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Conformation-independent structural comparison of macromolecules with ProSMART - PubMed

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Comparative Study

Conformation-independent structural comparison of macromolecules with ProSMART

Robert A Nicholls et al. Acta Crystallogr D Biol Crystallogr. 2014 Sep.

Abstract

The identification and exploration of (dis)similarities between macromolecular structures can help to gain biological insight, for instance when visualizing or quantifying the response of a protein to ligand binding. Obtaining a residue alignment between compared structures is often a prerequisite for such comparative analysis. If the conformational change of the protein is dramatic, conventional alignment methods may struggle to provide an intuitive solution for straightforward analysis. To make such analyses more accessible, the Procrustes Structural Matching Alignment and Restraints Tool (ProSMART) has been developed, which achieves a conformation-independent structural alignment, as well as providing such additional functionalities as the generation of restraints for use in the refinement of macromolecular models. Sensible comparison of protein (or DNA/RNA) structures in the presence of conformational changes is achieved by enforcing neither chain nor domain rigidity. The visualization of results is facilitated by popular molecular-graphics software such as CCP4mg and PyMOL, providing intuitive feedback regarding structural conservation and subtle dissimilarities between close homologues that can otherwise be hard to identify. Automatically generated colour schemes corresponding to various residue-based scores are provided, which allow the assessment of the conservation of backbone and side-chain conformations relative to the local coordinate frame. Structural comparison tools such as ProSMART can help to break the complexity that accompanies the constantly growing pool of structural data into a more readily accessible form, potentially offering biological insight or influencing subsequent experiments.

Keywords: ProSMART; Procrustes; alignment; external restraints; refinement; structural comparison.

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Figures

Figure 1
Figure 1

Structural comparison of the backbone in the presence of ligand-induced conformational changes. Illustrations of results from the default ProSMART comparison of open (PDB entry

2cex

chain A) and closed (PDB entry

3b50

chain A) forms of the SiaP TRAP sialic acid-binding protein, coloured using a colour gradient according to main-chain dissimilarity scores (yellow implies similarity and red relative dissimilarity; white, not applicable). Since the two models do not superpose well, for clarity only

2cex

chain A is shown in (b)–(d). The Procrustes score (b) allows easy identification of locally distorted regions (such as hinges). The Flexible score (c) helps to identify regions that are at all similar, despite any global conformational change (note that the whole structure is coloured yellow, indicating high local similarity despite different global conformations). The Hinging score (d) is useful for identifying subtle backbone deformations (including hinges) that can otherwise be very hard to identify. These complementary depictions allow quick visual identification of exactly which regions are structurally very similar and which exhibit differences. (a) Open (

2cex

chain A, left) and closed (

3b50

chain A, right) forms of SiaP. (b) Coloured by the Procrustes score. (c) Coloured by the Flexible score. (d) Coloured by the Hinging score.

Figure 2
Figure 2

Comparison of structures sharing low sequence homology. ProSMART structural comparison of a sialic acid-binding protein (PDB entry

2cex

chain A) and a sodium α-keto acid-binding protein (PDB entry

2hzk

chain A), which share only 14% sequence identity despite exhibiting the same overall global fold. In (b) and (c) the models are coloured by the Flexible score using a colour gradient (yellow implies similarity and red relative dissimilarity; white, not applicable). This representation allows quick and easy visual identification of exactly which regions are structurally similar and which exhibit differences; note that this level of insight could not be achieved by simple superposition (a). (a)

2cex

chain A and

2hzk

chain A superposed. (b)

2cex

chain A coloured by the Flexible score. (c)

2hzk

chain A coloured by the Flexible score.

Figure 3
Figure 3

Conformation-independent structural comparison in the presence of domain swaps. Models of barnase with different biological assemblies are compared; the model

1yvs

chain A corresponds to the trimeric domain-swapped form, unlike the sequence-identical model

2za4

chain A. To help illustrate the nature of the conformational change, in (a) the N-terminus is labelled N and the N-terminal helix is labelled H1. The models are coloured by (a) the Flexible score and (b) the side-chain r.m.s.d. score using a colour gradient (yellow implies similarity and red relative dissimilarity; white, not applicable). This demonstrates the ability to analyse structural conservation despite the presence of large conformational changes such as domain swaps, noting that this approach does not require spatial relationships to be conserved nor domains to be intact; only the conservation of local structure is of relevance. (a) Flexible score:

1yvs

chain A (top) and

2za4

chain A (bottom). (b) Side-chain r.m.s.d. score:

1yvs

chain A (top) and

2za4

chain A (bottom).

Figure 4
Figure 4

Application of comparative structural analysis in crystallographic model building and refinement. Comparative analysis of the backbone (left) and side chains (right) of (a) the 3.5 Å resolution model

1ryx

of ovotransferrin before and after re-refinement with external restraints from the sequence-identical 2.15 Å resolution model

2d3i

and (b)

1ryx

after re-refinement using external restraints and the reference model

2d3i

. For clarity, the reference model

2d3i

is not shown. The models are coloured according to the Flexible backbone score (left) and the side-chain r.m.s.d. score (right) using a colour gradient (yellow implies similarity and red relative dissimilarity; white, not applicable). (a) Comparison of

1ryx

before and after re-refinement (superposed). (b) Comparison of

1ryx

after re-refinement and

2d3i

(not shown).

Figure 5
Figure 5

Processing ensembles from other methods, such as from NMR spectroscopy. Multi-model comparative analysis of a solution NMR structure of hen egg-white lysozyme (PDB entry

1e8l

). All models are coloured using the same scheme, using a colour gradient (yellow implies similarity and red relative dissimilarity; white, not applicable). Residues in the ensemble are coloured according to the maximum (worst) Flexible score over all models in the ensemble, using the first model as the target.

Figure 6
Figure 6

Structural comparison of nucleic acids. Local comparative analysis of the P-site and E-site fMet-tRNA models from a 70S ribosome (PDB entry

3d5a

chains Y and Z). The models are superposed and coloured according to the Flexible backbone score using a colour gradient (yellow implies similarity and red relative dissimilarity). The C1′, C4′, O3′ and O5′ atoms were used for the comparison in rough analogy with the four backbone atoms in proteins (any selection of atoms common to all nucleotides might have been selected). This allows straightforward visual identification of regions with low structural conservation (centre and left), whereas other regions (right) might visually appear dissimilar when superposed but are actually more conserved locally. This highlights how ProSMART can provide complementary information that cannot be readily achieved simply by looking at superposed structures or considering r.m.s.d. values.

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