Structure-based statistical analysis of transmembrane helices

Abstract

Recent advances in high-resolution structure determination of membrane proteins enable now the analysis of the main features of amino acids in transmembrane (TM) segments in comparison with amino acids in watersoluble helices. In this work, we introduced a large-scale analysis of amino acid propensities using a data set of 170 structures of integral membrane proteins obtained from MPTopo database and 930 structures of water-soluble helical proteins obtained from the Protein Data Bank. Large hydrophobic residues (Leu, Val, Ile and Phe) plus Gly had a clear preference for TM helices, while polar residues (Glu, Lys, Asp, Arg and Gln) were less frequent in this type of helices. The distribution of residues along the TM helices was also examined. As expected, hydrophobic and slightly polar amino acids are commonly found in the hydrophobic core of the membrane, while aromatic (Trp and Tyr) and Pro together with hydrophilic (Asn, His, and Gln) residues are frequent in the interface regions. Charged residues also have statistically preferred locations avoiding the hydrophobic core of the membrane, but while acidic residues are frequently found at both the cytoplasmic and extracytoplasmic interfaces, basic residues cluster at the cytoplasmic interface.These results strongly support the experimentally demonstrated biased distribution of positively charged residues (that is, the so-called the positiveinside rule) with structural data.

Intracellular Trafficking of the KV1.3 Potassium Channel Is Regulated by the Prodomain of a Matrix Metalloprotease

“…Helix ␣1 is slightly longer than expected for typical trans-membrane proteins found within the ER or Golgi (20 residues) (36). However, the N-terminal region of helix ␣1 (residues Glu-17-Trp-20, comprising the N-terminal capping motif) contains residues that are known to prefer the polar/nonpolar interface of lipid bilayers (32). These residues are partially flexible and solvent-exposed, suggesting that the N-terminal portion of ␣1 may protrude from the surface of the membrane.…”

“…The data indicate that a disruption in the TMD ␣1 helix several residues upstream of Pro-32 around residues Ala-27-Leu-28 introduces some flexibility into the helix in this region. Proline residues are known to be helixdestabilizing in water-soluble proteins but are surprisingly common in trans-membrane proteins (32,37). They often introduce a region of flexibility and a kink in trans-membrane helices because of steric conflicts with the preceding residue and loss of a backbone hydrogen bond (38).…”

“…) contains residues that are often found at the membrane interface of TMDs (32). The prediction of secondary structure is variable in the region just C-terminal to the TMD, although there is a propensity for helical content in this region.…”

Hydrophobic Blocks Facilitate Lipid Compatibility and Translocon Recognition of Transmembrane Protein Sequences

“…We therefore designed 19-residue TM sequences that contain an equal number of polar and hydrophobic residues, nine Ser and nine Leu residues, each with a centrally positioned Trp residue as a fluorescent probe. As the most commonly occurring amino acid in native TM helices, Leu was a natural choice, 22 while Ser is the most commonly occurring polar residue (similar to Thr) and can participate in both side chain–side chain and side chain–backbone H-bonds. 22 In addition, synthesis requirements of β-branch-rich peptides rendered Thr as a less feasible choice.…”

Charge Pair Interactions in Transmembrane Helices and Turn Propensity of the Connecting Sequence Promote Helical Hairpin Insertion

“…While many studies addressing the formation of helical hairpins in membranes have been carried out on model hydrophobic TM segments, [6][7][8][9] naturally occurring helical hairpins are not always highly hydrophobic, 10 and the role of helix-helix interactions and turn propensities of the residues interconnecting the two helices in their folding and stability is poorly understood. We previously showed that poliovirus (PV) 2B, which is a small protein involved in PV virulence, is a double-spanning integral membrane protein, in which the two TM segments are interconnected by a short turn forming a putative helical hairpin.…”