Structure alignment of membrane proteins: Accuracy of available tools and a consensus strategy

Abstract

Protein structure alignment methods are used for the detection of evolutionary and functionally related positions in proteins. A wide array of different methods are available, but the choice of the best method is often not apparent to the user. Several studies have assessed the alignment accuracy and consistency of structure alignment methods, but none of these explicitly considered membrane proteins, which are important targets for drug development and have distinct structural features. Here, we compared 13 widely-used pairwise structural alignment methods on a test set of homologous membrane protein structures (called HOMEP3). Each pair of structures was aligned and the corresponding sequence alignment was used to construct homology models. The model accuracy compared to the known structures was assessed using scoring functions not incorporated in the tested structural alignment methods. The analysis shows that fragment-based approaches such as FR-TM-align are the most useful for aligning structures of membrane proteins. Moreover, fragment-based approaches are more suitable for comparison of protein structures that have undergone large conformational changes. Nevertheless, no method was clearly superior to all other methods. Additionally, all methods lack a measure to rate the reliability of a position within a structure alignment. To solve both of these problems, we propose a consensus-type approach, combining alignments from four different methods, namely FR-TM-align, DaliLite, MATT and FATCAT. Agreement between the methods is used to assign confidence values to each position of the alignment. Overall, we conclude that there remains scope for the improvement of structural alignment methods for membrane proteins.

Global alignment and assessment of TRP channel transmembrane domain structures to explore functional mechanisms

“…The TM regions of these channels were aligned using Fr-TM-Align ( Pandit and Skolnick, 2008 ; Zhang and Skolnick, 2005 ), which aligns structures pairwise by optimizing for the global template-modeling-score (TM-score), a measure of backbone fold similarity that is independent of protein length (see Materials and methods). As a fragment-based alignment method, Fr-TM-Align is effective even in cases with large conformational differences ( Stamm and Forrest, 2015 ). Alignments of the TM regions of the TRP family structures generally have TM-scores of >0.6, indicating that they share similar global folds ( Figure 2 ; Xu and Zhang, 2010 ).…”

“…To obtain a structure-based, sequence-agnostic sequence alignment, structures were first aligned pairwise using Fr-TM-Align version 1.0, a fragment-based alignment approach that aligns residues based on patterns of secondary structure ( Pandit and Skolnick, 2008 ). Fr-TM-Align has been tested on membrane proteins and is robust even to large conformational changes ( Stamm and Forrest, 2015 ). As with other methods, the aligned structures are iteratively aligned and scored for alignment match before the alignment with the best pairwise TM-score is chosen.…”

Family resemblances: A common fold for some dimeric ion-coupled secondary transporters

“…4R1I ; Su et al, 2015 ), and YdaH (PDB accession no. 4R0C ; Bolla et al, 2015 ) was performed using the fragment-based structure alignment program Fr-TM-align ( Pandit and Skolnick, 2008 ), which is one of the most accurate methods for structurally aligning membrane proteins ( Stamm and Forrest, 2015 ). Several alignments were performed; in each case, we compared all combinations of the three structures, namely MtrF aligned with VcINDY, YdaH aligned with VcINDY, and MtrF aligned with YdaH.…”

Evaluation of Transmembrane Protein Structural Models Using HPMScore

“…The membrane protein dataset was derived from the HOMEP dataset [57]. This set of proteins is composed of 76 membrane proteins, separated in 23 categories, depending on their biological function (https://zenodo.org/record/2646540#.Y7b99C3pNTY, accessed on 1 March 2023).…”