* Corresponding Author(s);
Pre-prints
(68) Manjula, R.; Ghanem, L.; Skeens, E.; Bai, L.; Lisi, G.P.; Lolis, E.J.; Bennett, A.M.* Functional Coupling between the α4-α5 Loop and Allosteric Site on MKP5 is a Critical Determinant of Catalysis bioRxiv. 2026. DOI: 10.64898/2026.06.01.729370
(67) Knight, A.L.; Belato, H.B.; Dresser, C.S.; Pindi, C.; Mercado, B.J.; Lasekan, P.; Luo, J.; Arantes, P.R.; Jogl, G.*; Palermo, G.*: Lisi, G.P.* Orthosteric and Allosteric Effects of anti-CRISPR II-C1 Inhibition on GeoCas9 from Integrated Structural Biophysics bioRxiv. 2026. DOI: 10.64898/2026.04.08.717222
(66) Cui, D.S.; Anderson, E.O.; Zavala, E.; Lisi, G.P.; Loria, J.P.* Facilitating NMR Resonance Assignment with Metabolic Tampering bioRxiv. 2026. DOI: 10.64898/2026.04.29.721603
(65) East, K.W.; Leith, A.; Ragavendran, A.; Delaglio, F.; Lisi, G.P.* NMRdock: Lightweight and Modular NMR Processing bioRxiv. 2019. DOI: 10.1101/679688
2026
(64) Ahsan, M.; Knight, A.L.; Saha, A.; Ramos, D.; Strohkendl, I.; Skeens, E.; West, M.S.; Luo, J.; Dresser, C.S.; Taylor, D.W.; Lisi, G.P.*; Palermo, G.* A Cryptic Binding Pocket Regulates the Metal-dependent Activity of Cas9 Nature Communications. 2026. In press (MA and ALK contributed equally)
(63) Handelmann, C.R.; Skeens, E.; Lisi, G.P.; Buck, M.J.* Evaluating High-fidelity CRISPR-Cas Nucleases in Nucleosomal Contexts using a Quantitative Framework Frontiers in Genome Editing. 2026. 8. DOI: 10.3389/fgeed.2026.1759382
(62) Cui, J.Y.; Varghese, I; Bock, A.S.; Floody, M.; Zhang, F.; Rubenstein, B.M.; Lisi, G.P.* Exploring the GM-CSF Histidine Triad as a Modulator of Structure, Molecular Motion, and Ligand Binding RSC Chemical Biology. 2026. 7. 1409-1419 (JYC and IV contributed equally)
(61) Wu, Z.; Widjaja, V.; Skeens, E.; van der Velde, J.J.H.; Zahran, M.; Zhang, J.; Cool, R.H.; Poelarends, G.J.; Lisi, G.P.; Dekker, F.J.* Discovery of Furan-2-carboxylic Acid Derivatives as Novel D-dopachrome Tautomerase (D-DT) and Macrophage Migration Inhibitory Factor-1 (MIF-1) Dual Inhibitors Journal of Medicinal Chemistry. 2026. 69. 5712-5728
(60) Molina, C.E.; Knight, A.L.; Lisi, G.P.* Comparative Thermodynamic and Kinetic Properties Governing the Nucleic Acid Interactions of CRISPR-Cas9 And Cas12a Physical Biology. 2026. 23. 021001-021012
(59) Lisi, G.P.* Disorder, Dynamics, and Regulation of Proteins and Nucleic Acids Journal of Structural Biology. 2026. 218. 108258
2025
(58) Vieyra, F.H.; Pindi, C.; Lisi, G.P.; Morzan, U.N.*; Palermo, G.* Design Rules for Expanding PAM Compatibility in CRISPR-Cas9 from the VQR, VRER, and EQR Variants Journal of Physical Chemistry B. 2025. 129. 11949-11958 (FHV and CP contributed equally)
(57) Widjaja, V.; D'Orazio, S.M.; Das, P.; Rajendran, D.T.; Takada, X.; Shi, Y.; Varghese, I.; Lam, Y.; DaSilva, N.; Wang, J.; Batista, V.S.; Bhandari, V.; Lisi, G.P.* Atomistic Modulation of MIF-2 Structure, Catalysis, and Biological Signaling via Cysteine Residues and a Small Molecule, Ebselen Protein Science. 2025. 34. e70344-e70359
(56) Knight, A.L.; Luo, J.; Lisi, G.P.* Assessing Temperature-dependent DNA Cleavage by CRISPR-Cas9 Bio-protocol. 2025. 15. e5463-e5474
(55) Skeens, E.; Maschietto, F.; Ramu, M.; Shillingford, S.; Murphy, J.W.; Lolis, E.J.;* Batista, V.S.;* Bennett, A.M.*; Lisi, G.P.* Dynamic and Structural Insights into Allosteric Regulation on MKP5, A Dual-specificity Phosphatase Nature Communications. 2025. 16. 7011-7024 (ES and FM contributed equally)
(54) Knight, A.L.; Lisi, G.P.* Spy-ing on Nucleic Acids: Atomic Resolution of the S. pyogenes CRISPR-Cas9 Surveillance State Structure. 2025. 33. 636-638
- Structure Spotlight
(53) Clark, M.E.; Farinha, A.; Morrison, A.R.*; Lisi, G.P.* Structural, Biological, and Biomedical Implications of mRNA Interactions with the Master Regulator HuR NAR Molecular Medicine. 2025. DOI: 10.1093/narmme/ugaf002
2024
(52) Sajko, S.; Skeens, E.; Schinagl, A.; Ferhat, M.; Mirkina, I.; Mayer, J.; Rossmueller, G.; Thiele, M.*; Lisi, G.P.* Redox-dependent Plasticity of oxMIF Facilitates its Interaction with CD74 and Therapeutic Antibodies Redox Biology. 2024. 75. 103264-103278
(51) Belato, H.B.; Knight, A.L.; D'Ordine, A.M.; Pindi, C.; Fan, Z.; Luo, J.; Palermo, G.; Jogl, G.; Lisi, G.P.* Structural and Dynamic Impacts of Single-atom Disruptions to Guide RNA Interactions within the Recognition Lobe of Geobacillus stearothermophilus Cas9 eLife. 2024. 13. RP99275- RP99296 (HBB and ALK contributed equally)
(50) Monteiro da Silva, G.; Cui, J.Y.; Dalgarno, D.C.; Lisi, G.P.; Rubenstein, B.M.* High-throughput Prediction of Protein Conformational Distributions with Subsampled AlphaFold2 Nature Communications. 2024. 15. 2464-2476
- "New Technique for Predicting Protein Dynamics May Prove Big Breakthrough for Drug Discovery" (Press - Blavatnik Family Foundation)
(49) Skeens, E.; Sinha, S.; Ahsan, M.; D'Ordine, A.M.; Jogl, G.; Palermo, G.*; Lisi, G.P.* High-fidelity, Hyper-accurate, and Evolved Mutants Rewire Atomic Level Communication in CRISPR-Cas9 Science Advances. 2024. 10. eadl1045-1056 (ES and SS contributed equally)
2023
(48) Wang, J.; Maschietto, F.; Qiu, T.; Arantes, P.R.; Skeens, E.; Palermo, G.*; Lisi, G.P.*; Batista, V.S.* Substrate-indpendent Activation Pathways of the CRISPR-Cas9 HNH Nuclease Biophysical Journal. 2023. 122. 4635-4644
(47) Knight, A.L.; Widjaja, V.; Lisi, G.P.* Temperature as a Modulator of Allosteric Motions and Crosstalk in Mesophilic and Thermophilic Enzymes Frontiers in Molecular Biosciences. 2023. DOI: 10.3389/fmolb.2023.1281062 (ALK and VW contributed equally)
- Thematic issue "Allosteric Functions and Inhibitions: Structural Insights"
(46) Chen E.; Widjaja, V.; Kyro, G.; Allen, B.; Das, P.; Prahaladan, V.M.; Bhandari, V.; Lolis, E.J.; Batista, V.S.*; Lisi, G.P.* Mapping N- to C-terminal Allosteric Coupling through Disruption of a Putative CD74 Activation Site in D-dopachrome Tautomerase Journal of Biological Chemistry. 2023. 299, 104729-104740 (EC and VW contributed equally)
(45) Parkins, A.; Chen E.; Rangel, V.; Singh, M.; Xue, L.; Lisi, G.P.; Pantouris, G.* Ligand-induced Conformational Changes Enable Intersubunit Communications in D-dopachrome Tautomerase Biophysical Journal. 2023. 122, 1268-1276
(44) Maschietto, F.; Qiu, T.; Wang, J.*; Shi, Y.; Allen, B.; Lisi, G.P.; Lolis, E.; Batista, V.S.* Valproate Coenzyme-A Conjugate Blocks Opening of Receptor Binding Domains in the Spike Trimer of SARS-CoV-2 through an Allosteric Mechanism Computational and Structural Biotechnology Journal. 2023. 21. 1066-1076
(43) Belato, H.B.; Lisi, G.P.* The Many (Inter)faces of Anti-CRISPRs: Modulation of CRISPR-Cas Structure and Dynamics by Mechanistically Diverse Inhibitors Biomolecules. 2023. 13. 264-277
- Feature paper in Molecular Structure and Dynamics
(42) Skeens, E.; Lisi, G.P.* Analysis of Coordinated NMR Chemical Shifts to Map Allosteric Networks in Proteins Methods. 2023. 209. 40-47
- Thematic issue "New Methods in Biomolecular NMR Spectroscopy"
(41) Wang, J.*; Arantes, P.R.; Ahsan, M.; Sinha, S.; Kyro, G.W.; Maschietto, F.; Allen, B.; Skeens, E.; Lisi, G.P.*; Batista, V.S.*; Palermo, G.* Twisting and Swiveling Domain Motions in Cas9 to Recognize Target DNA Duplexes, Make Double-stranded Breaks, and Release Cleaved Duplexes Frontiers in Molecular Biosciences. 2023. DOI: 10.3389/fmolb.2022.1072733
2022
(40) Belato, H.B.; Norbrun, C.; Luo, J.; Pindi, C.; Sinha, S.; D'Ordine, A.M.; Jogl, G.; Palermo, G.*; Lisi, G.P.* Disruption of Electrostatic Contacts in the HNH Nuclease from a Thermophilic Cas9 Rewires Allosteric Motions and Enhances High-temperature DNA Cleavage Journal of Chemical Physics. 2022. 157. 225103-225113
- Thematic collection "New Views of Allostery"
(39) Fredericks, A.M.; East, K.W.; Shi, Y.; Liu, J.; Maschietto, F.; Ayala, A.; Cioffi, W.G.; Cohen, M.; Fairbrother, W.G.; Lefort, C.T.; Nau, G.;J.; Levy, M.M.; Wang, J.; Batista, V.S. Lisi, G.P.*; Monaghan, S.F.* Identification and Mechanistic Basis of non-ACE2 Blocking Neutralizing Antibodies from COVID-19 Patients with Deep RNA Sequencing and Molecular Dynamics Simulations Frontiers in Molecular Biosciences. 2022. DOI: 10.3389/fmolb.2022.1080964 (AMF, KWE, and YS contributed equally)
(38) Wang, J.*; Liu, J.; Gisriel, C.J.; Wu, S.; Maschietto, F.; Flesher, D.A.; Lolis, E.; Lisi, G.P.; Brudvig, G.W.; Xiong, Y.; Batista, V.S. How to Correct Relative Voxel Scale Factors for Calculations of Vector-difference Fourier Maps in Cryo-EM Journal of Structural Biology. 2022. 214. 107902-107915
(37) Wang, J.*; Shi, Y.; Reiss, K.; Maschietto, F.; Lolis, E.; Konigsberg, W.; Lisi, G.P.; Batista, V.S.* Structural Insights into Binding of Remdesivir Triphosphate within the Replication-transcription Complex of SARS-CoV-2 Biochemistry. 2022. 61. 1966-1973
(36) Nierzwicki, L.; East, K.W.; Binz, J.; Hsu, R.V.; Arantes, P.R.; Ahsan, M.; Skeens, E.; Pacesa, M.; Jinek, M.; Lisi, G.P.*; Palermo, G.* Principles of Target DNA Cleavage and the Role of Mg2+ in the Catalysis of CRISPR-Cas9 Nature Catalysis. 2022. 5. 912-922
(35) Wang, J.*; Skeens, E.; Arantes, P.R.; Maschietto, F.; Allen, B.; Kyro, G.; Lisi, G.P.*; Palermo, G.*; Batista, V.S.* Structural Basis for Reduced Dynamics of Three Engineered HNH Endonuclease Lys-to-Ala Mutants of the CRISPR-Cas9 Enzyme Biochemistry. 2022. 61. 785-794.
(34) Lisi, G.P.*; Rivalta, I.*; Venditti, V.* Editorial: Structural and Dynamic Aspects of Protein Function and Allostery Frontiers in Molecular Biosciences. 2022. DOI: 10.3389/fmolb.2022.876499
(33) Wang, J.; Shi, Y.; Reiss, K.; Allen, B.; Maschietto, F.; Lolis, E.J.; Konigsberg, W.; Lisi, G.P.; Batista, V.S.* Insights into Binding of Single-stranded Viral RNA Template to the Replication-transcription Complex of SARS-CoV-2 for the Priming Reaction from Molecular Dynamics Simulations Biochemistry. 2022. 61. 424-432
(32) Skeens, E.; Gadzuk-Shea, M.M.; Shah, D.; Bhandari, V.; Schweppe, D.K.; Berlow, R.B.*; Lisi, G.P.* Redox-dependent Structure and Dynamics of Macrophage Migration Inhibitory Factor Reveal Sites of Latent Allostery Structure. 2022. 30. 840-850
- Commentary in Structure 2022 "Cytokine Aerobics: Oxidation Controls Cytokine Dynamics and Function"
(31) Skeens, E.; Pantouris, G.; Shah, D.; Manjula, R.; Ombrello, M.J.; Maluf, N.K.; Bhandari, V.; Lisi, G.P.*; Lolis, E.J.* A Cysteine Variant at an Allosteric Site Alters MIF Dynamics and Biological Function in Homo- and Heterotrimeric Assemblies Frontiers in Molecular Biosciences. 2022. 9. DOI: 10.3389/fmolb.2022.783669 (ES and GP contributed equally)
2021
(30) Nierzwicki, L.; East, K.W.; Morzan, U.N.; Arantes, P.R.; Batista, V.S.; Lisi, G.P.*; Palermo, G.* Enhanced Specificity Mutations Perturb Allosteric Signaling in CRISPR-Cas9 eLife. 2021. 10. e73601 (LN and KWE contributed equally)
- Journal Cover Art
(29) Belato, H.B.; D'Ordine, A.M.; Nierzwicki, L.; Arantes, P.R.; Jogl, G.; Palermo, G.*; Lisi, G.P.* Structural and Dynamic Insights into the HNH Nuclease of Divergent Cas9 Species Journal of Structural Biology. 2021. 214. 107814-107824
(28) Cui, J.Y.; Lisi, G.P.* Molecular Level Insights into the Structural and Dynamic Factors Driving Cytokine Function Frontiers in Molecular Biosciences. 2021. DOI: 10.3389/fmolb.2021.773252
- Thematic issue "Structural and Dynamic Aspects of Protein Function and Allostery"
(27) Parkins, A.; Skeens, E.; McCallum, C.M.; Lisi, G.P.*; Pantouris, G.* The N-terminus of MIF Regulates the Dynamic Profile of Residues Involved in CD74 Activation Biophysical Journal. 2021. 120. 1-8
(26) Chen, E.; Reiss, K.; Shah, D.; Manjula, R.; Allen, B.; Murphy, E.L.; Murphy, J.W.; Batista, V.S.; Bhandari, V.; Lolis, E.J.*; Lisi, G.P.* A Structurally Preserved Allosteric Site in the MIF Superfamily Affects Enzymatic Activity and CD74 Activation in D-dopachrome Tautomerase Journal of Biological Chemistry. 2021. 297. 101061-101073
(25) Wang, J.*; Reiss, K.; Shi, Y.; Lolis, E.; Lisi, G.P.; Batista, V.S.* Mechanism of Inhibition of the Reproduction of SARS-CoV-2 and Ebola Viruses by Remdesivir Biochemistry. 2021. 60. 1869-1875
(24) East, K.W.; Delaglio, F.; Lisi, G.P.* A Simple Approach for Reconstruction of Non-uniformly Sampled Pseudo-3D NMR Data for Accurate Measurement of Spin Relaxation Parameters Journal of Biomolecular NMR. 2021. 75. 213-219
2020
(23) Skeens, E.; East, K.W.; Lisi, G.P.* 1H, 13C, 15N Backbone Resonance Assignment of the Recognition Lobe Subdomain 3 (Rec3) from Streptococcus pyogenes CRISPR-Cas9 Biomolecular NMR Assignments. 2020. 15. 25-28
(22) Cui, J.Y.; Zhang, F.; Nierzwicki, L.; Palermo, G.; Linhardt, R.J.: Lisi, G.P.* Mapping the Structural and Dynamic Determinants of pH-sensitive Heparin Binding to Granulocyte Macrophage-colony Stimulating Factor Biochemistry. 2020. 59. 3541-3553
(21) Murphy, J.W.; Rajasekaran, D.; Merkel, J.; Skeens, E.; Keeler, C.; Hodsdon, M.; Lisi, G.P.; Lolis, E.J.* High-throughput Screening of a Functional Human CXCL12-CXCR4 Signaling Axis in a Genetically Modified S. cerevisiae: Discovery of a Novel Up-regulator of CXCR4 Activity Frontiers in Molecular Biosciences. 2020. 7. DOI: 10.389/fmolb.2020.00164
(20) Pantouris, G.*; Khurana, L.; Ma, A.; Skeens, E.; Reiss, K.; Batista, V.S.; Lisi, G.P.*; Lolis, E.J.* Regulation of MIF Enzymatic Activity by an Allosteric Site at the Central Solvent Channel Cell Chemical Biology. 2020. 27. 740-750
(19) East, K.W.; Newton, J.C.; Morzan, U.N.; Narkhede, Y.; Acharya, A.; Skeens, E.; Jogl, G.; Batista, V.S.; Palermo, G.*; Lisi, G.P.* Allosteric Motions of the CRISPR-Cas9 HNH Nuclease Probed by NMR and Molecular Dynamics Journal of the American Chemical Society. 2020. 142. 1348-1358
- Highlighted in Biochemistry 2020 "Allosteric Control of Enzyme Activity: From Ancient Origins to Recent Genome-editing Technologies"
- Editor's selection for JACS 2021 virtual issue dedicated to outstanding early career investigators
(18) East, K.W.; Skeens, E.; Cui, J.Y.; Belato, H.B.; Mitchell, B.; Hsu, R.; Batista, V.S.; Palermo, G.; Lisi, G.P.* NMR and Computational Methods for Molecular Resolution of Allosteric Pathways in Enzyme Complexes Biophysical Reviews. 2020. 12. 155-174
2019
(17) Belato, H.B.; East, K.W.; Lisi, G.P.* 1H, 13C, 15N Backbone and Side Chain Resonance Assignments of the HNH Nuclease from Streptococcus pyogenes CRISPR-Cas9 Biomolecular NMR Assignments. 2019. 13. 367-370 (HBB and KWE contributed equally)
2018
(16) Negre, C.F.A.*; Morzan, U.N.*; Hendrickson, H.P.; Pal, R.; Lisi, G.P.; Loria, J.P.; Rivalta, I.*; Batista, V.S.* Eigenvector Centrality for Characterization of Protein Allosteric Pathways PNAS. 2018. 115. E12201-E12208
(15) Lisi, G.P.; Currier, A.A.; Loria, J.P.* Glutamine Hydrolysis by Imidazole Glycerol Phosphate Synthase Displays Temperature-Dependent Allosteric Activation Frontiers in Molecular Biosciences. 2018. 5. DOI: 10.3389/fmolb.2018.0004
2017
(14) Lisi, G.P.*; Loria, J.P.* Allostery in Enzyme Catalysis Current Opinion in Structural Biology. 2017. 47. 123-130
- Thematic issue "Catalysis and Regulation"
(13) Lisi, G.P.; East, K.W.; Batista, V.S.; Loria, J.P.* Altering the Allosteric Pathway in IGPS Suppresses Millisecond Motions and Catalytic Activity PNAS. 2017. 114. E3414-E3423
2016
(12) Rivalta, I.*; Lisi, G.P.; Snoeberger, N.-S.; Manley, G.A.; Loria, J.P.*; Batista, V.S.* Allosteric Communication Disrupted by a Small Molecule Binding to the Imidazole Glycerol Phosphate Synthase Protein-Protein Interface Biochemistry. 2016. 55. 6484-6494
(11) Lisi, G.P.; Hughes, R.P.; Wilcox, D.E.* Coordination Contributions to Protein Stability in Metal-Substituted Carbonic Anhydrase Journal of Biological Inorganic Chemistry. 2016. 21. 659-667
(10) Lisi, G.P.; Manley, G.A.; Hendrickson, H.; Rivalta, I.; Batista, V.S.; Loria, J.P.* Dissecting Dynamic Allosteric Pathways using Chemically Related Small Molecule Activators Structure. 2016. 24. 1155-1166
- Feature article
(9) Lisi, G.P.*; Loria, J.P.* Solution NMR Spectroscopy for the Study of Enzyme Allostery Chemical Reviews. 2016. 116. 6323-6369
- Thematic issue "Protein Ensembles and Allostery"
(8) Lisi, G.P.; Loria, J.P.* Using NMR Spectroscopy to Elucidate the Role of Molecular Motions in Enzyme Function Progress in NMR Spectroscopy. 2016. 92-93. 1-17
2015
(7) Amacher, J.F.; Zhong, F.; Lisi, G.P.; Zhu, M.Q.; Alden, S.L.; Hoke, K.H.; Madden, D.R.; Pletneva, E.V.* A Compact Structure of Cytochrome c Trapped in a Lysine-Ligated State: Loop Refolding and Functional Implications of a Conformational Switch Journal of the American Chemical Society. 2015. 137. 8435-8449
2014
(6) Lisi, G.P.; Png, C.Y.M.; Wilcox, D.E.* Thermodynamic Contributions to the Stability of the Insulin Hexamer Biochemistry. 2014. 53. 3576-3584
(5) Zhong, F.; Lisi, G.P.; Collins, D.P.; Dawson, J.H.; Pletneva, E.V.* Redox-Dependent Stability, Protonation, and Reactivity of Cysteine-Bound Heme Proteins PNAS. 2014. 111. E306-E315
2012
(4) Harper-Leatherman, A.S.*; Iftikhar, M.; Ndoi, A.; Scappaticci, S.J.; Lisi, G.P.; Buzard, K.L.; Garvey, E.M. Simplified Procedure for Encapsulating Cytochrome c in Silica Aerogel Nanoarchitectures While Retaining Gas-Phase Bioactivity Langmuir. 2012. 28. 14756-14765
(3) Miecznikowski, J.R.*; Lo, W.; Lynn, M.A.; Jain, S.; Keilich, L.C.; Kloczko, N.F.; O’Loughlin, B.E.; DiMarzio, A.P.; Foley, K.M.; Lisi, G.P.; Kwiecien, D.J.; Butrick, E.E.; Powers, E.; Al-Abbasee, R. Syntheses, Characterization, Density Functional Theory Calculations and Activity of Tridentate SNS Zinc Pincer Complexes Based on Bis-Imidazole or Bis-Triazole Precursors Inorganica Chimica Acta. 2012. 387. 25-36
2011
(2) Miecznikowski, J.R.*; Lo, W.; Lynn, M.A.; O’Loughlin, B.E.; DiMarzio, A.P.; Martinez, A.M.; Lampe, L.; Foley, K.M.; Keilich, L.C.; Lisi, G.P.; Kwiecien, D.J.; Pires, C.M.; Kelly, W.J.; Kloczko, N.F.; Morio, K.N. Syntheses, Characterization, Density Functional Theory Calculations and Activity of Tridentate SNS Zinc Pincer Complexes Inorganica Chimica Acta. 2011. 376. 515-524
(1) Miecznikowski, J.R.*; Caradonna, J.P.; Foley, K.M.; Kwiecien, D.J.; Lisi, G.P.; Martinez, A.M. Introduction to Homogenous Catalysis with Ruthenium-Catalyzed Oxidation of Alcohols: An Experiment for Undergraduate Advanced Inorganic Chemistry Students Journal of Chemical Education. 2011. 88. 657-661
Pre-prints
(68) Manjula, R.; Ghanem, L.; Skeens, E.; Bai, L.; Lisi, G.P.; Lolis, E.J.; Bennett, A.M.* Functional Coupling between the α4-α5 Loop and Allosteric Site on MKP5 is a Critical Determinant of Catalysis bioRxiv. 2026. DOI: 10.64898/2026.06.01.729370
(67) Knight, A.L.; Belato, H.B.; Dresser, C.S.; Pindi, C.; Mercado, B.J.; Lasekan, P.; Luo, J.; Arantes, P.R.; Jogl, G.*; Palermo, G.*: Lisi, G.P.* Orthosteric and Allosteric Effects of anti-CRISPR II-C1 Inhibition on GeoCas9 from Integrated Structural Biophysics bioRxiv. 2026. DOI: 10.64898/2026.04.08.717222
(66) Cui, D.S.; Anderson, E.O.; Zavala, E.; Lisi, G.P.; Loria, J.P.* Facilitating NMR Resonance Assignment with Metabolic Tampering bioRxiv. 2026. DOI: 10.64898/2026.04.29.721603
(65) East, K.W.; Leith, A.; Ragavendran, A.; Delaglio, F.; Lisi, G.P.* NMRdock: Lightweight and Modular NMR Processing bioRxiv. 2019. DOI: 10.1101/679688
2026
(64) Ahsan, M.; Knight, A.L.; Saha, A.; Ramos, D.; Strohkendl, I.; Skeens, E.; West, M.S.; Luo, J.; Dresser, C.S.; Taylor, D.W.; Lisi, G.P.*; Palermo, G.* A Cryptic Binding Pocket Regulates the Metal-dependent Activity of Cas9 Nature Communications. 2026. In press (MA and ALK contributed equally)
(63) Handelmann, C.R.; Skeens, E.; Lisi, G.P.; Buck, M.J.* Evaluating High-fidelity CRISPR-Cas Nucleases in Nucleosomal Contexts using a Quantitative Framework Frontiers in Genome Editing. 2026. 8. DOI: 10.3389/fgeed.2026.1759382
(62) Cui, J.Y.; Varghese, I; Bock, A.S.; Floody, M.; Zhang, F.; Rubenstein, B.M.; Lisi, G.P.* Exploring the GM-CSF Histidine Triad as a Modulator of Structure, Molecular Motion, and Ligand Binding RSC Chemical Biology. 2026. 7. 1409-1419 (JYC and IV contributed equally)
(61) Wu, Z.; Widjaja, V.; Skeens, E.; van der Velde, J.J.H.; Zahran, M.; Zhang, J.; Cool, R.H.; Poelarends, G.J.; Lisi, G.P.; Dekker, F.J.* Discovery of Furan-2-carboxylic Acid Derivatives as Novel D-dopachrome Tautomerase (D-DT) and Macrophage Migration Inhibitory Factor-1 (MIF-1) Dual Inhibitors Journal of Medicinal Chemistry. 2026. 69. 5712-5728
(60) Molina, C.E.; Knight, A.L.; Lisi, G.P.* Comparative Thermodynamic and Kinetic Properties Governing the Nucleic Acid Interactions of CRISPR-Cas9 And Cas12a Physical Biology. 2026. 23. 021001-021012
(59) Lisi, G.P.* Disorder, Dynamics, and Regulation of Proteins and Nucleic Acids Journal of Structural Biology. 2026. 218. 108258
2025
(58) Vieyra, F.H.; Pindi, C.; Lisi, G.P.; Morzan, U.N.*; Palermo, G.* Design Rules for Expanding PAM Compatibility in CRISPR-Cas9 from the VQR, VRER, and EQR Variants Journal of Physical Chemistry B. 2025. 129. 11949-11958 (FHV and CP contributed equally)
(57) Widjaja, V.; D'Orazio, S.M.; Das, P.; Rajendran, D.T.; Takada, X.; Shi, Y.; Varghese, I.; Lam, Y.; DaSilva, N.; Wang, J.; Batista, V.S.; Bhandari, V.; Lisi, G.P.* Atomistic Modulation of MIF-2 Structure, Catalysis, and Biological Signaling via Cysteine Residues and a Small Molecule, Ebselen Protein Science. 2025. 34. e70344-e70359
(56) Knight, A.L.; Luo, J.; Lisi, G.P.* Assessing Temperature-dependent DNA Cleavage by CRISPR-Cas9 Bio-protocol. 2025. 15. e5463-e5474
(55) Skeens, E.; Maschietto, F.; Ramu, M.; Shillingford, S.; Murphy, J.W.; Lolis, E.J.;* Batista, V.S.;* Bennett, A.M.*; Lisi, G.P.* Dynamic and Structural Insights into Allosteric Regulation on MKP5, A Dual-specificity Phosphatase Nature Communications. 2025. 16. 7011-7024 (ES and FM contributed equally)
(54) Knight, A.L.; Lisi, G.P.* Spy-ing on Nucleic Acids: Atomic Resolution of the S. pyogenes CRISPR-Cas9 Surveillance State Structure. 2025. 33. 636-638
- Structure Spotlight
(53) Clark, M.E.; Farinha, A.; Morrison, A.R.*; Lisi, G.P.* Structural, Biological, and Biomedical Implications of mRNA Interactions with the Master Regulator HuR NAR Molecular Medicine. 2025. DOI: 10.1093/narmme/ugaf002
2024
(52) Sajko, S.; Skeens, E.; Schinagl, A.; Ferhat, M.; Mirkina, I.; Mayer, J.; Rossmueller, G.; Thiele, M.*; Lisi, G.P.* Redox-dependent Plasticity of oxMIF Facilitates its Interaction with CD74 and Therapeutic Antibodies Redox Biology. 2024. 75. 103264-103278
(51) Belato, H.B.; Knight, A.L.; D'Ordine, A.M.; Pindi, C.; Fan, Z.; Luo, J.; Palermo, G.; Jogl, G.; Lisi, G.P.* Structural and Dynamic Impacts of Single-atom Disruptions to Guide RNA Interactions within the Recognition Lobe of Geobacillus stearothermophilus Cas9 eLife. 2024. 13. RP99275- RP99296 (HBB and ALK contributed equally)
(50) Monteiro da Silva, G.; Cui, J.Y.; Dalgarno, D.C.; Lisi, G.P.; Rubenstein, B.M.* High-throughput Prediction of Protein Conformational Distributions with Subsampled AlphaFold2 Nature Communications. 2024. 15. 2464-2476
- "New Technique for Predicting Protein Dynamics May Prove Big Breakthrough for Drug Discovery" (Press - Blavatnik Family Foundation)
(49) Skeens, E.; Sinha, S.; Ahsan, M.; D'Ordine, A.M.; Jogl, G.; Palermo, G.*; Lisi, G.P.* High-fidelity, Hyper-accurate, and Evolved Mutants Rewire Atomic Level Communication in CRISPR-Cas9 Science Advances. 2024. 10. eadl1045-1056 (ES and SS contributed equally)
2023
(48) Wang, J.; Maschietto, F.; Qiu, T.; Arantes, P.R.; Skeens, E.; Palermo, G.*; Lisi, G.P.*; Batista, V.S.* Substrate-indpendent Activation Pathways of the CRISPR-Cas9 HNH Nuclease Biophysical Journal. 2023. 122. 4635-4644
(47) Knight, A.L.; Widjaja, V.; Lisi, G.P.* Temperature as a Modulator of Allosteric Motions and Crosstalk in Mesophilic and Thermophilic Enzymes Frontiers in Molecular Biosciences. 2023. DOI: 10.3389/fmolb.2023.1281062 (ALK and VW contributed equally)
- Thematic issue "Allosteric Functions and Inhibitions: Structural Insights"
(46) Chen E.; Widjaja, V.; Kyro, G.; Allen, B.; Das, P.; Prahaladan, V.M.; Bhandari, V.; Lolis, E.J.; Batista, V.S.*; Lisi, G.P.* Mapping N- to C-terminal Allosteric Coupling through Disruption of a Putative CD74 Activation Site in D-dopachrome Tautomerase Journal of Biological Chemistry. 2023. 299, 104729-104740 (EC and VW contributed equally)
(45) Parkins, A.; Chen E.; Rangel, V.; Singh, M.; Xue, L.; Lisi, G.P.; Pantouris, G.* Ligand-induced Conformational Changes Enable Intersubunit Communications in D-dopachrome Tautomerase Biophysical Journal. 2023. 122, 1268-1276
(44) Maschietto, F.; Qiu, T.; Wang, J.*; Shi, Y.; Allen, B.; Lisi, G.P.; Lolis, E.; Batista, V.S.* Valproate Coenzyme-A Conjugate Blocks Opening of Receptor Binding Domains in the Spike Trimer of SARS-CoV-2 through an Allosteric Mechanism Computational and Structural Biotechnology Journal. 2023. 21. 1066-1076
(43) Belato, H.B.; Lisi, G.P.* The Many (Inter)faces of Anti-CRISPRs: Modulation of CRISPR-Cas Structure and Dynamics by Mechanistically Diverse Inhibitors Biomolecules. 2023. 13. 264-277
- Feature paper in Molecular Structure and Dynamics
(42) Skeens, E.; Lisi, G.P.* Analysis of Coordinated NMR Chemical Shifts to Map Allosteric Networks in Proteins Methods. 2023. 209. 40-47
- Thematic issue "New Methods in Biomolecular NMR Spectroscopy"
(41) Wang, J.*; Arantes, P.R.; Ahsan, M.; Sinha, S.; Kyro, G.W.; Maschietto, F.; Allen, B.; Skeens, E.; Lisi, G.P.*; Batista, V.S.*; Palermo, G.* Twisting and Swiveling Domain Motions in Cas9 to Recognize Target DNA Duplexes, Make Double-stranded Breaks, and Release Cleaved Duplexes Frontiers in Molecular Biosciences. 2023. DOI: 10.3389/fmolb.2022.1072733
2022
(40) Belato, H.B.; Norbrun, C.; Luo, J.; Pindi, C.; Sinha, S.; D'Ordine, A.M.; Jogl, G.; Palermo, G.*; Lisi, G.P.* Disruption of Electrostatic Contacts in the HNH Nuclease from a Thermophilic Cas9 Rewires Allosteric Motions and Enhances High-temperature DNA Cleavage Journal of Chemical Physics. 2022. 157. 225103-225113
- Thematic collection "New Views of Allostery"
(39) Fredericks, A.M.; East, K.W.; Shi, Y.; Liu, J.; Maschietto, F.; Ayala, A.; Cioffi, W.G.; Cohen, M.; Fairbrother, W.G.; Lefort, C.T.; Nau, G.;J.; Levy, M.M.; Wang, J.; Batista, V.S. Lisi, G.P.*; Monaghan, S.F.* Identification and Mechanistic Basis of non-ACE2 Blocking Neutralizing Antibodies from COVID-19 Patients with Deep RNA Sequencing and Molecular Dynamics Simulations Frontiers in Molecular Biosciences. 2022. DOI: 10.3389/fmolb.2022.1080964 (AMF, KWE, and YS contributed equally)
(38) Wang, J.*; Liu, J.; Gisriel, C.J.; Wu, S.; Maschietto, F.; Flesher, D.A.; Lolis, E.; Lisi, G.P.; Brudvig, G.W.; Xiong, Y.; Batista, V.S. How to Correct Relative Voxel Scale Factors for Calculations of Vector-difference Fourier Maps in Cryo-EM Journal of Structural Biology. 2022. 214. 107902-107915
(37) Wang, J.*; Shi, Y.; Reiss, K.; Maschietto, F.; Lolis, E.; Konigsberg, W.; Lisi, G.P.; Batista, V.S.* Structural Insights into Binding of Remdesivir Triphosphate within the Replication-transcription Complex of SARS-CoV-2 Biochemistry. 2022. 61. 1966-1973
(36) Nierzwicki, L.; East, K.W.; Binz, J.; Hsu, R.V.; Arantes, P.R.; Ahsan, M.; Skeens, E.; Pacesa, M.; Jinek, M.; Lisi, G.P.*; Palermo, G.* Principles of Target DNA Cleavage and the Role of Mg2+ in the Catalysis of CRISPR-Cas9 Nature Catalysis. 2022. 5. 912-922
(35) Wang, J.*; Skeens, E.; Arantes, P.R.; Maschietto, F.; Allen, B.; Kyro, G.; Lisi, G.P.*; Palermo, G.*; Batista, V.S.* Structural Basis for Reduced Dynamics of Three Engineered HNH Endonuclease Lys-to-Ala Mutants of the CRISPR-Cas9 Enzyme Biochemistry. 2022. 61. 785-794.
(34) Lisi, G.P.*; Rivalta, I.*; Venditti, V.* Editorial: Structural and Dynamic Aspects of Protein Function and Allostery Frontiers in Molecular Biosciences. 2022. DOI: 10.3389/fmolb.2022.876499
(33) Wang, J.; Shi, Y.; Reiss, K.; Allen, B.; Maschietto, F.; Lolis, E.J.; Konigsberg, W.; Lisi, G.P.; Batista, V.S.* Insights into Binding of Single-stranded Viral RNA Template to the Replication-transcription Complex of SARS-CoV-2 for the Priming Reaction from Molecular Dynamics Simulations Biochemistry. 2022. 61. 424-432
(32) Skeens, E.; Gadzuk-Shea, M.M.; Shah, D.; Bhandari, V.; Schweppe, D.K.; Berlow, R.B.*; Lisi, G.P.* Redox-dependent Structure and Dynamics of Macrophage Migration Inhibitory Factor Reveal Sites of Latent Allostery Structure. 2022. 30. 840-850
- Commentary in Structure 2022 "Cytokine Aerobics: Oxidation Controls Cytokine Dynamics and Function"
(31) Skeens, E.; Pantouris, G.; Shah, D.; Manjula, R.; Ombrello, M.J.; Maluf, N.K.; Bhandari, V.; Lisi, G.P.*; Lolis, E.J.* A Cysteine Variant at an Allosteric Site Alters MIF Dynamics and Biological Function in Homo- and Heterotrimeric Assemblies Frontiers in Molecular Biosciences. 2022. 9. DOI: 10.3389/fmolb.2022.783669 (ES and GP contributed equally)
2021
(30) Nierzwicki, L.; East, K.W.; Morzan, U.N.; Arantes, P.R.; Batista, V.S.; Lisi, G.P.*; Palermo, G.* Enhanced Specificity Mutations Perturb Allosteric Signaling in CRISPR-Cas9 eLife. 2021. 10. e73601 (LN and KWE contributed equally)
- Journal Cover Art
(29) Belato, H.B.; D'Ordine, A.M.; Nierzwicki, L.; Arantes, P.R.; Jogl, G.; Palermo, G.*; Lisi, G.P.* Structural and Dynamic Insights into the HNH Nuclease of Divergent Cas9 Species Journal of Structural Biology. 2021. 214. 107814-107824
(28) Cui, J.Y.; Lisi, G.P.* Molecular Level Insights into the Structural and Dynamic Factors Driving Cytokine Function Frontiers in Molecular Biosciences. 2021. DOI: 10.3389/fmolb.2021.773252
- Thematic issue "Structural and Dynamic Aspects of Protein Function and Allostery"
(27) Parkins, A.; Skeens, E.; McCallum, C.M.; Lisi, G.P.*; Pantouris, G.* The N-terminus of MIF Regulates the Dynamic Profile of Residues Involved in CD74 Activation Biophysical Journal. 2021. 120. 1-8
(26) Chen, E.; Reiss, K.; Shah, D.; Manjula, R.; Allen, B.; Murphy, E.L.; Murphy, J.W.; Batista, V.S.; Bhandari, V.; Lolis, E.J.*; Lisi, G.P.* A Structurally Preserved Allosteric Site in the MIF Superfamily Affects Enzymatic Activity and CD74 Activation in D-dopachrome Tautomerase Journal of Biological Chemistry. 2021. 297. 101061-101073
(25) Wang, J.*; Reiss, K.; Shi, Y.; Lolis, E.; Lisi, G.P.; Batista, V.S.* Mechanism of Inhibition of the Reproduction of SARS-CoV-2 and Ebola Viruses by Remdesivir Biochemistry. 2021. 60. 1869-1875
(24) East, K.W.; Delaglio, F.; Lisi, G.P.* A Simple Approach for Reconstruction of Non-uniformly Sampled Pseudo-3D NMR Data for Accurate Measurement of Spin Relaxation Parameters Journal of Biomolecular NMR. 2021. 75. 213-219
2020
(23) Skeens, E.; East, K.W.; Lisi, G.P.* 1H, 13C, 15N Backbone Resonance Assignment of the Recognition Lobe Subdomain 3 (Rec3) from Streptococcus pyogenes CRISPR-Cas9 Biomolecular NMR Assignments. 2020. 15. 25-28
(22) Cui, J.Y.; Zhang, F.; Nierzwicki, L.; Palermo, G.; Linhardt, R.J.: Lisi, G.P.* Mapping the Structural and Dynamic Determinants of pH-sensitive Heparin Binding to Granulocyte Macrophage-colony Stimulating Factor Biochemistry. 2020. 59. 3541-3553
(21) Murphy, J.W.; Rajasekaran, D.; Merkel, J.; Skeens, E.; Keeler, C.; Hodsdon, M.; Lisi, G.P.; Lolis, E.J.* High-throughput Screening of a Functional Human CXCL12-CXCR4 Signaling Axis in a Genetically Modified S. cerevisiae: Discovery of a Novel Up-regulator of CXCR4 Activity Frontiers in Molecular Biosciences. 2020. 7. DOI: 10.389/fmolb.2020.00164
(20) Pantouris, G.*; Khurana, L.; Ma, A.; Skeens, E.; Reiss, K.; Batista, V.S.; Lisi, G.P.*; Lolis, E.J.* Regulation of MIF Enzymatic Activity by an Allosteric Site at the Central Solvent Channel Cell Chemical Biology. 2020. 27. 740-750
(19) East, K.W.; Newton, J.C.; Morzan, U.N.; Narkhede, Y.; Acharya, A.; Skeens, E.; Jogl, G.; Batista, V.S.; Palermo, G.*; Lisi, G.P.* Allosteric Motions of the CRISPR-Cas9 HNH Nuclease Probed by NMR and Molecular Dynamics Journal of the American Chemical Society. 2020. 142. 1348-1358
- Highlighted in Biochemistry 2020 "Allosteric Control of Enzyme Activity: From Ancient Origins to Recent Genome-editing Technologies"
- Editor's selection for JACS 2021 virtual issue dedicated to outstanding early career investigators
(18) East, K.W.; Skeens, E.; Cui, J.Y.; Belato, H.B.; Mitchell, B.; Hsu, R.; Batista, V.S.; Palermo, G.; Lisi, G.P.* NMR and Computational Methods for Molecular Resolution of Allosteric Pathways in Enzyme Complexes Biophysical Reviews. 2020. 12. 155-174
2019
(17) Belato, H.B.; East, K.W.; Lisi, G.P.* 1H, 13C, 15N Backbone and Side Chain Resonance Assignments of the HNH Nuclease from Streptococcus pyogenes CRISPR-Cas9 Biomolecular NMR Assignments. 2019. 13. 367-370 (HBB and KWE contributed equally)
2018
(16) Negre, C.F.A.*; Morzan, U.N.*; Hendrickson, H.P.; Pal, R.; Lisi, G.P.; Loria, J.P.; Rivalta, I.*; Batista, V.S.* Eigenvector Centrality for Characterization of Protein Allosteric Pathways PNAS. 2018. 115. E12201-E12208
(15) Lisi, G.P.; Currier, A.A.; Loria, J.P.* Glutamine Hydrolysis by Imidazole Glycerol Phosphate Synthase Displays Temperature-Dependent Allosteric Activation Frontiers in Molecular Biosciences. 2018. 5. DOI: 10.3389/fmolb.2018.0004
2017
(14) Lisi, G.P.*; Loria, J.P.* Allostery in Enzyme Catalysis Current Opinion in Structural Biology. 2017. 47. 123-130
- Thematic issue "Catalysis and Regulation"
(13) Lisi, G.P.; East, K.W.; Batista, V.S.; Loria, J.P.* Altering the Allosteric Pathway in IGPS Suppresses Millisecond Motions and Catalytic Activity PNAS. 2017. 114. E3414-E3423
2016
(12) Rivalta, I.*; Lisi, G.P.; Snoeberger, N.-S.; Manley, G.A.; Loria, J.P.*; Batista, V.S.* Allosteric Communication Disrupted by a Small Molecule Binding to the Imidazole Glycerol Phosphate Synthase Protein-Protein Interface Biochemistry. 2016. 55. 6484-6494
(11) Lisi, G.P.; Hughes, R.P.; Wilcox, D.E.* Coordination Contributions to Protein Stability in Metal-Substituted Carbonic Anhydrase Journal of Biological Inorganic Chemistry. 2016. 21. 659-667
(10) Lisi, G.P.; Manley, G.A.; Hendrickson, H.; Rivalta, I.; Batista, V.S.; Loria, J.P.* Dissecting Dynamic Allosteric Pathways using Chemically Related Small Molecule Activators Structure. 2016. 24. 1155-1166
- Feature article
(9) Lisi, G.P.*; Loria, J.P.* Solution NMR Spectroscopy for the Study of Enzyme Allostery Chemical Reviews. 2016. 116. 6323-6369
- Thematic issue "Protein Ensembles and Allostery"
(8) Lisi, G.P.; Loria, J.P.* Using NMR Spectroscopy to Elucidate the Role of Molecular Motions in Enzyme Function Progress in NMR Spectroscopy. 2016. 92-93. 1-17
2015
(7) Amacher, J.F.; Zhong, F.; Lisi, G.P.; Zhu, M.Q.; Alden, S.L.; Hoke, K.H.; Madden, D.R.; Pletneva, E.V.* A Compact Structure of Cytochrome c Trapped in a Lysine-Ligated State: Loop Refolding and Functional Implications of a Conformational Switch Journal of the American Chemical Society. 2015. 137. 8435-8449
2014
(6) Lisi, G.P.; Png, C.Y.M.; Wilcox, D.E.* Thermodynamic Contributions to the Stability of the Insulin Hexamer Biochemistry. 2014. 53. 3576-3584
(5) Zhong, F.; Lisi, G.P.; Collins, D.P.; Dawson, J.H.; Pletneva, E.V.* Redox-Dependent Stability, Protonation, and Reactivity of Cysteine-Bound Heme Proteins PNAS. 2014. 111. E306-E315
2012
(4) Harper-Leatherman, A.S.*; Iftikhar, M.; Ndoi, A.; Scappaticci, S.J.; Lisi, G.P.; Buzard, K.L.; Garvey, E.M. Simplified Procedure for Encapsulating Cytochrome c in Silica Aerogel Nanoarchitectures While Retaining Gas-Phase Bioactivity Langmuir. 2012. 28. 14756-14765
(3) Miecznikowski, J.R.*; Lo, W.; Lynn, M.A.; Jain, S.; Keilich, L.C.; Kloczko, N.F.; O’Loughlin, B.E.; DiMarzio, A.P.; Foley, K.M.; Lisi, G.P.; Kwiecien, D.J.; Butrick, E.E.; Powers, E.; Al-Abbasee, R. Syntheses, Characterization, Density Functional Theory Calculations and Activity of Tridentate SNS Zinc Pincer Complexes Based on Bis-Imidazole or Bis-Triazole Precursors Inorganica Chimica Acta. 2012. 387. 25-36
2011
(2) Miecznikowski, J.R.*; Lo, W.; Lynn, M.A.; O’Loughlin, B.E.; DiMarzio, A.P.; Martinez, A.M.; Lampe, L.; Foley, K.M.; Keilich, L.C.; Lisi, G.P.; Kwiecien, D.J.; Pires, C.M.; Kelly, W.J.; Kloczko, N.F.; Morio, K.N. Syntheses, Characterization, Density Functional Theory Calculations and Activity of Tridentate SNS Zinc Pincer Complexes Inorganica Chimica Acta. 2011. 376. 515-524
(1) Miecznikowski, J.R.*; Caradonna, J.P.; Foley, K.M.; Kwiecien, D.J.; Lisi, G.P.; Martinez, A.M. Introduction to Homogenous Catalysis with Ruthenium-Catalyzed Oxidation of Alcohols: An Experiment for Undergraduate Advanced Inorganic Chemistry Students Journal of Chemical Education. 2011. 88. 657-661
