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Adasme-Carreño F, Caballero J, Ireta J. PSIQUE: Protein Secondary Structure Identification on the Basis of Quaternions and Electronic Structure Calculations. J Chem Inf Model 2021; 61:1789-1800. [PMID: 33769809 DOI: 10.1021/acs.jcim.0c01343] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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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Affiliation(s)
- Francisco Adasme-Carreño
- Departamento de Bioinformática, Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Campus Talca, 1 Poniente No. 1141, Casilla 721, Talca 3460000, Chile
| | - Julio Caballero
- Departamento de Bioinformática, Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Campus Talca, 1 Poniente No. 1141, Casilla 721, Talca 3460000, Chile
| | - Joel Ireta
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, A.P. 55-534, Ciudad de Mexico 09340, Mexico
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Brinkjost T, Ehrt C, Koch O, Mutzel P. SCOT: Rethinking the classification of secondary structure elements. Bioinformatics 2020; 36:2417-2428. [PMID: 31742326 DOI: 10.1093/bioinformatics/btz826] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 10/02/2019] [Accepted: 11/16/2019] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Secondary structure classification is one of the most important issues in structure-based analyses due to its impact on secondary structure prediction, structural alignment and protein visualization. There are still open challenges concerning helix and sheet assignments which are currently not addressed by a single multi-purpose software. RESULTS We introduce SCOT (Secondary structure Classification On Turns) as a novel secondary structure element assignment software which supports the assignment of turns, right-handed α-, 310- and π-helices, left-handed α- and 310-helices, 2.27- and polyproline II helices, β-sheets and kinks. We demonstrate that the introduction of helix Purity values enables a clear differentiation between helix classes. SCOT's unique strengths are highlighted by comparing it to six state-of-the-art methods (DSSP, STRIDE, ASSP, SEGNO, DISICL and SHAFT). The assignment approaches were compared concerning geometric consistency, protein structure quality and flexibility dependency and their impact on secondary structure element-based structural alignments. We show that only SCOT's combination of hydrogen bonds, geometric criteria and dihedral angles enables robust assignments independent of the structure quality and flexibility. We demonstrate that this combination and the elaborate kink detection lead to SCOT's clear superiority for protein alignments. As the resulting helices and strands are provided in a PDB conform output format, they can immediately be used for structure alignment algorithms. Taken together, the application of our new method and the straight-forward visualization using the accompanying PyMOL scripts enable the comprehensive analysis of regular backbone geometries in proteins. AVAILABILITY AND IMPLEMENTATION https://this-group.rocks. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tobias Brinkjost
- Department of Computer Science.,Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund 44227, Germany
| | - Christiane Ehrt
- Department of Computer Science.,Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund 44227, Germany
| | - Oliver Koch
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund 44227, Germany
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Batkhishig D, Enkhbayar P, Kretsinger RH, Matsushima N. A strong correlation between consensus sequences and unique super secondary structures in leucine rich repeats. Proteins 2020; 88:840-852. [DOI: 10.1002/prot.25876] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/03/2020] [Accepted: 01/25/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Dashdavaa Batkhishig
- Laboratory of Bioinformatics and Systems Biology, Department of Information and Computer Science, School of Engineering and Applied SciencesNational University of Mongolia Ulaanbaatar Mongolia
- Department of Physics, School of Mathematics and Natural SciencesMongolian National University of Education Ulaanbaatar Mongolia
| | - Purevjav Enkhbayar
- Laboratory of Bioinformatics and Systems Biology, Department of Information and Computer Science, School of Engineering and Applied SciencesNational University of Mongolia Ulaanbaatar Mongolia
| | | | - Norio Matsushima
- Division of Bioinformatics, Institute of Tandem Repeats Noboribetsu Japan
- Center for Medical Education, Sapporo Medical University Sapporo Japan
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Matsushima N, Miyashita H, Tamaki S, Kretsinger RH. Polyproline II Helix as a Recognition Motif of Plant Peptide Hormones and Flagellin Peptide flg22. Protein Pept Lett 2019; 26:684-690. [DOI: 10.2174/0929866526666190408125441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/01/2019] [Accepted: 04/02/2019] [Indexed: 02/07/2023]
Abstract
Background:
Plant peptide hormones play a crucial role in plant growth and
development. A group of these peptide hormones are signaling peptides with 5 - 23 amino acids.
Flagellin peptide (flg22) also elicits an immune response in plants. The functions are expressed
through recognition of the peptide hormones and flg22. This recognition relies on membrane
localized receptor kinases with extracellular leucine rich repeats (LRR-RKs). The structures of
plant peptide hormones - AtPep1, IDA, IDL1, RGFs 1- 3, TDIF/CLE41 - and of flg22 complexed
with LRR domains of corresponding LRRRKs and co-receptors SERKs have been determined.
However, their structures are well not analyzed and characterized in detail. The structures of PIP,
CEP, CIF, and HypSys are still unknown.
Objective:
Our motivation is to clarify structural features of these plant, small peptides and Flg22 in
their bound states.
Methods:
In this article, we performed secondary structure assignments and HELFIT analyses
(calculating helix axis, pitch, radius, residues per turn, and handedness) based on the atomic
coordinates from the crystal structures of AtPep1, IDA, IDL1, RGFs 1- 3, TDIF/CLE41 - and of
flg22. We also performed sequence analysis of the families of PIP, CEP, CIF, and HypSys in order
to predict their secondary structures.
Results:
Following AtPep1 with 23 residues adopts two left handed polyproline helices (PPIIs)
with six and four residues. IDA, IDL1, RGFs 1 - 2, and TDIF/CLE41 with 12 or 13 residues adopt
a four residue PPII; RGF3 adopts two PPIIs with four residues. Flg22 with 22 residues also adopts a
six residue PPII. The other peptide hormones – PIP, CEP, CIF, and HypSys – that are rich in
proline or hydroxyproline presumably prefer PPII.
Conclusion:
The present analysis indicates that PPII helix in the plant small peptide hormones and
in flg22 is crucial for recognition of the LRR domains in receptors.
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Affiliation(s)
| | | | | | - Robert H. Kretsinger
- Department of Biology, University of Virginia, Charlottesville, VA 22904, United States
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Batkhishig D, Bilguun K, Enkhbayar P, Miyashita H, Kretsinger RH, Matsushima N. Super Secondary Structure Consisting of a Polyproline II Helix and a β-Turn in Leucine Rich Repeats in Bacterial Type III Secretion System Effectors. Protein J 2019; 37:223-236. [PMID: 29651716 PMCID: PMC5976695 DOI: 10.1007/s10930-018-9767-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
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.
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Affiliation(s)
- Dashdavaa Batkhishig
- Laboratory of Bioinformatics and Systems Biology, Department of Information and Computer Science, School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, 14201, Mongolia.,Department of Physics, School of Mathematics and Natural Sciences, Mongolian National University of Education, Ulaanbaatar, 210648, Mongolia
| | - Khurelbaatar Bilguun
- Laboratory of Bioinformatics and Systems Biology, Department of Information and Computer Science, School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, 14201, Mongolia.,Institute of Physics and Technology, Mongolian Academy of Sciences, Enkhtaivan avenue 54B, Ulaanbaatar, 210651, Mongolia
| | - Purevjav Enkhbayar
- Laboratory of Bioinformatics and Systems Biology, Department of Information and Computer Science, School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, 14201, Mongolia.
| | - Hiroki Miyashita
- Hokubu Rinsho Co., Ltd, Sapporo, 060-0061, Japan.,Institute of Tandem Repeats, Sapporo, 004-0882, Japan
| | | | - Norio Matsushima
- Laboratory of Bioinformatics and Systems Biology, Department of Information and Computer Science, School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, 14201, Mongolia. .,Institute of Tandem Repeats, Sapporo, 004-0882, Japan. .,Sapporo Medical University, Sapporo, 060-8556, Japan.
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Kamihara T, Mizuno T, Shoji A, Takegoshi K. Conformational Characterization of Left-Handed Helices in Poly(β-benzyl l-aspartate) by 13C Chemical Shift Anisotropy Using Solid-State NMR. Macromolecules 2015. [DOI: 10.1021/ma502165u] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Takayuki Kamihara
- Division of Chemistry,
Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | | | - Akira Shoji
- Department of Chemistry and Chemical Biology, Graduate School of
Engineering, Gunma University, Kiryu, Gunma 376-8515, Japan
| | - K. Takegoshi
- Division of Chemistry,
Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
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