Liam M. Longo

Specially Appointed Associate Professor

Earth-Life Science Institute

Institute of Science Tokyo(formerly Tokyo Institute of Technology)

Associate Research Scientist

Blue Marble Space Institute of Science

Publications

*Corresponding or Co-corresponding, ^Equal contributions

Preprints

  • Seya K^, Corlett TS^, Giaffar H^, Buttelli AL, Lemay-St-Denis C, Fujishima K, Kamerlin SCL, Kolodny R, Smith E*, Longo LM*, Nucleotide-binding motifs nucleated folding of the first enzymes. bioRxiv
  • Modrusan P, Brkic A, Buttelli AL, Leibundgut M, Zivkovic I, Ban N*, Longo LM*, Gruic-Sovulj I*, C-terminal evolutionary remodelling of isoleucyl-tRNA synthetases is a prokaryote-specific strategy for tuning aminoacylation rate. bioRxiv

2026

  • Cherepashuk I, Makarov M, Soucek R, Verner V, Krystufek R, Hadravova R, Giacobelli VG, Fujishima K, Jordan SF*, Longo LM*, Hlouchova K*, Peptides at vesicle and mineral prebiotic interfaces. Astrobiology 2026; (Accepted)
  • Corlett TS, Smith HB*, Smith E, Goldford JE, Longo LM*, The history of enzyme evolution embedded in metabolism. Proceedings of the National Academy of Sciences 2026; 123(33): e2609531123. PubMed / Journal
  • Yanai G, Axel G, Longo LM*, Ben-Tal N*, Kolodny R*, Contrastive learning unites sequence and structure in a global representation of protein space. Proceedings of the National Academy of Sciences 2026; 123(32): e2532702123. PubMed / Journal
  • Chen S, Corlett T, Kitadai N, Nakamura R, Miyauchi M, Longo LM*, Yamaguchi A*, Primitive basic amino acids promote mineral-catalyzed electrochemical reduction of H+ and CO2. Journal of Physical Chemistry C 2026; 130(26): 9040-9047. Journal
  • Seya K, Brownless AR, Kamerlin SCL*, Longo LM*, The borderlands of foldability: lessons from simplified proteins. Trends in Chemistry 2026; 8(5): 362-376. Journal
  • Matsumoto R^, Watanabe T^, Yamazaki E, Kagawa A, Longo LM*, Matsuura T*, A universal polyphosphate kinase powers in vitro transcription. Nature Communications 2026; 17(1): 1252. PubMed / Journal

2025

  • Seal M^, Edelstein I^, Scolnik Y, Weil-Ktorza O, Metanis N, Levy Y*, Longo LM*, Goldfarb D*, RNA Binding and Coacervation Promote Preservation of Peptide Form and Function Across the Heterochiral-Homochiral Divide. Protein Science 2025; 34(9): e70273. PubMed / Journal
  • Sarrias MH, Wheat CW, Longo LM*, Arvestad L*, Exonize: a tool for finding and classifying exon duplications in annotated genomes. Bioinformatics Advances 2025; vbaf177. PubMed / Journal
  • Vyas P*^, Santra K^, Preeyanka, N, Gupta, A, Weil-Ktorza O, Zhu, Q, Metanis N, Fransson, J, Longo LM, Naaman, R*, Role of Electron Spin, Chirality, and Charge Dynamics in Promoting the Persistence of Nascent Nucleic Acid–Peptide Complexes. Journal of Physical Chemistry B 2025; 129(16): 3978-3987. PubMed / Journal
  • Weil-Ktorza O^, Naveh-Tassa S^, Fridmann-Sirkis Y^, Despotović D^, Cherukuri KP, Corlett T, Levy Y*, Metanis N*, Longo LM*, Functional ambidexterity of an ancient nucleic acid-binding domain. Angewandte Chemie 2025; 64(25): e202505188. PubMed / Journal
  • Demkiv AO, Toledo-Patiño S, Medina-Carmona E, Berg A, Pinto G, Parracino A, Sanchez-Ruiz JM, Hengge AC, Laurino P, Longo LM*, Kamerlin SCL*, Redefining the limits of functional continuity in the early evolution of P-loop NTPases. Molecular Biology and Evolution 2025; 42(4): msaf055. PubMed / Journal
  • Matsumoto R, Matsuura T*, Longo LM*, Distribution of polyphosphate kinase 2 genes in bacteria underscores a dynamic evolutionary history. Proteins 2025; 93(5): 972-980. PubMed / Journal

2024

  • Goldford JE*^, Smith HB^, Longo LM^, Wing BA, McGlynn SE*, Primitive purine biosynthesis connects ancient geochemistry to modern metabolism. Nature Ecology and Evolution 2024; 8(5): 999-1009. PubMed / Journal
  • Longo LM, Evolution of folded domains from short, oligomerizing peptides through coacervation. Seibutsu Butsuri 2024; 64(4): 181-184. Journal

    • Cover Article

2022

  • Longo LM*, Hirai H, McGlynn SE*, An Evolutionary History of the CoA-Binding Protein Nat/Ivy. Protein Science 2022; 31(10): e4463. PubMed / Journal
  • Seal M, Weil-Ktorza O, Despotović D, Tawfik DS, Levy Y, Metanis N, Longo LM*, Goldfarb D*, Peptide-RNA Coacervates as a Cradle for the Evolution of Folded Domains. Journal of the American Chemical Society 2022; 144(31): 14150-14160. PubMed / Journal
  • Despotović D*, Aharon E^, Trofimyuk O^, Dubovetskyi A^, Cherukuri KP^, Ashani Y, Eliason O, Sperfeld M, Leader H, Castelli A, Fumagalli L, Savidor A, Levin Y, Longo LM*, Segev E*, Tawfik DS, Utilization of diverse organophosphorus pollutants by marine bacteria. Proceedings of the National Academy of Sciences 2022; 119(32): e2203604119. PubMed / Journal
  • Gruic-Sovulj I*, Longo LM, Jabłońska J, Tawfik DS*, The evolutionary history of the HUP domain. Critical Reviews in Biochemistry and Molecular Biology 2022; 57(1): 1-15. PubMed / Journal

2021

  • Longo LM*, Kolodny R*, McGlynn SE*, Evidence for the Emergence of β-Trefoils by 'Peptide Budding' from an IgG-like β-Sandwich. PLOS Computational Biology 2021; 18(2): e1009833. PubMed / Journal
  • Vyas P, Trofimyuk O, Longo LM, Deshmukh FK, Sharon M, Tawfik DS*, Helicase-like functions in phosphate loop containing beta-alpha polypeptides. Proceedings of the National Academy of Sciences 2021; 118(16): e2016131118. PubMed / Journal

2020

  • Longo LM, Jabłońska J, Vyas P, Kanade M, Kolodny R*, Ben-Tal N*, Tawfik DS*, On the emergence of P-Loop NTPase and Rossmann enzymes from a Beta-Alpha-Beta ancestral fragment. Elife 2020; 9: e64415. PubMed / Journal
  • Despotović D*^, Longo LM^, Aharon E, Kahana A, Scherf T, Gruic-Sovulj I, Tawfik DS*, Polyamines mediate folding of primordial hyperacidic helical proteins. Biochemistry 2020; 59(46): 4456-4462. PubMed / Journal
  • Longo LM^, Despotović D^, Weil-Ktorza O^, Walker MJ, Jabłońska J, Fridmann-Sirkis Y, Varani G, Metanis N*, Tawfik DS*, Primordial emergence of a nucleic acid binding protein via phase separation and statistical ornithine to arginine conversion. Proceedings of the National Academy of Sciences 2020; 117(27): 15731-15739. PubMed / Journal

    • Faculty Opinions Recommendation

  • Tenorio CA, Longo LM, Parker JB, Lee J, Blaber M*, Ab initio folding of a trefoil‐fold motif reveals structural similarity with a β‐propeller blade motif. Protein Science 2020; 29(5): 1172-1185. PubMed / Journal
  • Longo LM, Petrović D, Kamerlin SCL, Tawfik DS*, Short and simple sequences favored the emergence of N-helix phospho-ligand binding sites in the first enzymes. Proceedings of the National Academy of Sciences 2020; 117(10): 5310-5318. PubMed / Journal

2018

  • Davidi D*, Longo LM, Jabłońska J, Milo R, Tawfik DS*, A bird’s-eye view of enzyme evolution: Chemical, physicochemical, and physiological considerations. Chemical reviews 2018; 118(18): 8786-8797. PubMed / Journal
  • Longo LM^, Gao Y^, Tenorio CA, Wang G, Paravastu AK*, Blaber M*, Folding nucleus structure persists in thermally‐aggregated FGF‐1. Protein Science 2018; 27(2): 431-440. PubMed / Journal

2017

  • Noda‐Garcia L, Romero Romero ML, Longo LM, Kolodkin‐Gal I, Tawfik DS*, Bacilli glutamate dehydrogenases diverged via coevolution of transcription and enzyme regulation. EMBO reports 2017; 18(7): 1139-1149. PubMed / Journal

2016

  • Xia X^, Longo LM^, Sutherland MA, Blaber M*, Evolution of a protein folding nucleus. Protein Science 2016; 25(7): 1227-1240. PubMed / Journal
  • Longo LM, Blaber M*, Proteins: folding, misfolding, disordered proteins, and related diseases. Encyclopedia of Cell Biology 2016; 1: 108-114. Academic Press, Oxford. Journal

2015

  • Xia X, Longo LM, Blaber M*, Mutation choice to eliminate buried free cysteines in protein therapeutics. Journal of pharmaceutical sciences 2015; 104(2): 566-576. PubMed / Journal
  • Longo LM, Tenorio CA, Kumru OS, Middaugh CR, Blaber M*, A single aromatic core mutation converts a designed “primitive” protein from halophile to mesophile folding. Protein Science 2015; 24(1): 27-37. PubMed / Journal

2014

  • Longo LM, Kumru OS, Middaugh CR, Blaber M*, Evolution and design of protein structure by folding nucleus symmetric expansion. Structure 2014; 22(10): 1377-1384. PubMed / Journal
  • Longo LM, Blaber M*, Symmetric protein architecture in protein design: top-down symmetric deconstruction. Protein Design 2014; 161-182. PubMed / Journal

    • Cover Article

  • Longo LM, Blaber M*, Prebiotic protein design supports a halophile origin of foldable proteins. Frontiers in microbiology 2014; 4: 418-419. PubMed / Journal
  • Stefanovic L, Longo LM, Zhang Y, Stefanovic B*, Characterization of binding of LARP6 to the 5’stem-loop of collagen mRNAs: Implications for synthesis of type I collagen. RNA biology 2014; 11(11): 1386-1401. PubMed / Journal

2013

  • Longo LM, Lee J, Blaber M*, Simplified protein design biased for prebiotic amino acids yields a foldable, halophilic protein. Proceedings of the National Academy of Sciences 2013; 110(6): 2135-2139. PubMed / Journal

    • 2013 Kasha Award

    • Faculty Opinions Recommendation

  • Longo LM^, Lee J^, Tenorio CA, Blaber M*, Alternative folding nuclei definitions facilitate the evolution of a symmetric protein fold from a smaller peptide motif. Structure 2013; 21(11): 2042-2050. PubMed / Journal
  • Longo LM, Blaber M*, Biophysical characterization of a thermoalkalophilic esterase from Geobacillus sp.. Journal of Proteins and Proteomics 2013; 4(2): 123-128. Journal
  • Phipps HW, Longo LM, Blaber SI, Blaber M, VanLandingham JW*, Kallikrein-related peptidase 6: A biomarker for traumatic brain injury in the rat. Brain Injury 2013; 27(13-14): 1698-1706. PubMed / Journal

2012

  • Longo LM, Lee J, Blaber M*, Experimental support for the foldability–function tradeoff hypothesis: Segregation of the folding nucleus and functional regions in fibroblast growth factor‐1. Protein Science 2012; 21(12): 1911-1920. PubMed / Journal

    • 2012 Protein Science Best Paper Award

  • Longo LM, Blaber M*, Protein design at the interface of the pre-biotic and biotic worlds. Archives of biochemistry and biophysics 2012; 526(1): 16-21. PubMed / Journal
  • Blaber M*, Lee J, Longo LM, Emergence of symmetric protein architecture from a simple peptide motif: evolutionary models. Cellular and Molecular Life Sciences 2012; 69(23): 3999-4006. PubMed / Journal
  • Longo LM, Blaber M*, Protein design — a vast unexploited resource. Journal of Proteins and Proteomics 2012; 3(2): 79-83. Journal

2008

  • Lee J, Dubey VK, Longo LM, Blaber M*, A logical OR redundancy within the Asx-Pro-Asx-Gly type I beta-turn motif.. J Mol Biol 2008; 377(4): 1251-1264. PubMed / Journal

2007

  • Hacisalihoglu G*, Ji P, Longo LM, Olson S, Momol TM, Bacterial wilt induced changes in nutrient distribution and biomass and the effect of acibenzolar-S-methyl on bacterial wilt in tomato. Crop Protection 2007; 26(7): 978-982. Journal

2005

  • Hacisalihoglu G*, Duke ER, Longo LM, Differential response of common bean genotypes to mycorrhizal colonization. Proceedings of the Florida State Horticultural Society 2005; 118: 150-152. Journal