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Mechanisms for stabilisation and the maintenance of solubility in proteins from thermophiles.

Greaves RB, Warwicker J - BMC Struct. Biol. (2007)

Bottom Line: A dataset of 291 thermophile-derived protein structures is compared with mesophile proteins.An exception is increased burial of alanine and proline residues and decreased burial of phenylalanine, methionine, tyrosine and tryptophan in hyperthermophile proteins compared to those from mesophiles.With regard to our observation that aromatic sidechains are less buried in hyperthermophile proteins, further analysis indicates that the placement of some of these groups may facilitate the reduction of folding fluctuations in proteins of the higher growth temperature organisms.

View Article: PubMed Central - HTML - PubMed

Affiliation: Faculty of Life Sciences, Michael Smith Building, University of Manchester, Manchester, UK. r.greaves@manchester.ac.uk <r.greaves@manchester.ac.uk>

ABSTRACT

Background: The database of protein structures contains representatives from organisms with a range of growth temperatures. Various properties have been studied in a search for the molecular basis of protein adaptation to higher growth temperature. Charged groups have emerged as key distinguishing factors for proteins from thermophiles and mesophiles.

Results: A dataset of 291 thermophile-derived protein structures is compared with mesophile proteins. Calculations of electrostatic interactions support the importance of charges, but indicate that increases in charge contribution to folded state stabilisation do not generally correlate with the numbers of charged groups. Relative propensities of charged groups vary, such as the substitution of glutamic for aspartic acid sidechains. Calculations suggest an energetic basis, with less dehydration for longer sidechains. Most other properties studied show weak or insignificant separation of proteins from moderate thermophiles or hyperthermophiles and mesophiles, including an estimate of the difference in sidechain rotameric entropy upon protein folding. An exception is increased burial of alanine and proline residues and decreased burial of phenylalanine, methionine, tyrosine and tryptophan in hyperthermophile proteins compared to those from mesophiles.

Conclusion: Since an increase in the number of charged groups for hyperthermophile proteins is separable from charged group contribution to folded state stability, we hypothesise that charged group propensity is important in the context of protein solubility and the prevention of aggregation. Accordingly we find some separation between mesophile and hyperthermophile proteins when looking at the largest surface patch that does not contain a charged sidechain. With regard to our observation that aromatic sidechains are less buried in hyperthermophile proteins, further analysis indicates that the placement of some of these groups may facilitate the reduction of folding fluctuations in proteins of the higher growth temperature organisms.

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Separation by GminN. Cumulative frequency distributions of GminN calculated for each protein in the dataset and grouped according to origin as mesophile, moderate thermophile or hyperthermophile. (a) The 291 set. (b) The 67 subset of homologous pairs with E-value < 10-2 and a chain length difference of less than 30 residues.
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Figure 2: Separation by GminN. Cumulative frequency distributions of GminN calculated for each protein in the dataset and grouped according to origin as mesophile, moderate thermophile or hyperthermophile. (a) The 291 set. (b) The 67 subset of homologous pairs with E-value < 10-2 and a chain length difference of less than 30 residues.

Mentions: The minimum of the curve describing the pH-dependence of ionisable group contribution to the free energy of folding (Gmin, Figure 1), divided by the number of residues in the chain (GminN), was examined. Normalisation was performed to reduce the effect of length differences between proteins. Cumulative frequency distributions of GminN are separated for both the 291 sets and 67 subsets of hyperthermophile- and mesophile-derived proteins (Figure 2a,b), reflecting the anticipated greater contribution of charged group interactions to the free energy of stabilisation for proteins from hyperthermophiles. We also explored the ionisable group contributions at notional pH extremes that relate to full protonation or full deprotonation, again normalised by the protein length. Although some separation in the curves for the hyperthermophile and mesophile sets was observed (not shown), these appeared to recapitulate the GminN result and were not analysed further.


Mechanisms for stabilisation and the maintenance of solubility in proteins from thermophiles.

Greaves RB, Warwicker J - BMC Struct. Biol. (2007)

Separation by GminN. Cumulative frequency distributions of GminN calculated for each protein in the dataset and grouped according to origin as mesophile, moderate thermophile or hyperthermophile. (a) The 291 set. (b) The 67 subset of homologous pairs with E-value < 10-2 and a chain length difference of less than 30 residues.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1851960&req=5

Figure 2: Separation by GminN. Cumulative frequency distributions of GminN calculated for each protein in the dataset and grouped according to origin as mesophile, moderate thermophile or hyperthermophile. (a) The 291 set. (b) The 67 subset of homologous pairs with E-value < 10-2 and a chain length difference of less than 30 residues.
Mentions: The minimum of the curve describing the pH-dependence of ionisable group contribution to the free energy of folding (Gmin, Figure 1), divided by the number of residues in the chain (GminN), was examined. Normalisation was performed to reduce the effect of length differences between proteins. Cumulative frequency distributions of GminN are separated for both the 291 sets and 67 subsets of hyperthermophile- and mesophile-derived proteins (Figure 2a,b), reflecting the anticipated greater contribution of charged group interactions to the free energy of stabilisation for proteins from hyperthermophiles. We also explored the ionisable group contributions at notional pH extremes that relate to full protonation or full deprotonation, again normalised by the protein length. Although some separation in the curves for the hyperthermophile and mesophile sets was observed (not shown), these appeared to recapitulate the GminN result and were not analysed further.

Bottom Line: A dataset of 291 thermophile-derived protein structures is compared with mesophile proteins.An exception is increased burial of alanine and proline residues and decreased burial of phenylalanine, methionine, tyrosine and tryptophan in hyperthermophile proteins compared to those from mesophiles.With regard to our observation that aromatic sidechains are less buried in hyperthermophile proteins, further analysis indicates that the placement of some of these groups may facilitate the reduction of folding fluctuations in proteins of the higher growth temperature organisms.

View Article: PubMed Central - HTML - PubMed

Affiliation: Faculty of Life Sciences, Michael Smith Building, University of Manchester, Manchester, UK. r.greaves@manchester.ac.uk <r.greaves@manchester.ac.uk>

ABSTRACT

Background: The database of protein structures contains representatives from organisms with a range of growth temperatures. Various properties have been studied in a search for the molecular basis of protein adaptation to higher growth temperature. Charged groups have emerged as key distinguishing factors for proteins from thermophiles and mesophiles.

Results: A dataset of 291 thermophile-derived protein structures is compared with mesophile proteins. Calculations of electrostatic interactions support the importance of charges, but indicate that increases in charge contribution to folded state stabilisation do not generally correlate with the numbers of charged groups. Relative propensities of charged groups vary, such as the substitution of glutamic for aspartic acid sidechains. Calculations suggest an energetic basis, with less dehydration for longer sidechains. Most other properties studied show weak or insignificant separation of proteins from moderate thermophiles or hyperthermophiles and mesophiles, including an estimate of the difference in sidechain rotameric entropy upon protein folding. An exception is increased burial of alanine and proline residues and decreased burial of phenylalanine, methionine, tyrosine and tryptophan in hyperthermophile proteins compared to those from mesophiles.

Conclusion: Since an increase in the number of charged groups for hyperthermophile proteins is separable from charged group contribution to folded state stability, we hypothesise that charged group propensity is important in the context of protein solubility and the prevention of aggregation. Accordingly we find some separation between mesophile and hyperthermophile proteins when looking at the largest surface patch that does not contain a charged sidechain. With regard to our observation that aromatic sidechains are less buried in hyperthermophile proteins, further analysis indicates that the placement of some of these groups may facilitate the reduction of folding fluctuations in proteins of the higher growth temperature organisms.

Show MeSH
Related in: MedlinePlus