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

Abstract

BackgroundMost 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.ResultsBioSuper 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.ConclusionsBioSuper 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.

Conformational plasticity of RepB, the replication initiator protein of promiscuous streptococcal plasmid pMV158

“…In all three simulations, the OBDs moved considerably during the trajectories as reflected by their final RMSD with respect to their starting X-ray structures (C2 = 8.41 Å, C3 = 8.51 Å, C6B = 9.56 Å) (see Supplementary Fig. S3 ; note that we included rotational symmetry in the RMSD calculation 19 ). These values are clearly higher than those expected for a globular protein of this size 20 21 , suggesting high flexibility for these systems.…”

“…All trajectories were generated using NAMD2 program 54 at the MareNostrum supercomputer at the Barcelona Supercomputing Centre. Analysis of trajectories was performed using ptraj 55 , VMD 56 , ICM 57 , BioSuper web server 19 , as well as in-house software developed specifically for this project.…”

Molecular docking and dynamic simulation of conserved B cell epitope of SARS-CoV-2 glycoprotein Indonesian isolates: an immunoinformatic approach

“…The resulting spike glycoprotein SARS-CoV-2 models of Indonesian isolates in this study had similarity values of 90-100% with the references in the database through the 3D alignment process ( Figure 1 ). 32 …”

“…The resulting spike glycoprotein SARS-CoV-2 models of Indonesian isolates in this study had similarity values of 90-100% with the references in the database through the 3D alignment process (Figure 1). 32 Mapping of conserved B cell and T CD4+ epitope Indonesian isolate MZ026853.1 was chosen for SARS-COV-2 seed vaccine candidate as it is the dominant variant found in Indonesia. 33 Prediction of B cell epitope recognition was carried out on the template of Indonesian isolate MZ026853.1 using IEDB Analysis Tools with the BepiPred method.…”

Internal symmetry in protein structures: prevalence, functional relevance and evolution

“…Comparative analysis of evolutionarily related structures with internal symmetry is a challenge, especially if there has been extensive divergence between them, as it is non-trivial to determine equivalent domains or units. However, a recently developed computational method aims to overcome this by providing an optimal alignment between structures in question [53] analogous to methods such as CE, MUSTANG and VAST for protein structural alignment [54][55][56]. Further internal symmetric axes in protein tertiary structures could be exploited to get an optimal alignment of symmetric units as in the case of EF-hand domains such as CTER and S100 [57,58].…”