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SAMPLEX: automatic mapping of perturbed and unperturbed regions of proteins and complexes.

Krzeminski M, Loth K, Boelens R, Bonvin AM - BMC Bioinformatics (2010)

Bottom Line: Its performance is demonstrated for different applications including the prediction of disordered regions in partially unfolded proteins and of interacting regions in protein complexes.The proposed approach is suitable for partially unfolded states of proteins, local perturbations due to small ligands and protein-protein interfaces.The method is not restricted to NMR data, but is generic and can be applied to a wide variety of information.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, 3584 CH, Utrecht, The Netherlands.

ABSTRACT

Background: The activity of proteins within the cell is characterized by their motions, flexibility, interactions or even the particularly intriguing case of partially unfolded states. In the last two cases, a part of the protein is affected either by binding or unfolding and the detection of the respective perturbed and unperturbed region(s) is a fundamental part of the structural characterization of these states. This can be achieved by comparing experimental data of the same protein in two different states (bound/unbound, folded/unfolded). For instance, measurements of chemical shift perturbations (CSPs) from NMR 1H-15N HSQC experiments gives an excellent opportunity to discriminate both moieties.

Results: We describe an innovative, automatic and unbiased method to distinguish perturbed and unperturbed regions in a protein existing in two distinct states (folded/partially unfolded, bound/unbound). The SAMPLEX program takes as input a set of data and the corresponding three-dimensional structure and returns the confidence for each residue to be in a perturbed or unperturbed state. Its performance is demonstrated for different applications including the prediction of disordered regions in partially unfolded proteins and of interacting regions in protein complexes.

Conclusions: The proposed approach is suitable for partially unfolded states of proteins, local perturbations due to small ligands and protein-protein interfaces. The method is not restricted to NMR data, but is generic and can be applied to a wide variety of information.

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Chemical shift perturbations and derived confidences as function of the residue sequence for CI2 (unbound and bound to BPN'). Top: Raw CSP data; Middle: Starting confidences; Bottom: Confidences after homogenization. The triangles filled in black show residues involved in the interaction between CI-2 and BPN', the ones filled in grey show the selection made by SAMPLEX and the open ones, residues in an intermediate state.
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Figure 1: Chemical shift perturbations and derived confidences as function of the residue sequence for CI2 (unbound and bound to BPN'). Top: Raw CSP data; Middle: Starting confidences; Bottom: Confidences after homogenization. The triangles filled in black show residues involved in the interaction between CI-2 and BPN', the ones filled in grey show the selection made by SAMPLEX and the open ones, residues in an intermediate state.

Mentions: Subtilisin BPN' is a serine protease [7] which can be inhibited by the chymotrypsin inhibitor 2, an 83 amino acid protein with a disordered N-terminal tail [8]. Figure 1 shows the evolution of the residue selection for the CI2 subunit of the Subtilisin/CI2 complex as a function of the raw CSP data (C. van Heijnoort and L. Koharudin, personal communication), starting confidences and the resulting homogenized confidences. In this case we took for the selection process the structures from the complex (PDB entry 1LW6) [8].


SAMPLEX: automatic mapping of perturbed and unperturbed regions of proteins and complexes.

Krzeminski M, Loth K, Boelens R, Bonvin AM - BMC Bioinformatics (2010)

Chemical shift perturbations and derived confidences as function of the residue sequence for CI2 (unbound and bound to BPN'). Top: Raw CSP data; Middle: Starting confidences; Bottom: Confidences after homogenization. The triangles filled in black show residues involved in the interaction between CI-2 and BPN', the ones filled in grey show the selection made by SAMPLEX and the open ones, residues in an intermediate state.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2823710&req=5

Figure 1: Chemical shift perturbations and derived confidences as function of the residue sequence for CI2 (unbound and bound to BPN'). Top: Raw CSP data; Middle: Starting confidences; Bottom: Confidences after homogenization. The triangles filled in black show residues involved in the interaction between CI-2 and BPN', the ones filled in grey show the selection made by SAMPLEX and the open ones, residues in an intermediate state.
Mentions: Subtilisin BPN' is a serine protease [7] which can be inhibited by the chymotrypsin inhibitor 2, an 83 amino acid protein with a disordered N-terminal tail [8]. Figure 1 shows the evolution of the residue selection for the CI2 subunit of the Subtilisin/CI2 complex as a function of the raw CSP data (C. van Heijnoort and L. Koharudin, personal communication), starting confidences and the resulting homogenized confidences. In this case we took for the selection process the structures from the complex (PDB entry 1LW6) [8].

Bottom Line: Its performance is demonstrated for different applications including the prediction of disordered regions in partially unfolded proteins and of interacting regions in protein complexes.The proposed approach is suitable for partially unfolded states of proteins, local perturbations due to small ligands and protein-protein interfaces.The method is not restricted to NMR data, but is generic and can be applied to a wide variety of information.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, 3584 CH, Utrecht, The Netherlands.

ABSTRACT

Background: The activity of proteins within the cell is characterized by their motions, flexibility, interactions or even the particularly intriguing case of partially unfolded states. In the last two cases, a part of the protein is affected either by binding or unfolding and the detection of the respective perturbed and unperturbed region(s) is a fundamental part of the structural characterization of these states. This can be achieved by comparing experimental data of the same protein in two different states (bound/unbound, folded/unfolded). For instance, measurements of chemical shift perturbations (CSPs) from NMR 1H-15N HSQC experiments gives an excellent opportunity to discriminate both moieties.

Results: We describe an innovative, automatic and unbiased method to distinguish perturbed and unperturbed regions in a protein existing in two distinct states (folded/partially unfolded, bound/unbound). The SAMPLEX program takes as input a set of data and the corresponding three-dimensional structure and returns the confidence for each residue to be in a perturbed or unperturbed state. Its performance is demonstrated for different applications including the prediction of disordered regions in partially unfolded proteins and of interacting regions in protein complexes.

Conclusions: The proposed approach is suitable for partially unfolded states of proteins, local perturbations due to small ligands and protein-protein interfaces. The method is not restricted to NMR data, but is generic and can be applied to a wide variety of information.

Show MeSH