{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T15:50:11Z","timestamp":1785426611173,"version":"3.56.0"},"reference-count":83,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,12,30]],"date-time":"2024-12-30T00:00:00Z","timestamp":1735516800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000854","name":"Human Frontier Science Program","doi-asserted-by":"publisher","award":["RGY0072\/2021"],"award-info":[{"award-number":["RGY0072\/2021"]}],"id":[{"id":"10.13039\/501100000854","id-type":"DOI","asserted-by":"publisher"}]},{"name":"NASA Exobiology","award":["NNH23ZDA001N"],"award-info":[{"award-number":["NNH23ZDA001N"]}]},{"DOI":"10.13039\/501100001503","name":"ICAR","doi-asserted-by":"publisher","award":["80NSSC17K0296"],"award-info":[{"award-number":["80NSSC17K0296"]}],"id":[{"id":"10.13039\/501100001503","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Margarita Salas Postdoctoral Fellowship"},{"name":"Uni\u00f3n Europea","award":["B.C.Z.; UP2021-035"],"award-info":[{"award-number":["B.C.Z.; UP2021-035"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Ribulose-1,5-bisphosphate carboxylase\/oxygenase (RuBisCO) is an ancient protein critical for CO2-fixation and global biogeochemistry. Form-I RuBisCO complexes uniquely harbor small subunits that form a hexadecameric complex together with their large subunits. The small subunit protein is thought to have significantly contributed to RuBisCO's response to the atmospheric rise of O2 \u223c2.5 billion years ago, marking a pivotal point in the enzyme's evolutionary history. Here, we performed a comprehensive evolutionary analysis of extant and ancestral RuBisCO sequences and structures to explore the impact of the small subunit's earliest integration on the molecular dynamics of the overall complex. Our simulations suggest that the small subunit restricted the conformational flexibility of the large subunit early in its history, impacting the evolutionary trajectory of the Form-I RuBisCO complex. Molecular dynamics investigations of CO2 and O2 gas distribution around predicted ancient RuBisCO complexes suggest that a proposed \u201cCO2-reservoir\u201d role for the small subunit is not conserved throughout the enzyme's evolutionary history. The evolutionary and biophysical response of RuBisCO to changing atmospheric conditions on ancient Earth showcase multi-level and trackable responses of enzymes to environmental shifts over long timescales.<\/jats:p>","DOI":"10.1093\/molbev\/msae268","type":"journal-article","created":{"date-parts":[[2024,12,27]],"date-time":"2024-12-27T15:28:55Z","timestamp":1735313335000},"source":"Crossref","is-referenced-by-count":13,"title":["Evolutionary Dynamics of RuBisCO: Emergence of the Small Subunit and its Impact Through Time"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-5270-3451","authenticated-orcid":false,"given":"Kaustubh","family":"Amritkar","sequence":"first","affiliation":[{"name":"Department of Bacteriology, University of Wisconsin-Madison , Madison, WI ,","place":["USA"]},{"name":"Biophysics Graduate Degree Program, University of Wisconsin-Madison , Madison, WI ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1479-9442","authenticated-orcid":false,"given":"Bruno","family":"Cuevas-Zuvir\u00eda","sequence":"additional","affiliation":[{"name":"Department of Bacteriology, University of Wisconsin-Madison , Madison, WI ,","place":["USA"]},{"name":"Centro de Biotecnolog\u00eda y Gen\u00f3mica de Plantas, Universidad Polit\u00e9cnica de Madrid , Madrid ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0482-2357","authenticated-orcid":false,"given":"Bet\u00fcl","family":"Ka\u00e7ar","sequence":"additional","affiliation":[{"name":"Department of Bacteriology, University of Wisconsin-Madison , Madison, WI ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,12,30]]},"reference":[{"key":"2025013112385221600_msae268-B1","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1007\/978-1-4939-8736-8_8","volume-title":"Computational methods in protein evolution","author":"Aadland","year":"2019"},{"issue":"11","key":"2025013112385221600_msae268-B2","doi-asserted-by":"publisher","first-page":"444","DOI":"10.1016\/S0968-0004(98)01298-5","article-title":"Iterated profile searches with PSI-BLAST\u2014a tool for discovery in protein databases","volume":"23","author":"Altschul","year":"1998","journal-title":"Trends Biochem Sci"},{"issue":"17","key":"2025013112385221600_msae268-B3","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"2025013112385221600_msae268-B4","doi-asserted-by":"publisher","first-page":"160","DOI":"10.1006\/jmbi.1996.0310","article-title":"Large structures at high resolution: the 1.6 \u00c5 crystal structure of spinach ribulose-1,5- bisphosphate carboxylase\/oxygenase complexed with 2-carboxyarabinitol bisphosphate","volume":"259","author":"Andersson","year":"1996","journal-title":"J Mol Biol"},{"issue":"7","key":"2025013112385221600_msae268-B5","doi-asserted-by":"publisher","first-page":"1555","DOI":"10.1093\/jxb\/ern091","article-title":"Catalysis and regulation in rubisco","volume":"59","author":"Andersson","year":"2008","journal-title":"J Exp Bot"},{"issue":"25","key":"2025013112385221600_msae268-B6","doi-asserted-by":"publisher","first-page":"12213","DOI":"10.1016\/S0021-9258(18)37741-X","article-title":"Catalysis by cyanobacterial ribulose-bisphosphate carboxylase large subunits in the complete absence of small subunits","volume":"263","author":"Andrews","year":"1988","journal-title":"J Biol Chem"},{"issue":"5-6","key":"2025013112385221600_msae268-B7","doi-asserted-by":"publisher","first-page":"611","DOI":"10.1016\/j.resmic.2005.01.014","article-title":"Was photosynthetic RuBisCO recruited by acquisitive evolution from RuBisCO-like proteins involved in sulfur metabolism?","volume":"156","author":"Ashida","year":"2005","journal-title":"Res Microbiol"},{"issue":"2","key":"2025013112385221600_msae268-B8","doi-asserted-by":"publisher","first-page":"200","DOI":"10.1016\/j.cbpa.2009.11.028","article-title":"What makes an enzyme promiscuous?","volume":"14","author":"Babtie","year":"2010","journal-title":"Curr Opin Chem Biol"},{"issue":"11","key":"2025013112385221600_msae268-B9","doi-asserted-by":"publisher","first-page":"1575","DOI":"10.1093\/bioinformatics\/btr168","article-title":"Prody: protein dynamics inferred from theory and experiments","volume":"27","author":"Bakan","year":"2011","journal-title":"Bioinformatics"},{"issue":"9","key":"2025013112385221600_msae268-B10","doi-asserted-by":"publisher","first-page":"1158","DOI":"10.1038\/s41477-020-00762-4","article-title":"Novel bacterial clade reveals origin of form I rubisco","volume":"6","author":"Banda","year":"2020","journal-title":"Nat Plants"},{"issue":"43","key":"2025013112385221600_msae268-B11","doi-asserted-by":"publisher","first-page":"e2308600120","DOI":"10.1073\/pnas.2308600120","article-title":"Identification of a carbonic anhydrase\u2013rubisco complex within the alpha-carboxysome","volume":"120","author":"Blikstad","year":"2023","journal-title":"Proc Natl Acad Sci U S A."},{"issue":"11","key":"2025013112385221600_msae268-B12","doi-asserted-by":"publisher","first-page":"e2321050121","DOI":"10.1073\/pnas.2321050121","article-title":"Rubisco is evolving for improved catalytic efficiency and CO2 assimilation in plants","volume":"121","author":"Bouvier","year":"2024","journal-title":"Proc Natl Acad Sci U S A."},{"issue":"1","key":"2025013112385221600_msae268-B13","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1146\/annurev-arplant-043015-111633","article-title":"Biogenesis and metabolic maintenance of rubisco","volume":"68","author":"Bracher","year":"2017","journal-title":"Annu Rev Plant Biol"},{"issue":"11","key":"2025013112385221600_msae268-B14","doi-asserted-by":"publisher","first-page":"201700174","DOI":"10.1002\/bies.201700174","article-title":"RubisCO and the search for biomolecular culprits of planetary change","volume":"39","author":"Caetano-Anoll\u00e9s","year":"2017","journal-title":"Bioessays"},{"issue":"12","key":"2025013112385221600_msae268-B15","doi-asserted-by":"publisher","first-page":"1761","DOI":"10.3390\/biom11121761","article-title":"An insight of RuBisCO evolution through a multilevel approach","volume":"11","author":"Camel","year":"2021","journal-title":"Biomolecules"},{"issue":"6","key":"2025013112385221600_msae268-B16","doi-asserted-by":"publisher","first-page":"997","DOI":"10.1093\/sysbio\/syw037","article-title":"Terrace aware data structure for phylogenomic inference from supermatrices","volume":"65","author":"Chernomor","year":"2016","journal-title":"Syst Biol"},{"key":"2025013112385221600_msae268-B17","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1007\/978-1-62703-658-0_11","article-title":"Principal component analysis: a method for determining the essential dynamics of proteins","volume":"1084","author":"David","year":"2014","journal-title":"Methods Mol Biol"},{"issue":"7","key":"2025013112385221600_msae268-B18","doi-asserted-by":"publisher","first-page":"e1005659","DOI":"10.1371\/journal.pcbi.1005659","article-title":"OpenMM 7: rapid development of high performance algorithms for molecular dynamics","volume":"13","author":"Eastman","year":"2017","journal-title":"PLOS Comput Biol"},{"key":"2025013112385221600_msae268-B19","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1016\/j.copbio.2017.07.017","article-title":"A short history of RubisCO: the rise and fall (? ) of Nature's predominant CO2 fixing enzyme","volume":"49","author":"Erb","year":"2018","journal-title":"Curr Opin Biotechnol"},{"issue":"3","key":"2025013112385221600_msae268-B20","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1007\/s11120-013-9916-0","article-title":"Substitutions at the opening of the rubisco central solvent channel affect holoenzyme stability and CO2\/O2 specificity but not activation by rubisco Activase","volume":"118","author":"Esquivel","year":"2013","journal-title":"Photosynth Res"},{"issue":"5879","key":"2025013112385221600_msae268-B21","doi-asserted-by":"publisher","first-page":"1034","DOI":"10.1126\/science.1153213","article-title":"The microbial engines that drive Earth's biogeochemical cycles","volume":"320","author":"Falkowski","year":"2008","journal-title":"Science"},{"issue":"4","key":"2025013112385221600_msae268-B22","doi-asserted-by":"publisher","first-page":"666","DOI":"10.1111\/tpj.14669","article-title":"Wasteful, essential, evolutionary stepping stone? The multiple personalities of the photorespiratory pathway","volume":"102","author":"Fernie","year":"2020","journal-title":"Plant J"},{"issue":"31","key":"2025013112385221600_msae268-B23","doi-asserted-by":"publisher","first-page":"3365","DOI":"10.1021\/acs.biochem.9b00237","article-title":"Revisiting trade-offs between rubisco kinetic parameters","volume":"58","author":"Flamholz","year":"2019","journal-title":"Biochemistry"},{"issue":"8","key":"2025013112385221600_msae268-B24","doi-asserted-by":"publisher","first-page":"2183","DOI":"10.1038\/s41396-021-00971-5","article-title":"The curious consistency of carbon biosignatures over billions of years of earth-life coevolution","volume":"15","author":"Garcia","year":"2021","journal-title":"ISME J"},{"issue":"1-2","key":"2025013112385221600_msae268-B25","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1007\/BF00047686","article-title":"Synthesis and assembly of bacterial and higher plant rubisco subunits in Escherichia coli","volume":"17","author":"Gatenby","year":"1988","journal-title":"Photosynth Res"},{"issue":"26","key":"2025013112385221600_msae268-B26","doi-asserted-by":"publisher","first-page":"19833","DOI":"10.1074\/jbc.M110.124230","article-title":"Functional hybrid rubisco enzymes with plant small subunits and algal large subunits: engineered rbcS cDNA for expression in Chlamydomonas","volume":"285","author":"Genkov","year":"2010","journal-title":"J Biol Chem"},{"issue":"1","key":"2025013112385221600_msae268-B27","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1007\/s11120-007-9240-7","article-title":"Ribulose-1,5-bisphosphate carboxylase\/oxygenase from thermophilic cyanobacterium thermosynechococcus elongatus","volume":"95","author":"Gubernator","year":"2008","journal-title":"Photosynth Res"},{"key":"2025013112385221600_msae268-B28","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1007\/978-1-59745-177-2_5","volume-title":"Molecular modeling of proteins. Methods molecular BiologyTM","author":"Hayward","year":"2008"},{"issue":"7838","key":"2025013112385221600_msae268-B29","doi-asserted-by":"publisher","first-page":"503","DOI":"10.1038\/s41586-020-3021-2","article-title":"A hydrophobic ratchet entrenches molecular complexes","volume":"588","author":"Hochberg","year":"2020","journal-title":"Nature"},{"issue":"7","key":"2025013112385221600_msae268-B30","doi-asserted-by":"publisher","first-page":"167462","DOI":"10.1016\/j.jmb.2022.167462","article-title":"Adventures on the routes of protein evolution\u2014in memoriam dan salah tawfik (1955\u20132021)","volume":"434","author":"Jackson","year":"2022","journal-title":"J Mol Biol"},{"issue":"2","key":"2025013112385221600_msae268-B31","doi-asserted-by":"publisher","first-page":"926","DOI":"10.1063\/1.445869","article-title":"Comparison of simple potential functions for simulating liquid water","volume":"79","author":"Jorgensen","year":"1983","journal-title":"J Chem Phys"},{"issue":"2","key":"2025013112385221600_msae268-B32","doi-asserted-by":"publisher","first-page":"1066","DOI":"10.1074\/jbc.M114.613091","article-title":"Role of small subunit in mediating assembly of red-type form I rubisco","volume":"290","author":"Joshi","year":"2015","journal-title":"J Biol Chem"},{"issue":"1","key":"2025013112385221600_msae268-B33","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1146\/annurev-micro-041522-103400","article-title":"Reconstructing early microbial life","volume":"78","author":"Ka\u00e7ar","year":"2024","journal-title":"Annu Rev Microbiol"},{"issue":"5","key":"2025013112385221600_msae268-B34","doi-asserted-by":"publisher","first-page":"628","DOI":"10.1111\/gbi.12243","article-title":"Constraining the timing of the great oxidation event within the rubisco phylogenetic tree","volume":"15","author":"Kacar","year":"2017","journal-title":"Geobiology"},{"issue":"6","key":"2025013112385221600_msae268-B35","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: fast model selection for accurate phylogenetic estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat Methods"},{"issue":"14","key":"2025013112385221600_msae268-B36","doi-asserted-by":"publisher","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform","volume":"30","author":"Katoh","year":"2002","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"2025013112385221600_msae268-B37","doi-asserted-by":"publisher","first-page":"110726","DOI":"10.1016\/j.celrep.2022.110726","article-title":"Resurrected rubisco suggests uniform carbon isotope signatures over geologic time","volume":"39","author":"K\u0119dzior","year":"2022","journal-title":"Cell Rep"},{"issue":"1","key":"2025013112385221600_msae268-B38","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1016\/S0022-2836(05)80100-7","article-title":"Crystallographic analysis of ribulose 1,5-bisphosphate carboxylase from spinach at 2.4 A resolution subunit interactions and active site","volume":"215","author":"Knight","year":"1990","journal-title":"J Mol Biol"},{"issue":"2","key":"2025013112385221600_msae268-B39","doi-asserted-by":"publisher","first-page":"793","DOI":"10.1111\/nph.16195","article-title":"Cyanobacterial carboxysomes contain an unique rubisco-Activase-like protein","volume":"225","author":"Lechno-Yossef","year":"2020","journal-title":"New Phytol"},{"issue":"40","key":"2025013112385221600_msae268-B40","doi-asserted-by":"publisher","first-page":"9352","DOI":"10.1021\/bi00492a007","article-title":"Purification of recombinant ribulose-1,5-bisphosphate carboxylase\/oxygenase large subunits suitable for reconstitution and assembly of active L8S8 enzyme","volume":"29","author":"Lee","year":"1990","journal-title":"Biochemistry"},{"issue":"13","key":"2025013112385221600_msae268-B41","doi-asserted-by":"publisher","first-page":"1658","DOI":"10.1093\/bioinformatics\/btl158","article-title":"Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences","volume":"22","author":"Li","year":"2006","journal-title":"Bioinformatics"},{"issue":"34","key":"2025013112385221600_msae268-B42","doi-asserted-by":"publisher","first-page":"eadc9440","DOI":"10.1126\/sciadv.adc9440","article-title":"Structural plasticity enables evolution and innovation of RuBisCO assemblies","volume":"8","author":"Liu","year":"2022","journal-title":"Sci Adv"},{"issue":"7278","key":"2025013112385221600_msae268-B43","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1038\/nature08651","article-title":"Coupled chaperone action in folding and assembly of hexadecameric rubisco","volume":"463","author":"Liu","year":"2010","journal-title":"Nature"},{"issue":"8","key":"2025013112385221600_msae268-B44","doi-asserted-by":"publisher","first-page":"3696","DOI":"10.1021\/acs.jctc.5b00255","article-title":"ff14SB: improving the accuracy of protein Side chain and backbone parameters from ff99SB","volume":"11","author":"Maier","year":"2015","journal-title":"J Chem Theory Comput"},{"issue":"2","key":"2025013112385221600_msae268-B45","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1093\/jxb\/erac309","article-title":"The small subunit of rubisco and its potential as an engineering target","volume":"74","author":"Mao","year":"2023","journal-title":"J Exp Bot"},{"issue":"11","key":"2025013112385221600_msae268-B46","doi-asserted-by":"publisher","first-page":"1570","DOI":"10.1016\/j.molp.2020.08.012","article-title":"Hybrid rubisco with complete replacement of rice rubisco small subunits by Sorghum counterparts confers C4 plant-like high catalytic activity","volume":"13","author":"Matsumura","year":"2020","journal-title":"Mol Plant"},{"issue":"10","key":"2025013112385221600_msae268-B47","doi-asserted-by":"publisher","first-page":"2319","DOI":"10.1002\/jcc.21787","article-title":"MDAnalysis: a toolkit for the analysis of molecular dynamics simulations","volume":"32","author":"Michaud-Agrawal","year":"2011","journal-title":"J Comput Chem"},{"issue":"6","key":"2025013112385221600_msae268-B48","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1038\/s41592-022-01488-1","article-title":"ColabFold: making protein folding accessible to all","volume":"19","author":"Mirdita","year":"2022","journal-title":"Nat Methods"},{"key":"2025013112385221600_msae268-B49","doi-asserted-by":"publisher","first-page":"160","DOI":"10.1016\/j.sbi.2021.04.007","article-title":"Epistasis and intramolecular networks in protein evolution","volume":"69","author":"Miton","year":"2021","journal-title":"Curr Opin Struct Biol"},{"issue":"1392","key":"2025013112385221600_msae268-B50","doi-asserted-by":"publisher","first-page":"1923","DOI":"10.1098\/rstb.1999.0532","article-title":"Life: past, present and future","volume":"354","author":"Nealson","year":"1999","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"issue":"1","key":"2025013112385221600_msae268-B51","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: a fast and effective stochastic algorithm for estimating Maximum-likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol Biol Evol"},{"issue":"2","key":"2025013112385221600_msae268-B52","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1038\/nbt1519","article-title":"Protein promiscuity and its implications for biotechnology","volume":"27","author":"Nobeli","year":"2009","journal-title":"Nat Biotechnol"},{"key":"2025013112385221600_msae268-B53","first-page":"2825","article-title":"Scikit-learn: machine learning in python","volume":"12","author":"Pedregosa","year":"2011","journal-title":"J Mach Learn Res"},{"issue":"10","key":"2025013112385221600_msae268-B54","doi-asserted-by":"publisher","first-page":"e1009541","DOI":"10.1371\/journal.pcbi.1009541","article-title":"TwinCons: conservation score for uncovering deep sequence similarity and divergence","volume":"17","author":"Penev","year":"2021","journal-title":"PLoS Comput Biol"},{"issue":"144","key":"2025013112385221600_msae268-B55","doi-asserted-by":"publisher","first-page":"20180330","DOI":"10.1098\/rsif.2018.0330","article-title":"Conformational dynamics and enzyme evolution","volume":"15","author":"Petrovi\u0107","year":"2018","journal-title":"J R Soc Interface"},{"issue":"13","key":"2025013112385221600_msae268-B56","doi-asserted-by":"publisher","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF chimera\u2014a visualization system for exploratory research and analysis","volume":"25","author":"Pettersen","year":"2004","journal-title":"J Comput Chem"},{"issue":"48","key":"2025013112385221600_msae268-B57","doi-asserted-by":"publisher","first-page":"30451","DOI":"10.1073\/pnas.2018939117","article-title":"Biophysical analysis of the structural evolution of substrate specificity in RuBisCO","volume":"117","author":"Poudel","year":"2020","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"5768","key":"2025013112385221600_msae268-B58","doi-asserted-by":"publisher","first-page":"1764","DOI":"10.1126\/science.1118439","article-title":"The effect of oxygen on biochemical networks and the evolution of complex life","volume":"311","author":"Raymond","year":"2006","journal-title":"Science"},{"issue":"6","key":"2025013112385221600_msae268-B59","doi-asserted-by":"publisher","first-page":"554","DOI":"10.1016\/j.tim.2023.03.011","article-title":"Enigmatic evolution of microbial nitrogen fixation: insights from Earth's past","volume":"32","author":"Rucker","year":"2024","journal-title":"Trends Microbiol"},{"issue":"8","key":"2025013112385221600_msae268-B60","doi-asserted-by":"publisher","first-page":"2593","DOI":"10.1074\/jbc.RA118.006330","article-title":"The small RbcS-like domains of the \u03b2-carboxysome structural protein CcmM bind RubisCO at a site distinct from that binding the RbcS subunit","volume":"294","author":"Ryan","year":"2019","journal-title":"J Biol Chem"},{"issue":"2","key":"2025013112385221600_msae268-B61","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1002\/wcms.1121","article-title":"An overview of the amber biomolecular simulation package","volume":"3:","author":"Salomon-Ferrer","year":"2013","journal-title":"Wiley Interdiscip Rev Comput Mol Sci"},{"key":"2025013112385221600_msae268-B62","author":"Schmidt"},{"issue":"6616","key":"2025013112385221600_msae268-B63","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1126\/science.abq1416","article-title":"Evolution of increased complexity and specificity at the Dawn of form I rubiscos","volume":"378","author":"Schulz","year":"2022","journal-title":"Science"},{"issue":"2","key":"2025013112385221600_msae268-B64","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1016\/S0003-9861(03)00171-1","article-title":"Role of the small subunit in ribulose-1,5-bisphosphate carboxylase\/oxygenase","volume":"414","author":"Spreitzer","year":"2003","journal-title":"Arch Biochem Biophys"},{"issue":"46","key":"2025013112385221600_msae268-B65","doi-asserted-by":"publisher","first-page":"18785","DOI":"10.1073\/pnas.1210754109","article-title":"Structural mechanism of RuBisCO activation by carbamylation of the active site lysine","volume":"109","author":"Stec","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"22","key":"2025013112385221600_msae268-B66","doi-asserted-by":"publisher","first-page":"15655","DOI":"10.1074\/jbc.274.22.15655","article-title":"Crystal structure of carboxylase reaction-oriented ribulose 1,5-bisphosphate carboxylase\/oxygenase from a thermophilic red alga, Galdieria partita","volume":"274","author":"Sugawara","year":"1999","journal-title":"J Biol Chem"},{"issue":"W1","key":"2025013112385221600_msae268-B67","doi-asserted-by":"publisher","first-page":"W65","DOI":"10.1093\/nar\/gkaa276","article-title":"Zebra2: advanced and easy-to-use web-server for bioinformatic analysis of subfamily-specific and conserved positions in diverse protein superfamilies","volume":"48","author":"Suplatov","year":"2020","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"2025013112385221600_msae268-B68","doi-asserted-by":"publisher","first-page":"576","DOI":"10.1128\/MMBR.00015-07","article-title":"Function, structure, and evolution of the RubisCO-like proteins and their RubisCO homologs","volume":"71","author":"Tabita","year":"2007","journal-title":"Microbiol Mol Biol Rev"},{"issue":"7","key":"2025013112385221600_msae268-B69","doi-asserted-by":"publisher","first-page":"1515","DOI":"10.1093\/jxb\/erm361","article-title":"Distinct form I, II, III, and IV rubisco proteins from the three kingdoms of life provide clues about rubisco evolution and structure\/function relationships","volume":"59","author":"Tabita","year":"2008","journal-title":"J Exp Bot"},{"issue":"5924","key":"2025013112385221600_msae268-B70","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1126\/science.1169375","article-title":"Protein dynamism and evolvability","volume":"324","author":"Tokuriki","year":"2009","journal-title":"Science"},{"issue":"34","key":"2025013112385221600_msae268-B71","doi-asserted-by":"publisher","first-page":"13033","DOI":"10.1074\/jbc.RA118.003518","article-title":"Structural and functional analyses of rubisco from Arctic diatom species reveal unusual posttranslational modifications","volume":"293","author":"Valeg\u00e5rd","year":"2018","journal-title":"J Biol Chem"},{"issue":"8","key":"2025013112385221600_msae268-B72","doi-asserted-by":"publisher","first-page":"3165","DOI":"10.1021\/ja411579b","article-title":"CO2 and O2 distribution in rubisco suggests the small subunit functions as a CO2 reservoir","volume":"136","author":"Van Lun","year":"2014","journal-title":"J Am Chem Soc"},{"issue":"5","key":"2025013112385221600_msae268-B73","doi-asserted-by":"publisher","first-page":"1083","DOI":"10.1016\/j.jmb.2011.06.052","article-title":"Subunit interface dynamics in hexadecameric rubisco","volume":"411","author":"Van Lun","year":"2011","journal-title":"J Mol Biol"},{"issue":"97","key":"2025013112385221600_msae268-B74","doi-asserted-by":"publisher","first-page":"20131190","DOI":"10.1098\/rsif.2013.1190","article-title":"Spaces of the possible: universal darwinism and the wall between technological and biological innovation","volume":"11","author":"Wagner","year":"2014","journal-title":"J R Soc Interface"},{"issue":"7742","key":"2025013112385221600_msae268-B75","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1038\/s41586-019-0880-5","article-title":"Rubisco condensate formation by CcmM in \u03b2-carboxysome biogenesis","volume":"566","author":"Wang","year":"2019","journal-title":"Nature"},{"issue":"9","key":"2025013112385221600_msae268-B76","doi-asserted-by":"publisher","first-page":"1157","DOI":"10.1002\/jcc.20035","article-title":"Development and testing of a general amber force field","volume":"25","author":"Wang","year":"2004","journal-title":"J Comput Chem"},{"issue":"1","key":"2025013112385221600_msae268-B77","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1093\/molbev\/msq232","article-title":"A universal molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenation","volume":"28","author":"Wang","year":"2011","journal-title":"Mol Biol Evol"},{"key":"2025013112385221600_msae268-B78","doi-asserted-by":"publisher","first-page":"188","DOI":"10.1016\/j.freeradbiomed.2019.01.049","article-title":"The evolution and productivity of carbon fixation pathways in response to changes in oxygen concentration over geological time","volume":"140","author":"Ward","year":"2019","journal-title":"Free Radic Biol Med"},{"key":"2025013112385221600_msae268-B79","doi-asserted-by":"publisher","author":"West-Roberts","DOI":"10.1101\/2021.08.23.457424"},{"issue":"1-3","key":"2025013112385221600_msae268-B80","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1016\/S0166-1280(00)00487-5","article-title":"Restrained electrostatic potential atomic partial charges for condensed-phase simulations of carbohydrates","volume":"527","author":"Woods","year":"2000","journal-title":"J Mol Struct"},{"issue":"8","key":"2025013112385221600_msae268-B81","doi-asserted-by":"publisher","first-page":"1586","DOI":"10.1093\/molbev\/msm088","article-title":"PAML 4: phylogenetic analysis by Maximum likelihood","volume":"24","author":"Yang","year":"2007","journal-title":"Mol Biol Evol"},{"issue":"1588","key":"2025013112385221600_msae268-B82","doi-asserted-by":"publisher","first-page":"483","DOI":"10.1098\/rstb.2011.0145","article-title":"Adaptive signals in algal rubisco reveal a history of ancient atmospheric carbon dioxide","volume":"367","author":"Young","year":"2012","journal-title":"Philos Trans R Soc B Biol Sci"},{"issue":"1","key":"2025013112385221600_msae268-B83","doi-asserted-by":"publisher","first-page":"132","DOI":"10.1093\/molbev\/msu281","article-title":"Evolution of conformational dynamics determines the conversion of a promiscuous generalist into a specialist enzyme","volume":"32","author":"Zou","year":"2015","journal-title":"Mol Biol Evol"}],"container-title":["Molecular Biology and Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/mbe\/advance-article-pdf\/doi\/10.1093\/molbev\/msae268\/61297226\/msae268.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/mbe\/article-pdf\/42\/1\/msae268\/61297226\/msae268.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/mbe\/article-pdf\/42\/1\/msae268\/61297226\/msae268.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,31]],"date-time":"2025-01-31T07:39:24Z","timestamp":1738309164000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/mbe\/article\/doi\/10.1093\/molbev\/msae268\/7934943"}},"subtitle":[],"editor":[{"given":"Julian","family":"Echave","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2024,12,30]]},"references-count":83,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2025,1,6]]}},"URL":"https:\/\/doi.org\/10.1093\/molbev\/msae268","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.06.06.597628","asserted-by":"object"}]},"ISSN":["0737-4038","1537-1719"],"issn-type":[{"value":"0737-4038","type":"print"},{"value":"1537-1719","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,1]]},"published":{"date-parts":[[2024,12,30]]},"article-number":"msae268"}}