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Cold-active enzymes studied by comparative molecular dynamics simulation

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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.

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

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References

  1. Collins T, Meuwis MA, Gerday C, Feller G (2003) J Mol Biol 328:419–428 DOI 10.1016/S0022-2836(03)00287-0

    Article  CAS  Google Scholar 

  2. Russell NJ (1997) Comp Biochem Physiol A Physiol 118:489–493

    Article  CAS  Google Scholar 

  3. Aghajari N, Feller G, Gerday C, Haser R (1998) Structure 6:1503–1516 DOI 10.1016/S0969-2126(98)00149-X

    Article  CAS  Google Scholar 

  4. Russell RJ, Gerike U, Danson MJ, Hough DW, Taylor GL (1998) Structure 6:351–361 DOI 10.1016/S0969-2126(98)00037-9

    Article  CAS  Google Scholar 

  5. Kim SY, Hwang KY, Kim SH, Sung HC, Han YS, Cho Y (1999) J Biol Chem 274:11761–11767

    Article  CAS  Google Scholar 

  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

    Article  CAS  Google Scholar 

  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

    Article  Google Scholar 

  8. Arnorsdottir J, Kristjansson MM, Ficner R (2005) FEBS J 272:832–845 DOI 10.1111/j.1742-4658.2005.04523.x

    Article  CAS  Google Scholar 

  9. Alvarez M, Zeelen JP, Mainfroid V, Rentier-Delrue F, Martial JA, Wyns L, Wierenga RK, Maes D (1998) J Biol Chem 273:2199–2206

    Article  CAS  Google Scholar 

  10. Bae E, Phillips GN Jr (2004) J Biol Chem 279:28202–28208 DOI 10.1074/jbc.M401865200

    Article  CAS  Google Scholar 

  11. Gianese G, Bossa F, Pascarella S (2002) Proteins 47:236–249 DOI 10.1002/prot.10084

    Article  CAS  Google Scholar 

  12. Gianese G, Argos P, Pascarella S (2001) Protein Eng 14:141–148

    Article  CAS  Google Scholar 

  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

    Article  CAS  Google Scholar 

  14. Zavodszky P, Kardos J, Svingor, Petsko GA (1998) Proc Natl Acad Sci USA 95:7406–7411

    Article  CAS  Google Scholar 

  15. Shoichet BK, Baase WA, Kuroki R, Matthews BW (1995) Proc Natl Acad Sci USA 92:452–456

    Article  CAS  Google Scholar 

  16. Beadle BM, Shoichet BK (2002) J Mol Biol 321:285–296 DOI 10.1016/S0022-2836(02)00599-5

    Article  CAS  Google Scholar 

  17. Olufsen M, Smalas AO, Moe E, Brandsdal BO (2005) J Biol Chem 280:18042–18048 DOI 10.1074/jbc.M500948200

    Article  CAS  Google Scholar 

  18. Taverna DM, Goldstein RA (2002) Proteins 46:105–109 DOI 10.1002/prot.10016

    Article  CAS  Google Scholar 

  19. Heimstad ES, Hansen LK, Smalas AO (1995) Protein Eng 8:379–399

    Article  CAS  Google Scholar 

  20. Brandsdal BO, Heimstad ES, Sylte I, Smalas AO (1999) J Biomol Struct Dyn 17:493–506

    CAS  Google Scholar 

  21. Brandsdal BO, Aqvist J, Smalas AO (2001) Protein Sci 10:1584–1595

    Article  CAS  Google Scholar 

  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

    Article  CAS  Google Scholar 

  23. Brandsdal BO, Smalas AO, Aqvist J (2001) FEBS Lett 499:171–175 DOI 10.1016/S0014-5793(01)02552-2

    Article  CAS  Google Scholar 

  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

    Article  CAS  Google Scholar 

  25. D’Amico S, Gerday C, Feller G (2002) J Biol Chem 277:46110–46115 DOI 10.1074/jbc.M207253200

    Article  CAS  Google Scholar 

  26. Mavromatis K, Feller G, Kokkinidis M, Bouriotis V (2003) Protein Eng 16:497–503

    Article  CAS  Google Scholar 

  27. Mavromatis K, Tsigos I, Tzanodaskalaki M, Kokkinidis M, Bouriotis V (2002) Eur J Biochem 269:2330–2335

    Article  CAS  Google Scholar 

  28. Narinx E, Baise E, Gerday C (1997) Protein Eng 10:1271–1279

    Article  CAS  Google Scholar 

  29. Ohtani N, Haruki M, Morikawa M, Kanaya S (2001) Protein Eng 14:975–982

    Article  CAS  Google Scholar 

  30. Agarwal PK (2006) Microb Cell Fact 5 DOI 10.1186/1475-2859-5-2

  31. McCammon JA, Gelin BR, Karplus M (1977) Nature 276:585–590 DOI 10.1038/267585a0

    Article  Google Scholar 

  32. Hayward JA, Finney JL, Daniel RM, Smith JC (2003) Biophys J 85:679–685

    CAS  Google Scholar 

  33. Stocker U, Spiegel K, van Gunsteren WF (2000) J Biomol NMR 18:1–12 DOI 10.1023/A:1008379605403

    Article  CAS  Google Scholar 

  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

    Article  CAS  Google Scholar 

  35. Grottesi A, Ceruso MA, Colosimo A, Di Nola A (2002) Proteins 46:287–294 DOI 10.1002/prot.10045

    Article  CAS  Google Scholar 

  36. Lazaridis T, Lee I, Karplus M (1997) Protein Sci 6:2589–2605

    CAS  Google Scholar 

  37. Amadei A, Linssen AB, Berendsen HJ (1993) Proteins 17:412–425 DOI 10.1002/prot.340170408

    Article  CAS  Google Scholar 

  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

    CAS  Google Scholar 

  39. Guda C, Lu S, Scheeff ED, Bourne PE, Shindyalov IN (2004) Nucleic Acids Res 32:W100–W103 DOI 10.1093/nar/gkh464

    Article  CAS  Google Scholar 

  40. Sali A, Blundell TL (1993) J Mol Biol 234:779–815 DOI 10.1006/jmbi.1993.1626

    Article  CAS  Google Scholar 

  41. Canutescu AA, Shelenkov AA, Dunbrack RL Jr (2003) Protein Sci 12:2001–2014

    Article  CAS  Google Scholar 

  42. Feller G, Bussy O, Houssier C, Gerday C (1996) J Biol Chem 271:23836–23841

    Article  CAS  Google Scholar 

  43. Ravaud S, Gouet P, Haser R, Aghajari N (2003) J Bacteriol 185:4195–4203 DOI 10.1128/JB.185.14.4195-4203

    Article  CAS  Google Scholar 

  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 forces

  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

    Article  CAS  Google Scholar 

  46. Lindahl E, Hess B, van der Spoel D (2001) J Mol Mod 7:306–317 DOI 10.1007/s008940100045

    CAS  Google Scholar 

  47. Berendsen HJC, Postma JPM, DiNola A, Haak JR (1984) J Chem Phys 81:3684–3690 DOI 10.1063/1.448118

    Article  CAS  Google Scholar 

  48. Parrinello M, Rahman A (1981) J Appl Phys 52:7182–7190 DOI 10.1063/1.328693

    Article  CAS  Google Scholar 

  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

    Article  CAS  Google Scholar 

  50. Fan H, Mark AE (2003) Proteins 53:111–120 DOI 10.1002/prot.10496

    Article  CAS  Google Scholar 

  51. Rost B (2002) Curr Opin Struct Biol 12:409–416 DOI 10.1016/S0959-440X(02)00337-8

    Article  CAS  Google Scholar 

  52. Fitter J, Heberle J (2000) Biophys J 79:1629–1637

    CAS  Google Scholar 

  53. Roccatano D, Mark AE, Hayward S (2001) J Mol Biol 310:1039–1054 DOI 10.1006/jmbi.2001.4808

    Article  CAS  Google Scholar 

  54. Kurz LC, Drysdale G, Riley M, Tomar MA, Chen J, Russell RJ, Danson MJ (2000) Biochemistry 39:2283–2297 DOI 10.1021/bi991982r

    Article  CAS  Google Scholar 

  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

    Article  CAS  Google Scholar 

  56. Ferrand M, Dianoux AJ, Petry W, Zaccai G (1993) Proc Natl Acad Sci USA 90:9668–9672

    Article  CAS  Google Scholar 

  57. Rasmussen BF, Stock AM, Ringe D, Petsko GA (1992) Nature 357:423–424 DOI 10.1038/357423a0

    Article  CAS  Google Scholar 

  58. Daniel RM, Smith JC, Ferrand M, Hery S, Dunn R, Finney JL (1998) Biophys J 75:2504–2507

    Article  CAS  Google Scholar 

  59. Dunn RV, Reat V, Finney J, Ferrand M, Smith JC, Daniel RM (2000) Biochem J 346:355–358

    Article  CAS  Google Scholar 

  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

    Article  CAS  Google Scholar 

  61. Qian M, Nahoum V, Bonicel J, Bischoff H, Henrissat B, Payan F (2001) Biochemistry 40:7700–7709 DOI 10.1021/bi0102050

    CAS  Google Scholar 

  62. Russell RJ, Ferguson JM, Hough DW, Danson MJ, Taylor GL (1997) Biochemistry 36:9983–9994 DOI 10.1021/bi9705321

    Article  CAS  Google Scholar 

  63. to be published

  64. Baumann U, Wu S, Flaherty KM, McKay DB (1993) EMBO J 12:3357–3364

    CAS  Google Scholar 

  65. Alzari PM, Souchon H, Dominguez R (1996) Structure 4:265–275 DOI 10.1016/S0969-2126(96)00031-7

    Article  CAS  Google Scholar 

Download references

Acknowledgment

This work was supported by the Academy of Sciences of the Czech Republic (GAAV KJB 500500512) and the Ministry of Education, Youth and Sports (MSM 6046137305). The authors would like to acknowledge colleagues from the Department of Biochemistry and Microbiology, Institute of Chemical Technology Prague who have lent their personal computers during holiday periods for performing some of the computations presented herein. They are listed on the following web site: biomikro.vscht.cz/groups/lab211/holiday.

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Authors and Affiliations

  1. Department of Biochemistry and Microbiology, Institute of Chemical Technology Prague, Technická 5, Prague 6, 166 28, Czech Republic

    Vojtěch Spiwok, Petra Lipovová & Blanka Králová

  2. Institute of Macromolecular Chemistry, The Academy of Sciences of the Czech Republic, Heyrovského nám.2, Prague 6, 162 06, Czech Republic

    Tereza Skálová, Jarmila Dušková, Jan Dohnálek & Jindřich Hašek

  3. Department of Agricultural Sciences, Imperial College London, Wye campus, Ashford, Kent, TN25 5AH, UK

    Nicholas J. Russell

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  1. Vojtěch Spiwok
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Correspondence to Vojtěch Spiwok.

Electronic Supplementary Material

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Supplementary material is available. Supplementary material contains sequence alignments, RMSD profiles, 3D illustrations of flexibility profiles, correlation of flexibilities for corresponding residues and results of essential dynamics analysis.

Fig. 1

(a–e) 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)

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Fig. 2

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

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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)

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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),

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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)

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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)

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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)

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Spiwok, V., Lipovová, P., Skálová, T. et al. Cold-active enzymes studied by comparative molecular dynamics simulation. J Mol Model 13, 485–497 (2007). https://doi.org/10.1007/s00894-006-0164-5

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