Sequence and conformational preferences at termini of α‐helices in membrane proteins: Role of the helix environment

Abstract

α-Helices are amongst the most common secondary structural elements seen in membrane proteins and are packed in the form of helix bundles. These α-helices encounter varying external environments (hydrophobic, hydrophilic) that may influence the sequence preferences at their N and C-termini. The role of the external environment in stabilization of the helix termini in membrane proteins is still unknown. Here we analyze α-helices in a high-resolution dataset of integral α-helical membrane proteins and establish that their sequence and conformational preferences differ from those in globular proteins. We specifically examine these preferences at the N and C-termini in helices initiating/terminating inside the membrane core as well as in linkers connecting these transmembrane helices. We find that the sequence preferences and structural motifs at capping (Ncap and Ccap) and near-helical (N' and C') positions are influenced by a combination of features including the membrane environment and the innate helix initiation and termination property of residues forming structural motifs. We also find that a large number of helix termini which do not form any particular capping motif are stabilized by formation of hydrogen bonds and hydrophobic interactions contributed from the neighboring helices in the membrane protein. We further validate the sequence preferences obtained from our analysis with data from an ultradeep sequencing study that identifies evolutionarily conserved amino acids in the rat neurotensin receptor. The results from our analysis provide insights for the secondary structure prediction, modeling and design of membrane proteins.

A model of the interactions between the FtsQLB and the FtsWI peptidoglycan synthase complex in bacterial cell division

“…In the structural context of the model, P 39 appears to have the dual purpose of inducing a helical break while also stabilizing the TM helix as a favorable N-capping residue, as observed, for example, in certain integrin molecules (51). We tested a P39N substitution, which lacks the helical break function but can act as an N-capping residue (52), as well as a P39A substitution, which would lead to the loss of both functions. Both mutations resulted in very mild cell division defects (11% elongated cells; supplementary Fig.…”

N–H···N Hydrogen Bonds Involving Histidine Imidazole Nitrogen Atoms: A New Structural Role for Histidine Residues in Proteins

“…This preference is pronounced if the donor N–H group is contributed by residues that are two positions apart from histidine ( i + 2) with a proline residue occupying the middle position ( i + 1). Several N-terminal capping motifs have been identified, and their possible role in biological function has been investigated. ,− In a recent study of membrane protein structures, Shelar and Bansal have reported an example of a histidine residue participating in helix-capping interaction in a transmembrane helix of a membrane protein. The current study has clearly shown frequent instances of histidine residues at the N-cap position participating in the N–H···N type of hydrogen bond with the main-chain N–H group as the HB donor at position N2 in helices.…”

The Topology of the l -Arginine Exporter ArgO Conforms to an N in -C out Configuration in Escherichia coli: Requirement for the Cytoplasmic N-Terminal Domain, Functional Helical Interactions, and an Aspartate Pair for ArgO Function

“…The average length of TM segments has been thought to vary from 20 to 40 residues (52). Furthermore, a recent analysis has catalogued the lengths of ␣-helical TM segments in a high-resolution data set to note that the median TM segment length can vary from 16 to 30 amino acids (53). The assigned lengths of the TM segments in ArgO are compatible overall with the aforementioned findings on TM lengths in integral membrane proteins It is worth noting, in this context, that while PhoA reporter fusion analysis of C. glutamicum LysE suggested a five-TM ␣-helical spanner topology (13), members of this family are believed to adopt a six-TM topology (14).…”