The π‐helix translates structure into function

Weaver, Todd

doi:10.1110/ps.9.1.201

Cited by 106 publications

(83 citation statements)

References 31 publications

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“…The π-bulges form a particular kind of discontinuity in helical structures. Like the π-helices [64], they are not frequently observed but they seem to be directly associated to protein function [70]. For instance, Erb2 protein transmembrane domain has been shown, using molecular dynamics approaches [71][72][73], to HAL author manuscript inserm-00175058, version 1 display a transition state from an α-helix to a π-bulge motif, and this has further been confirmed by experimental approaches [74].…”

Section: Secondary Structuresmentioning

confidence: 81%

“…Weaver found in 8 out of 10 confirmed crystal structures which contained π-helices, that its unique conformation was directly linked to the formation or stabilization of a specific binding site within the protein [64]. A dynamic relationship would exist between the different kinds of helices as shown for instance between α-and π-helices [65].…”

Section: Secondary Structuresmentioning

confidence: 89%

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Local Protein Structures

Offmann¹,

Tyagi²,

Brevern

2007

CBIO

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Protein structures are classically described as composed of two regular states, the α-helices and the β-strands and one non-regular and variable state, the coil. Nonetheless, this simple definition of secondary structures hides numerous limitations. In fact, the rules for secondary structure assignment are complex. Thus, numerous assignment methods based on different criteria have emerged leading to heterogeneous and diverging results. In the same way, 3 states may over-simplify the description of protein structure; 50% of all residues, i.e., the coil, are not genuinely described even when it encompass precise local protein structures.Description of local protein structures have hence focused on the elaboration of complete sets of small prototypes or "structural alphabets", able to analyze local protein structures and to approximate every part of the protein backbone. They have also been used to predict the protein backbone conformation and in ab initio / de novo methods. In this paper, we review different approaches towards the description of local structures, mainly through their description in terms of secondary structures and in terms of structural alphabets. We provide some insights into their potential applications.

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Section: Secondary Structuresmentioning

confidence: 81%

Section: Secondary Structuresmentioning

confidence: 89%

Local Protein Structures

Offmann¹,

Tyagi²,

Brevern

2007

CBIO

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“…This behavior is not accurately modeled using available methods, which rather, artifactually skew and twist the helical axis. Other approaches to identify helical perturbations that result in wide turns, also called -bulges, require the presence of one or more (i 3 iϪ5) hydrogen-bonds (H-bonds) (Kabasch and Sander, 1983;Richards and Kundrot, 1988;Frishman and Argos, 1995;Labesse et al, 1997;Weaver, 2000;Fodje and Al-Karadaghi, 2002) and a turn of ␣-helix before and after the wide turn (Cartailler and Luecke, 2004). As a result, wide turns not bounded by complete ␣-helical turns may not be identified.…”

mentioning

confidence: 99%

Wide Turn Diversity in Protein Transmembrane Helices Implications for G-Protein-Coupled Receptor and Other Polytopic Membrane Protein Structure and Function

Riek

Finch²,

Begg³

et al. 2008

Mol Pharmacol

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Previously, we showed that perturbations of protein transmembrane helices are manifested as one of three types of noncanonical structures (wide turns, tight turns, and kinks), which, compared with ␣-helices, are evident by distinctive C␣ i 3 C␣ x distances. In this study, we report the analysis of more than 3000 transmembrane helices in 244 crystal structures from which we identified 70 wide turns (29 proline-and 41 nonproline-induced). Based on differences in the C␣ i 3 C␣ iϪ4 and C␣ i 3 C␣ iϪ5 profiles, we show that wide turns can be subclassified into three distinct subclasses (W 1 , W 2 , and W 3 ) that differ with regard to the number and position of backbone i 3 iϪ5 H-bonds formed N-terminal to the perturbing or signature proline or nonproline residue. Although wide turns generally produce changes in helical direction of 20°to 30°and a lateral shift in the helical axis, some of the W 3 subclass are associated with changes of Ͻ5°. We also show that the distinct architectural features of wide turns allow the carbonyl bond of the iϪ4th residue, which is located on the widened loop of a wide turn, to be directed away from the helical axis. This provides regions of flexibility within helical regions allowing, for example, unique opportunities for interhelical H-bonding, including interactions with glycine zipper motifs, and for ion and cofactor binding. Furthermore, differences in wide-turn subtype usage by related protein family members, such as the G-protein-coupled receptors rhodopsin and the ␤2-adrenergic receptor, can significantly affect the orientation and position of residues critical for ligand binding and receptor activation.More than 70% of helices in proteins are curved or contain one or more kinks or other non-␣-helical structures (e.g., -bulges, 3 10

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“…5 type isotactic helix is the postulated (p-helix that has actually only recently been observed experimentally (Weaver 2000). The syndiotactic helix corresponds to B L /B D regions of /, w space (Fig.…”

Section: Chirality Defining Secondary Structure Of a Polypeptidementioning

confidence: 77%