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

DOI: 10.1007/s00894-006-0164-5

Cite this article as:
Spiwok, V., Lipovová, P., Skálová, T. et al. J Mol Model (2007) 13: 485. doi:10.1007/s00894-006-0164-5

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.

https://static-content.springer.com/image/art%3A10.1007%2Fs00894-006-0164-5/MediaObjects/894_2006_164_Figa_HTML.gif
Figure

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

Keywords

Cold-active enzymesPsychrophilesExtremophilesMolecular dynamicsFlexibility

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)
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894_2006_164_Fig1b_ESM.tif (260 kb)
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894_2006_164_Fig1c_ESM.tif (228 kb)
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894_2006_164_Fig1d_ESM.tif (303 kb)
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894_2006_164_Fig1e_ESM.tif (274 kb)
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894_2006_164_Fig2_ESM.jpg (275 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_Fig2_ESM.tif (883 kb)
High resolution image file (TIFF 904 KB)
894_2006_164_Fig3_ESM.jpg (254 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_Fig3_ESM.tif (453 kb)
High resolution image file (TIFF 463 KB)
894_2006_164_Fig4a_ESM.jpg (216 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_Fig4b_ESM.jpg (172 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_Fig4c_ESM.jpg (171 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_Fig4d_ESM.jpg (219 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_Fig4e_ESM.jpg (214 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_Fig4a_ESM.tif (1.8 mb)
High resolution image file (TIFF 1 906 KB)
894_2006_164_Fig4b_ESM.tif (1.4 mb)
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894_2006_164_Fig4c_ESM.tif (1.3 mb)
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894_2006_164_Fig4d_ESM.tif (1.8 mb)
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894_2006_164_Fig4e_ESM.tif (1.9 mb)
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894_2006_164_Fig5_ESM.jpg (245 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_Fig5_ESM.tif (432 kb)
High resolution image file (TIFF 442 KB)
894_2006_164_Fig6_ESM.jpg (236 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_Fig6_ESM.tif (372 kb)
High resolution image file (TIFF 381 KB)
894_2006_164_Fig7_ESM.jpg (171 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_Fig7_ESM.tif (819 kb)
High resolution image file (TIFF 838 KB)

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