrosine phosphatases, DNA polymerases, and archaeal phosphatases, utilizing techniques like high-resolution relaxometry to understand enzyme behavior and regulation. His work aims to elucidate the molecular basis of enzyme function and its implications in cellular processes and disease.

Research topics

• Biochemistry
• Cell biology
• Chemistry
• Biology
• Biophysics
• Virology
• Mathematics
• Microbiology
• Computational biology

Selected publications

• Distal Mutations Rewire Allosteric Networks to Control Substrate Specificity in PTP1B

  Biochemistry · 2025-11-26 · 2 citations

  articleOpen accessSenior authorCorresponding

  Protein tyrosine phosphatase 1B (PTP1B) is a key regulator of cellular signaling pathways, and its dysregulation is linked to diabetes, obesity, cancer, and immune dysfunction. While the catalytic mechanism of PTP1B is conserved across protein tyrosine phosphatases, its regulation by distal allosteric sites remains less understood. Here, we investigate how mutations at four allosteric sites (Y153, I275, M282, and E297) alter the PTP1B substrate specificity and enzymatic dynamics. Kinetic analyses with phosphotyrosine peptides and p-nitrophenylphosphate reveal that allosteric mutants display distinct changes in catalytic efficiency (kcat/Km), in some cases reversing substrate preference relative to the wild-type enzyme. Solution NMR spectroscopy and microsecond molecular dynamics simulations demonstrate that these mutations perturb long-range communication networks, disrupting coupling between helices α3 and α7 and altering acid-loop flexibility and active-site dynamics. Notably, the E297A mutation has the most pronounced effects, rigidifying the acid loop and weakening allosteric communication to the catalytic center. Community network analysis highlights the acid loop and helix α7 as central hubs linking distal sites to the active site. Together, these results establish that distal mutations can reshape PTP1B’s dynamic landscape, thereby modulating substrate specificity. This work expands our understanding of allosteric regulation in PTP1B and provides a framework for targeting dynamic networks to control phosphatase activity.

  PublisherOA PDFDOI

• Conformational Dynamics and Catalytic Backups in a Hyper-thermostable Engineered Archaeal Protein Tyrosine Phosphatase

  JACS Au · 2025-12-10

  articleOpen access

  Protein tyrosine phosphatases (PTPs) are a family of enzymes that play important roles in regulating cellular signaling pathways. The activity of these enzymes is regulated by the motion of a catalytic loop that places a critical conserved aspartic acid side chain into the active site for acid-base catalysis upon loop closure. These enzymes also have a conserved phosphate-binding loop that is typically highly rigid and forms a well-defined anion-binding nest. The intimate links between loop dynamics and chemistry in these enzymes make PTPs an excellent model system for understanding the role of loop dynamics in protein function and evolution. In this context, archaeal PTPs, which have often evolved in extremophilic organisms, are highly understudied, despite their unusual biophysical properties. We present here an engineered chimeric PTP (ShufPTP) generated by shuffling the amino acid sequence of five extant hyperthermophilic archaeal PTPs. Despite ShufPTP's high sequence similarity to its natural counterparts, it presents a suite of unique properties, including high flexibility of the phosphate binding P-loop, facile oxidation of the active-site cysteine, mechanistic promiscuity, and, most notably, hyperthermostability, with a denaturation temperature likely >130 °C (>8 °C higher than the highest recorded growth temperature of any archaeal strain). Our combined structural, biochemical, biophysical, and computational analysis provides insight both into how small steps in evolutionary space can radically modulate the biophysical properties of an enzyme and showcases the tremendous potential of archaeal enzymes for biotechnology, to generate novel enzymes capable of operating under extreme conditions.

  PublisherDOI

• Conformational Dynamics and Catalytic Backups in a Hyper-Thermostable Engineered Archaeal Protein Tyrosine Phosphatase

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-03-26

  preprintOpen access

  Protein tyrosine phosphatases (PTPs) are a family of enzymes that play important roles in regulating cellular signaling pathways. The activity of these enzymes is regulated by the motion of a catalytic loop that places a critical conserved aspartic acid side chain into the active site for acid-base catalysis upon loop closure. These enzymes also have a conserved phosphate binding loop that is typically highly rigid and forms a well-defined anion binding nest. The intimate links between loop dynamics and chemistry in these enzymes make PTPs an excellent model system for understanding the role of loop dynamics in protein function and evolution. In this context, archaeal PTPs, which have evolved in extremophilic organisms, are highly understudied, despite their unusual biophysical properties. We present here an engineered chimeric PTP (ShufPTP) generated by shuffling the amino acid sequence of five extant hyperthermophilic archaeal PTPs. Despite ShufPTP's high sequence similarity to its natural counterparts, ShufPTP presents a suite of unique properties, including high flexibility of the phosphate binding P-loop, facile oxidation of the active site cysteine, mechanistic promiscuity, and most notably, hyperthermostability, with a denaturation temperature likely >130 °C (>8°C higher than the highest recorded growth temperature of any archaeal strain). Our combined structural, biochemical, biophysical and computational analysis provides insight both into how small steps in evolutionary space can radically modulate the biophysical properties of an enzyme, and showcase the tremendous potential of archaeal enzymes for biotechnology, to generate novel enzymes capable of operating under extreme conditions.

  PublisherOA PDFDOI

• Conformational Dynamics and Catalytic Backups in a Hyper-Thermostable Engineered Archaeal Protein Tyrosine Phosphatase

  SSRN Electronic Journal · 2025-01-01

  preprintOpen access
  PublisherDOI

• Unbiased clustering of residues undergoing synchronous motions in proteins using NMR spin relaxation data

  Biophysical Chemistry · 2025-02-15 · 2 citations

  articleOpen access
  PublisherOA PDFDOI

• A salt bridge of the C‐terminal carboxyl group regulates <scp>PHPT1</scp> substrate affinity and catalytic activity

  Protein Science · 2024-05-15 · 5 citations

  articleOpen accessSenior authorCorresponding

  Abstract PHPT1 is a histidine phosphatase that modulates signaling in eukaryotes through its catalytic activity. Here, we present an analysis of the structure and dynamics of PHPT1 through a combination of solution NMR, molecular dynamics, and biochemical experiments. We identify a salt bridge formed between the R78 guanidinium moiety and the C‐terminal carboxyl group on Y125 that is critical for ligand binding. Disruption of the salt bridge by appending a glycine residue at the C‐terminus (G126) leads to a decrease in catalytic activity and binding affinity for the pseudo substrate, para‐nitrophenylphosphate (pNPP), as well as the active site inhibitor, phenylphosphonic acid (PPA). We show through NMR chemical shift, 15 N relaxation measurements, and analysis of molecular dynamics trajectories, that removal of this salt bridge results in an active site that is altered both structurally and dynamically thereby significantly impacting enzymatic function and confirming the importance of this electrostatic interaction.

  PublisherOA PDFDOI

• Unbiased Clustering of Residues Undergoing Synchronous Motions in Proteins Using Nmr Spin Relaxation Data

  SSRN Electronic Journal · 2024-01-01

  preprintOpen access
  PublisherDOI

• Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase

  Nature Communications · 2023-04-19 · 16 citations

  articleOpen access

  Allosteric drugs have the potential to revolutionize biomedicine due to their enhanced selectivity and protection against overdosage. However, we need to better understand allosteric mechanisms in order to fully harness their potential in drug discovery. In this study, molecular dynamics simulations and nuclear magnetic resonance spectroscopy are used to investigate how increases in temperature affect allostery in imidazole glycerol phosphate synthase. Results demonstrate that temperature increase triggers a cascade of local amino acid-to-amino acid dynamics that remarkably resembles the allosteric activation that takes place upon effector binding. The differences in the allosteric response elicited by temperature increase as opposed to effector binding are conditional to the alterations of collective motions induced by either mode of activation. This work provides an atomistic picture of temperature-dependent allostery, which could be harnessed to more precisely control enzyme function.

  PublisherDOI

• Author Correction: Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase

  Nature Communications · 2023-05-05

  erratumOpen access
  PublisherOA PDFDOI

• CCDC 2115742: Experimental Crystal Structure Determination

  The Cambridge Structural Database · 2023-01-04

  datasetOpen access

  An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  PublisherDOI

Recent grants

• CAREER: The Role of Dynamics in Enzyme Function by NMR, Chemical Synthesis, and Biochemistry

  NSF · $538k · 2003–2008

• NIH Grant R01GM099990

  NIH · $1.2M · 2017

• Computational and Biochemical Studies of Temperature Effects on Allostery in the Imidazole Glycerol Phosphate Synthase (IGPS) from T. maritima

  NIH · $2.0M · 2014–2023

• Predoctoral Program in Biophysics

  NIH · $12.8M · 1988–2023

• Allosteric control of loop motions

  NSF · $900k · 2016–2021

Frequent coauthors

• Ivan Rivalta

  23 shared

• Víctor S. Batista

  Yale University

  19 shared

• Arthur G. Palmer

  Columbia University

  18 shared

• Rebecca B. Berlow

  University of North Carolina at Chapel Hill

  16 shared

• James Kempf

  13 shared

• Mark Rance

  13 shared

• J.M. Lipchock

  Montgomery College

  12 shared

• Alvan C. Hengge

  12 shared

Labs

• Loria LabPI

  Not provided

Awards & honors

• Camille and Henry Dreyfus New Faculty award (2001)
• NSF CAREER Award (2003)
• Alfred P. Sloan Fellow (2004)