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An automatic method for assessing structural importance of amino acid positions.

Sadowski MI, Jones DT - BMC Struct. Biol. (2009)

Bottom Line: Some buried residues were found to be less informative than expected, particularly residues involved in active sites and the binding of small molecules.The correlation-based method generates predictions of structural importance for superfamily positions which agree well with previous results of manual analyses, and may be of use in automated residue annotation piplines.A PERL script which implements the method is provided.

View Article: PubMed Central - HTML - PubMed

Affiliation: Computer Science Department, University College London, Gower St, London, WC1E 6BT, UK. msadows@nimr.mrc.ac.uk

ABSTRACT

Background: A great deal is known about the qualitative aspects of the sequence-structure relationship, for example that buried residues are usually more conserved between structurally similar homologues, but no attempts have been made to quantitate the relationship between evolutionary conservation at a sequence position and change to global tertiary structure. In this paper we demonstrate that the Spearman correlation between sequence and structural change is suitable for this purpose.

Results: Buried residues, bends, cysteines, prolines and leucines were significantly more likely to occupy positions highly correlated with structural change than expected by chance. Some buried residues were found to be less informative than expected, particularly residues involved in active sites and the binding of small molecules.

Conclusion: The correlation-based method generates predictions of structural importance for superfamily positions which agree well with previous results of manual analyses, and may be of use in automated residue annotation piplines. A PERL script which implements the method is provided.

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Related in: MedlinePlus

Significantly selected positions in chicken haemoglobin. The structure of chicken haemoglobin (PDB:1hbr) chain A is shown; residue backbones are coloured blue to orange from N to C terminal. Residues most strongly correlated with structural change are depicted in red. Figure created with PyMol (Delano Scientific, San Carlos, CA, USA).
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Figure 2: Significantly selected positions in chicken haemoglobin. The structure of chicken haemoglobin (PDB:1hbr) chain A is shown; residue backbones are coloured blue to orange from N to C terminal. Residues most strongly correlated with structural change are depicted in red. Figure created with PyMol (Delano Scientific, San Carlos, CA, USA).

Mentions: Figure 2 depicts the top 10 positions selected in the globin family mapped on the structure of chicken haemoglobin [PDB:1hbr chain A; [15]].


An automatic method for assessing structural importance of amino acid positions.

Sadowski MI, Jones DT - BMC Struct. Biol. (2009)

Significantly selected positions in chicken haemoglobin. The structure of chicken haemoglobin (PDB:1hbr) chain A is shown; residue backbones are coloured blue to orange from N to C terminal. Residues most strongly correlated with structural change are depicted in red. Figure created with PyMol (Delano Scientific, San Carlos, CA, USA).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2667441&req=5

Figure 2: Significantly selected positions in chicken haemoglobin. The structure of chicken haemoglobin (PDB:1hbr) chain A is shown; residue backbones are coloured blue to orange from N to C terminal. Residues most strongly correlated with structural change are depicted in red. Figure created with PyMol (Delano Scientific, San Carlos, CA, USA).
Mentions: Figure 2 depicts the top 10 positions selected in the globin family mapped on the structure of chicken haemoglobin [PDB:1hbr chain A; [15]].

Bottom Line: Some buried residues were found to be less informative than expected, particularly residues involved in active sites and the binding of small molecules.The correlation-based method generates predictions of structural importance for superfamily positions which agree well with previous results of manual analyses, and may be of use in automated residue annotation piplines.A PERL script which implements the method is provided.

View Article: PubMed Central - HTML - PubMed

Affiliation: Computer Science Department, University College London, Gower St, London, WC1E 6BT, UK. msadows@nimr.mrc.ac.uk

ABSTRACT

Background: A great deal is known about the qualitative aspects of the sequence-structure relationship, for example that buried residues are usually more conserved between structurally similar homologues, but no attempts have been made to quantitate the relationship between evolutionary conservation at a sequence position and change to global tertiary structure. In this paper we demonstrate that the Spearman correlation between sequence and structural change is suitable for this purpose.

Results: Buried residues, bends, cysteines, prolines and leucines were significantly more likely to occupy positions highly correlated with structural change than expected by chance. Some buried residues were found to be less informative than expected, particularly residues involved in active sites and the binding of small molecules.

Conclusion: The correlation-based method generates predictions of structural importance for superfamily positions which agree well with previous results of manual analyses, and may be of use in automated residue annotation piplines. A PERL script which implements the method is provided.

Show MeSH
Related in: MedlinePlus