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Definition of a New Information-Based Per-Residue Quality Parameter

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Abstract

For biomolecular NMR structures typically only a poor correspondence is observed between statistics derived from the experimental input data and structural quality indicators obtained from the structure ensembles. Here, we investigate the relationship between the amount of available NMR data and structure quality. By generating datasets with a predetermined information content and evaluating the quality of the resulting structure ensembles we show that there is, in contrast to previous findings, a linear relation between the information contained in experimental data and structural quality. From this relation, a new quality parameter is derived that provides direct insight, on a per-residue basis, into the extent to which structural quality is governed by the experimental input data.

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References

  • L. Banci I. Bertini G. Cavallaro A. Giachetti C. Luchinat G. Parigi (2004) J. Biomol. NMR 28 249–261 Occurrence Handle10.1023/B:JNMR.0000013703.30623.f7 Occurrence Handle14752258

    Article  PubMed  Google Scholar 

  • L. Banci I. Bertini G.G. Savellini A. Romagnoli P. Turano M.A. Cremonini C. Luchinat H.B. Gray (1997) Proteins 29 68–76 Occurrence Handle10.1002/(SICI)1097-0134(199709)29:1<68::AID-PROT5>3.0.CO;2-B Occurrence Handle9294867

    Article  PubMed  Google Scholar 

  • A.T. Brünger P.D. Adams G.M. Clore W.L. Delano P. Gros R.W. Grosse-Kunstleve J.-S. Jiang J. Kuszewski M. Nilges N.S. Pannu R.J. Read L.M. Rice T. Simonson G.L. Warren (1998) Acta Cryst. D54 905–921

    Google Scholar 

  • A.T. Brünger G.M. Clore A.M. Gronenborn R. Saffrich M. Nilges (1993) Science 261 328–331 Occurrence Handle8332897

    PubMed  Google Scholar 

  • G.M. Clore M.A. Robien A.M. Gronenborn (1993) J. Mol. Biol. 231 82–102 Occurrence Handle10.1006/jmbi.1993.1259 Occurrence Handle8496968

    Article  PubMed  Google Scholar 

  • G.M. Clore M.R. Starich C.A. Bewley M.L. Cai J. Kuszewski (1999) J. Am. Chem. Soc. 121 6513–6514 Occurrence Handle10.1021/ja991143s

    Article  Google Scholar 

  • G. Cornilescu J.L. Marquardt M. Ottiger A. Bax (1998) J. Am. Chem. Soc. 120 6836–6837 Occurrence Handle10.1021/ja9812610

    Article  Google Scholar 

  • J.F. Doreleijers S. Mading D. Maziuk K. Sojourner L. Yin J. Zhu J.L. Markley E.L. Ulrich (2003) J. Biomol. NMR 26 139–146 Occurrence Handle10.1023/A:1023514106644 Occurrence Handle12766409

    Article  PubMed  Google Scholar 

  • J.F. Doreleijers M.L. Raves T. Rullmann R. Kaptein (1999) J. Biomol. NMR 14 123–132 Occurrence Handle10.1023/A:1008335423527 Occurrence Handle10610141

    Article  PubMed  Google Scholar 

  • J.F. Doreleijers J.A. Rullmann R. Kaptein (1998) J. Mol. Biol. 281 149–164 Occurrence Handle10.1006/jmbi.1998.1808 Occurrence Handle9680482

    Article  PubMed  Google Scholar 

  • T. Gallagher P. Alexander P. Bryan G.L. Gilliland (1994) Biochemistry 33 4721–4729 Occurrence Handle10.1021/bi00181a032 Occurrence Handle8161530

    Article  PubMed  Google Scholar 

  • D.S. Garrett J. Kuszewski T.J. Hancock P.J. Lodi G.W. Vuister A.M. Gronenborn G.M. Clore (1994) J. Magn. Reson. B 104 99–103 Occurrence Handle10.1006/jmrb.1994.1061 Occurrence Handle8025816

    Article  PubMed  Google Scholar 

  • B.J. Goodfellow J.S. Dias G.C. Ferreira P. Henklein V. Wray A.L. Macedo (2001) FEBS Lett. 505 325–331 Occurrence Handle10.1016/S0014-5793(01)02818-6 Occurrence Handle11566198

    Article  PubMed  Google Scholar 

  • P. Güntert (2003) Prog. NMR Spec. 43 105–125 Occurrence Handle10.1016/S0079-6565(03)00021-9

    Article  Google Scholar 

  • R.W. Hooft C. Sander G. Vriend (1997) Comp. Appl. Biosci. 13 425–330 Occurrence Handle9283757

    PubMed  Google Scholar 

  • R.W. Hooft G. Vriend C. Sander E.E. Abola (1996) Nature 381 272 Occurrence Handle10.1038/381272a0 Occurrence Handle8692262

    Article  PubMed  Google Scholar 

  • Y. Kim J.H. Prestegard (1990) Proteins 8 377–385 Occurrence Handle10.1002/prot.340080411 Occurrence Handle2091027

    Article  PubMed  Google Scholar 

  • G.J. Kleywegt T.A. Jones (1995) Structure 3 535–540 Occurrence Handle10.1016/S0969-2126(01)00187-3 Occurrence Handle8590014

    Article  PubMed  Google Scholar 

  • G.J. Kleywegt T.A. Jones (1996) Structure 4 1395–1400 Occurrence Handle10.1016/S0969-2126(96)00147-5 Occurrence Handle8994966

    Article  PubMed  Google Scholar 

  • G.J. Kleywegt T.A. Jones (2002) Structure 10 465–472 Occurrence Handle10.1016/S0969-2126(02)00743-8 Occurrence Handle11937051

    Article  PubMed  Google Scholar 

  • C.P. Kloks C.A. Spronk E. Lasonder A. Hoffmann G.W. Vuister S. Grzesiek C.W. Hilbers (2002) J. Mol. Biol. 316 317–326 Occurrence Handle10.1006/jmbi.2001.5334 Occurrence Handle11851341

    Article  PubMed  Google Scholar 

  • J. Kuszewski A.M. Gronenborn G.M. Clore (1995a) J. Magn. Reson. B 107 293–297 Occurrence Handle10.1006/jmrb.1995.1093

    Article  Google Scholar 

  • J. Kuszewski A.M. Gronenborn G.M. Clore (1999) J. Am. Chem. Soc. 121 2337–2338 Occurrence Handle10.1021/ja9843730

    Article  Google Scholar 

  • J. Kuszewski J. Qin A.M. Gronenborn G.M. Clore (1995b) J. Magn. Reson. B 106 92–96 Occurrence Handle10.1006/jmrb.1995.1017

    Article  Google Scholar 

  • J.P. Linge M. Nilges (1999) J. Biomol. NMR 13 51–59 Occurrence Handle10.1023/A:1008365802830 Occurrence Handle10905826

    Article  PubMed  Google Scholar 

  • J.P. Linge M.A. Williams C.A. Spronk A.M. Bonvin M. Nilges (2003) Proteins 50 496–506 Occurrence Handle10.1002/prot.10299 Occurrence Handle12557191

    Article  PubMed  Google Scholar 

  • Y. Liu D. Zhao R. Altman O. Jardetzky (1992) J. Biomol. NMR 2 373–388 Occurrence Handle10.1007/BF01874815 Occurrence Handle1511237

    Article  PubMed  Google Scholar 

  • D.F. Mierke T. Huber H. Kessler (1994) J. Comput. Aided Mol. Des. 8 29–40 Occurrence Handle10.1007/BF00124347 Occurrence Handle8035210

    Article  PubMed  Google Scholar 

  • S.B. Nabuurs A.J. Nederveen W. Vranken J.F. Doreleijers A.M. Bonvin G.W. Vuister G. Vriend C.A. Spronk (2004) Proteins 55 483–486 Occurrence Handle10.1002/prot.20118 Occurrence Handle15103611

    Article  PubMed  Google Scholar 

  • S.B. Nabuurs C.A. Spronk E. Krieger H. Maassen G. Vriend G.W. Vuister (2003) J. Am. Chem. Soc. 125 12026–12034 Occurrence Handle10.1021/ja035440f Occurrence Handle14505424

    Article  PubMed  Google Scholar 

  • A.J. Nederveen J.F. Doreleijers W. Vranken Z. Miller C.A. Spronk S.B. Nabuurs P. Guntert M. Livny J.L. Markley M. Nilges E.L. Ulrich R. Kaptein A.M. Bonvin (2005) Proteins 59 662–672 Occurrence Handle10.1002/prot.20408 Occurrence Handle15822098

    Article  PubMed  Google Scholar 

  • C.M. Oshiro J. Thomason I.D. Kuntz (1991) Biopolymers 31 1049–1064 Occurrence Handle10.1002/bip.360310905 Occurrence Handle1786338

    Article  PubMed  Google Scholar 

  • D.A. Snyder A. Bhattacharya Y.J. Huang G.T. Montelione (2005) Proteins 59 655–661 Occurrence Handle10.1002/prot.20499 Occurrence Handle15822105

    Article  PubMed  Google Scholar 

  • C.A. Spronk J.P. Linge C.W. Hilbers G.W. Vuister (2002) J. Biomol. NMR 22 281–289 Occurrence Handle10.1023/A:1014971029663 Occurrence Handle11991356

    Article  PubMed  Google Scholar 

  • C.A. Spronk S.B. Nabuurs A.M. Bonvin E. Krieger G.W. Vuister G. Vriend (2003) J. Biomol. NMR 25 225–234 Occurrence Handle10.1023/A:1022819716110 Occurrence Handle12652134

    Article  PubMed  Google Scholar 

  • C.A. Spronk S.B. Nabuurs E. Krieger G. Vriend G.W. Vuister (2004) Prog. Nucl. Magn. Reson. Spectrosc 45 315–337 Occurrence Handle10.1016/j.pnmrs.2004.08.003

    Article  Google Scholar 

  • N. Tjandra D.S. Garrett A.M. Gronenborn A. Bax G.M. Clore (1997a) Nat. Struct. Biol. 4 443–449 Occurrence Handle10.1038/nsb0697-443

    Article  Google Scholar 

  • N. Tjandra J. Marquardt G.M. Clore (2000) J. Magn. Reson. 142 393–396 Occurrence Handle10.1006/jmre.1999.1985 Occurrence Handle10648162

    Article  PubMed  Google Scholar 

  • N. Tjandra J.G. Omichinski A.M. Gronenborn G.M. Clore A. Bax (1997b) Nat. Struct. Biol. 4 732–738 Occurrence Handle10.1038/nsb0997-732

    Article  Google Scholar 

  • S. Vijay-Kumar C.E. Bugg W.J. Cook (1987) J. Mol. Biol. 194 531–544 Occurrence Handle10.1016/0022-2836(87)90679-6 Occurrence Handle3041007

    Article  PubMed  Google Scholar 

  • G. Vriend (1990) J. Mol. Graph 8 IssueID29 52–56 Occurrence Handle10.1016/0263-7855(90)80070-V Occurrence Handle2268628

    Article  PubMed  Google Scholar 

  • T. Walma J. Aelen S.B. Nabuurs M. Oostendorp L. Berk Particlevan den W. Hendriks G.W. Vuister (2004) Structure (Camb) 12 11–20 Occurrence Handle10.1016/j.str.2003.11.023

    Article  Google Scholar 

  • D. Zhao O. Jardetzky (1994) J. Mol. Biol. 239 601–607 Occurrence Handle10.1006/jmbi.1994.1402 Occurrence Handle8014985

    Article  PubMed  Google Scholar 

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Correspondence to Geerten W. Vuister.

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Nabuurs, S.B., Krieger, E., Spronk, C.A.E.M. et al. Definition of a New Information-Based Per-Residue Quality Parameter. J Biomol NMR 33, 123–134 (2005). https://doi.org/10.1007/s10858-005-2826-5

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  • DOI: https://doi.org/10.1007/s10858-005-2826-5

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