Protein beta-turn assignments

Bornot, Aurélie; Brevern, Alexandre G. de

doi:10.6026/97320630001153

Cited by 31 publications

(30 citation statements)

References 16 publications

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“…They are as recurrent as the PolyProline helix II conformation 34 or the frequent types of b-turns. 35 Chan and coworkers 16 analyzed only 362 b-bulges from 170 proteins. In this work, the dataset used is 66 times bigger, nevertheless a similar distribution of b-bulges was found (see Supporting Information Table S1).…”

Section: Analysis Of the Secondary Structuresmentioning

confidence: 99%

β‐Bulges: Extensive structural analyses of β‐sheets irregularities

et al. 2013

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b-Sheets are quite frequent in protein structures and are stabilized by regular main-chain hydrogen bond patterns. Irregularities in b-sheets, named b-bulges, are distorted regions between two consecutive hydrogen bonds. They disrupt the classical alternation of side chain direction and can alter the directionality of b-strands. They are implicated in protein-protein interactions and are introduced to avoid b-strand aggregation. Five different types of b-bulges are defined. Previous studies on b-bulges were performed on a limited number of protein structures or one specific family. These studies evoked a potential conservation during evolution. In this work, we analyze the bbulge distribution and conservation in terms of local backbone conformations and amino acid composition. Our dataset consists of 66 times more b-bulges than the last systematic study (Chan et al. Protein Science 1993, 2:1574-1590. Novel amino acid preferences are underlined and local structure conformations are highlighted by the use of a structural alphabet. We observed that bbulges are preferably localized at the N-and C-termini of b-strands, but contrary to the earlier studies, no significant conservation of b-bulges was observed among structural homologues. Displacement of b-bulges along the sequence was also investigated by Molecular Dynamics simulations.

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Section: Analysis Of the Secondary Structuresmentioning

confidence: 99%

β‐Bulges: Extensive structural analyses of β‐sheets irregularities

et al. 2013

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“…These results show the difficulties for defining an appropriate length for α-helices, β-strands and coils and locating their ends. Another recent study has also shown the consequences of this differences on β-turn assignment [255]. DEFINE always remains distinct from all these methods because it over-assigns regular secondary structure and, with respect to this, is closer to PALSSE than the other SSAMs.…”

Section: Secondary Structuresmentioning

confidence: 99%

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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“…In the same way, analysis of PUs in terms of secondary structures did not show any significant tendency in comparison to the entire databank. The Protein Blocks [56,75,85,88,99,[101][102][103][104][105][106][107][108] give a finer description than secondary structures [109], they so give more precise description of protein contacts and even some insights in signature of specific regions of protein loops in the PUs (e.g., PBs h and i).…”

Section: Discussionmentioning

confidence: 99%

Analysis of protein contacts into Protein Units

2009

Self Cite

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Three-dimensional structures of proteins are the support of their biological functions.Their folds are maintained by inter-residue interactions which are one of the main focuses to understand the mechanisms of protein folding and stability. Furthermore, protein structures can be composed of single or multiple functional domains that can fold and function independently. Hence, dividing a protein into domains is useful for obtaining an accurate structure and function determination.In previous studies, we enlightened protein contact properties according to different

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Protein beta-turn assignments

Cited by 31 publications

References 16 publications

β‐Bulges: Extensive structural analyses of β‐sheets irregularities

β‐Bulges: Extensive structural analyses of β‐sheets irregularities

Local Protein Structures

Analysis of protein contacts into Protein Units

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