Abstract
BackgroundTransmembrane helices (TMHs) frequently occur amongst protein architectures as means for proteins to attach to or embed into biological membranes. Physical constraints such as the membrane’s hydrophobicity and electrostatic potential apply uniform requirements to TMHs and their flanking regions; consequently, they are mirrored in their sequence patterns (in addition to TMHs being a span of generally hydrophobic residues) on top of variations enforced by the specific protein’s biological functions.ResultsWith statistics derived from a large body of protein sequences, we demonstrate that, in addition to the positive charge preference at the cytoplasmic inside (positive-inside rule), negatively charged residues preferentially occur or are even enriched at the non-cytoplasmic flank or, at least, they are suppressed at the cytoplasmic flank (negative-not-inside/negative-outside (NNI/NO) rule). As negative residues are generally rare within or near TMHs, the statistical significance is sensitive with regard to details of TMH alignment and residue frequency normalisation and also to dataset size; therefore, this trend was obscured in previous work. We observe variations amongst taxa as well as for organelles along the secretory pathway. The effect is most pronounced for TMHs from single-pass transmembrane (bitopic) proteins compared to those with multiple TMHs (polytopic proteins) and especially for the class of simple TMHs that evolved for the sole role as membrane anchors.ConclusionsThe charged-residue flank bias is only one of the TMH sequence features with a role in the anchorage mechanisms, others apparently being the leucine intra-helix propensity skew towards the cytoplasmic side, tryptophan flanking as well as the cysteine and tyrosine inside preference. These observations will stimulate new prediction methods for TMHs and protein topology from a sequence as well as new engineering designs for artificial membrane proteins.
Highlights
Transmembrane helices (TMHs) frequently occur amongst protein architectures as means for proteins to attach to or embed into biological membranes
Acidic residues within and nearby TMH segments are rare In order to reliably compare the amino acid sequence properties of TMHs, we assembled datasets of TMH proteins from what are likely to be the best in terms of quality and comprehensiveness of annotation in eukaryotic and prokaryotic representative genomes, as well as composite datasets to represent larger taxonomic groups and to consider subcellular locations
The UniProt datasets used included only manually curated records; it is still necessary to check for systematic bias due to the prediction methods used by UniProt for TMH annotation in the majority of cases without direct experimental evidence
Summary
Transmembrane helices (TMHs) frequently occur amongst protein architectures as means for proteins to attach to or embed into biological membranes. The classic concept of a transmembrane helical region was a rather simple story: Typical transmembrane proteins were thought to be anchored in the membrane by membrane-spanning bundles of nonpolar α-helices of roughly 20 residues in length, with a consistent orientation of being perpendicular to the membrane surface This is broadly true, hundreds of high-quality membrane structures have elucidated that membrane-embedded helices can adopt a plethora of lengths and orientations within the membrane. From the biological function point of view, many TMHs have multiple roles besides being just hydrophobic anchors; for example, certain TMHs have been identified as regulators of protein quality control and trafficking mechanisms [4] As these additional biological functions are mirrored in the TMHs’ sequence patterns, TMHs can be classified as simple (just hydrophobic anchors) and complex sequence segments [5,6,7]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
