PepEngine: A Manually Curated Structural Database of Peptides Containing α, β- Dehydrophenylalanine (ΔPhe) and α-Amino Isobutyric Acid (Aib)
Tóm tắt
Protein design is the systematic and rational design of protein/peptide molecules for various purposes such as improved activity, novel function, understanding structure–activity relationships (SARs) etc. A common approach to protein design involves methodical and sequential linking of various independently stable structural motifs to arrive at the desired global architecture. Non-standard amino acids which are not present in the classical set of 20 naturally coded amino acids have been utilized to induce, reinforce and stabilize certain desired secondary conformations. Hence, peptides containing non-standard residues can be utilized as structural blocks towards protein/peptide design. To facilitate the above, ‘PepEngine’: a manually curated database providing detailed structural information of synthetic peptides containing non-standard amino acid residues; α, β-dehydrophenylalanine (ΔPhe/ΔF) and α-aminoisobutyric acid (Aib); has been designed. 100 peptides were modelled with accurate, experimentally derived structural information (φ/ψ angles) using the Maestro suite of Schrödinger™. The database was further expanded to include information such as conformation type, terminal modifications, dihedral angles, original references etc. The database was then hosted as a web service including a comprehensive search function with interactive 3D visualization tools to enable wide public dissemination enhancing its utility. Apart from protein/peptide design; PepEngine can also be utilized as a benchmarking dataset for testing computational conformational sampling approaches and validating minimum energy state prediction algorithms. Further expansion of the database has been planned to include other classes of non-standard residues along with a text mining-based pipeline to automatically search the relevant literature for novel peptides. The database is available at
www.pepengine.in
Tài liệu tham khảo
Allgaeir H, Jung G, Werner RG et al (1986) Epidermin: sequencing of a heterodet tetracyclic 21-peptide amide antibiotic. Eur J Biochem. https://doi.org/10.1111/j.1432-1033.1986.tb09933.x
Aravinda S, Shamala N, Roy RS, Balaram P (2003) Non-protein amino acids in peptide design. Proc Indian Acad Sci Chem Sci. https://doi.org/10.1007/bf02708230
Ashok Kumar T (2013) CFSSP: Chou and Fasman secondary structure prediction server. Wide Spectr. https://doi.org/10.5281/zenodo.50733
Banerjee R, Basu G (2002) A short Aib/Ala-based peptide helix is as stable as an Ala-based peptide helix double its length. ChemBioChem. https://doi.org/10.1002/1439-7633(20021202)3:12%3c1263::AID-CBIC1263%3e3.0.CO;2-O
Bhardwaj G, Mulligan VK, Bahl CD et al (2016) Accurate de novo design of hyperstable constrained peptides. Nature. https://doi.org/10.1038/nature19791
Bozovičar K, Bratkovič T (2021) Small and simple, yet sturdy: Conformationally constrained peptides with remarkable properties. Int. J. Mol. Sci.
Buchan DWA, Jones DT (2019) The PSIPRED protein analysis workbench: 20 years on. Nucleic Acids Res. https://doi.org/10.1093/nar/gkz297
Castro TG, Micaêlo NM (2014) Conformational and thermodynamic properties of non-canonical α, α-dialkyl glycines in the peptaibol alamethicin: Molecular dynamics studies. J Phys Chem B. https://doi.org/10.1021/jp505400q
Clerici F, Erba E, Gelmi ML, Pellegrino S (2016) Non-standard amino acids and peptides: From self-assembly to nanomaterials. Tetrahedron Lett.
Ding Y, Ting JP, Liu J, et al (2020) Impact of non-proteinogenic amino acids in the discovery and development of peptide therapeutics. Amino Acids
Dubey SP, Gopalakrishna Kini N, Sathish Kumar M, Balaji S (2016) Ab initio protein structure prediction using GPU computing. Perspect Sci. https://doi.org/10.1016/j.pisc.2016.06.046
Duclohier H (2010) Antimicrobial Peptides and Peptaibols. Curr Pharm Des, Substitutes for Conventional Antibiotics. https://doi.org/10.2174/138161210793292500
Geng H, Chen F, Ye J, Jiang F (2019) Applications of Molecular Dynamics Simulation in Structure Prediction of Peptides and Proteins. Comput. Struct. Biotechnol. J.
Georgakopoulos ND, Talapatra SK, Gatliff J et al (2018) Modified Peptide Inhibitors of the Keap1–Nrf2 Protein-Protein Interaction Incorporating Unnatural Amino Acids. ChemBioChem. https://doi.org/10.1002/cbic.201800170
Gromiha MM, Selvaraj S (2004) Inter-residue interactions in protein folding and stability. Prog. Biophys. Mol. Biol.
Gupta M, Chauhan VS (2011) De novo design of α, β-didehydrophenylalanine containing peptides: From models to applications. Biopolymers. https://doi.org/10.1002/bip.21561
Gupta M, Bagaria A, Mishra A et al (2007) Self-assembly of a dipeptide-containing conformationally restricted dehydrophenylalanine residue to form ordered nanotubes. Adv Mater. https://doi.org/10.1002/adma.200601774
Henchey LK, Jochim AL, Arora PS (2008) Contemporary strategies for the stabilization of peptides in the α-helical conformation. Curr Opin Chem Biol 12:692–697
Huang S, Huang JT (2013) Inter-residue interaction is a determinant of protein folding kinetics. J Theor Biol. https://doi.org/10.1016/j.jtbi.2012.10.003
Ishida H, Inoue Y (1999) Peptides that contain unnatural amino acids: Toward artificial proteins. Rev. Heteroat. Chem. 19:79–142
Isidro-Llobet A, Álvarez M, Albericio F (2009) Amino acid-protecting groups. Chem Rev. https://doi.org/10.1021/cr800323s
Jin X, Park OJ, Hong SH (2019) Incorporation of non-standard amino acids into proteins: challenges, recent achievements, and emerging applications. Appl Microbiol Biotechnol 103:2947–2958
Karle IL, Das C, Balaram P (2000) De novo protein design: Crystallographic characterization of a synthetic peptide containing independent helical and hairpin domains. Proc Natl Acad Sci U S A. https://doi.org/10.1073/pnas.97.7.3034
Karnes MA, Schettler SL, Werner HM et al (2016) Thermodynamic and Structural Impact of α, α-Dialkylated Residue Incorporation in a β-Hairpin Peptide. Org Lett. https://doi.org/10.1021/acs.orglett.6b01936
Krüger DM, Glas A, Bier D et al (2017) Structure-based design of non-natural macrocyclic peptides that inhibit protein-Protein interactions. J Med Chem. https://doi.org/10.1021/acs.jmedchem.7b01221
Lee HS, Wang SH, Daniel JT et al (2020) Exploring the use of helicogenic amino acids for optimising single chain relaxin-3 peptide agonists. Biomedicines. https://doi.org/10.3390/biomedicines8100415
Mabonga L, Kappo AP (2020) Peptidomimetics: A synthetic tool for inhibiting protein-protein interactions in cancer. Int J Pept Res Ther 26:225–241
Mandal S, Moudgil M, Mandal SK (2009) Rational drug design. Eur J Pharmacol 625:90–100
Mathur P, Ramakumar S, Chauhan VS (2004) Peptide Design Using α, β-Dehydro Amino Acids: From β-Turns to Helical Hairpins. Biopolymers - Peptide Science Section 76:150–161
Mavromoustakos T, Durdagi S, Koukoulitsa C et al (2011) Strategies in the Rational Drug Design. Curr Med Chem. https://doi.org/10.2174/092986711795933731
Oliva R, Chino M, Pane K et al (2018) Exploring the role of unnatural amino acids in antimicrobial peptides. Sci Rep. https://doi.org/10.1038/s41598-018-27231-5
Panda JJ, Kaul A, Alam S et al (2011) Designed peptides as model self-assembling nanosystems: Characterization and potential biomedical applications. Ther Deliv. https://doi.org/10.4155/tde.10.93
Pathak S, Singh Chauhan V (2011) Rationale-based, de novo design of dehydrophenylalanine-containing antibiotic peptides and systematic modification in sequence for enhanced potency. Antimicrob Agents Chemother. https://doi.org/10.1128/AAC.01493-10
Qvit N, Rubin SJS, Urban TJ, et al (2017) Peptidomimetic therapeutics: scientific approaches and opportunities. Drug Discov. Today
Rai J, Raghothama S, Sahal D (2007) De novo design of ΔF-containing heme-binding peptides. Chem Biol Drug Des. https://doi.org/10.1111/j.1747-0285.2007.00480.x
Ramagopal UA, Ramakumar S, Mathur P et al (2002) Dehydrophenylalanine zippers: Strong helix-helix clamping through a network of weak interactions. Protein Eng. https://doi.org/10.1093/protein/15.4.331
Rashid MA, Shatabda S, Newton MAH et al (2014) A parallel framework for multipoint spiral search in ab initio protein structure prediction. Adv Bioinformatics. https://doi.org/10.1155/2014/985968
Regan L, Caballero D, Hinrichsen MR, et al (2015) Protein design: Past, present, and future. Biopolymers
Rost B, Sander C, Schneider R (1994) PHD-an automatic mail server for protein secondary structure prediction. Bioinformatics. https://doi.org/10.1093/bioinformatics/10.1.53
Sen TZ, Jernigan RL, Garnier J, Kloczkowski A (2005) GOR V server for protein secondary structure prediction. Bioinformatics. https://doi.org/10.1093/bioinformatics/bti408
Singh S, Singh H, Tuknait A et al (2015) PEPstrMOD: Structure prediction of peptides containing natural, non-natural and modified residues. Biol Direct. https://doi.org/10.1186/s13062-015-0103-4
Tsuji G, Misawa T, Doi M, Demizu Y (2018) Extent of helical induction caused by introducing α-aminoisobutyric acid into an oligovaline sequence. ACS Omega. https://doi.org/10.1021/acsomega.8b01030
Tugyi R, Uray K, Iván D et al (2005) Partial D-amino acid substitution: Improved enzymatic stability and preserved Ab recognition of a MUC2 epitope peptide. Proc Natl Acad Sci U S A. https://doi.org/10.1073/pnas.0407677102
Uma K, Balaram P (1989) Peptide Design - An Analysis Of Studies Using Alpha-Aminoisobutyric-Acid (Aib) And Z-Alpha, Beta Dehydrophenylalanine (Delta-Z-Phe). Indian J Chem - Sect B Org Med Chem 28:705–710
Wang T, Liang C, Xu H et al (2020) Incorporation of nonstandard amino acids into proteins: principles and applications. World J Microbiol Biotechnol 36:1–14
Werle M, Bernkop-Schnürch A (2006) Strategies to improve plasma half life time of peptide and protein drugs. Amino Acids 30:351–367
Werner HM, Cabalteja CC, Horne WS (2016) Peptide Backbone composition and protease susceptibility: impact of modification type, position, and tandem substitution. ChemBioChem. https://doi.org/10.1002/cbic.201500312
Yakimov AP, Afanaseva AS, Khodorkovskiy MA, Petukhov MG (2016) Design of Stable a-Helical Peptides and Thermostable Proteins in Biotechnology and Biomedicine. Acta Naturae. https://doi.org/10.32607/20758251-2016-8-4-70-81
Yennamalli RM (2018) Protein design Encyclopedia of Bioinformatics and Computational Biology ABC of Bioinformatics. Polymers 13:2533
Yin H (2012) Constrained peptides as miniature protein structures. ISRN Biochem. https://doi.org/10.5402/2012/692190
Yousef M, Abdelkader T, El-Bahnasy K (2019) Performance comparison of ab initio protein structure prediction methods. Ain Shams Eng J. https://doi.org/10.1016/j.asej.2019.03.004