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BioSuper: a web tool for the superimposition of biomolecules and assemblies with rotational symmetry.

Rueda M, Orozco M, Totrov M, Abagyan R - BMC Struct. Biol. (2013)

Bottom Line: Despite the myriad of superimposition tools in the literature, we could not find any able to account for rotational symmetry and display the graphical results in the web browser.To the best of our knowledge, BioSuper is the first tool of its kind that provides immediate interactive visualization of the graphical results in the browser, biomolecule generator capabilities, different levels of atom selection, sequence-dependent and structure-based superimposition types, and is the only web tool that takes into account the equivalence of atoms in side chains displaying symmetry ambiguity.BioSuper uses ICM program functionality as a core for the superimpositions and displays the results as text, HTML tables and 3D interactive molecular objects that can be visualized in the browser or in Android and iOS platforms with a free plugin.

View Article: PubMed Central - HTML - PubMed

Affiliation: Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. rabagyan@ucsd.edu.

ABSTRACT

Background: Most of the proteins in the Protein Data Bank (PDB) are oligomeric complexes consisting of two or more subunits that associate by rotational or helical symmetries. Despite the myriad of superimposition tools in the literature, we could not find any able to account for rotational symmetry and display the graphical results in the web browser.

Results: BioSuper is a free web server that superimposes and calculates the root mean square deviation (RMSD) of protein complexes displaying rotational symmetry. To the best of our knowledge, BioSuper is the first tool of its kind that provides immediate interactive visualization of the graphical results in the browser, biomolecule generator capabilities, different levels of atom selection, sequence-dependent and structure-based superimposition types, and is the only web tool that takes into account the equivalence of atoms in side chains displaying symmetry ambiguity. BioSuper uses ICM program functionality as a core for the superimpositions and displays the results as text, HTML tables and 3D interactive molecular objects that can be visualized in the browser or in Android and iOS platforms with a free plugin.

Conclusions: BioSuper is a fast and functional tool that allows for pairwise superimposition of proteins and assemblies displaying rotational symmetry. The web server was created after our own frustration when attempting to superimpose flexible oligomers. We strongly believe that its user-friendly and functional design will be of great interest for structural and computational biologists who need to superimpose oligomeric proteins (or any protein). BioSuper web server is freely available to all users at http://ablab.ucsd.edu/BioSuper.

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Schematic representation of the two major issues found when attempting to superimpose protein complexes displaying rotational symmetry: a) the order of the protomers differs in both complexes; b) flexible protomers fluctuate between conformational states.
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Figure 1: Schematic representation of the two major issues found when attempting to superimpose protein complexes displaying rotational symmetry: a) the order of the protomers differs in both complexes; b) flexible protomers fluctuate between conformational states.

Mentions: The superimposition of complexes with perfect rotational symmetry is not an issue because RMSD becomes invariant to rotations. However, symmetry in biomolecules is rarely perfect and often is broken in functionally-relevant conformational changes. For instance, assemblies can adopt quasi-symmetry, in which subunits with identical sequence adopt distinct conformations (e.g., flexible proteins fluctuating between states) [24]), or pseudo-symmetry, in which different chains form almost symmetrical complexes (e.g., hemoglobin) [22,25,26]. The presence of “imperfect” symmetry (very common in biomolecular systems) generates a hurdle in the superimposition of structures (see Figure 1) by currently available software [14,18,27-31].


BioSuper: a web tool for the superimposition of biomolecules and assemblies with rotational symmetry.

Rueda M, Orozco M, Totrov M, Abagyan R - BMC Struct. Biol. (2013)

Schematic representation of the two major issues found when attempting to superimpose protein complexes displaying rotational symmetry: a) the order of the protomers differs in both complexes; b) flexible protomers fluctuate between conformational states.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3924234&req=5

Figure 1: Schematic representation of the two major issues found when attempting to superimpose protein complexes displaying rotational symmetry: a) the order of the protomers differs in both complexes; b) flexible protomers fluctuate between conformational states.
Mentions: The superimposition of complexes with perfect rotational symmetry is not an issue because RMSD becomes invariant to rotations. However, symmetry in biomolecules is rarely perfect and often is broken in functionally-relevant conformational changes. For instance, assemblies can adopt quasi-symmetry, in which subunits with identical sequence adopt distinct conformations (e.g., flexible proteins fluctuating between states) [24]), or pseudo-symmetry, in which different chains form almost symmetrical complexes (e.g., hemoglobin) [22,25,26]. The presence of “imperfect” symmetry (very common in biomolecular systems) generates a hurdle in the superimposition of structures (see Figure 1) by currently available software [14,18,27-31].

Bottom Line: Despite the myriad of superimposition tools in the literature, we could not find any able to account for rotational symmetry and display the graphical results in the web browser.To the best of our knowledge, BioSuper is the first tool of its kind that provides immediate interactive visualization of the graphical results in the browser, biomolecule generator capabilities, different levels of atom selection, sequence-dependent and structure-based superimposition types, and is the only web tool that takes into account the equivalence of atoms in side chains displaying symmetry ambiguity.BioSuper uses ICM program functionality as a core for the superimpositions and displays the results as text, HTML tables and 3D interactive molecular objects that can be visualized in the browser or in Android and iOS platforms with a free plugin.

View Article: PubMed Central - HTML - PubMed

Affiliation: Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. rabagyan@ucsd.edu.

ABSTRACT

Background: Most of the proteins in the Protein Data Bank (PDB) are oligomeric complexes consisting of two or more subunits that associate by rotational or helical symmetries. Despite the myriad of superimposition tools in the literature, we could not find any able to account for rotational symmetry and display the graphical results in the web browser.

Results: BioSuper is a free web server that superimposes and calculates the root mean square deviation (RMSD) of protein complexes displaying rotational symmetry. To the best of our knowledge, BioSuper is the first tool of its kind that provides immediate interactive visualization of the graphical results in the browser, biomolecule generator capabilities, different levels of atom selection, sequence-dependent and structure-based superimposition types, and is the only web tool that takes into account the equivalence of atoms in side chains displaying symmetry ambiguity. BioSuper uses ICM program functionality as a core for the superimpositions and displays the results as text, HTML tables and 3D interactive molecular objects that can be visualized in the browser or in Android and iOS platforms with a free plugin.

Conclusions: BioSuper is a fast and functional tool that allows for pairwise superimposition of proteins and assemblies displaying rotational symmetry. The web server was created after our own frustration when attempting to superimpose flexible oligomers. We strongly believe that its user-friendly and functional design will be of great interest for structural and computational biologists who need to superimpose oligomeric proteins (or any protein). BioSuper web server is freely available to all users at http://ablab.ucsd.edu/BioSuper.

Show MeSH