• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of narLink to Publisher's site
Nucleic Acids Res. Sep 15, 1998; 26(18): 4280–4290.
PMCID: PMC147832

A database of macromolecular motions.

Abstract

We describe a database of macromolecular motions meant to be of general use to the structural community. The database, which is accessible on the World Wide Web with an entry point at http://bioinfo.mbb.yale.edu/MolMovDB , attempts to systematize all instances of protein and nucleic acid movement for which there is at least some structural information. At present it contains >120 motions, most of which are of proteins. Protein motions are further classified hierarchically into a limited number of categories, first on the basis of size (distinguishing between fragment, domain and subunit motions) and then on the basis of packing. Our packing classification divides motions into various categories (shear, hinge, other) depending on whether or not they involve sliding over a continuously maintained and tightly packed interface. In addition, the database provides some indication about the evidence behind each motion (i.e. the type of experimental information or whether the motion is inferred based on structural similarity) and attempts to describe many aspects of a motion in terms of a standardized nomenclature (e.g. the maximum rotation, the residue selection of a fixed core, etc.). Currently, we use a standard relational design to implement the database. However, the complexity and heterogeneity of the information kept in the database makes it an ideal application for an object-relational approach, and we are moving it in this direction. Specifically, in terms of storing complex information, the database contains plausible representations for motion pathways, derived from restrained 3D interpolation between known endpoint conformations. These pathways can be viewed in a variety of movie formats, and the database is associated with a server that can automatically generate these movies from submitted coordinates.

Full Text

The Full Text of this article is available as a PDF (418K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Abad-Zapatero C, Griffith JP, Sussman JL, Rossmann MG. Refined crystal structure of dogfish M4 apo-lactate dehydrogenase. J Mol Biol. 1987 Dec 5;198(3):445–467. [PubMed]
  • Abola EE, Sussman JL, Prilusky J, Manning NO. Protein Data Bank archives of three-dimensional macromolecular structures. Methods Enzymol. 1997;277:556–571. [PubMed]
  • Altman RB, Abernethy NF, Chen RO. Standardized representations of the literature: combining diverse sources of ribosomal data. Proc Int Conf Intell Syst Mol Biol. 1997;5:15–24. [PubMed]
  • Anderson BF, Baker HM, Norris GE, Rumball SV, Baker EN. Apolactoferrin structure demonstrates ligand-induced conformational change in transferrins. Nature. 1990 Apr 19;344(6268):784–787. [PubMed]
  • Anderson CM, Zucker FH, Steitz TA. Space-filling models of kinase clefts and conformation changes. Science. 1979 Apr 27;204(4391):375–380. [PubMed]
  • Bairoch A, Boeckmann B. The SWISS-PROT protein sequence data bank. Nucleic Acids Res. 1992 May 11;20 (Suppl):2019–2022. [PMC free article] [PubMed]
  • Bairoch A, Bucher P, Hofmann K. The PROSITE database, its status in 1995. Nucleic Acids Res. 1996 Jan 1;24(1):189–196. [PMC free article] [PubMed]
  • Bennett WS, Huber R. Structural and functional aspects of domain motions in proteins. CRC Crit Rev Biochem. 1984;15(4):291–384. [PubMed]
  • Bennett WS, Jr, Steitz TA. Glucose-induced conformational change in yeast hexokinase. Proc Natl Acad Sci U S A. 1978 Oct;75(10):4848–4852. [PMC free article] [PubMed]
  • Berman HM, Olson WK, Beveridge DL, Westbrook J, Gelbin A, Demeny T, Hsieh SH, Srinivasan AR, Schneider B. The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys J. 1992 Sep;63(3):751–759. [PMC free article] [PubMed]
  • Blake CC, Rice DW, Cohen FE. A "helix-scissors" mechanism for the hinge-bending conformational change in phosphoglycerate kinase. Int J Pept Protein Res. 1986 May;27(5):443–448. [PubMed]
  • Boutonnet NS, Rooman MJ, Wodak SJ. Automatic analysis of protein conformational changes by multiple linkage clustering. J Mol Biol. 1995 Nov 3;253(4):633–647. [PubMed]
  • Brenner SE, Chothia C, Hubbard TJ. Population statistics of protein structures: lessons from structural classifications. Curr Opin Struct Biol. 1997 Jun;7(3):369–376. [PubMed]
  • Bullough PA, Hughson FM, Skehel JJ, Wiley DC. Structure of influenza haemagglutinin at the pH of membrane fusion. Nature. 1994 Sep 1;371(6492):37–43. [PubMed]
  • Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Kundrot CE, Cech TR, Doudna JA. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science. 1996 Sep 20;273(5282):1678–1685. [PubMed]
  • Chan DC, Fass D, Berger JM, Kim PS. Core structure of gp41 from the HIV envelope glycoprotein. Cell. 1997 Apr 18;89(2):263–273. [PubMed]
  • Chasman DI, Flaherty KM, Sharp PA, Kornberg RD. Crystal structure of yeast TATA-binding protein and model for interaction with DNA. Proc Natl Acad Sci U S A. 1993 Sep 1;90(17):8174–8178. [PMC free article] [PubMed]
  • Chik JK, Lindberg U, Schutt CE. The structure of an open state of beta-actin at 2.65 A resolution. J Mol Biol. 1996 Nov 8;263(4):607–623. [PubMed]
  • Chothia C. Proteins. One thousand families for the molecular biologist. Nature. 1992 Jun 18;357(6379):543–544. [PubMed]
  • Chothia C, Lesk AM, Dodson GG, Hodgkin DC. Transmission of conformational change in insulin. Nature. 1983 Apr 7;302(5908):500–505. [PubMed]
  • Chuprina VP, Rullmann JA, Lamerichs RM, van Boom JH, Boelens R, Kaptein R. Structure of the complex of lac repressor headpiece and an 11 base-pair half-operator determined by nuclear magnetic resonance spectroscopy and restrained molecular dynamics. J Mol Biol. 1993 Nov 20;234(2):446–462. [PubMed]
  • Donne DG, Viles JH, Groth D, Mehlhorn I, James TL, Cohen FE, Prusiner SB, Wright PE, Dyson HJ. Structure of the recombinant full-length hamster prion protein PrP(29-231): the N terminus is highly flexible. Proc Natl Acad Sci U S A. 1997 Dec 9;94(25):13452–13457. [PMC free article] [PubMed]
  • Flaherty KM, McKay DB, Kabsch W, Holmes KC. Similarity of the three-dimensional structures of actin and the ATPase fragment of a 70-kDa heat shock cognate protein. Proc Natl Acad Sci U S A. 1991 Jun 1;88(11):5041–5045. [PMC free article] [PubMed]
  • Genick UK, Borgstahl GE, Ng K, Ren Z, Pradervand C, Burke PM, Srajer V, Teng TY, Schildkamp W, McRee DE, et al. Structure of a protein photocycle intermediate by millisecond time-resolved crystallography. Science. 1997 Mar 7;275(5305):1471–1475. [PubMed]
  • Gerstein M, Altman RB. Average core structures and variability measures for protein families: application to the immunoglobulins. J Mol Biol. 1995 Aug 4;251(1):161–175. [PubMed]
  • Gerstein M, Chothia C. Packing at the protein-water interface. Proc Natl Acad Sci U S A. 1996 Sep 17;93(19):10167–10172. [PMC free article] [PubMed]
  • Gerstein M, Chothia C. Analysis of protein loop closure. Two types of hinges produce one motion in lactate dehydrogenase. J Mol Biol. 1991 Jul 5;220(1):133–149. [PubMed]
  • Gerstein M, Anderson BF, Norris GE, Baker EN, Lesk AM, Chothia C. Domain closure in lactoferrin. Two hinges produce a see-saw motion between alternative close-packed interfaces. J Mol Biol. 1993 Nov 20;234(2):357–372. [PubMed]
  • Gerstein M, Lesk AM, Chothia C. Structural mechanisms for domain movements in proteins. Biochemistry. 1994 Jun 7;33(22):6739–6749. [PubMed]
  • Gerstein M, Schulz G, Chothia C. Domain closure in adenylate kinase. Joints on either side of two helices close like neighboring fingers. J Mol Biol. 1993 Jan 20;229(2):494–501. [PubMed]
  • Gilson MK, Straatsma TP, McCammon JA, Ripoll DR, Faerman CH, Axelsen PH, Silman I, Sussman JL. Open "back door" in a molecular dynamics simulation of acetylcholinesterase. Science. 1994 Mar 4;263(5151):1276–1278. [PubMed]
  • Gregoret LM, Cohen FE. Novel method for the rapid evaluation of packing in protein structures. J Mol Biol. 1990 Feb 20;211(4):959–974. [PubMed]
  • Harlos K, Vas M, Blake CF. Crystal structure of the binary complex of pig muscle phosphoglycerate kinase and its substrate 3-phospho-D-glycerate. Proteins. 1992 Feb;12(2):133–144. [PubMed]
  • Harpaz Y, Gerstein M, Chothia C. Volume changes on protein folding. Structure. 1994 Jul 15;2(7):641–649. [PubMed]
  • Harrison PM, Bamborough P, Daggett V, Prusiner SB, Cohen FE. The prion folding problem. Curr Opin Struct Biol. 1997 Feb;7(1):53–59. [PubMed]
  • Hogue CW, Ohkawa H, Bryant SH. A dynamic look at structures: WWW-Entrez and the Molecular Modeling Database. Trends Biochem Sci. 1996 Jun;21(6):226–229. [PubMed]
  • Holm L, Sander C. The FSSP database of structurally aligned protein fold families. Nucleic Acids Res. 1994 Sep;22(17):3600–3609. [PMC free article] [PubMed]
  • Holm L, Sander C. Mapping the protein universe. Science. 1996 Aug 2;273(5275):595–603. [PubMed]
  • Hubbard SJ, Argos P. Cavities and packing at protein interfaces. Protein Sci. 1994 Dec;3(12):2194–2206. [PMC free article] [PubMed]
  • Hubbard SJ, Argos P. A functional role for protein cavities in domain: domain motions. J Mol Biol. 1996 Aug 16;261(2):289–300. [PubMed]
  • Hubbard TJ, Murzin AG, Brenner SE, Chothia C. SCOP: a structural classification of proteins database. Nucleic Acids Res. 1997 Jan 1;25(1):236–239. [PMC free article] [PubMed]
  • Janin J, Wodak SJ. Structural domains in proteins and their role in the dynamics of protein function. Prog Biophys Mol Biol. 1983;42(1):21–78. [PubMed]
  • Johnson LN, Barford D. Glycogen phosphorylase. The structural basis of the allosteric response and comparison with other allosteric proteins. J Biol Chem. 1990 Feb 15;265(5):2409–2412. [PubMed]
  • Joseph D, Petsko GA, Karplus M. Anatomy of a conformational change: hinged "lid" motion of the triosephosphate isomerase loop. Science. 1990 Sep 21;249(4975):1425–1428. [PubMed]
  • Kim Y, Geiger JH, Hahn S, Sigler PB. Crystal structure of a yeast TBP/TATA-box complex. Nature. 1993 Oct 7;365(6446):512–520. [PubMed]
  • Knowles JR. Enzyme catalysis: not different, just better. Nature. 1991 Mar 14;350(6314):121–124. [PubMed]
  • Knowles JR. To build an enzyme.... Philos Trans R Soc Lond B Biol Sci. 1991 May 29;332(1263):115–121. [PubMed]
  • Koonin EV, Tatusov RL, Rudd KE. Protein sequence comparison at genome scale. Methods Enzymol. 1996;266:295–322. [PubMed]
  • Koshland DE. Application of a Theory of Enzyme Specificity to Protein Synthesis. Proc Natl Acad Sci U S A. 1958 Feb;44(2):98–104. [PMC free article] [PubMed]
  • Koshland DE., Jr Protein and biological control. Sci Am. 1973 Oct;229(4):52–64. [PubMed]
  • Kuntz ID. Structure-based strategies for drug design and discovery. Science. 1992 Aug 21;257(5073):1078–1082. [PubMed]
  • Lawson CL, Zhang RG, Schevitz RW, Otwinowski Z, Joachimiak A, Sigler PB. Flexibility of the DNA-binding domains of trp repressor. Proteins. 1988;3(1):18–31. [PubMed]
  • Lesk AM, Chothia C. Mechanisms of domain closure in proteins. J Mol Biol. 1984 Mar 25;174(1):175–191. [PubMed]
  • Lesk AM, Chothia C. Elbow motion in the immunoglobulins involves a molecular ball-and-socket joint. Nature. 1988 Sep 8;335(6186):188–190. [PubMed]
  • Levitt M, Gerstein M, Huang E, Subbiah S, Tsai J. Protein folding: the endgame. Annu Rev Biochem. 1997;66:549–579. [PubMed]
  • Lewis M, Chang G, Horton NC, Kercher MA, Pace HC, Schumacher MA, Brennan RG, Lu P. Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. Science. 1996 Mar 1;271(5253):1247–1254. [PubMed]
  • Mangel WF, Lin BH, Ramakrishnan V. Characterization of an extremely large, ligand-induced conformational change in plasminogen. Science. 1990 Apr 6;248(4951):69–73. [PubMed]
  • McPhalen CA, Vincent MG, Picot D, Jansonius JN, Lesk AM, Chothia C. Domain closure in mitochondrial aspartate aminotransferase. J Mol Biol. 1992 Sep 5;227(1):197–213. [PubMed]
  • Meador WE, Means AR, Quiocho FA. Target enzyme recognition by calmodulin: 2.4 A structure of a calmodulin-peptide complex. Science. 1992 Aug 28;257(5074):1251–1255. [PubMed]
  • Moffat K. Time-resolved macromolecular crystallography. Annu Rev Biophys Biophys Chem. 1989;18:309–332. [PubMed]
  • Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol. 1995 Apr 7;247(4):536–540. [PubMed]
  • Newman M, Strzelecka T, Dorner LF, Schildkraut I, Aggarwal AK. Structure of Bam HI endonuclease bound to DNA: partial folding and unfolding on DNA binding. Science. 1995 Aug 4;269(5224):656–663. [PubMed]
  • Olson AJ, Bricogne G, Harrison SC. Structure of tomato busy stunt virus IV. The virus particle at 2.9 A resolution. J Mol Biol. 1983 Nov 25;171(1):61–93. [PubMed]
  • Orengo CA, Jones DT, Thornton JM. Protein superfamilies and domain superfolds. Nature. 1994 Dec 15;372(6507):631–634. [PubMed]
  • Peretz D, Williamson RA, Matsunaga Y, Serban H, Pinilla C, Bastidas RB, Rozenshteyn R, James TL, Houghten RA, Cohen FE, et al. A conformational transition at the N terminus of the prion protein features in formation of the scrapie isoform. J Mol Biol. 1997 Oct 31;273(3):614–622. [PubMed]
  • Perutz MF. Mechanisms of cooperativity and allosteric regulation in proteins. Q Rev Biophys. 1989 May;22(2):139–237. [PubMed]
  • Pley HW, Flaherty KM, McKay DB. Three-dimensional structure of a hammerhead ribozyme. Nature. 1994 Nov 3;372(6501):68–74. [PubMed]
  • Ponder JW, Richards FM. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J Mol Biol. 1987 Feb 20;193(4):775–791. [PubMed]
  • Povey S, White J, Nahmias J, Wain H. Problems of nomenclature. Nature. 1997 Nov 27;390(6658):329–329. [PubMed]
  • Rayment I, Rypniewski WR, Schmidt-Bäse K, Smith R, Tomchick DR, Benning MM, Winkelmann DA, Wesenberg G, Holden HM. Three-dimensional structure of myosin subfragment-1: a molecular motor. Science. 1993 Jul 2;261(5117):50–58. [PubMed]
  • Rees B, Cavarelli J, Moras D. Conformational flexibility of tRNA: structural changes in yeast tRNA(Asp) upon binding to aspartyl-tRNA synthetase. Biochimie. 1996;78(7):624–631. [PubMed]
  • Remington S, Wiegand G, Huber R. Crystallographic refinement and atomic models of two different forms of citrate synthase at 2.7 and 1.7 A resolution. J Mol Biol. 1982 Jun 15;158(1):111–152. [PubMed]
  • Richards FM. Areas, volumes, packing and protein structure. Annu Rev Biophys Bioeng. 1977;6:151–176. [PubMed]
  • Richards FM. Calculation of molecular volumes and areas for structures of known geometry. Methods Enzymol. 1985;115:440–464. [PubMed]
  • Richards FM, Lim WA. An analysis of packing in the protein folding problem. Q Rev Biophys. 1993 Nov;26(4):423–498. [PubMed]
  • Ruff M, Krishnaswamy S, Boeglin M, Poterszman A, Mitschler A, Podjarny A, Rees B, Thierry JC, Moras D. Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). Science. 1991 Jun 21;252(5013):1682–1689. [PubMed]
  • Sampson NS, Knowles JR. Segmental movement: definition of the structural requirements for loop closure in catalysis by triosephosphate isomerase. Biochemistry. 1992 Sep 15;31(36):8482–8487. [PubMed]
  • Sayle RA, Milner-White EJ. RASMOL: biomolecular graphics for all. Trends Biochem Sci. 1995 Sep;20(9):374–374. [PubMed]
  • Schlichting I, Almo SC, Rapp G, Wilson K, Petratos K, Lentfer A, Wittinghofer A, Kabsch W, Pai EF, Petsko GA, et al. Time-resolved X-ray crystallographic study of the conformational change in Ha-Ras p21 protein on GTP hydrolysis. Nature. 1990 May 24;345(6273):309–315. [PubMed]
  • Schmidt R, Gerstein M, Altman RB. LPFC: an Internet library of protein family core structures. Protein Sci. 1997 Jan;6(1):246–248. [PMC free article] [PubMed]
  • Schuler GD, Epstein JA, Ohkawa H, Kans JA. Entrez: molecular biology database and retrieval system. Methods Enzymol. 1996;266:141–162. [PubMed]
  • Scott WG, Finch JT, Klug A. The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell. 1995 Jun 30;81(7):991–1002. [PubMed]
  • Shilton BH, Flocco MM, Nilsson M, Mowbray SL. Conformational changes of three periplasmic receptors for bacterial chemotaxis and transport: the maltose-, glucose/galactose- and ribose-binding proteins. J Mol Biol. 1996 Nov 29;264(2):350–363. [PubMed]
  • Shon KJ, Kim Y, Colnago LA, Opella SJ. NMR studies of the structure and dynamics of membrane-bound bacteriophage Pf1 coat protein. Science. 1991 May 31;252(5010):1303–1305. [PubMed]
  • Stein P, Chothia C. Serpin tertiary structure transformation. J Mol Biol. 1991 Sep 20;221(2):615–621. [PubMed]
  • Stevens RC, Gouaux JE, Lipscomb WN. Structural consequences of effector binding to the T state of aspartate carbamoyltransferase: crystal structures of the unligated and ATP- and CTP-complexed enzymes at 2.6-A resolution. Biochemistry. 1990 Aug 21;29(33):7691–7701. [PubMed]
  • Stevens RC, Lipscomb WN. A molecular mechanism for pyrimidine and purine nucleotide control of aspartate transcarbamoylase. Proc Natl Acad Sci U S A. 1992 Jun 15;89(12):5281–5285. [PMC free article] [PubMed]
  • Subramaniam S, Gerstein M, Oesterhelt D, Henderson R. Electron diffraction analysis of structural changes in the photocycle of bacteriorhodopsin. EMBO J. 1993 Jan;12(1):1–8. [PMC free article] [PubMed]
  • Tsai CJ, Lin SL, Wolfson HJ, Nussinov R. A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique. J Mol Biol. 1996 Jul 26;260(4):604–620. [PubMed]
  • Vonrhein C, Schlauderer GJ, Schulz GE. Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases. Structure. 1995 May 15;3(5):483–490. [PubMed]
  • Vyas NK, Vyas MN, Quiocho FA. Comparison of the periplasmic receptors for L-arabinose, D-glucose/D-galactose, and D-ribose. Structural and Functional Similarity. J Biol Chem. 1991 Mar 15;266(8):5226–5237. [PubMed]
  • Wade RC, Davis ME, Luty BA, Madura JD, McCammon JA. Gating of the active site of triose phosphate isomerase: Brownian dynamics simulations of flexible peptide loops in the enzyme. Biophys J. 1993 Jan;64(1):9–15. [PMC free article] [PubMed]
  • Williams N. How to get databases talking the same language. Science. 1997 Jan 17;275(5298):301–302. [PubMed]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

  • PubMed
    PubMed
    PubMed citations for these articles
  • Substance
    Substance
    PubChem Substance links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...