Water and side‐chain embedded π‐turns

DasGupta, Bhaskar; Dey, Sucharita; Chakrabarti, Pinak

doi:10.1002/bip.22401

Cited by 6 publications

(6 citation statements)

References 42 publications

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“…Numerous review articles on this fundamental 3D-structural motif, which consists of four amino acid residues, two of which are entirely incorporated into the pseudo-ring form, were subsequently published. 18,19 2. They are the a-turn (1 ' 5 intramolecularly H-bonded or C 13 form), 4,12-15 d-turn (2 -3 intramolecularly H-bonded or C 8 form), 4,16,17 e-turn (2 -4 intramolecularly H-bonded or C 11 form), 4 and p-turn (1 ' 6 intramolecularly H-bonded or C 16 form).…”

Section: Introductionmentioning

confidence: 99%

Single and multiple peptide γ-turns: literature survey and recent progress

et al. 2015

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In contrast to the extensively investigated b-turn conformation in peptides and proteins, single and multiple g-turns have been much less commonly studied. Single and non-contiguous multiple g-turns have been relatively often authenticated in small cyclic peptides, but these important peptide mainchain reversal motifs have not been examined carefully either in linear peptides or in globular proteins.This Perspective article summarizes literature data on this aspect of peptide stereochemistry, expanding the discussion also to the rarely found, contiguous multiple g-turns which generate incipient or fullydeveloped 2.2 7 -(g-) helices. Unpublished results of recent research activities on this topic ongoing in our laboratories are also briefly outlined.L-amino acids are labeled. In C, a g-turn enclosed into a larger e-turn (C 11 form) is illustrated.

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Section: Introductionmentioning

confidence: 99%

Single and multiple peptide γ-turns: literature survey and recent progress

et al. 2015

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“…At this point, it is worth pointing out that by purpose in this review we did not take into consideration possible intramolecularly H-bonded 3D structures occurring in longer systems of (five or six) covalently linked peptide units, for example, the C 16 2 (or p-) turn for the "common way" and the C 14 2 and C 17 2 turns for "the other way around" H-bonding (for a selection of articles, see Refs. [38][39][40][41][42][43][44][45][46][47]. We planned to investigate these three types of wider turns in peptides and proteins in the near future.…”

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confidence: 99%

Intramolecular backbone···backbone hydrogen bonds in polypeptide conformations. The other way around: ɛ‐turn

et al. 2017

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In this study, we performed a detailed literature survey of the ɛ-turn in peptides and proteins. This three-dimensional structural feature is characterized by an eleven-membered pseudo-cycle closed by an intramolecular backbone…backbone H-bond. Interestingly, in this motif the direction of the N-H…O = C H-bond runs opposite to that of the much more popular and extensively investigated α-, β-, and γ-turns. We did not authenticate unequivocally the ɛ-turn main-chain reversal topology in any linear short peptide. However, it is frequently observed in small cyclic peptides formed by four, five, and six amino acid residues with stringent geometric requirements. Rather surprisingly, ɛ-turns do occur in proteins, although to a relatively moderate extent, as an isolated feature or in the turn segment of hairpin motifs based on two antiparallel, pleated β-strands. Moreover, the ɛ-turn may also host not only the seven-membered, intramolecularly H-bonded, pseudo-cycle termed γ-turn, either of the classic or inverse type, but also one (or even two) cis peptide bond(s) or a β-bulge conformation. Based on their ϕ, ψ backbone torsion angles, we were able to classify the protein ɛ-turns in six different families. Conformational energy computations using the DFT methodology were also performed on the ɛ-turns adopted by the amino acid triplet -Gly-Gly-Gly- (Gly is the most commonly found residue at each of the three positions in our analysis of proteins). Again, in this computational study, six families of turns were identified, but only some of them resemble rather closely those extracted from our investigation on proteins.

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“…Sequence and motif preferences at α‐helix termini for globular proteins have been extensively studied in the past few decades . However, to the best of our knowledge, such studies have not been carried out for a high resolution dataset of membrane proteins.…”

Section: Discussionmentioning

confidence: 99%

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

Shelar

Bansal

2014

Proteins

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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.

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Water and side‐chain embedded π‐turns

Cited by 6 publications

References 42 publications

Single and multiple peptide γ-turns: literature survey and recent progress

Single and multiple peptide γ-turns: literature survey and recent progress

Intramolecular backbone···backbone hydrogen bonds in polypeptide conformations. The other way around: ɛ‐turn

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

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