ArticlePloS one2013
Alignment of helical membrane protein sequences using AlignMe.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed, 73 citations in OpenAlex.
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- Refining pairwise sequence alignments of membrane proteins by the incorporation of anchors.PloS one · 2021Article
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- Unraveling the structural elements of pH sensitivity and substrate binding in the human zinc transporter SLC39A2 (ZIP2).The Journal of biological chemistry · 2019Article
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- Efflux Pumps Represent Possible Evolutionary Convergence onto the β-Barrel Fold.Structure (London, England : 1993) · 2018Article
- Structural relationship between the putative hair cell mechanotransduction channel TMC1 and TMEM16 proteins.eLife · 2018Article
- A Comparative Study of Modern Homology Modeling Algorithms for Rhodopsin Structure Prediction.ACS omega · 2018Article
- Homology modeling and docking studies of a Δ9-fatty acid desaturase from a Cold-tolerantPeerJ · 2018Article
- Refined topology model of the STT3/Stt3 protein subunit of the oligosaccharyltransferase complex.The Journal of biological chemistry · 2017Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Few sequence alignment methods have been designed specifically for integral membrane proteins, even though these important proteins have distinct evolutionary and structural properties that might affect their alignments. Existing approaches typically consider membrane-related information either by using membrane-specific substitution matrices or by assigning distinct penalties for gap creation in transmembrane and non-transmembrane regions. Here, we ask whether favoring matching of predicted transmembrane segments within a standard dynamic programming algorithm can improve the accuracy of pairwise membrane protein sequence alignments. We tested various strategies using a specifically designed program called AlignMe. An updated set of homologous membrane protein structures, called HOMEP2, was used as a reference for optimizing the gap penalties. The best of the membrane-protein optimized approaches were then tested on an independent reference set of membrane protein sequence alignments from the BAliBASE collection. When secondary structure (S) matching was combined with evolutionary information (using a position-specific substitution matrix (P)), in an approach we called AlignMePS, the resultant pairwise alignments were typically among the most accurate over a broad range of sequence similarities when compared to available methods. Matching transmembrane predictions (T), in addition to evolutionary information, and secondary-structure predictions, in an approach called AlignMePST, generally reduces the accuracy of the alignments of closely-related proteins in the BAliBASE set relative to AlignMePS, but may be useful in cases of extremely distantly related proteins for which sequence information is less informative. The open source AlignMe code is available at https://sourceforge.net/projects/alignme/, and at http://www.forrestlab.org, along with an online server and the HOMEP2 data set.
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