{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T18:24:13Z","timestamp":1778869453035,"version":"3.51.4"},"reference-count":47,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2014,3,6]],"date-time":"2014-03-06T00:00:00Z","timestamp":1394064000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1003484","type":"journal-article","created":{"date-parts":[[2014,3,6]],"date-time":"2014-03-06T21:27:07Z","timestamp":1394141227000},"page":"e1003484","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":11,"title":["Structural Insights into E. coli Porphobilinogen Deaminase during Synthesis and Exit of 1-Hydroxymethylbilane"],"prefix":"10.1371","volume":"10","author":[{"given":"Navneet","family":"Bung","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Meenakshi","family":"Pradhan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Harini","family":"Srinivasan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gopalakrishnan","family":"Bulusu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2014,3,6]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1016\/S1369-5266(98)80112-X","article-title":"Novel insights in the control of tetrapyrrole metabolism of higher plants","volume":"1","author":"B Grimm","year":"1998","journal-title":"Curr Opin Plant Biol"},{"key":"ref2","volume":"Vol 19","unstructured":"Jordan PM (1991) The biosynthesis of 5-aminolaevulinic acid and its transformation to uroporphyrinogen III. In: Neuberger A, Van Deenen LLM, (Eds.) andJordan PM, (Vol. Ed). New Comprehensive Biochemistry, <volume>Vol 19<\/volume> , Biosynthesis of Tetrapyrroles. Elsevier, Amsterdam p. l\u201366."},{"key":"ref3","doi-asserted-by":"crossref","first-page":"1137","DOI":"10.1002\/pro.405","article-title":"Structure and function of enzymes in heme biosynthesis","volume":"19","author":"G Layer","year":"2010","journal-title":"Protein Sci"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1016\/j.bbamcr.2006.05.005","article-title":"Biosynthesis of heme in mammals","volume":"1763","author":"RS Ajioka","year":"2006","journal-title":"Biochim Biophys Acta"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1042\/BJ20082077","article-title":"Structure of human porphobilinogen deaminase at 2.8 \u00c5: the molecular basis of acute intermittent porphyria","volume":"420","author":"R Gill","year":"2009","journal-title":"Biochem J"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1046\/j.1365-2958.2003.03589.x","article-title":"Leptospira spp. possess a complete haem biosynthetic pathway and are able to use exogenous haem sources","volume":"49","author":"R Guegan","year":"2003","journal-title":"Mol Microbiol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1016\/j.ijpara.2008.10.011","article-title":"Localisation of Plasmodium falciparum uroporphyrinogen III decarboxylase of the heme-biosynthetic pathway in the apicoplast and characterisation of its catalytic properties","volume":"39","author":"VA Nagaraj","year":"2009","journal-title":"Int J Parasitol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1038\/359033a0","article-title":"Structure of porphobilinogen deaminase reveals a flexible multidomain polymerase with a single catalytic site","volume":"359","author":"GV Louie","year":"1992","journal-title":"Nature"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1039\/B201331B","article-title":"Time-resolved and static-ensemble structural chemistry of hydroxymethylbilane synthase","volume":"122","author":"JR Helliwell","year":"2003","journal-title":"Faraday Discuss"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"2615","DOI":"10.1039\/a802217h","article-title":"Time-resolved structures of hydroxymethylbilane synthase (Lys59Gln Mutant) as it is loaded with substrate in the crystal determined by Laue diffraction","volume":"94","author":"JR Helliwell","year":"1998","journal-title":"J Chem Soc, Faraday Trans"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"995","DOI":"10.1107\/S0909049599006342","article-title":"Accurate and highly complete synchrotron protein crystal Laue diffraction data using the ESRF CCD and the Daresbury Laue software","volume":"6","author":"YP Nieh","year":"1999","journal-title":"J. Synchrotron Radn"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1107\/S0907444998014711","article-title":"Determination of the structure of seleno-methionine-labelled hydroxymethylbilane synthase in its active form by multi-wavelength anomalous dispersion","volume":"55","author":"A Hadener","year":"1999","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1096\/fj.08-115469","article-title":"Structural insight into acute intermittent porphyria","volume":"23","author":"G Song","year":"2009","journal-title":"FASEB J"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1107\/S0907444912052134","article-title":"Insights into the mechanism of pyrrole polymerization catalyzed by porphobilinogen deaminase: high-resolution X-ray studies of the Arabidopsis thaliana enzyme","volume":"69","author":"A Roberts","year":"2013","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"HM Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1002\/(SICI)1097-0134(199605)25:1<48::AID-PROT5>3.0.CO;2-G","article-title":"The three-dimensional structure of Escherichia coli porphobilinogen deaminase at 1.76 \u00c5 resolution","volume":"25","author":"GV Louie","year":"1996","journal-title":"Proteins"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1042\/bj2800445","article-title":"Mutagenesis of arginine residues in the catalytic cleft of Escherichia coli porphobilinogen deaminase that affects dipyrromethane cofactor assembly and tetrapyrrole chain initiation and elongation","volume":"280","author":"PM Jordan","year":"1991","journal-title":"Biochem J"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1042\/bj2750447","article-title":"Studies on the mechanism of hydroxymethylbilane synthase concerning the role of arginine residues in substrate binding","volume":"275","author":"M Lander","year":"1991","journal-title":"Biochem J"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1042\/bj2710487","article-title":"Investigation of putative active-site lysine residues in hydroxymethylbilane synthase. Preparation and characterization of mutants in which (a) Lys-55, (b) Lys-59 and (c) both Lys-55 and Lys-59 have been replaced by glutamine","volume":"271","author":"A Hadener","year":"1990","journal-title":"Biochem J"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"2688","DOI":"10.1021\/bi00175a043","article-title":"Evidence for participation of aspartate-84 as a catalytic group at the active site of porphobilinogen deaminase obtained by site-directed mutagenesis of the hemC gene from Escherichia coli","volume":"33","author":"SC Woodcock","year":"1994","journal-title":"Biochem"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1042\/bst0310731","article-title":"Human porphobilinogen deaminase mutations in the investigation of the mechanism of dipyrromethane cofactor assembly and tetrapyrrole formation","volume":"31","author":"PM Shoolingin-Jordan","year":"2003","journal-title":"Biochem Soc Trans"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1074\/jbc.M706861200","article-title":"Unique properties of Plasmodium falciparum porphobilinogen deaminase","volume":"283","author":"VA Nagaraj","year":"2008","journal-title":"J Biol Chem"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"21839","DOI":"10.1074\/jbc.272.35.21839","article-title":"Heme biosynthesis by the malarial parasite. Import of delta-aminolevulinate dehydrase from the host red cell","volume":"272","author":"ZQ Bonday","year":"1997","journal-title":"J Biol Chem"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/j.tibs.2007.09.005","article-title":"An alternative model for heme biosynthesis in the malarial parasite","volume":"32","author":"G Padmanaban","year":"2007","journal-title":"Trends Biochem Sci"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1016\/j.jbbm.2007.10.006","article-title":"A steered molecular dynamics method with direction optimization and its applications on ligand molecule dissociation","volume":"70","author":"X Liu","year":"2008","journal-title":"J Biochem Biophys Methods"},{"key":"ref26","doi-asserted-by":"crossref","unstructured":"Pradhan M, Srinivasan H, Bung N, Bulusu G (2013) Structural dynamics of E.coli porphobilinogen deaminase during the tetrapolymerisation of porphobilinogen. In: Bansal M, Srinivasan N, editors. Biomolecular Forms and Functions. IISc Press-World Scientific. pp. 455\u2013467.","DOI":"10.1142\/9789814449144_0035"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1006\/jmbi.2000.4155","article-title":"How do substrates enter and products exit the buried active site of cytochrome P450cam? 2. Steered molecular dynamics and adiabatic mapping of substrate pathways","volume":"303(5)","author":"SK L\u00fcdemann","year":"2000","journal-title":"J Mol Biol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"328","DOI":"10.2174\/092986611794654003","article-title":"Role of protein conformational dynamics in the catalysis by 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase","volume":"18(4)","author":"H Yan","year":"2011","journal-title":"Protein Pept Lett"},{"key":"ref29","first-page":"357","article-title":"Domain closure in lactoferrin. Two hinges produce a see-saw motion between alternative close-packed interfaces","volume":"234(2)","author":"M Gerstein","year":"1993","journal-title":"J Mol Biol"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"2093","DOI":"10.1016\/S0006-3495(00)76756-7","article-title":"Proteins with similar architecture exhibit similar large-scale dynamic behavior","volume":"78","author":"O Keskin","year":"2000","journal-title":"Biophys J"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"1672","DOI":"10.1002\/pro.2143","article-title":"Molecular dynamics simulation of the last step of a catalytic cycle: product release from the active site of the enzyme chorismate mutase from Mycobacterium tuberculosis","volume":"21","author":"A Choutko","year":"2012","journal-title":"Protein Sci"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1016\/S0076-6879(03)74020-8","article-title":"Modeller: generation and refinement of homology-based protein structure models","volume":"374","author":"A Fizer","year":"2003","journal-title":"Methods Enzymol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1021\/ct700301q","article-title":"GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation","volume":"4","author":"B Hess","year":"2008","journal-title":"J Chem Theory Comput"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"1656","DOI":"10.1002\/jcc.20090","article-title":"A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6","volume":"25","author":"C Oostenbrink","year":"2004","journal-title":"J Comput Chem"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"4026","DOI":"10.1021\/ct200196m","article-title":"An Automated force field Topology Builder (ATB) and repository: version 1.0","volume":"7","author":"AK Malde","year":"2011","journal-title":"J Chem Theory Comput"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"6269","DOI":"10.1021\/j100308a038","article-title":"The missing term in effective pair potentials","volume":"91","author":"HJC Berendsen","year":"1987","journal-title":"J Phys Chem"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"014101","DOI":"10.1063\/1.2408420","article-title":"Canonical sampling through velocity rescaling","volume":"126","author":"G Bussi","year":"2007","journal-title":"J Chem Phys"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"7182","DOI":"10.1063\/1.328693","article-title":"Polymorphic transitions in single crystals: A new molecular dynamics method","volume":"52","author":"M Parrinello","year":"1981","journal-title":"J Appl Phys"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1002\/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H","article-title":"LINCS: A linear constraint solver for molecular simulations","volume":"18","author":"B Hess","year":"1997","journal-title":"J Comput Chem"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"10089","DOI":"10.1063\/1.464397","article-title":"Particle mesh Ewald: An N.log(N) method for Ewald sums in large systems","volume":"98","author":"T Darden","year":"1993","journal-title":"J Chem Phys"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"8577","DOI":"10.1063\/1.470117","article-title":"A smooth particle mesh Ewald method","volume":"103","author":"U Essmann","year":"1995","journal-title":"J Chem Phys"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"E1002708","DOI":"10.1371\/journal.pcbi.1002708","article-title":"CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures","volume":"8","author":"E Chovancova","year":"2012","journal-title":"PLoS Comput Biol"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: visual molecular dynamics,","volume":"14","author":"W Humphrey","year":"1996","journal-title":"J Mol Graph"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1002\/prot.340220107","article-title":"The essential dynamics of thermolysin: confirmation of the hinge-bending motion and comparison of simulations in vacuum and water","volume":"22","author":"DM van Aalten","year":"1995","journal-title":"Proteins"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"1147","DOI":"10.1016\/S0006-3495(97)78147-5","article-title":"Molecular dynamics study of time-correlated protein domain motions and molecular flexibility: cytochrome P450BM-3","volume":"73(3)","author":"GE Arnold","year":"1997","journal-title":"Biophys J"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"1575","DOI":"10.1093\/bioinformatics\/btr168","article-title":"ProDy: Protein dynamics inferred from theory and experiments","volume":"27","author":"A Bakan","year":"2011","journal-title":"Bioinformatics"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1016\/j.jmgm.2010.10.007","article-title":"POVME: an algorithm for measuring binding-pocket volumes","volume":"29","author":"JD Durrant","year":"2011","journal-title":"J Mol Graph Model"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003484","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,9]],"date-time":"2020-05-09T12:54:42Z","timestamp":1589028882000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003484"}},"subtitle":[],"editor":[{"given":"Rebecca C.","family":"Wade","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2014,3,6]]},"references-count":47,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2014,3,6]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1003484","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,3,6]]}}}