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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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Lack of separation by SdiffN. SdiffN is shown for mesophile, moderate thermophile, and hyperthermophile proteins, at two values of the van der Waals tolerance parameter (used in sidechain packing), 0.8 and 1.2 Å.
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Figure 5: Lack of separation by SdiffN. SdiffN is shown for mesophile, moderate thermophile, and hyperthermophile proteins, at two values of the van der Waals tolerance parameter (used in sidechain packing), 0.8 and 1.2 Å.

Mentions: The quantity SdiffN is the (protein length normalised) difference between StotalN and the fold-restricted case, estimated from mean field calculations of rotameric restriction in the folded state. As such, SdiffN is a measure of sidechain 'lock down' in the folded state of the protein. SdiffN was not a useful discriminator between proteins from moderate thermophiles or hyperthermophiles and mesophiles (Figure 5). These calculations are affected by the van der Waals tolerance allowed for atom clashes in sidechain packing. A value of about 0.8 Å is generally required to pack back the experimentally-derived rotamers, relating to overlap required for some interactions in a United Atom model. Calculation of SdiffN was repeated for several values of clash tolerance (0.4, 0.8, 1.0, 1.2, 1.4, 1.6 and 2.0 Å). The best discrimination of SdiffN distributions was apparent for the tolerance parameter set to 1.2Å (Figure 5). We interpret SdiffN as related to conformational flexibility, for sidechains, so that the current result is roughly in accord with the observation [48] that any increase in sidechain flexibility in thermophile proteins compared to mesophile proteins is small. It has been hypothesised that the basis for thermophile proteins containing a greater proportion of Lys over Arg, is a difference in the number of accessible rotameric states [48]. In a subsequent section we look at variations in dehydration energy that could contribute to changes in the percentages of charged residue classes.


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

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

Lack of separation by SdiffN. SdiffN is shown for mesophile, moderate thermophile, and hyperthermophile proteins, at two values of the van der Waals tolerance parameter (used in sidechain packing), 0.8 and 1.2 Å.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Lack of separation by SdiffN. SdiffN is shown for mesophile, moderate thermophile, and hyperthermophile proteins, at two values of the van der Waals tolerance parameter (used in sidechain packing), 0.8 and 1.2 Å.
Mentions: The quantity SdiffN is the (protein length normalised) difference between StotalN and the fold-restricted case, estimated from mean field calculations of rotameric restriction in the folded state. As such, SdiffN is a measure of sidechain 'lock down' in the folded state of the protein. SdiffN was not a useful discriminator between proteins from moderate thermophiles or hyperthermophiles and mesophiles (Figure 5). These calculations are affected by the van der Waals tolerance allowed for atom clashes in sidechain packing. A value of about 0.8 Å is generally required to pack back the experimentally-derived rotamers, relating to overlap required for some interactions in a United Atom model. Calculation of SdiffN was repeated for several values of clash tolerance (0.4, 0.8, 1.0, 1.2, 1.4, 1.6 and 2.0 Å). The best discrimination of SdiffN distributions was apparent for the tolerance parameter set to 1.2Å (Figure 5). We interpret SdiffN as related to conformational flexibility, for sidechains, so that the current result is roughly in accord with the observation [48] that any increase in sidechain flexibility in thermophile proteins compared to mesophile proteins is small. It has been hypothesised that the basis for thermophile proteins containing a greater proportion of Lys over Arg, is a difference in the number of accessible rotameric states [48]. In a subsequent section we look at variations in dehydration energy that could contribute to changes in the percentages of charged residue classes.

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