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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 Born (desolvation) energy of ionisable groups, summed over each protein. (a) Aspartic acid. The inset in this and other panels shows the relative composition for the given amino acid(s). Thus aspartic acid is most common in mesophiles and least in hyperthermophiles. (b) Glutamic acid. (c) All ionisable groups likely to be charged at neutral pH.
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Figure 7: Separation by Born (desolvation) energy of ionisable groups, summed over each protein. (a) Aspartic acid. The inset in this and other panels shows the relative composition for the given amino acid(s). Thus aspartic acid is most common in mesophiles and least in hyperthermophiles. (b) Glutamic acid. (c) All ionisable groups likely to be charged at neutral pH.

Mentions: The GminN analysis looked at charge-charge interactions with a simple Debye-Hűckel (DH) model that neglects desolvation energies. A Finite Difference Poisson-Boltzmann (FDPB) calculation was used to estimate dehydration energies for ionisable groups likely to be charged at neutral pH. It was found that hyperthermophile and mesophile proteins are differentiated by the Born energy summed over all titratable groups that are likely to carry net charge at neutral pH (Figure 7c). This differentiation was principally due to Glu, Lys and Arg, and generally relates to more solvent exposure in the folded form. For example, Asp possesses a shorter sidechain (Figure 7a) and is less able to achieve the same level of solvent exposure as Glu (Figure 7b). It can be seen that overall Born energy is lower for Glu than Asp and lower still in hyperthermophiles. Aspartic acid sidechains presumably are unable to adapt conformationally to reduce Born energy, consistent with their substitution by Glu residues in thermophiles (particularly hyperthermophiles, note the relative abundance histograms in Figure 7). Individually these energy components are relatively small, but are more significant summed over a protein. We are able to rationalise changes between amino acid compositions in energetic terms (e.g. Glu for Asp), but this desolvation argument does not account for the overall increase in ionisable groups. This is investigated (in later sections) in terms of protein solubility, i.e. differences between folded and aggregated states rather than between folded and unfolded states.


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

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

Separation by Born (desolvation) energy of ionisable groups, summed over each protein. (a) Aspartic acid. The inset in this and other panels shows the relative composition for the given amino acid(s). Thus aspartic acid is most common in mesophiles and least in hyperthermophiles. (b) Glutamic acid. (c) All ionisable groups likely to be charged at neutral pH.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 7: Separation by Born (desolvation) energy of ionisable groups, summed over each protein. (a) Aspartic acid. The inset in this and other panels shows the relative composition for the given amino acid(s). Thus aspartic acid is most common in mesophiles and least in hyperthermophiles. (b) Glutamic acid. (c) All ionisable groups likely to be charged at neutral pH.
Mentions: The GminN analysis looked at charge-charge interactions with a simple Debye-Hűckel (DH) model that neglects desolvation energies. A Finite Difference Poisson-Boltzmann (FDPB) calculation was used to estimate dehydration energies for ionisable groups likely to be charged at neutral pH. It was found that hyperthermophile and mesophile proteins are differentiated by the Born energy summed over all titratable groups that are likely to carry net charge at neutral pH (Figure 7c). This differentiation was principally due to Glu, Lys and Arg, and generally relates to more solvent exposure in the folded form. For example, Asp possesses a shorter sidechain (Figure 7a) and is less able to achieve the same level of solvent exposure as Glu (Figure 7b). It can be seen that overall Born energy is lower for Glu than Asp and lower still in hyperthermophiles. Aspartic acid sidechains presumably are unable to adapt conformationally to reduce Born energy, consistent with their substitution by Glu residues in thermophiles (particularly hyperthermophiles, note the relative abundance histograms in Figure 7). Individually these energy components are relatively small, but are more significant summed over a protein. We are able to rationalise changes between amino acid compositions in energetic terms (e.g. Glu for Asp), but this desolvation argument does not account for the overall increase in ionisable groups. This is investigated (in later sections) in terms of protein solubility, i.e. differences between folded and aggregated states rather than between folded and unfolded states.

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