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PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality.

Dehouck Y, Kwasigroch JM, Gilis D, Rooman M - BMC Bioinformatics (2011)

Bottom Line: Future breakthroughs in medical research may also be expected from an improved understanding of the effect of naturally occurring disease-causing mutations on the molecular level.It is moreover very fast, allowing the prediction of the stability changes resulting from all possible mutations in a medium size protein in less than a minute.This sequence optimality data is also expected to have significant implications in the prediction and the analysis of particular structural or functional protein regions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatique génomique et structurale, Université Libre de Bruxelles, Av, Fr, Roosevelt 50, CP165/61, 1050 Brussels, Belgium. ydehouck@ulb.ac.be

ABSTRACT

Background: The rational design of modified proteins with controlled stability is of extreme importance in a whole range of applications, notably in the biotechnological and environmental areas, where proteins are used for their catalytic or other functional activities. Future breakthroughs in medical research may also be expected from an improved understanding of the effect of naturally occurring disease-causing mutations on the molecular level.

Results: PoPMuSiC-2.1 is a web server that predicts the thermodynamic stability changes caused by single site mutations in proteins, using a linear combination of statistical potentials whose coefficients depend on the solvent accessibility of the mutated residue. PoPMuSiC presents good prediction performances (correlation coefficient of 0.8 between predicted and measured stability changes, in cross validation, after exclusion of 10% outliers). It is moreover very fast, allowing the prediction of the stability changes resulting from all possible mutations in a medium size protein in less than a minute. This unique functionality is user-friendly implemented in PoPMuSiC and is particularly easy to exploit. Another new functionality of our server concerns the estimation of the optimality of each amino acid in the sequence, with respect to the stability of the structure. It may be used to detect structural weaknesses, i.e. clusters of non-optimal residues, which represent particularly interesting sites for introducing targeted mutations. This sequence optimality data is also expected to have significant implications in the prediction and the analysis of particular structural or functional protein regions. To illustrate the interest of this new functionality, we apply it to a dataset of known catalytic sites, and show that a much larger than average concentration of structural weaknesses is detected, quantifying how these sites have been optimized for function rather than stability.

Conclusion: The freely available PoPMuSiC-2.1 web server is highly useful for identifying very rapidly a list of possibly relevant mutations with the desired stability properties, on which subsequent experimental studies can be focused. It can also be used to detect sequence regions corresponding to structural weaknesses, which could be functionally important or structurally delicate regions, with obvious applications in rational protein design.

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Sequence optimality in the active site of the PRAI-IGPS enzyme. A. Sample output of the PoPMuSiC-2.1 web server, corresponding to residues 41-120 of the bifunctional enzyme PRAI:IGPS from E. Coli (PDB code: 1PIIpdb1PII). The sequence optimality score Γ is plotted as a function of the position in the sequence. The elements of secondary structure are distinguished by the associated colour: helices in red, strands in blue, and coils in green. B. Schematic representation of the PRAI:IGPS enzyme. The residues identified by PoPMuSiC as being non-optimal with respect to the stability (Γ ≤ -5 kcal/mol) are highlighted in red (helix), blue (beta strand), or green (coil region). The residues recorded as catalytic residues in the Catalytic Site Atlas are represented as spheres, while those identified by PoPMuSiC but not recorded in the Catalytic Site Atlas are represented as sticks. Catalytic residues that are not identified by PoPMuSiC are colored in magenta.
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Figure 2: Sequence optimality in the active site of the PRAI-IGPS enzyme. A. Sample output of the PoPMuSiC-2.1 web server, corresponding to residues 41-120 of the bifunctional enzyme PRAI:IGPS from E. Coli (PDB code: 1PIIpdb1PII). The sequence optimality score Γ is plotted as a function of the position in the sequence. The elements of secondary structure are distinguished by the associated colour: helices in red, strands in blue, and coils in green. B. Schematic representation of the PRAI:IGPS enzyme. The residues identified by PoPMuSiC as being non-optimal with respect to the stability (Γ ≤ -5 kcal/mol) are highlighted in red (helix), blue (beta strand), or green (coil region). The residues recorded as catalytic residues in the Catalytic Site Atlas are represented as spheres, while those identified by PoPMuSiC but not recorded in the Catalytic Site Atlas are represented as sticks. Catalytic residues that are not identified by PoPMuSiC are colored in magenta.

Mentions: The sequence optimality scores (Γ) are automatically computed for each "Systematic" query. A second plain text file, containing the Γ-values for each position in the sequence is then given as output. In addition, an interactive figure is created, which allows the user to view the distribution of Γ-values along the sequence, and to easily identify the individual contribution of each mutation (Figure 2A).


PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality.

Dehouck Y, Kwasigroch JM, Gilis D, Rooman M - BMC Bioinformatics (2011)

Sequence optimality in the active site of the PRAI-IGPS enzyme. A. Sample output of the PoPMuSiC-2.1 web server, corresponding to residues 41-120 of the bifunctional enzyme PRAI:IGPS from E. Coli (PDB code: 1PIIpdb1PII). The sequence optimality score Γ is plotted as a function of the position in the sequence. The elements of secondary structure are distinguished by the associated colour: helices in red, strands in blue, and coils in green. B. Schematic representation of the PRAI:IGPS enzyme. The residues identified by PoPMuSiC as being non-optimal with respect to the stability (Γ ≤ -5 kcal/mol) are highlighted in red (helix), blue (beta strand), or green (coil region). The residues recorded as catalytic residues in the Catalytic Site Atlas are represented as spheres, while those identified by PoPMuSiC but not recorded in the Catalytic Site Atlas are represented as sticks. Catalytic residues that are not identified by PoPMuSiC are colored in magenta.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3113940&req=5

Figure 2: Sequence optimality in the active site of the PRAI-IGPS enzyme. A. Sample output of the PoPMuSiC-2.1 web server, corresponding to residues 41-120 of the bifunctional enzyme PRAI:IGPS from E. Coli (PDB code: 1PIIpdb1PII). The sequence optimality score Γ is plotted as a function of the position in the sequence. The elements of secondary structure are distinguished by the associated colour: helices in red, strands in blue, and coils in green. B. Schematic representation of the PRAI:IGPS enzyme. The residues identified by PoPMuSiC as being non-optimal with respect to the stability (Γ ≤ -5 kcal/mol) are highlighted in red (helix), blue (beta strand), or green (coil region). The residues recorded as catalytic residues in the Catalytic Site Atlas are represented as spheres, while those identified by PoPMuSiC but not recorded in the Catalytic Site Atlas are represented as sticks. Catalytic residues that are not identified by PoPMuSiC are colored in magenta.
Mentions: The sequence optimality scores (Γ) are automatically computed for each "Systematic" query. A second plain text file, containing the Γ-values for each position in the sequence is then given as output. In addition, an interactive figure is created, which allows the user to view the distribution of Γ-values along the sequence, and to easily identify the individual contribution of each mutation (Figure 2A).

Bottom Line: Future breakthroughs in medical research may also be expected from an improved understanding of the effect of naturally occurring disease-causing mutations on the molecular level.It is moreover very fast, allowing the prediction of the stability changes resulting from all possible mutations in a medium size protein in less than a minute.This sequence optimality data is also expected to have significant implications in the prediction and the analysis of particular structural or functional protein regions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatique génomique et structurale, Université Libre de Bruxelles, Av, Fr, Roosevelt 50, CP165/61, 1050 Brussels, Belgium. ydehouck@ulb.ac.be

ABSTRACT

Background: The rational design of modified proteins with controlled stability is of extreme importance in a whole range of applications, notably in the biotechnological and environmental areas, where proteins are used for their catalytic or other functional activities. Future breakthroughs in medical research may also be expected from an improved understanding of the effect of naturally occurring disease-causing mutations on the molecular level.

Results: PoPMuSiC-2.1 is a web server that predicts the thermodynamic stability changes caused by single site mutations in proteins, using a linear combination of statistical potentials whose coefficients depend on the solvent accessibility of the mutated residue. PoPMuSiC presents good prediction performances (correlation coefficient of 0.8 between predicted and measured stability changes, in cross validation, after exclusion of 10% outliers). It is moreover very fast, allowing the prediction of the stability changes resulting from all possible mutations in a medium size protein in less than a minute. This unique functionality is user-friendly implemented in PoPMuSiC and is particularly easy to exploit. Another new functionality of our server concerns the estimation of the optimality of each amino acid in the sequence, with respect to the stability of the structure. It may be used to detect structural weaknesses, i.e. clusters of non-optimal residues, which represent particularly interesting sites for introducing targeted mutations. This sequence optimality data is also expected to have significant implications in the prediction and the analysis of particular structural or functional protein regions. To illustrate the interest of this new functionality, we apply it to a dataset of known catalytic sites, and show that a much larger than average concentration of structural weaknesses is detected, quantifying how these sites have been optimized for function rather than stability.

Conclusion: The freely available PoPMuSiC-2.1 web server is highly useful for identifying very rapidly a list of possibly relevant mutations with the desired stability properties, on which subsequent experimental studies can be focused. It can also be used to detect sequence regions corresponding to structural weaknesses, which could be functionally important or structurally delicate regions, with obvious applications in rational protein design.

Show MeSH
Related in: MedlinePlus