Abstract
BackgroundProtein 3D structure is the support of its function. Comparison of 3D protein structures provides insight on their evolution and their functional specificities and can be done efficiently via protein structure superimposition analysis. Multiple approaches have been developed to perform such task and are often based on structural superimposition deduced from sequence alignment, which does not take into account structural features. Our methodology is based on the use of a Structural Alphabet (SA), i.e. a library of 3D local protein prototypes able to approximate protein backbone. The interest of a SA is to translate into 1D sequences into the 3D structures.ResultsWe used Protein blocks (PB), a widely used SA consisting of 16 prototypes, each representing a conformation of the pentapeptide skeleton defined in terms of dihedral angles. Proteins are described using PB from which we have previously developed a sequence alignment procedure based on dynamic programming with a dedicated PB Substitution Matrix. We improved the procedure with a specific two-step search: (i) very similar regions are selected using very high weights and aligned, and (ii) the alignment is completed (if possible) with less stringent parameters. Our approach, iPBA, has shown to perform better than other available tools in benchmark tests. To facilitate the usage of iPBA, we designed and implemented iPBAvizu, a plugin for PyMOL that allows users to run iPBA in an easy way and analyse protein superimpositions.ConclusionsiPBAvizu is an implementation of iPBA within the well-known and widely used PyMOL software. iPBAvizu enables to generate iPBA alignments, create and interactively explore structural superimposition, and assess the quality of the protein alignments.
Highlights
Protein 3D structure is the support of its function
Protein backbone conformation can be characterized by a set of local structure prototypes, namely Structural Alphabets (SAs), which enables the transformation of 3D information into a 1D sequence of alphabets [4]
We present here a plugin, iPBAvizu, which integrates the efficient protein structure alignment approach iPBA with the very popular molecular graphics viewer PyMOL (The PyMOL Molecular Graphics System, Version 1.7, Schrödinger, LLC) from which several plugins like PyKnoT [16] or PyETV [17] have been integrated in. iPBAvizu enables interactive visualization and analysis of protein structure superposition and the resulting sequence alignment
Summary
Protein 3D structure is the support of its function. Comparison of 3D protein structures provides insight on their evolution and their functional specificities and can be done efficiently via protein structure superimposition analysis. The detection of structural analogy between protein folds requires development of methods and tools to compare and classify them. This is extremely helpful for studying evolutionary relationships between proteins especially in the low sequence identity ranges [1]. An optimal superposition is far from being a trivial task Popular methods such as DALI [2] and CE [3], use a reduced representation of backbone conformation in terms of distance matrices. A SA consisting of 16 pentapeptide conformations, called Protein Blocks (PBs), was developed in our group [5] Based on this library, a protein superimposition approach was developed.
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