{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,9]],"date-time":"2026-03-09T14:14:31Z","timestamp":1773065671000,"version":"3.50.1"},"reference-count":38,"publisher":"Springer Science and Business Media LLC","issue":"S16","license":[{"start":{"date-parts":[[2013,10,1]],"date-time":"2013-10-01T00:00:00Z","timestamp":1380585600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2013,10]]},"DOI":"10.1186\/1471-2105-14-s16-s11","type":"journal-article","created":{"date-parts":[[2013,10,22]],"date-time":"2013-10-22T05:06:31Z","timestamp":1382418391000},"source":"Crossref","is-referenced-by-count":9,"title":["Structural analysis on mutation residues and interfacial water molecules for human TIM disease understanding"],"prefix":"10.1186","volume":"14","author":[{"given":"Zhenhua","family":"Li","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ying","family":"He","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qian","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liang","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Limsoon","family":"Wong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chee Keong","family":"Kwoh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hung","family":"Nguyen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinyan","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2013,10,22]]},"reference":[{"issue":"5","key":"6130_CR1","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1056\/NEJM196502042720503","volume":"272","author":"AS Schneider","year":"1965","unstructured":"Schneider AS, Valentine WN, Hattori M, Heins HL: Hereditary Hemolytic Anemia with Triosephosphate Isomerase Deficiency. N Engl J Med. 1965, 272 (5): 229-235. 10.1056\/NEJM196502042720503.","journal-title":"N Engl J Med"},{"key":"6130_CR2","doi-asserted-by":"publisher","first-page":"1335","DOI":"10.1093\/brain\/awp023","volume":"132","author":"FX Guix","year":"2009","unstructured":"Guix FX, Ill-Raga G, Bravo R, Nakaya T, de Fabritiis G, Coma M, Miscione GP, Villa-Freixa J, Suzuki T, Fernandez-Busquets X, Valverde MA, de Strooper B, Munoz FJ: Amyloid-dependent triosephosphate isomerase nitrotyrosination induces glycation and tau fibrillation. Brain. 2009, 132: 1335-1345. 10.1093\/brain\/awp023.","journal-title":"Brain"},{"key":"6130_CR3","first-page":"43","volume":"28","author":"M Tajes","year":"2013","unstructured":"Tajes M, Guivernau B, Ramos-Fern\u00e1ndez E, Bosch-Morat\u00f3 M, Palomer E, Guix FX, Mu\u00f1oz FJ: The patho-physiology of triose phosphate isomerase dysfunction in Alzheimer's disease. Histol Histopathol. 2013, 28: 43-51.","journal-title":"Histol Histopathol"},{"issue":"12","key":"6130_CR4","doi-asserted-by":"publisher","first-page":"703","DOI":"10.1080\/15216540601115960","volume":"58","author":"F Orosz","year":"2006","unstructured":"Orosz F, Ol\u00e1h J, Ov\u00e1di J: Triosephosphate isomerase deficiency: Facts and doubts. IUBMB Life. 2006, 58 (12): 703-715. 10.1080\/15216540601115960.","journal-title":"IUBMB Life"},{"key":"6130_CR5","volume-title":"Neurobiology of Disease","author":"SL Hrizo","year":"2013","unstructured":"Hrizo SL, Fisher IJ, Long DR, Hutton JA, Liu Z, Palladino MJ: Early mitochondrial dysfunction leads to altered redox chemistry underlying pathogenesis of TPI deficiency. Neurobiology of Disease. 2013,"},{"key":"6130_CR6","doi-asserted-by":"publisher","first-page":"1168","DOI":"10.1016\/j.bbadis.2009.09.012","volume":"1792","author":"F Orosz","year":"2009","unstructured":"Orosz F, Ol\u00e1h J, Ov\u00e1di J: Triosephosphate isomerase deficiency: new insights into an enigmatic disease. Biochim. Biophys. Acta. 2009, 1792: 1168-1174. 10.1016\/j.bbadis.2009.09.012.","journal-title":"Biochim. Biophys. Acta"},{"issue":"20","key":"6130_CR7","doi-asserted-by":"publisher","first-page":"7903","DOI":"10.1073\/pnas.83.20.7903","volume":"83","author":"IO Daar","year":"1986","unstructured":"Daar IO, Artymiuk PJ, Phillips DC, Maquat LE: Human triose-phosphate isomerase deficiency: a single amino acid substitution results in a thermolabile enzyme. Proc Natl Acad Sci USA. 1986, 83 (20): 7903-7907. 10.1073\/pnas.83.20.7903.","journal-title":"Proc Natl Acad Sci USA"},{"key":"6130_CR8","unstructured":"Neubauer BA, Pekrun A, Beauregard SW, Lakomek M, Schroeter W: Relation between genetic defect, altered protein structure, and enzyme function in triose-phosphate isomerase (TPI) deficiency. Eur J Pediatr. 1992, 232-232. Suppl 151"},{"issue":"5","key":"6130_CR9","doi-asserted-by":"publisher","first-page":"486","DOI":"10.1007\/BF00216456","volume":"92","author":"S Hollan","year":"1993","unstructured":"Hollan S, Fujii H, Hirono A, Hirono K, Karro H, Miwa S, Harsanyi V, Gyodi E, Inselt-Kovacs M: Hereditary triosephosphate isomerase (TPI) deficiency: two severely affected brothers one with and one without neurological symptoms. Hum Genet. 1993, 92 (5): 486-490. 10.1007\/BF00216456.","journal-title":"Hum Genet"},{"issue":"4","key":"6130_CR10","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1002\/(SICI)1098-1004(1997)10:4<290::AID-HUMU4>3.0.CO;2-L","volume":"10","author":"R Arya","year":"1997","unstructured":"Arya R, Lalloz MRA, Bellingham AJ, Layton DM: Evidence for founder effect of the glu104asp substitution and identification of new mutations in triosephosphate isomerase deficiency. Human Mutation. 1997, 10 (4): 290-294. 10.1002\/(SICI)1098-1004(1997)10:4<290::AID-HUMU4>3.0.CO;2-L.","journal-title":"Human Mutation"},{"issue":"4","key":"6130_CR11","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1111\/j.1399-0004.1995.tb03955.x","volume":"47","author":"A Pekrun","year":"1995","unstructured":"Pekrun A, Neubauer BA, Eber SW, Lakomek M, Seidel H, Schroter W: Triosephosphate isomerase deficiency: biochemical and molecular genetic analysis for prenatal diagnosis. Clin Genet. 1995, 47 (4): 175-179.","journal-title":"Clin Genet"},{"issue":"4","key":"6130_CR12","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1002\/ajh.2830500407","volume":"50","author":"A Schneider","year":"1995","unstructured":"Schneider A, Westwood B, Yim C, Prchal J, Berkow R, Labotka R, Warrier R, Beutler E: Triosephosphate isomerase deficiency: repetitive occurrence of point mutation in amino acid 104 in multiple apparently unrelated families. Am J Hematol. 1995, 50 (4): 263-268. 10.1002\/ajh.2830500407.","journal-title":"Am J Hematol"},{"issue":"6","key":"6130_CR13","doi-asserted-by":"publisher","first-page":"553","DOI":"10.3109\/08880019809018318","volume":"15","author":"RE Linarello","year":"1998","unstructured":"Linarello RE, Shetty AK, Thomas T, Warrier RP: Triosephosphate isomerase deficiency in a child with congenital hemolytic anemia and severe hypotonia. Pediatr Hematol Oncol. 1998, 15 (6): 553-556. 10.3109\/08880019809018318.","journal-title":"Pediatr Hematol Oncol"},{"issue":"12","key":"6130_CR14","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1006\/bcmd.1996.0019","volume":"22","author":"A Schneider","year":"1996","unstructured":"Schneider A, Westwood B, Yim C, Cohen-Solal M, Rosa R, Labotka R, Eber S, Wolf R, Lammi A, Beutler E: The 1591C mutation in triosephosphate isomerase (TPI) deficiency. Tightly linked polymorphisms and a common haplotype in all known families. Blood Cells Mol Dis. 1996, 22 (12): 115-125.","journal-title":"Blood Cells Mol Dis"},{"issue":"5","key":"6130_CR15","doi-asserted-by":"publisher","first-page":"810","DOI":"10.1002\/pro.5560030510","volume":"3","author":"SC Mande","year":"1994","unstructured":"Mande SC, Mainfroid V, Kalk KH, Goraj K, Martial JA, Hol WG: Crystal structure of recombinant human triosephosphate isomerase at 2.8 \u00c5 resolution. Triosephosphate isomerase-related human genetic disorders and comparison with the trypanosomal enzyme. Protein Sci. 1994, 3 (5): 810-821.","journal-title":"Protein Sci"},{"key":"6130_CR16","doi-asserted-by":"publisher","first-page":"e30","DOI":"10.1371\/journal.pone.0000030","volume":"1","author":"M Ralser","year":"2006","unstructured":"Ralser M, Heeren G, Breitenbach M, Lehrach H, Krobitsch S: Triose Phosphate Isomerase Deficiency Is Caused by Altered Dimerization--not Catalytic Inactivity--of the Mutant Enzymes. PLoS ONE. 2006, 1: e30-10.1371\/journal.pone.0000030.","journal-title":"PLoS ONE"},{"issue":"34","key":"6130_CR17","doi-asserted-by":"publisher","first-page":"23254","DOI":"10.1074\/jbc.M802145200","volume":"283","author":"C Rodriguez-Almazan","year":"2008","unstructured":"Rodriguez-Almazan C, Arreola R, Rodriguez-Larrea D, Aguirre-Lopez B, de Gomez-Puyou MT, Perez-Montfort R, Costas M, Gomez-Puyou A, Torres-Larios A: Structural Basis of Human Triosephosphate Isomerase Deficiency: MUTATION E104D IS RELATED TO ALTERATIONS OF A CONSERVED WATER NETWORK AT THE DIMER INTERFACE. J Biol Chem. 2008, 283 (34): 23254-23263. 10.1074\/jbc.M802145200.","journal-title":"J Biol Chem"},{"issue":"46","key":"6130_CR18","doi-asserted-by":"publisher","first-page":"7745","DOI":"10.1002\/anie.200602795","volume":"45","author":"MT Reetz","year":"2006","unstructured":"Reetz MT, Carballeira JD, Vogel A: Iterative Saturation Mutagenesis on the Basis of B Factors as a Strategy for Increasing Protein Thermostability. Angew Chem Int Ed. 2006, 45 (46): 7745-7751. 10.1002\/anie.200602795.","journal-title":"Angew Chem Int Ed"},{"issue":"6","key":"6130_CR19","doi-asserted-by":"publisher","first-page":"1712","DOI":"10.1002\/bit.22202","volume":"102","author":"MT Reetz","year":"2009","unstructured":"Reetz MT, Soni P, Fern\u00e1ndez L: Knowledge-guided laboratory evolution of protein thermolability. Biotechnol Bioeng. 2009, 102 (6): 1712-1717. 10.1002\/bit.22202.","journal-title":"Biotechnol Bioeng"},{"key":"6130_CR20","doi-asserted-by":"publisher","first-page":"3961","DOI":"10.1007\/s00018-010-0473-9","volume":"67","author":"R Wierenga","year":"2010","unstructured":"Wierenga R, Kapetaniou E, Venkatesan R: Triosephosphate isomerase: a highly evolved biocatalyst. Cell Mol Life Sci. 2010, 67: 3961-3982. 10.1007\/s00018-010-0473-9.","journal-title":"Cell Mol Life Sci"},{"key":"6130_CR21","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1002\/1097-0134(20001001)41:1<47::AID-PROT80>3.0.CO;2-8","volume":"41","author":"H Ponstingl","year":"2000","unstructured":"Ponstingl H, Henrick K, Thornton JM: Discriminating between homodimeric and monomeric proteins in the crystalline state. Proteins Struct Funct Bioinf. 2000, 41: 47-57. 10.1002\/1097-0134(20001001)41:1<47::AID-PROT80>3.0.CO;2-8.","journal-title":"Proteins Struct Funct Bioinf"},{"issue":"4","key":"6130_CR22","doi-asserted-by":"publisher","first-page":"943","DOI":"10.1016\/j.jmb.2003.12.073","volume":"336","author":"RP Bahadur","year":"2004","unstructured":"Bahadur RP, Chakrabarti P, Rodier F, Janin J: A dissection of specific and non-specific protein-protein interfaces. J Mol Biol. 2004, 336 (4): 943-955. 10.1016\/j.jmb.2003.12.073.","journal-title":"J Mol Biol"},{"issue":"31","key":"6130_CR23","doi-asserted-by":"publisher","first-page":"10930","DOI":"10.1073\/pnas.0502667102","volume":"102","author":"J Mintseris","year":"2005","unstructured":"Mintseris J, Weng Z: Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci USA. 2005, 102 (31): 10930-10935. 10.1073\/pnas.0502667102.","journal-title":"Proc Natl Acad Sci USA"},{"key":"6130_CR24","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1186\/1471-2105-7-27","volume":"7","author":"H Zhu","year":"2006","unstructured":"Zhu H, Domingues F, Sommer I, Lengauer T: NOXclass: prediction of protein-protein interaction types. BMC Bioinf. 2006, 7: 27-10.1186\/1471-2105-7-27.","journal-title":"BMC Bioinf"},{"issue":"70","key":"6130_CR25","doi-asserted-by":"publisher","first-page":"209","DOI":"10.2307\/2276207","volume":"9","author":"MO Lorenz","year":"1905","unstructured":"Lorenz MO: Methods of Measuring the Concentration of Wealth. Publications of the American Statistical Association. 1905, 9 (70): 209-219. 10.2307\/2276207.","journal-title":"Publications of the American Statistical Association"},{"key":"6130_CR26","volume-title":"The PyMOL Molecular Graphics System, Version 1.3r1","author":"LLC Schr\u00f6dinger","year":"2010","unstructured":"Schr\u00f6dinger LLC: The PyMOL Molecular Graphics System, Version 1.3r1. 2010"},{"issue":"Pt 2","key":"6130_CR27","doi-asserted-by":"publisher","first-page":"479","DOI":"10.1107\/S0907444998012086","volume":"55","author":"O Carugo","year":"1999","unstructured":"Carugo O, Bordo D: How many water molecules can be detected by protein crystallography?. Acta Crystallogr D Biol Crystallogr. 1999, 55 (Pt 2): 479-483.","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"6130_CR28","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","volume":"14","author":"W Humphrey","year":"1996","unstructured":"Humphrey W, Dalke A, Schulten K: VMD: Visual molecular dynamics. Journal of Molecular Graphics. 1996, 14: 33-38. 10.1016\/0263-7855(96)00018-5.","journal-title":"Journal of Molecular Graphics"},{"issue":"18","key":"6130_CR29","doi-asserted-by":"publisher","first-page":"3586","DOI":"10.1021\/jp973084f","volume":"102","author":"AD MacKerell","year":"1998","unstructured":"MacKerell AD, Bashford D, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wi\u00f3rkiewicz-Kuczera J, Yin D, Karplus M: All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins. The Journal of Physical Chemistry B. 1998, 102 (18): 3586-3616. 10.1021\/jp973084f.","journal-title":"The Journal of Physical Chemistry B"},{"issue":"13","key":"6130_CR30","doi-asserted-by":"publisher","first-page":"1584","DOI":"10.1002\/jcc.20082","volume":"25","author":"AD Mackerell","year":"2004","unstructured":"Mackerell AD: Empirical force fields for biological macromolecules: Overview and issues. Journal of Computational Chemistry. 2004, 25 (13): 1584-1604. 10.1002\/jcc.20082.","journal-title":"Journal of Computational Chemistry"},{"issue":"12","key":"6130_CR31","doi-asserted-by":"publisher","first-page":"10089","DOI":"10.1063\/1.464397","volume":"98","author":"T Darden","year":"1993","unstructured":"Darden T, York D, Pedersen L: Particle mesh Ewald: An N.log(N) method for Ewald sums in large systems. The Journal of Chemical Physics. 1993, 98 (12): 10089-10092. 10.1063\/1.464397.","journal-title":"The Journal of Chemical Physics"},{"issue":"16","key":"6130_CR32","doi-asserted-by":"publisher","first-page":"1781","DOI":"10.1002\/jcc.20289","volume":"26","author":"JC Phillips","year":"2005","unstructured":"Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kal\u00e9 L, Schulten K: Scalable molecular dynamics with NAMD. J Comput Chem. 2005, 26 (16): 1781-1802. 10.1002\/jcc.20289.","journal-title":"J Comput Chem"},{"key":"6130_CR33","doi-asserted-by":"publisher","first-page":"51+","DOI":"10.1186\/1471-2105-13-51","volume":"13","author":"Z Li","year":"2012","unstructured":"Li Z, He Y, Wong L, Li J: Progressive dry-core-wet-rim hydration trend in a nested-ring topology of protein binding interfaces. BMC Bioinf. 2012, 13: 51+-10.1186\/1471-2105-13-51.","journal-title":"BMC Bioinf"},{"issue":"17","key":"6130_CR34","doi-asserted-by":"publisher","first-page":"9613","DOI":"10.1073\/pnas.96.17.9613","volume":"96","author":"S Fischer","year":"1999","unstructured":"Fischer S, Verma CS: Binding of buried structural water increases the flexibility of proteins. Proc Natl Acad Sci USA. 1999, 96 (17): 9613-9615. 10.1073\/pnas.96.17.9613.","journal-title":"Proc Natl Acad Sci USA"},{"key":"6130_CR35","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"HM Berman","year":"2000","unstructured":"Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000, 28: 235-242. 10.1093\/nar\/28.1.235.","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"6130_CR36","doi-asserted-by":"publisher","first-page":"1270","DOI":"10.1073\/pnas.94.4.1270","volume":"94","author":"PJ Keeling","year":"1997","unstructured":"Keeling PJ, Doolittle WF: Evidence that eukaryotic triosephosphate isomerase is of alpha-proteobacterial origin. Proc Natl Acad Sci USA. 1997, 94 (4): 1270-1275. 10.1073\/pnas.94.4.1270.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"suppl 2","key":"6130_CR37","doi-asserted-by":"publisher","first-page":"W529","DOI":"10.1093\/nar\/gkq399","volume":"38","author":"H Ashkenazy","year":"2010","unstructured":"Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N: ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res. 2010, 38 (suppl 2): W529-W533.","journal-title":"Nucleic Acids Res"},{"key":"6130_CR38","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1073\/pnas.93.1.13","volume":"93","author":"S Jones","year":"1996","unstructured":"Jones S, Thornton JM: Principles of protein-protein interactions. Proc Natl Acad Sci USA. 1996, 93: 13-20. 10.1073\/pnas.93.1.13.","journal-title":"Proc Natl Acad Sci USA"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-S16-S11.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-14-S16-S11\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-S16-S11.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T19:38:14Z","timestamp":1548185894000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-14-S16-S11"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,10]]},"references-count":38,"journal-issue":{"issue":"S16","published-print":{"date-parts":[[2013,10]]}},"alternative-id":["6130"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-14-s16-s11","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,10]]},"article-number":"S11"}}