Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Comparative Study
. 2014 Sep;70(Pt 9):2487-99.
doi: 10.1107/S1399004714016241. Epub 2014 Aug 29.

Conformation-independent structural comparison of macromolecules with ProSMART

Robert A Nicholls  1 , Marcus Fischer  2 , Stuart McNicholas  3 , Garib N Murshudov  1
Affiliations
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.

PubMed Disclaimer

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.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Alexandrov, N. N., Takahashi, K. & Go, N. (1992). J. Mol. Biol. 225, 5–9. - PubMed
    1. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990). J. Mol. Biol. 215, 403–410. - PubMed
    1. Aung, Z. & Tan, K. L. (2006). J. Bioinform. Comput. Biol. 4, 1197–1216. - PubMed
    1. Berman, H. et al. (2002). Acta Cryst. D58, 899–907. - PubMed
    1. Bertsekas, D. (2005). Dynamic Programming and Optimal Control, Vol 1. Nashua: Athena Scientific.

Publication types

MeSH terms

Substances