ω-Helices in Proteins

Enkhbayar, Purevjav; Boldgiv, Bazartseren; Matsushima, Norio

doi:10.1007/s10930-010-9245-5

Cited by 6 publications

(8 citation statements)

References 38 publications

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“…No plateau or minima are observed at the same region on the surface without dispersion correction but rather a smooth slope connected to the energy basins of the extended structures. No other minimum connected to rare secondary structures such as ω-helix and α-sheet are found. The unique features of the newly calculated PES over that reported by Ireta and Scheffler make it more adequate for secondary structure classification and assignment.…”

Section: Resultsmentioning

confidence: 93%

PSIQUE: Protein Secondary Structure Identification on the Basis of Quaternions and Electronic Structure Calculations

Adasme‐Carreño

Caballero

Ireta

2021

J. Chem. Inf. Model.

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The secondary structure is important in protein structure analysis, classification, and modeling. We have developed a novel method for secondary structure assignment, termed PSIQUE, based on the potential energy surface (PES) of polyalanine obtained using an infinitely long chain model and density functional theory calculations. First, uniform protein segments are determined in terms of a difference of quaternions between neighboring amino acids along the protein backbone. Then, the identification of the secondary structure motifs is carried out based on the minima found in the PES. PSIQUE shows good agreement with other secondary structure assignment methods. However, it provides better discrimination of subtle secondary structures (e.g., helix types) and termini and produces more uniform segments while also accounting for local distortions. Overall, PSIQUE provides a precise and reliable assignment of secondary structures, so it should be helpful for the detailed characterization of the protein structure.

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Section: Resultsmentioning

confidence: 93%

PSIQUE: Protein Secondary Structure Identification on the Basis of Quaternions and Electronic Structure Calculations

Adasme‐Carreño

Caballero

Ireta

2021

J. Chem. Inf. Model.

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“…The p parameter is independent of the number of data points or helix length ( n ). The criterion for regular 3(10)‐helices as well α‐helices is p ≤ .10 Å …”

Section: Methodsmentioning

confidence: 99%

“…The HELFIT program determines helix parameters (helix axis, pitch, radius, residues per turn, and handedness, perfectness) of helix structures; it needs only four data points . We calculated real helix parameters of α‐helix, 3(10)‐helix, PPII, and β‐turn in proteins . We also applied it for geometrical analysis of LRR solenoid structures .…”

Section: Introductionmentioning

confidence: 99%

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A strong correlation between consensus sequences and unique super secondary structures in leucine rich repeats

et al. 2020

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Leucine rich repeats (LRRs) are present in over 430 000 proteins from viruses to eukaryotes. The LRRs are 20 to 30 residues long and occur in tandem. Individual LRRs are separated into a highly conserved segment with the consensus of LxxLxLxxNxL or LxxLxLxxNxxL (HCS) and a variable segment (VS). In LRRs parallel stacking of short β‐strands (at positions 3‐5 in HCS) form a super helix arrangement called a solenoid structure. Many classes have been recognized. All three classes of Plant specific, Leptospira‐like, and SDS22‐like LRRs which are 24, 23, and 22 residues long, respectively, form a 3(10)‐helix in the VS part. To get a deeper understanding of sequence, structure correlations in LRR structures, we utilized secondary structure assignment and HELFIT analysis (calculating helix axis, pitch, radius, residues per turn, and handedness) based on the atomic coordinates in crystal structures of 43 LRR proteins. We also defined three structural parameters using the three unit vectors of the helix axes of 3(10)‐helix, β‐turn, and LRR‐domain calculated by HELFIT. The combination of the secondary structure assignment and HELFIT reveals that their LRRs adopt unique super secondary structures consisting of a 3(10)‐helix and one or two Type I β‐turns. We propose one structural parameter as a geometrical invariant of LRR solenoid structures. The common LxxLxxL sequence (where “L” is Leu, Ile, Val, Phe or Cys) in the three classes is an essential determinant for the super secondary structures providing a medium range interaction.

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“…The criterion for regular PPII helices is p ≤ 0.10 Å. This same test is used for α-helices, ω-helices, and 3 10 -helices in proteins [ 63 , 64 ]. The HELFIT analysis requires only four data points: the coordinates of α-carbon (Cα) of each residue.…”

Section: Methodsmentioning

confidence: 99%

Super Secondary Structure Consisting of a Polyproline II Helix and a β-Turn in Leucine Rich Repeats in Bacterial Type III Secretion System Effectors

et al. 2018

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Leucine rich repeats (LRRs) are present in over 100,000 proteins from viruses to eukaryotes. The LRRs are 20–30 residues long and occur in tandem. LRRs form parallel stacks of short β-strands and then assume a super helical arrangement called a solenoid structure. Individual LRRs are separated into highly conserved segment (HCS) with the consensus of LxxLxLxxNxL and variable segment (VS). Eight classes have been recognized. Bacterial LRRs are short and characterized by two prolines in the VS; the consensus is xxLPxLPxx with Nine residues (N-subtype) and xxLPxxLPxx with Ten residues (T-subtype). Bacterial LRRs are contained in type III secretion system effectors such as YopM, IpaH3/9.8, SspH1/2, and SlrP from bacteria. Some LRRs in decorin, fribromodulin, TLR8/9, and FLRT2/3 from vertebrate also contain the motifs. In order to understand structural features of bacterial LRRs, we performed both secondary structures assignments using four programs—DSSP-PPII, PROSS, SEGNO, and XTLSSTR—and HELFIT analyses (calculating helix axis, pitch, radius, residues per turn, and handedness), based on the atomic coordinates of their crystal structures. The N-subtype VS adopts a left handed polyproline II helix (PPII) with four, five or six residues and a type I β-turn at the C-terminal side. Thus, the N-subtype is characterized by a super secondary structure consisting of a PPII and a β-turn. In contrast, the T-subtype VS prefers two separate PPIIs with two or three and two residues. The HELFIT analysis indicates that the type I β-turn is a right handed helix. The HELFIT analysis determines three unit vectors of the helix axes of PPII (P), β-turn (B), and LRR domain (A). Three structural parameters using these three helix axes are suggested to characterize the super secondary structure and the LRR domain.Electronic supplementary materialThe online version of this article (10.1007/s10930-018-9767-9) contains supplementary material, which is available to authorized users.

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ω-Helices in Proteins

Cited by 6 publications

References 38 publications

PSIQUE: Protein Secondary Structure Identification on the Basis of Quaternions and Electronic Structure Calculations

PSIQUE: Protein Secondary Structure Identification on the Basis of Quaternions and Electronic Structure Calculations

A strong correlation between consensus sequences and unique super secondary structures in leucine rich repeats

Super Secondary Structure Consisting of a Polyproline II Helix and a β-Turn in Leucine Rich Repeats in Bacterial Type III Secretion System Effectors

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