Impact of ancestral sequence reconstruction on mechanistic and structural enzymology
Tài liệu tham khảo
Merkl, 2016, Ancestral protein reconstruction: techniques and applications, Biol Chem, 397, 1, 10.1515/hsz-2015-0158
Starr, 2017, Alternative evolutionary histories in the sequence space of an ancient protein, Nature, 549, 409, 10.1038/nature23902
Risso, 2018, Biotechnological and protein-engineering implications of ancestral protein resurrection, Curr Opin Struct Biol, 51, 106, 10.1016/j.sbi.2018.02.007
Schupfner, 2020, Analysis of allosteric communication in a multienzyme complex by ancestral sequence reconstruction, Proc Natl Acad Sci U S A, 117, 346, 10.1073/pnas.1912132117
Pauling, 1963, Chemical paleogenetics, Acta Chem Scand, 17, S9, 10.3891/acta.chem.scand.17s-0009
Voordeckers, 2012, Reconstruction of ancestral metabolic enzymes reveals molecular mechanisms underlying evolutionary innovation through gene duplication, PLoS Biol, 10, 10.1371/journal.pbio.1001446
Hadzipasic, 2020, Ancient origins of allosteric activation in a Ser-Thr kinase, Science, 367, 912, 10.1126/science.aay9959
Kaczmarksi, 2020, Altered conformation sampling along an evolutionary trajectory changes the catalytic activity of an enzyme, Nat Commun, 11, 5945, 10.1038/s41467-020-19695-9
Dishman, 2021, Evolution of fold switching in a metamorphic protein, Science, 371, 86, 10.1126/science.abd8700
Yang, 2020, A mechanistic view of enzyme evolution, Protein Sci, 29, 1724, 10.1002/pro.3901
Thomson, 2022, Engineering functional thermostable proteins using ancestral sequence reconstruction, J Biol Chem, 298, 10.1016/j.jbc.2022.102435
Alonso-Lerma, 2023, Evolution of CRISPR-associated endonucleases as inferred from resurrected proteins, Nat Microbiol, 8, 77, 10.1038/s41564-022-01265-y
Mascotti, 2022, Resurrecting enzymes by ancestral sequence reconstruction, Enzyme Eng, 2397
Hochberg, 2017, Reconstructing ancient proteins to understand the causes of structure and function, Annu Rev Biophys, 46, 247, 10.1146/annurev-biophys-070816-033631
Harms, 2013, Evolutionary biochemistry: revealing the historical and physical causes of protein properties, Nat Rev Genet, 14, 559, 10.1038/nrg3540
Siddiq, 2017, Evolution of protein specificity: insights from ancestral protein reconstruction, Curr Opin Struct Biol, 47, 113, 10.1016/j.sbi.2017.07.003
Gerlt, 2009, Enzyme (re)design: lessons from natural evolution and computation, Curr Opin Chem Biol, 13, 10, 10.1016/j.cbpa.2009.01.014
Spence, 2021, Ancestral sequence reconstruction for protein engineers, Curr Opin Struct Biol, 69, 131, 10.1016/j.sbi.2021.04.001
Harris, 2022, Ancestral sequence reconstruction of a cytochrome P450 family involved in chemical defense reveals the functional evolution of a promiscuous, xenobiotic-metabolizing enzyme in vertebrates, Mol Biol Evol, 39, msac116, 10.1093/molbev/msac116
Nicoll, 2020, Ancestral-sequence reconstruction unveils the structural basis of function in mammalian FMOs, Nat Struct Mol Biol, 27, 14, 10.1038/s41594-019-0347-2
Bailleul, 2021, Ancestral reconstruction of mammalian FMO1 enables structural determination, revealing unique features that explain its catalytic properties, J Biol Chem, 296, 10.1074/jbc.RA120.016297
Sheng, 2001, Mechanistic studies of cyclohexanone monooxygenase: chemical properties of intermediates involved in catalysis, Biochemistry, 40, 11156, 10.1021/bi011153h
Bailleul, 2023, Evolution of enzyme functionality in the flavin-containing monooxygenases, Nat Commun, 14, 1042, 10.1038/s41467-023-36756-x
Gong, 2013, Stability-mediated epistasis constrains the evolution of an influenza protein, Elife, 2, 10.7554/eLife.00631
Starr, 2016, Epistasis in protein evolution, Protein Sci, 25, 1204, 10.1002/pro.2897
Campitelli, 2021, Substitutions at non-conserved rheostat positions modulate function by rewiring long-range, dynamic interactions, Mol Biol Evol, 38, 201, 10.1093/molbev/msaa202
Gamiz-Arco, 2021, Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase, Nat Commun, 12, 380, 10.1038/s41467-020-20630-1
Gutierrez-Rus, 2023, Protection of catalytic cofactors by polypeptides as a driver for the emergence of primordial enzymes, Mol Biol Evol, msad126, 10.1093/molbev/msad126
Valenti, 2022, Characterization of ancestral Fe/Mn superoxide dismutases indicates their cambialistic origin, Protein Sci, 31, e4423, 10.1002/pro.4423
Flamholz, 2019, Revisiting trade-offs between Rubisco kinetic parameters, Biochemistry, 58, 3365, 10.1021/acs.biochem.9b00237
Iñiguez, 2020, Evolutionary trends in RuBisCO kinetics and their co-evolution with CO2 concentrating mechanisms, Plant J, 101, 897, 10.1111/tpj.14643
Lin, 2022, Improving the efficiency of Rubisco by resurrecting its ancestors in the family Solanaceae, Sci Adv, 8, 10.1126/sciadv.abm6871
Schulz, 2022, Evolution of increased complexity and specificity at the dawn of form I Rubiscos, Science, 378, 155, 10.1126/science.abq1416
Chalupkova, 2019, Light-emitting dehalogenases: reconstruction of multifunctional biocatalysts, ACS Catal, 9, 4810, 10.1021/acscatal.9b01031
Risso, 2013, Hyperstability and substrate promiscuity in laboratory resurrections of Precambrian ꞵ-lactamases, J Am Chem Soc, 135, 2899, 10.1021/ja311630a
Devamani, 2016, Catalytic promiscuity of ancestral esterases and hydroxynitrile lyases, J Am Chem Soc, 138, 1046, 10.1021/jacs.5b12209
Chen, 2023, Big data mining, rational modification, and ancestral sequence reconstruction inferred multiple xylose isomerases for biorefinery, Sci Adv, 9
Livada, 2023, Ancestral sequence reconstruction enhances gene mining efforts for industrial ene reductases by expanding enzyme panels with thermostable catalysts, ACS Catal, 4, 2576, 10.1021/acscatal.2c03859
Joho, 2023, Ancestral sequence reconstruction identifies structural changes underlying the evolution of ideonella sakaiensis PETase and variants with improved stability and activity, Biochemistry, 62, 437, 10.1021/acs.biochem.2c00323
Kratzer, 2014, Evolutionary history and metabolic insights of ancient mammalian uricases, Proc Natl Acad Sci U S A, 111, 3763, 10.1073/pnas.1320393111
Zakas, 2017, Enhancing the pharmaceutical properties of protein drugs by ancestral sequence reconstruction, Nat Biotechnol, 35, 35, 10.1038/nbt.3677
Thomas, 2022, Survivor bias drives overestimation of stability in reconstructed ancestral proteins, bioRxiv
Williams, 2006, Assessing the accuracy of ancestral protein reconstruction methods, PLoS Comput Biol, 2, e69, 10.1371/journal.pcbi.0020069
Hobbs, 2012, On the origin and evolution of thermophily: reconstruction of functional precambrian enzymes from ancestors of Bacillus, Mol Biol Evol, 29, 825, 10.1093/molbev/msr253
Trudeau, 2016, On the potential origins of the high stability of reconstructed ancestral proteins, Mol Biol Evol, 33, 2633, 10.1093/molbev/msw138
Wheeler, 2016, The thermostability and specificity of ancient proteins, Curr Opin Struct Biol, 38, 37, 10.1016/j.sbi.2016.05.015
Saenko, 1999, Role of activation of the coagulation factor VIII in interaction with vWf, phospholipid, and functioning within the factor xase complex, Trends Cardiovasc Med, 9, 185, 10.1016/S1050-1738(00)00019-0
Schmidt, 2003, Structure–function relationships in factor IX and factor IXa, Trends Cardiovasc Med, 13, 39, 10.1016/S1050-1738(02)00210-4
Knight, 2021, Identification of coagulation factor IX variants with enhanced activity through ancestral sequence reconstruction, Blood Adv, 5, 3333, 10.1182/bloodadvances.2021004742
Simioni, 2009, X-linked thrombophilia with a mutant factor IX (factor IX Padua), N Engl J Med, 361, 1671, 10.1056/NEJMoa0904377
Ortlund, 2007, Crystal structure of an ancient protein: evolution by conformational epistasis, Science, 317, 1544, 10.1126/science.1142819
Pillai, 2020, Origin of complexity in haemoglobin evolution, Nature, 581, 480, 10.1038/s41586-020-2292-y
Hager, 2022, Substrate affinity versus catalytic efficiency: ancestral sequence reconstruction of tRNA nucleotidyltransferases solves an enzyme puzzle, Mol Biol Evol, 39, 10.1093/molbev/msac250
Dobzhansky, 1973, Nothing in biology Makes Sense except in the light of evolution, Am Biol Teach, 35, 125, 10.2307/4444260