Cyrus Chothia

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Template:Short description Template:DMCA Template:DMCA Script error: No such module "Template wrapper".Script error: No such module "Check for conflicting parameters". Cyrus Homi Chothia (19 February 1942 – 26 November 2019)[1] FRS[2][3] was an English biochemist who was an emeritus scientist at the Medical Research Council (MRC) Laboratory of Molecular Biology (LMB) at the University of Cambridge[4][5] and emeritus fellow of Wolfson College, Cambridge.[2][6][7][8][9][10][11]

Education

Chothia was educated at Alleyn's School,[12] then went to study at Durham University graduating with a Bachelor of Science degree in 1965.[1] Chothia then completed a Master of Science degree at Birkbeck College in 1967 and a PhD from University College London[13] under the supervision of Peter Pauling [Wikidata],[14] the son of Linus Pauling.

Research and career

After his PhD Chothia worked in the Laboratory of Molecular Biology (LMB) for three years. He then worked with Michael Levitt[15] at the Weizmann Institute of Science[16][17] followed by two years with Joel Janin at the Institut Pasteur in Paris.[18]

In 1976 Chothia returned to England to work at University College London and the LMB. With Arthur Lesk[19][20] he showed that proteins adapt to mutations by changes in structure.

In 1992 he proposed that most proteins are built of domains that come from a small number of families.[21] He collaborated with Alexey Murzin, Steven Brenner and Tim Hubbard to create the Structural Classification of Proteins database (SCOP),[22][23] a periodic table for all known protein structures. With Julian Gough[24] he created the Superfamily database[25] which uses Hidden Markov models to identify protein sequences that are related to those of known structures.

During his career, Chothia supervised 19 successful PhD students to completion[26] including Alex Bateman,[27] Steven E. Brenner,[28] Mark Bender Gerstein,[29] Julian Gough,[30] Sarah Teichmann,[31] Bissan Al-Lazikani,[32][33][34] Goga Apic,[35] Samantha Barré[citation needed][36] Matthew Bashton,[37][38][39][40] Dan Bolser,[41] Michael Bremang,[42] Bernard de Bono,[43][44] Emma Ganley (née Hill),[45][46][47] Martin Madera,[48][49] Siarhei Maslau,[50] Susan Miller,[51][52][53] Jong Park (aka Jong Bhak),[54][55][56] Rajkumar Sasidharan,[57][58] and Christine Vogel.[59][60]

Awards and honours

Chothia was elected a Fellow of the Royal Society (FRS) in 2000.[1] His certificate of election and candidature reads: Page Template:Blockquote/styles.css has no content.

Dr Chothia has shown how the amino sequences of proteins determine their structure, function and evolution. From an analysis of their structural regularities, he has developed a classification of protein structures that is now in general use. His picture of protein evolution suggests how proteins diverge and gain new functions. He has helped us to understand how their apparently limited set of slightly different structures allow immunoglobin to recognise an almost limitless variety of different antigens.[61]

In 2015, Chothia was elected a Fellow of the International Society for Computational Biology (ISCB)[62] and was awarded the ISCB Accomplishment by a Senior Scientist Award in honour of his work in using computational methods to understand protein structure.[63][64]

Alongside David Haussler and Michael Waterman, Chothia was awarded the 2015 Dan David Prize for his contributions to the field of bioinformatics.[65]

References

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  1. ^ a b c Script error: No such module "template wrapper". (Subscription or UK public library membership required.)
  2. ^ a b Page Module:Citation/CS1/styles.css has no content."Wolfson College: Emeritus Fellow Dr Cyrus Chothia MA MSc FRS". Archived from the original on 5 February 2012.
  3. ^ Page Module:Citation/CS1/styles.css has no content."Cyrus Chothia (1942–2019)". 27 November 2019. Retrieved 27 November 2019.
  4. ^ Page Module:Citation/CS1/styles.css has no content."Cyrus Chothia: The protein origins of biological complexity, LMB Emeritus". Archived from the original on 15 February 2012.
  5. ^ Page Module:Citation/CS1/styles.css has no content."Structural genomics and protein structure". Mrc-lmb.cam.ac.uk. Archived from the original on 14 February 2015. Retrieved 24 June 2014.
  6. ^ {{DBLP}} template missing ID and not present in Wikidata.
  7. ^ Page Module:Citation/CS1/styles.css has no content."cyrus chothia". Google Scholar. Retrieved 24 June 2014.
  8. ^ Page Module:Citation/CS1/styles.css has no content.Chothia, C.; Lesk, A. M.; Tramontano, A.; Levitt, M.; Smith-Gill, S. J.; Air, G.; Sheriff, S.; Padlan, E. A.; Davies, D.; Tulip, W. R.; Colman, P. M.; Spinelli, S.; Alzari, P. M.; Poljak, R. J. (1989). "Conformations of immunoglobulin hypervariable regions". Nature. 342 (6252): 877–883. Bibcode:1989Natur.342..877C. doi:10.1038/342877a0. PMID 2687698. S2CID 4241051.
  9. ^ Page Module:Citation/CS1/styles.css has no content.Lewis, T. E.; Sillitoe, I; Andreeva, A; Blundell, T. L.; Buchan, D. W.; Chothia, C; Cozzetto, D; Dana, J. M.; Filippis, I; Gough, J; Jones, D. T.; Kelley, L. A.; Kleywegt, G. J.; Minneci, F; Mistry, J; Murzin, A. G.; Ochoa-Montaño, B; Oates, M. E.; Punta, M; Rackham, O. J.; Stahlhacke, J; Sternberg, M. J.; Velankar, S; Orengo, C (2015). "Genome3D: Exploiting structure to help users understand their sequences". Nucleic Acids Research. 43 (Database issue): D382–6. doi:10.1093/nar/gku973. PMC 4384030. PMID 25348407.
  10. ^ Page Module:Citation/CS1/styles.css has no content.Chothia, C; Gough, J; Vogel, C; Teichmann, S. A. (2003). "Evolution of the protein repertoire". Science. 300 (5626): 1701–3. Bibcode:2003Sci...300.1701C. doi:10.1126/science.1085371. PMID 12805536. S2CID 27681885.
  11. ^ Cyrus Chothia's publications indexed by the Scopus bibliographic database. (subscription required)
  12. ^ Page Module:Citation/CS1/styles.css has no content."Dan David Prize Awarded to Dr Cyrus Chothia". Alleyn's School. Archived from the original on 23 March 2015.
  13. ^ Page Module:Citation/CS1/styles.css has no content.Chothia, Cyrus (1973). The crystal structures of some molecules active at cholinergic nerve receptors (PhD thesis). University College London. OCLC 926297115. Template:ProQuest.
  14. ^ Page Module:Citation/CS1/styles.css has no content.Chothia, C.; Pauling, P. (1969). "On the conformations of hallucinogenic molecules and their correlation". Proceedings of the National Academy of Sciences of the United States of America. 63 (4): 1063–1070. Bibcode:1969PNAS...63.1063C. doi:10.1073/pnas.63.4.1063. PMC 223427. PMID 4311249.
  15. ^ Page Module:Citation/CS1/styles.css has no content."Cyrus H. Chothia, Chemistry Tree". Archived from the original on 27 February 2015.
  16. ^ Page Module:Citation/CS1/styles.css has no content.Chothia, C.; Levitt, M.; Richardson, D. (1977). "Structure of proteins: Packing of alpha-helices and pleated sheets". Proceedings of the National Academy of Sciences of the United States of America. 74 (10): 4130–4134. Bibcode:1977PNAS...74.4130C. doi:10.1073/pnas.74.10.4130. PMC 431889. PMID 270659.
  17. ^ Page Module:Citation/CS1/styles.css has no content.Levitt, M.; Chothia, C. (1976). "Structural patterns in globular proteins". Nature. 261 (5561): 552–558. Bibcode:1976Natur.261..552L. doi:10.1038/261552a0. PMID 934293. S2CID 4154884.
  18. ^ Page Module:Citation/CS1/styles.css has no content.Sweet, R.; Wright, H.; Janin, J.; Chothia, C.; Blow, D. (1974). "Crystal structure of the complex of porcine trypsin with soybean trypsin inhibitor (Kunitz) at 2.6-A resolution". Biochemistry. 13 (20): 4212–4228. doi:10.1021/bi00717a024. PMID 4472048.
  19. ^ Page Module:Citation/CS1/styles.css has no content.Lesk, A.; Chothia, C. (1980). "How different amino acid sequences determine similar protein structures: The structure and evolutionary dynamics of the globins". Journal of Molecular Biology. 136 (3): 225–270. doi:10.1016/0022-2836(80)90373-3. PMID 7373651.
  20. ^ Page Module:Citation/CS1/styles.css has no content.Lesk, A.; Chothia, C. (1980). "Solvent accessibility, protein surfaces, and protein folding". Biophysical Journal. 32 (1): 35–47. Bibcode:1980BpJ....32...35L. doi:10.1016/S0006-3495(80)84914-9. PMC 1327253. PMID 7248454.
  21. ^ Page Module:Citation/CS1/styles.css has no content.Chothia, Cyrus (1992). "One thousand families for the molecular biologist". Nature. 357 (6379): 543–4. Bibcode:1992Natur.357..543C. doi:10.1038/357543a0. PMID 1608464. S2CID 4355476.
  22. ^ Page Module:Citation/CS1/styles.css has no content.Hubbard, T.; Murzin, A.; Brenner, S.; Chothia, C. (1997). "SCOP: A structural classification of proteins database". Nucleic Acids Research. 25 (1): 236–239. doi:10.1093/nar/25.1.236. PMC 146380. PMID 9016544.
  23. ^ Page Module:Citation/CS1/styles.css has no content."UK government grants awarded to Cyrus Chothia". Research Councils UK. Archived from the original on 15 October 2014.
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  25. ^ Page Module:Citation/CS1/styles.css has no content.Gough, J.; Chothia, C. (2002). "SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments". Nucleic Acids Research. 30 (1): 268–272. doi:10.1093/nar/30.1.268. PMC 99153. PMID 11752312.
  26. ^ Page Module:Citation/CS1/styles.css has no content.Alex Bateman (2015). "Cyrus Chothia's academic family tree". twitter. Archived from the original on 15 July 2015.
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  32. ^ Page Module:Citation/CS1/styles.css has no content.Al-Lazikani, Bissan (1999). Canonical structures of immunoglobulins and T cell receptors (PhD thesis). University of Cambridge.
  33. ^ Page Module:Citation/CS1/styles.css has no content."Dr Bissan Al-Lazikani Team leader". The Institute of Cancer Research. Archived from the original on 5 March 2015.
  34. ^ Page Module:Citation/CS1/styles.css has no content.Al-Lazikani, B; Lesk, A. M.; Chothia, C (2000). "Canonical structures for the hypervariable regions of T cell alphabeta receptors". Journal of Molecular Biology. 295 (4): 979–95. doi:10.1006/jmbi.1999.3358. PMID 10656805.
  35. ^ Page Module:Citation/CS1/styles.css has no content.Apic, Gordana (2003). Evolution of multidomain proteins in genomes. lib.cam.ac.uk (PhD thesis). University of Cambridge. OCLC 894594841. Template:EThOS.
  36. ^ Page Module:Citation/CS1/styles.css has no content.Barré, Samantha; Greenberg, Andrew S.; Flajnik, Martin F.; Chothia, Cyrus (1994). "Structural conservation of hypervariable regions in immunoglobulins evolution". Nature Structural Biology. 1 (12): 915–920. doi:10.1038/nsb1294-915. PMID 7773781. S2CID 39728494.
  37. ^ Page Module:Citation/CS1/styles.css has no content.Bashton, Matthew (2004). Functional analysis of domain combinations (PhD thesis). University of Cambridge.
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  39. ^ Page Module:Citation/CS1/styles.css has no content.Bashton, M; Chothia, C (2002). "The geometry of domain combination in proteins". Journal of Molecular Biology. 315 (4): 927–39. doi:10.1006/jmbi.2001.5288. PMID 11812158.
  40. ^ Page Module:Citation/CS1/styles.css has no content.Bashton, M; Chothia, C (2007). "The generation of new protein functions by the combination of domains". Structure. 15 (1): 85–99. doi:10.1016/j.str.2006.11.009. PMID 17223535.
  41. ^ Page Module:Citation/CS1/styles.css has no content.Bolser, Daniel Murray (2007). The surfaces involved in the formation of protein complexes (PhD thesis). University of Cambridge.
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  44. ^ Page Module:Citation/CS1/styles.css has no content.de Bono, B. (2003). "Exegesis: a procedure to improve gene predictions and its use to find immunoglobulin superfamily proteins in the human and mouse genomes". Nucleic Acids Research. 31 (21): 6096–6103. doi:10.1093/nar/gkg828. PMC 275470. PMID 14576296.
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  48. ^ Page Module:Citation/CS1/styles.css has no content.Madera, Martin (2005). Hidden Markov models for detection of remote homology (PhD thesis). University of Cambridge.
  49. ^ Page Module:Citation/CS1/styles.css has no content.Madera, M. (2004). "The SUPERFAMILY database in 2004: additions and improvements". Nucleic Acids Research. 32 (90001): 235D–239. doi:10.1093/nar/gkh117. PMC 308851. PMID 14681402.
  50. ^ Page Module:Citation/CS1/styles.css has no content.Maslau, Siarhei (2007). Formation of the small molecule metabolism of Escherichia coli (PhD thesis). University of Cambridge.
  51. ^ Page Module:Citation/CS1/styles.css has no content.Miller, G. S. P. (1987). Computer display and manufacture of 3-D models (PhD thesis). University of Cambridge. OCLC 59769936.
  52. ^ Page Module:Citation/CS1/styles.css has no content.Miller, Susan; Janin, Joël; Lesk, Arthur M.; Chothia, Cyrus (1987). "Interior and surface of monomeric proteins". Journal of Molecular Biology. 196 (3): 641–656. doi:10.1016/0022-2836(87)90038-6. PMID 3681970.
  53. ^ Page Module:Citation/CS1/styles.css has no content.Miller, Susan; Lesk, Arthur M.; Janin, Joël; Chothia, Cyrus (1987). "The accessible surface area and stability of oligomeric proteins". Nature. 328 (6133): 834–836. Bibcode:1987Natur.328..834M. doi:10.1038/328834a0. PMID 3627230. S2CID 4349684.
  54. ^ Page Module:Citation/CS1/styles.css has no content.Park, Jong Hwa (1997). Genome sequence analysis and methods (PhD thesis). University of Cambridge.
  55. ^ Cyrus Chothia publications indexed by Google ScholarTemplate:EditAtWikidata
  56. ^ Page Module:Citation/CS1/styles.css has no content."Jong Bhak's home page: An entrepreneur and a scientist". jongbhak.com. Archived from the original on 20 December 2014.
  57. ^ Page Module:Citation/CS1/styles.css has no content.Sasidharan, Rajkumar (2004). Protein evolution : the selection of acceptable mutations (PhD thesis). University of Cambridge.
  58. ^ Page Module:Citation/CS1/styles.css has no content.Sasidharan, R.; Chothia, C. (2007). "The selection of acceptable protein mutations". Proceedings of the National Academy of Sciences. 104 (24): 10080–10085. Bibcode:2007PNAS..10410080S. doi:10.1073/pnas.0703737104. PMC 1891269. PMID 17540730.
  59. ^ Page Module:Citation/CS1/styles.css has no content.Vogel, Christine (2004). A domain perspective on the evolution of the protein repertoire (PhD thesis). University of Cambridge.
  60. ^ Page Module:Citation/CS1/styles.css has no content.Vogel, Christine; Chothia, Cyrus (2006). "Protein Family Expansions and Biological Complexity". PLOS Computational Biology. 2 (5): e48. Bibcode:2006PLSCB...2...48V. doi:10.1371/journal.pcbi.0020048. PMC 1464810. PMID 16733546. Open access icon
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  62. ^ Page Module:Citation/CS1/styles.css has no content.Fogg, C. N.; Kovats, D. E. (2015). "Message from the ISCB: 2015 ISCB Accomplishment by a Senior Scientist Award: Cyrus Chothia". Bioinformatics. 31 (13): 2238–9. doi:10.1093/bioinformatics/btv218. PMID 26002905.
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