Journal of Molecular Modeling

, Volume 13, Issue 4, pp 485–497

Cold-active enzymes studied by comparative molecular dynamics simulation

  • Vojtěch Spiwok
  • Petra Lipovová
  • Tereza Skálová
  • Jarmila Dušková
  • Jan Dohnálek
  • Jindřich Hašek
  • Nicholas J. Russell
  • Blanka Králová
Original Paper

Abstract

Enzymes from cold-adapted species are significantly more active at low temperatures, even those close to zero Celsius, but the rationale of this adaptation is complex and relatively poorly understood. It is commonly stated that there is a relationship between the flexibility of an enzyme and its catalytic activity at low temperature. This paper gives the results of a study using molecular dynamics simulations performed for five pairs of enzymes, each pair comprising a cold-active enzyme plus its mesophilic or thermophilic counterpart. The enzyme pairs included α-amylase, citrate synthase, malate dehydrogenase, alkaline protease and xylanase. Numerous sites with elevated flexibility were observed in all enzymes; however, differences in flexibilities were not striking. Nevertheless, amino acid residues common in both enzymes of a pair (not present in insertions of a structure alignment) are generally more flexible in the cold-active enzymes. The further application of principle component analysis to the protein dynamics revealed that there are differences in the rate and/or extent of opening and closing of the active sites. The results indicate that protein dynamics play an important role in catalytic processes where structural rearrangements, such as those required for active site access by substrate, are involved. They also support the notion that cold adaptation may have evolved by selective changes in regions of enzyme structure rather than in global change to the whole protein.

Figure

Collective motions in Cα atoms of the active site of cold-active xylanase

Keywords

Cold-active enzymes Psychrophiles Extremophiles Molecular dynamics Flexibility 

Supplementary material

894_2006_164_Fig1a_ESM.jpg (347 kb)
Fig. 1

(ae) Sequence alignments of the studied enzymes calculated by Conformational Extension 3D alignment procedure. Figures were obtained using ESPript a(JPEG 355 KB), b(JPEG 277 KB), c(JPEG 269 KB), d(JPEG 368 KB), e(JPEG 242 KB)

894_2006_164_Fig1b_ESM.jpg (271 kb)
Fig. 1

(ae) Sequence alignments of the studied enzymes calculated by Conformational Extension 3D alignment procedure. Figures were obtained using ESPript a(JPEG 355 KB), b(JPEG 277 KB), c(JPEG 269 KB), d(JPEG 368 KB), e(JPEG 242 KB)

894_2006_164_Fig1c_ESM.jpg (264 kb)
Fig. 1

(ae) Sequence alignments of the studied enzymes calculated by Conformational Extension 3D alignment procedure. Figures were obtained using ESPript a(JPEG 355 KB), b(JPEG 277 KB), c(JPEG 269 KB), d(JPEG 368 KB), e(JPEG 242 KB)

894_2006_164_Fig1d_ESM.jpg (360 kb)
Fig. 1

(ae) Sequence alignments of the studied enzymes calculated by Conformational Extension 3D alignment procedure. Figures were obtained using ESPript a(JPEG 355 KB), b(JPEG 277 KB), c(JPEG 269 KB), d(JPEG 368 KB), e(JPEG 242 KB)

894_2006_164_Fig1e_ESM.jpg (237 kb)
Fig. 1

(ae) Sequence alignments of the studied enzymes calculated by Conformational Extension 3D alignment procedure. Figures were obtained using ESPript a(JPEG 355 KB), b(JPEG 277 KB), c(JPEG 269 KB), d(JPEG 368 KB), e(JPEG 242 KB)

894_2006_164_Fig1a_ESM.tif (333 kb)
High resolution image file (TIFF 340 KB)
894_2006_164_Fig1b_ESM.tif (260 kb)
High resolution image file (TIFF 266 KB)
894_2006_164_Fig1c_ESM.tif (228 kb)
High resolution image file (TIFF 232 KB)
894_2006_164_Fig1d_ESM.tif (303 kb)
High resolution image file (TIFF 310 KB)
894_2006_164_Fig1e_ESM.tif (274 kb)
High resolution image file (TIFF 280 KB)
894_2006_164_Fig2_ESM.jpg (275 kb)
Fig. 2

Root-mean-square deviation of structures of the studied enzymes from the initial structure during molecular dynamics simulation(JPEG 281 KB)

894_2006_164_Fig2_ESM.tif (883 kb)
High resolution image file (TIFF 904 KB)
894_2006_164_Fig3_ESM.jpg (254 kb)
Fig. 3

Root-mean-square deviation from the initial structure during molecular dynamics simulation at different temperatures calculated for the studied xylanases(JPEG 260 KB)

894_2006_164_Fig3_ESM.tif (453 kb)
High resolution image file (TIFF 463 KB)
894_2006_164_Fig4a_ESM.jpg (216 kb)
Fig. 4

3D representation of flexibility profiles of the studied enzymes. Flexibility defined as root-mean square fluctuation is indicated by colour (red - most flexible, blue - least flexible, scale attached)a(JPEG 221 KB), b(JPEG 176 KB), c(JPEG 175 KB), d(JPEG 223 KB), e(JPEG 219 KB),

894_2006_164_Fig4b_ESM.jpg (172 kb)
Fig. 4

3D representation of flexibility profiles of the studied enzymes. Flexibility defined as root-mean square fluctuation is indicated by colour (red - most flexible, blue - least flexible, scale attached)a(JPEG 221 KB), b(JPEG 176 KB), c(JPEG 175 KB), d(JPEG 223 KB), e(JPEG 219 KB),

894_2006_164_Fig4c_ESM.jpg (171 kb)
Fig. 4

3D representation of flexibility profiles of the studied enzymes. Flexibility defined as root-mean square fluctuation is indicated by colour (red - most flexible, blue - least flexible, scale attached)a(JPEG 221 KB), b(JPEG 176 KB), c(JPEG 175 KB), d(JPEG 223 KB), e(JPEG 219 KB),

894_2006_164_Fig4d_ESM.jpg (219 kb)
Fig. 4

3D representation of flexibility profiles of the studied enzymes. Flexibility defined as root-mean square fluctuation is indicated by colour (red - most flexible, blue - least flexible, scale attached)a(JPEG 221 KB), b(JPEG 176 KB), c(JPEG 175 KB), d(JPEG 223 KB), e(JPEG 219 KB),

894_2006_164_Fig4e_ESM.jpg (214 kb)
Fig. 4

3D representation of flexibility profiles of the studied enzymes. Flexibility defined as root-mean square fluctuation is indicated by colour (red - most flexible, blue - least flexible, scale attached)a(JPEG 221 KB), b(JPEG 176 KB), c(JPEG 175 KB), d(JPEG 223 KB), e(JPEG 219 KB),

894_2006_164_Fig4a_ESM.tif (1.8 mb)
High resolution image file (TIFF 1 906 KB)
894_2006_164_Fig4b_ESM.tif (1.4 mb)
High resolution image file (TIFF 1 430 KB)
894_2006_164_Fig4c_ESM.tif (1.3 mb)
High resolution image file (TIFF 1 365 KB)
894_2006_164_Fig4d_ESM.tif (1.8 mb)
High resolution image file (TIFF 1 892 KB)
894_2006_164_Fig4e_ESM.tif (1.9 mb)
High resolution image file (TIFF 1 993 KB)
894_2006_164_Fig5_ESM.jpg (245 kb)
Fig. 5

Correlation of flexibilities (RMSF) between corresponding residues in a cold-active and meso- or thermophilic counterpart. For detailed explanation see Fig. 5 and the text(JPEG 250 KB)

894_2006_164_Fig5_ESM.tif (432 kb)
High resolution image file (TIFF 442 KB)
894_2006_164_Fig6_ESM.jpg (236 kb)
Fig. 6

Results of essential dynamics analysis. Projection of trajectory on the first eigenvector for the meso- or thermophilic enzyme vs. projection on the first eigenvector for the cold-active enzyme (left). Projection on the second eigenvector for the meso- or thermophilic enzyme vs. projection on the second eigenvector for the cold-active enzyme (right)(JPEG 241 KB)

894_2006_164_Fig6_ESM.tif (372 kb)
High resolution image file (TIFF 381 KB)
894_2006_164_Fig7_ESM.jpg (171 kb)
Fig. 7

Results of essential dynamics analysis of xylanases simulated at different temperatures. Each plot shows projection on the second eigenvector vs. projection on the first eigenvector(JPEG 1 786 KB)

894_2006_164_Fig7_ESM.tif (819 kb)
High resolution image file (TIFF 838 KB)

References

  1. 1.
    Collins T, Meuwis MA, Gerday C, Feller G (2003) J Mol Biol 328:419–428 DOI 10.1016/S0022-2836(03)00287-0 CrossRefGoogle Scholar
  2. 2.
    Russell NJ (1997) Comp Biochem Physiol A Physiol 118:489–493CrossRefGoogle Scholar
  3. 3.
    Aghajari N, Feller G, Gerday C, Haser R (1998) Structure 6:1503–1516 DOI 10.1016/S0969-2126(98)00149-X CrossRefGoogle Scholar
  4. 4.
    Russell RJ, Gerike U, Danson MJ, Hough DW, Taylor GL (1998) Structure 6:351–361 DOI 10.1016/S0969-2126(98)00037-9 CrossRefGoogle Scholar
  5. 5.
    Kim SY, Hwang KY, Kim SH, Sung HC, Han YS, Cho Y (1999) J Biol Chem 274:11761–11767CrossRefGoogle Scholar
  6. 6.
    Aghajari N, van Petegem F, Villeret V, Chessa JP, Gerday C, Haser R, van Beeumen J (2003) Proteins 50:636–647 DOI 10.1002/prot.10264 CrossRefGoogle Scholar
  7. 7.
    van Petegem F, Collins T, Meuwis MA, Gerday C, Feller G, van Beeumen J (2003) J Biol Chem 278:7531–7539 DOI 10.1074/jbc.M206862200 CrossRefGoogle Scholar
  8. 8.
    Arnorsdottir J, Kristjansson MM, Ficner R (2005) FEBS J 272:832–845 DOI 10.1111/j.1742-4658.2005.04523.x CrossRefGoogle Scholar
  9. 9.
    Alvarez M, Zeelen JP, Mainfroid V, Rentier-Delrue F, Martial JA, Wyns L, Wierenga RK, Maes D (1998) J Biol Chem 273:2199–2206CrossRefGoogle Scholar
  10. 10.
    Bae E, Phillips GN Jr (2004) J Biol Chem 279:28202–28208 DOI 10.1074/jbc.M401865200 CrossRefGoogle Scholar
  11. 11.
    Gianese G, Bossa F, Pascarella S (2002) Proteins 47:236–249 DOI 10.1002/prot.10084 CrossRefGoogle Scholar
  12. 12.
    Gianese G, Argos P, Pascarella S (2001) Protein Eng 14:141–148CrossRefGoogle Scholar
  13. 13.
    Saunders NF, Thomas T, Curmi PM, Mattick JS, Kuczek E, Slade R, Davis J, Franzmann PD, Boone D, Rusterholtz K, Feldman R, Gates C, Bench S, Sowers K, Kadner K, Aerts A, Dehal P, Detter C, Glavina T, Lucas S, Richardson P, Larimer F, Hauser L, Land M, Cavicchioli R (2003) Genome Res 13:1580–1588 DOI 10.1101/gr.1180903 CrossRefGoogle Scholar
  14. 14.
    Zavodszky P, Kardos J, Svingor, Petsko GA (1998) Proc Natl Acad Sci USA 95:7406–7411CrossRefGoogle Scholar
  15. 15.
    Shoichet BK, Baase WA, Kuroki R, Matthews BW (1995) Proc Natl Acad Sci USA 92:452–456CrossRefGoogle Scholar
  16. 16.
    Beadle BM, Shoichet BK (2002) J Mol Biol 321:285–296 DOI 10.1016/S0022-2836(02)00599-5 CrossRefGoogle Scholar
  17. 17.
    Olufsen M, Smalas AO, Moe E, Brandsdal BO (2005) J Biol Chem 280:18042–18048 DOI 10.1074/jbc.M500948200 CrossRefGoogle Scholar
  18. 18.
    Taverna DM, Goldstein RA (2002) Proteins 46:105–109 DOI 10.1002/prot.10016 CrossRefGoogle Scholar
  19. 19.
    Heimstad ES, Hansen LK, Smalas AO (1995) Protein Eng 8:379–399CrossRefGoogle Scholar
  20. 20.
    Brandsdal BO, Heimstad ES, Sylte I, Smalas AO (1999) J Biomol Struct Dyn 17:493–506Google Scholar
  21. 21.
    Brandsdal BO, Aqvist J, Smalas AO (2001) Protein Sci 10:1584–1595CrossRefGoogle Scholar
  22. 22.
    Gorfe AA, Brandsdal BO, Leiros HK, Helland R, Smalas AO (2000) Proteins 40:207–217 DOI 10.1002/(SICI)1097-0134(20000801)40:2<207::AID-PROT40>3.0.CO;2-U CrossRefGoogle Scholar
  23. 23.
    Brandsdal BO, Smalas AO, Aqvist J (2001) FEBS Lett 499:171–175 DOI 10.1016/S0014-5793(01)02552-2 CrossRefGoogle Scholar
  24. 24.
    Moe E, Leiros I, Riise EK, Olufsen M, Lanes O, Smalas A, Willassen NP (2004) J Mol Biol 343:1221–1230 DOI 10.1016/j.jmb.2004.09.004 CrossRefGoogle Scholar
  25. 25.
    D’Amico S, Gerday C, Feller G (2002) J Biol Chem 277:46110–46115 DOI 10.1074/jbc.M207253200 CrossRefGoogle Scholar
  26. 26.
    Mavromatis K, Feller G, Kokkinidis M, Bouriotis V (2003) Protein Eng 16:497–503CrossRefGoogle Scholar
  27. 27.
    Mavromatis K, Tsigos I, Tzanodaskalaki M, Kokkinidis M, Bouriotis V (2002) Eur J Biochem 269:2330–2335CrossRefGoogle Scholar
  28. 28.
    Narinx E, Baise E, Gerday C (1997) Protein Eng 10:1271–1279CrossRefGoogle Scholar
  29. 29.
    Ohtani N, Haruki M, Morikawa M, Kanaya S (2001) Protein Eng 14:975–982CrossRefGoogle Scholar
  30. 30.
    Agarwal PK (2006) Microb Cell Fact 5 DOI 10.1186/1475-2859-5-2
  31. 31.
    McCammon JA, Gelin BR, Karplus M (1977) Nature 276:585–590 DOI 10.1038/267585a0 CrossRefGoogle Scholar
  32. 32.
    Hayward JA, Finney JL, Daniel RM, Smith JC (2003) Biophys J 85:679–685Google Scholar
  33. 33.
    Stocker U, Spiegel K, van Gunsteren WF (2000) J Biomol NMR 18:1–12 DOI 10.1023/A:1008379605403 CrossRefGoogle Scholar
  34. 34.
    Wintrode PL, Zhang D, Vaidehi N, Arnold FH, Goddard WA III (2003) J Mol Biol 327:745–757 DOI 10.1016/S0022-2836(03)00147-5 CrossRefGoogle Scholar
  35. 35.
    Grottesi A, Ceruso MA, Colosimo A, Di Nola A (2002) Proteins 46:287–294 DOI 10.1002/prot.10045 CrossRefGoogle Scholar
  36. 36.
    Lazaridis T, Lee I, Karplus M (1997) Protein Sci 6:2589–2605Google Scholar
  37. 37.
    Amadei A, Linssen AB, Berendsen HJ (1993) Proteins 17:412–425 DOI 10.1002/prot.340170408 CrossRefGoogle Scholar
  38. 38.
    Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S, Fagan P, Marvin J, Padilla D, Ravichandran V, Schneider B, Thanki N, Weissig H, Westbrook JD, Zardecki C (2002) Acta Cryst D58:899–907 DOI 10.1107/S0907444902003451 Google Scholar
  39. 39.
    Guda C, Lu S, Scheeff ED, Bourne PE, Shindyalov IN (2004) Nucleic Acids Res 32:W100–W103 DOI 10.1093/nar/gkh464 CrossRefGoogle Scholar
  40. 40.
    Sali A, Blundell TL (1993) J Mol Biol 234:779–815 DOI 10.1006/jmbi.1993.1626 CrossRefGoogle Scholar
  41. 41.
    Canutescu AA, Shelenkov AA, Dunbrack RL Jr (2003) Protein Sci 12:2001–2014CrossRefGoogle Scholar
  42. 42.
    Feller G, Bussy O, Houssier C, Gerday C (1996) J Biol Chem 271:23836–23841CrossRefGoogle Scholar
  43. 43.
    Ravaud S, Gouet P, Haser R, Aghajari N (2003) J Bacteriol 185:4195–4203 DOI 10.1128/JB.185.14.4195-4203 CrossRefGoogle Scholar
  44. 44.
    Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J (1981) Interaction models for water in relation to protein hydration. In: Pullman B (ed) Intermolecular forcesGoogle Scholar
  45. 45.
    Berendsen HJC, van der Spoel D, van Drunen R (1995) Comp Phys Comm 91:43–56 DOI 10.1016/0010-4655(95)00042-E CrossRefGoogle Scholar
  46. 46.
    Lindahl E, Hess B, van der Spoel D (2001) J Mol Mod 7:306–317 DOI 10.1007/s008940100045 Google Scholar
  47. 47.
    Berendsen HJC, Postma JPM, DiNola A, Haak JR (1984) J Chem Phys 81:3684–3690 DOI 10.1063/1.448118 CrossRefGoogle Scholar
  48. 48.
    Parrinello M, Rahman A (1981) J Appl Phys 52:7182–7190 DOI 10.1063/1.328693 CrossRefGoogle Scholar
  49. 49.
    Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) J Comp Chem 18:1463–1472 DOI 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H CrossRefGoogle Scholar
  50. 50.
    Fan H, Mark AE (2003) Proteins 53:111–120 DOI 10.1002/prot.10496 CrossRefGoogle Scholar
  51. 51.
    Rost B (2002) Curr Opin Struct Biol 12:409–416 DOI 10.1016/S0959-440X(02)00337-8 CrossRefGoogle Scholar
  52. 52.
    Fitter J, Heberle J (2000) Biophys J 79:1629–1637Google Scholar
  53. 53.
    Roccatano D, Mark AE, Hayward S (2001) J Mol Biol 310:1039–1054 DOI 10.1006/jmbi.2001.4808 CrossRefGoogle Scholar
  54. 54.
    Kurz LC, Drysdale G, Riley M, Tomar MA, Chen J, Russell RJ, Danson MJ (2000) Biochemistry 39:2283–2297 DOI 10.1021/bi991982r CrossRefGoogle Scholar
  55. 55.
    Tehei M, Franzetti B, Madern D, Ginzburg M, Ginzburg BZ, Giudici-Orticoni MT, Bruschi M, Zaccai G (2004) EMBO Rep 5:66–77 DOI 10.1038/sj.embor.7400049 CrossRefGoogle Scholar
  56. 56.
    Ferrand M, Dianoux AJ, Petry W, Zaccai G (1993) Proc Natl Acad Sci USA 90:9668–9672CrossRefGoogle Scholar
  57. 57.
    Rasmussen BF, Stock AM, Ringe D, Petsko GA (1992) Nature 357:423–424 DOI 10.1038/357423a0 CrossRefGoogle Scholar
  58. 58.
    Daniel RM, Smith JC, Ferrand M, Hery S, Dunn R, Finney JL (1998) Biophys J 75:2504–2507CrossRefGoogle Scholar
  59. 59.
    Dunn RV, Reat V, Finney J, Ferrand M, Smith JC, Daniel RM (2000) Biochem J 346:355–358CrossRefGoogle Scholar
  60. 60.
    Wolf-Watz M, Thai V, Henzler-Wildman K, Hadjipavlou G, Eisenmesser EZ, Kern D (2004) Nat Struct Mol Biol 11:945–949 DOI 10.1038/nsmb821 CrossRefGoogle Scholar
  61. 61.
    Qian M, Nahoum V, Bonicel J, Bischoff H, Henrissat B, Payan F (2001) Biochemistry 40:7700–7709 DOI 10.1021/bi0102050 Google Scholar
  62. 62.
    Russell RJ, Ferguson JM, Hough DW, Danson MJ, Taylor GL (1997) Biochemistry 36:9983–9994 DOI 10.1021/bi9705321 CrossRefGoogle Scholar
  63. 63.
    to be publishedGoogle Scholar
  64. 64.
    Baumann U, Wu S, Flaherty KM, McKay DB (1993) EMBO J 12:3357–3364Google Scholar
  65. 65.
    Alzari PM, Souchon H, Dominguez R (1996) Structure 4:265–275 DOI 10.1016/S0969-2126(96)00031-7 CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • Vojtěch Spiwok
    • 1
  • Petra Lipovová
    • 1
  • Tereza Skálová
    • 2
  • Jarmila Dušková
    • 2
  • Jan Dohnálek
    • 2
  • Jindřich Hašek
    • 2
  • Nicholas J. Russell
    • 3
  • Blanka Králová
    • 1
  1. 1.Department of Biochemistry and MicrobiologyInstitute of Chemical Technology PraguePrague 6Czech Republic
  2. 2.Institute of Macromolecular ChemistryThe Academy of Sciences of the Czech RepublicPrague 6Czech Republic
  3. 3.Department of Agricultural SciencesImperial College LondonAshfordUK

Personalised recommendations