Limits...
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.

Show MeSH

Related in: MedlinePlus

ProTherm data, and calculations. (a) Scatter plot with ΔGfold for 100 proteins in the ProTherm database and calculated Gmin. Whereas ProTherm records ΔGfold as more positive for a more favoured folded state, Gmin calculations are in the opposite sense. (b) Scatter plot with the melting temperatures for 140 proteins in the ProTherm database and calculated Gmin.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC1851960&req=5

Figure 11: ProTherm data, and calculations. (a) Scatter plot with ΔGfold for 100 proteins in the ProTherm database and calculated Gmin. Whereas ProTherm records ΔGfold as more positive for a more favoured folded state, Gmin calculations are in the opposite sense. (b) Scatter plot with the melting temperatures for 140 proteins in the ProTherm database and calculated Gmin.

Mentions: Given that we have a collection of properties that provide some distinction between proteins from organisms at different growth temperatures, we looked also at proteins for which stability data (ΔGfold and/or Tm) are available in the ProTherm database [71]. Experimental ΔGfold or Tm are plotted against the calculated Gmin (Figure 11a,b). A large majority of the ProTherm proteins are from mesophiles. There is no correlation between our calculated charge-charge interactions and stability, using either the computed values per protein (Gmin) or the values per amino acid (GminN, not shown). This result emphasises that protein stability is a complex mixture of components, any one of which will not necessarily be a reliable indicator. Charge-charge interactions contribute to separation of thermophile and mesophile proteins in our analysis, but not to separation within a mesophile set, indicating that organism growth temperature is an important factor.


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

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

ProTherm data, and calculations. (a) Scatter plot with ΔGfold for 100 proteins in the ProTherm database and calculated Gmin. Whereas ProTherm records ΔGfold as more positive for a more favoured folded state, Gmin calculations are in the opposite sense. (b) Scatter plot with the melting temperatures for 140 proteins in the ProTherm database and calculated Gmin.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 11: ProTherm data, and calculations. (a) Scatter plot with ΔGfold for 100 proteins in the ProTherm database and calculated Gmin. Whereas ProTherm records ΔGfold as more positive for a more favoured folded state, Gmin calculations are in the opposite sense. (b) Scatter plot with the melting temperatures for 140 proteins in the ProTherm database and calculated Gmin.
Mentions: Given that we have a collection of properties that provide some distinction between proteins from organisms at different growth temperatures, we looked also at proteins for which stability data (ΔGfold and/or Tm) are available in the ProTherm database [71]. Experimental ΔGfold or Tm are plotted against the calculated Gmin (Figure 11a,b). A large majority of the ProTherm proteins are from mesophiles. There is no correlation between our calculated charge-charge interactions and stability, using either the computed values per protein (Gmin) or the values per amino acid (GminN, not shown). This result emphasises that protein stability is a complex mixture of components, any one of which will not necessarily be a reliable indicator. Charge-charge interactions contribute to separation of thermophile and mesophile proteins in our analysis, but not to separation within a mesophile set, indicating that organism growth temperature is an important factor.

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