1
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Chen Q, Ge Y, He X, Li S, Fang Z, Li C, Chen H. Virtual-screening of xanthine oxidase inhibitory peptides: Inhibition mechanisms and prediction of activity using machine-learning. Food Chem 2024; 460:140741. [PMID: 39128372 DOI: 10.1016/j.foodchem.2024.140741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 08/13/2024]
Abstract
Xanthine oxidase (XO) inhibitory peptides can prevent XO-mediated hyperuricemia. Currently, QSAR about XO inhibitory peptides with different lengths remains to be enriched. Here, XO inhibitory peptides were obtained from porcine visceral proteins through virtual-screening. A prediction model was established by machine-learning. Virtual-screening retained four lengths of peptides, including 3-6. Molecular-docking recognized their binding sites with XO and showed residues W, F, and G were the key amino acids. Datasets of XO inhibitory peptides therewith were established. The optimal model was used to generalize the peptides reported. Results showed that the R2 of the tripeptide, tetrapeptide, pentapeptide and hexapeptide in the generalisation test were R2 = 0.81, R2 = 0.82, R2 = 0.83 and R2 = 0.83, respectively. Overall, this work can serve as a reference for explaining the activity mechanism of XO inhibitory peptides and predicting the activity of XO inhibitory peptides.
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Affiliation(s)
- Qian Chen
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China
| | - Yuxi Ge
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China
| | - Xiaoyu He
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China
| | - Shanshan Li
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China
| | - Zhengfeng Fang
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China
| | - Cheng Li
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China
| | - Hong Chen
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China.
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2
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Kandoor A, Martinez G, Hitchcock JM, Angel S, Campbell L, Rizvi S, Naegle KM. CoDIAC: A comprehensive approach for interaction analysis reveals novel insights into SH2 domain function and regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.18.604100. [PMID: 39091881 PMCID: PMC11291013 DOI: 10.1101/2024.07.18.604100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Protein domains are conserved structural and functional units and are the functional building blocks of proteins. Evolutionary expansion means that domain families are often represented by many members in a species, which are found in various configurations with other domains, which have evolved new specificity for interacting partners. Here, we develop a structure-based interface analysis to comprehensively map domain interfaces from available experimental and predicted structures, including interfaces with other macromolecules and intraprotein interfaces (such as might exist between domains in a protein). We hypothesized that a comprehensive approach to contact mapping of domains could yield new insights. Specifically, we use it to gain information about how domains selectivity interact with ligands, whether domain-domain interfaces of repeated domain partnerships are conserved across diverse proteins, and identify regions of conserved post-translational modifications, using relationship to interaction interfaces as a method to hypothesize the effect of post-translational modifications (and mutations). We applied this approach to the human SH2 domain family, an extensive modular unit that is the foundation of phosphotyrosine-mediated signaling, where we identified a novel approach to understanding the binding selectivity of SH2 domains and evidence that there is coordinated and conserved regulation of multiple SH2 domain binding interfaces by tyrosine and serine/threonine phosphorylation and acetylation, suggesting that multiple signaling systems can regulate protein activity and SH2 domain interactions in a regulated manner. We provide the extensive features of the human SH2 domain family and this modular approach, as an open source Python package for COmprehensive Domain Interface Analysis of Contacts (CoDIAC).
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Affiliation(s)
- Alekhya Kandoor
- Department of Biomedical Engineering and the Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Gabrielle Martinez
- Department of Biomedical Engineering and the Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Julianna M Hitchcock
- Department of Biomedical Engineering and the Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Savannah Angel
- Department of Biomedical Engineering and the Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Logan Campbell
- Department of Biomedical Engineering and the Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Saqib Rizvi
- Department of Biomedical Engineering and the Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Kristen M Naegle
- Department of Biomedical Engineering and the Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
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3
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Su J, Zhou P. Musical protein: Mapping the time sequence of music onto the spatial architecture of proteins. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2024; 252:108233. [PMID: 38781810 DOI: 10.1016/j.cmpb.2024.108233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND AND OBJECTIVE Music, the ubiquitous language across human cultures, is traditionally considered as a form of art but has been linked to biomolecules in recent years. However, previous efforts have only been addressed on sonification of nucleic acids and proteins to produce so-called life music, the soundscape from the basic building blocks of life. In this study, we attempted to, for the first time, conduct a reverse operation of this process, i.e. conversion of music to protein (CoMtP). METHODS A novel notion termed musical protein (MP) -- the protein defined by music -- was proposed and, on this basis, we described a computational strategy to map the time sequence of music onto the spatial architecture of proteins, which considered that each note in the stave of a music (target) can be simply characterized by two acoustical quantities and that each residue in the primary sequence of a protein (hit) was represented by amino acid descriptors. RESULTS A simulated annealing (SA) algorithm was applied to iteratively generate the best matched MP hit for a music target and structural bioinformatics was then used to model spatial advanced structure for the resulting MP. We also demonstrated that some small MPs derived from music segments may have potential biological functions, which, for example, can serve as antimicrobial peptides (AMPs) to inhibit clinical bacterial strains with moderate or high antibacterial potency. CONCLUSIONS This work may benefit many aspects; for example, it would open a door for the hearing-impaired persons to 'listen' music in a biological vision and could be a mean of exposing students to the concepts of biomolecules at an earlier age through the use of auditory characteristics. The CoMtP would also facilitate the rational design of proteins with biological and medicinal significance.
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Affiliation(s)
- Jun Su
- College of Music, Chengdu Normal University, No.99 Haike Road East Section, Wenjiang District, Chengdu 611130, China.
| | - Peng Zhou
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), No.2006 Xiyuan Ave West Hi-Tech Zone, Chengdu 611731, China.
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4
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Du A, Jia W, Zhang R. Machine learning methods for unveiling the potential of antioxidant short peptides in goat milk-derived proteins during in vitro gastrointestinal digestion. J Dairy Sci 2024:S0022-0302(24)00970-6. [PMID: 38945266 DOI: 10.3168/jds.2024-24887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 06/06/2024] [Indexed: 07/02/2024]
Abstract
Milk serves as an important dietary source of bioactive peptides, offering notable benefits to individuals. Among the antioxidant short peptides (di- and tripeptides) generated from gastrointestinal digestion are characterized by enhanced bioavailability and bioaccessibility, while assessing them individually presents a labor-intensive and expensive challenge. Based on 4 distinct types of amino acid descriptors (physicochemical, 3D structural, quantum, and topological attributes) and genetic algorithms for feature selection, 1 and 4 machine learning predicted models separately for di- and tripeptides with ABTS radical scavenging capacity exhibited excellent fitting and prediction ability with random forest regression as machine learning algorithm. Intriguingly, the electronic properties of N-terminal amino acid were considered as only factor affecting the antioxidant capacity of dipeptides containing both tyrosine and tryptophan. Four peptides from the potential di- and tripeptides exhibited highly predicted values by the constructed predicted models. Subsequently, a total of 45 dipeptides and 52 tripeptides were screened by a customized workflow in goat milk during in vitro simulated digestion. In addition to 5 known antioxidant dipeptides, 9 peptides were quantified during digestion, falling within the range of 0.04 to 1.78 mg L-1. Particularly noteworthy was the promising in vivo functionality of antioxidant dipeptides with N-terminal tyrosine, supported by in silico assays. Overall, this investigation explored crucial molecular properties influencing antioxidant short peptides and high-throughput screening potential peptides with antioxidant activity from goat milk aided by machine learning, thereby facilitating the identification of novel bioactive peptides from milk-derived proteins and paving the way for understanding their metabolites during digestion.
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Affiliation(s)
- An Du
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an 710021, China
| | - Wei Jia
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an 710021, China; Shaanxi Research Institute of Agricultural Products Processing Technology, Xi'an 710021, China.
| | - Rong Zhang
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an 710021, China
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5
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Xu Q, Zheng L, Huang M, Zhao M. Collagen derived Gly-Pro-type DPP-IV inhibitory peptides: Structure-activity relationship, inhibition kinetics and inhibition mechanism. Food Chem 2024; 441:138370. [PMID: 38199113 DOI: 10.1016/j.foodchem.2024.138370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/20/2023] [Accepted: 01/04/2024] [Indexed: 01/12/2024]
Abstract
Our previous study has demonstrated that both the amino acid at N3 position and peptide length affected the DPP-IV inhibitory activity of Gly-Pro-type peptides. To further elucidate their molecular mechanism, a combined approach of QSAR modeling, enzymatic kinetics and molecular docking was used. Results showed that the QSAR models of Gly-Pro-type tripeptides and Gly-Pro-type peptides containing 3-12 residues were successfully constructed by 5z-scale descriptor with R2 of 0.830 and 0.797, respectively. The lower values of electrophilicity, polarity, and side-chain bulk of amino acid at N3 position caused higher DPP-IV inhibitory activity of Gly-Pro-type peptides. Moreover, an appropriate increase in the length of Gly-Pro-type peptides did not change their competitive inhibition mode, but decreased their inhibition constants (Ki values) and increased interactions with DPP-IV. More importantly, the interactions between the residues at C-terminal of Gly-Pro-type peptides containing 5 ∼ 6 residues with S2 extensive subsites (Ser209, Phe357, Arg358) of DPP-IV increased the interactions of Gly residue at N1 position with the S2 subsites (Glu205, Glu206, Asn710, Arg125, Tyr662) and decreased the acylation level of DPP-IV-peptide complex, and thereby increasing peptides' DPP-IV inhibitory activity.
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Affiliation(s)
- Qiongyao Xu
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China; Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou 510650, China
| | - Lin Zheng
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China; Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou 510650, China.
| | - Mingtao Huang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China; Chaozhou Branch of Chemistry and Chemical Engineering Guangdong Laboratory, Chaozhou, 521000, China; Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou 510650, China
| | - Mouming Zhao
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China; Chaozhou Branch of Chemistry and Chemical Engineering Guangdong Laboratory, Chaozhou, 521000, China; Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou 510650, China.
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6
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Du A, Jia W. Bioaccessibility of novel antihypertensive short-chain peptides in goat milk using the INFOGEST static digestion model by effect-directed assays. Food Chem 2023; 427:136735. [PMID: 37392630 DOI: 10.1016/j.foodchem.2023.136735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/21/2023] [Accepted: 06/24/2023] [Indexed: 07/03/2023]
Abstract
Short-chain peptides (SCPs, 2-4 amino acids) offer potential health benefits. A customized workflow was designed to screen SCPs in goat milk during INFOGEST digestion in vitro and 186 SCPs were preliminarily identified. Based on a two-terminal position numbering method and genetic algorithm combined with a support vector machine, 22 SCPs with predicted IC50 values less than 10 μM were obtained using a quantitative structure-activity relationship (QSAR) model with satisfactory fitting and predictive capacity (R2, RMSE, Q2, and R2pre of 0.93, 0.27, 0.71, and 0.65, respectively). Four novel antihypertensive SCPs were confirmed by testing in vitro and molecular docking analysis, and their quantification results (0.06 to 1.53 mg L-1) suggested distinct metabolic fates. This study facilitated the discovery of unknown potential food-derived antihypertensive peptides and the understanding of bioaccessible peptides during digestion.
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Affiliation(s)
- An Du
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an 710021, China
| | - Wei Jia
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an 710021, China; Shaanxi Research Institute of Agricultural Products Processing Technology, Xi'an 710021, China.
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7
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Du A, Jia W. Virtual screening, identification, and potential antioxidant mechanism of novel bioactive peptides during aging by a short-chain peptidomics, quantitative structure-activity relationship analysis, and molecular docking. Food Res Int 2023; 172:113129. [PMID: 37689894 DOI: 10.1016/j.foodres.2023.113129] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 09/11/2023]
Abstract
Antioxidant peptides have received a great deal of attention. However, only a few studies have been conducted on the antioxidant peptides originating from Baijiu. A total of 1490 features deemed potential short-chain peptides (the amino acid number between 2 and 4, SCPs) were screened and analyzed by a customized short-chain peptidomics approach in Feng-flavor Baijiu (FFB) during 14 years of aging, with an obvious discrepancy between FFB aged for 3 years and 6 years being observed. Thirty-nine characteristic SCPs in total were identified and accurately quantified by high-throughput parallel reaction monitoring-based synthetic standards, with the contents ranging from 0.16 to 279.33 μg L-1. Combined with the absorption, distribution, metabolism, excretion, and toxicity analysis model, PGRW, WK, SC, and PAW, four novel antioxidant peptides with high ABTS radical scavenging capacity, were obtained using a customized quantitative structure-activity relationship (QSAR) model based on a two terminal position numbering method, with satisfied coefficients of determination (R2), internal cross-validated R2 (Q2), and external R2 (R2pre) of 0.925, 0.808, and 0.665, respectively. Furthermore, these 4 antioxidant peptides could block the Keap-Nrf2 interaction and promote the accumulation of Nrf2 by molecular docking analysis, and the interaction energy between peptide PGRW and Keap1 was higher than that between epigallocatechin gallate and Keap1 based on CHARMm forced field. Overall, this study facilitated the discovery of functional peptides in Baijiu and the understanding of aging mechanisms.
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Affiliation(s)
- An Du
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an 710021, China
| | - Wei Jia
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an 710021, China; Shaanxi Research Institute of Agricultural Products Processing Technology, Xi'an 710021, China.
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8
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Lin J, Wen L, Zhou Y, Wang S, Ye H, Su J, Li J, Shu J, Huang J, Zhou P. PepQSAR: a comprehensive data source and information platform for peptide quantitative structure-activity relationships. Amino Acids 2023; 55:235-242. [PMID: 36474016 DOI: 10.1007/s00726-022-03219-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 11/23/2022] [Indexed: 12/12/2022]
Abstract
Peptide quantitative structure-activity relationships (pQSARs) have been widely applied to the statistical modeling and empirical prediction of peptide activity, property and feature. In the procedure, the peptide structure is characterized at sequence level using amino acid descriptors (AADs) and then correlated with observations by machine learning methods (MLMs), consequently resulting in a variety of quantitative regression models used to explain the structural factors that govern peptide activities, to generalize peptide properties of unknown from known samples, and to design new peptides with desired features. In this study, we developed a comprehensive platform, termed PepQSAR database, which is a systematic collection and decomposition of various data sources and abundant information regarding the pQSARs, including AADs, MLMs, data sets, peptide sequences, measured activities, model statistics, and literatures. The database also provides a comparison function for the various previously built pQSAR models reported by different groups via distinct approaches. The structured and searchable PepQSAR database is expected to provide a useful resource and powerful tool for the computational peptidology community, which is freely available at http://i.uestc.edu.cn/PQsarDB .
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Affiliation(s)
- Jing Lin
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), No. 2006 Xiyuan Ave, West Hi-Tech Zone, Chengdu, 611731, China
| | - Li Wen
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), No. 2006 Xiyuan Ave, West Hi-Tech Zone, Chengdu, 611731, China
| | - Yuwei Zhou
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), No. 2006 Xiyuan Ave, West Hi-Tech Zone, Chengdu, 611731, China
| | - Shaozhou Wang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), No. 2006 Xiyuan Ave, West Hi-Tech Zone, Chengdu, 611731, China
| | - Haiyang Ye
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), No. 2006 Xiyuan Ave, West Hi-Tech Zone, Chengdu, 611731, China
| | - Jun Su
- College of Music, Chengdu Normal University, Chengdu, 611130, China
| | - Juelin Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), No. 2006 Xiyuan Ave, West Hi-Tech Zone, Chengdu, 611731, China
| | - Jianping Shu
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), No. 2006 Xiyuan Ave, West Hi-Tech Zone, Chengdu, 611731, China
| | - Jian Huang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), No. 2006 Xiyuan Ave, West Hi-Tech Zone, Chengdu, 611731, China.
| | - Peng Zhou
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), No. 2006 Xiyuan Ave, West Hi-Tech Zone, Chengdu, 611731, China.
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9
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Shao X, Kong W, Li Y, Zhang S. Quantitative structure-activity relationship modeling reveals the minimal sequence requirement and amino acid preference of sirtuin-1's deacetylation substrates in diabetes mellitus. J Bioinform Comput Biol 2022; 20:2250008. [PMID: 35451939 DOI: 10.1142/s0219720022500081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Sirtuin 1 (SIRT1) is a nicotinamide adenine dinucleotide (NAD[Formula: see text]-dependent deacetylase involved in multiple glucose metabolism pathways and plays an important role in the pathogenesis of diabetes mellitus (DM). The enzyme specifically recognizes its deacetylation substrates' peptide segments containing a central acetyl-lysine residue as well as a number of amino acids flanking the central residue. In this study, we attempted to ascertain the minimal sequence requirement (MSR) around the central acetyl-lysine residue of SIRT1 substrate-recognition sites as well as the amino acid preference (AAP) at different residues of the MSR window through quantitative structure-activity relationship (QSAR) strategy, which would benefit our understanding of SIRT1 substrate specificity at the molecular level and is also helpful to rationally design substrate-mimicking peptidic agents against DM by competitively targeting SIRT1 active site. In this procedure, a large-scale dataset containing 6801 13-mer acetyl-lysine peptides (and their SIRT1-catalyized deacetylation activities) were compiled to train 10 QSAR regression models developed by systematic combination of machine learning methods (PLS and SVM) and five amino acids descriptors (DPPS, T-scale, MolSurf, [Formula: see text]-score, and FASGAI). The two best QSAR models (PLS+FASGAI and SVM+DPPS) were then employed to statistically examine the contribution of residue positions to the deacetylation activity of acetyl-lysine peptide substrates, revealing that the MSR can be represented by 5-mer acetyl-lysine peptides that meet a consensus motif X[Formula: see text]X[Formula: see text]X[Formula: see text](AcK)0X[Formula: see text]. Structural analysis found that the X[Formula: see text] and (AcK)0 residues are tightly packed against the enzyme active site and confer both stability and specificity for the enzyme-substrate complex, whereas the X[Formula: see text], X[Formula: see text] and X[Formula: see text] residues are partially exposed to solvent but can also effectively stabilize the complex system. Subsequently, a systematic deacetylation activity change profile (SDACP) was created based on QSAR modeling, from which the AAP for each residue position of MSR was depicted. With the profile, we were able to rationally design an SDACP combinatorial library with promising deacetylation activity, from which nine MSR acetyl-lysine peptides as well as two known SIRT1 acetyl-lysine peptide substrates were tested by using SIRT1 deacetylation assay. It is revealed that the designed peptides exhibit a comparable or even higher activity than the controls, although the former is considerably shorter than the latter.
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Affiliation(s)
- X Shao
- Department of Nephrology, Suzhou Kowloon Hospital, Shanghai Jiao Tong University, School of Medicine, Suzhou 215000, P. R. China
| | - W Kong
- Department of Nephrology, Suzhou Kowloon Hospital, Shanghai Jiao Tong University, School of Medicine, Suzhou 215000, P. R. China
| | - Y Li
- Department of Nephrology, Suzhou Kowloon Hospital, Shanghai Jiao Tong University, School of Medicine, Suzhou 215000, P. R. China
| | - S Zhang
- Department of Nephrology, Suzhou Kowloon Hospital, Shanghai Jiao Tong University, School of Medicine, Suzhou 215000, P. R. China
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10
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Yin JY, Han YN, Liu MQ, Piao ZH, Zhang X, Xue YT, Zhang YH. Structure-guided discovery of antioxidant peptides bounded to the Keap1 receptor as hunter for potential dietary antioxidants. Food Chem 2022; 373:130999. [PMID: 34710694 DOI: 10.1016/j.foodchem.2021.130999] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 07/17/2021] [Accepted: 08/29/2021] [Indexed: 01/27/2023]
Abstract
Human health can be damaged by free radicals, and antioxidant peptides are excellent radical scavengers. Antioxidant tripeptides data set based on 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulofnic acid) (ABTS) assay was created, 9 types of descriptors were integrated and 4 quantitative structure-activity relationship (QSAR) models were constructed in this study. Several structural factors influencing the activity of antioxidant tripeptides and the dominant amino acids at each position of tripeptides were revealed by the optimal model. Ten food-derived tripeptides with higher activity were selected for synthesis and activity determination. Molecular docking results demonstrated that these tripeptides were stably bound to the Keap1 receptor, further elucidating the antioxidant mechanism. It was known from the simulation of gastrointestinal digestion experiments that the model results possessed a guiding effect on the selection of proteins with high antioxidant activity. The performance of the model was proved to be robust after validation.
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Affiliation(s)
- Jia-Yi Yin
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China; Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China
| | - Ya-Ning Han
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China; Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China
| | - Meng-Qi Liu
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China; Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China
| | - Zan-Hao Piao
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China; Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China
| | - Xu Zhang
- Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China
| | - Yu-Ting Xue
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China; Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China
| | - Ying-Hua Zhang
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China; Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China.
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11
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Bo W, Chen L, Qin D, Geng S, Li J, Mei H, Li B, Liang G. Application of quantitative structure-activity relationship to food-derived peptides: Methods, situations, challenges and prospects. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.05.031] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Zhou P, Liu Q, Wu T, Miao Q, Shang S, Wang H, Chen Z, Wang S, Wang H. Systematic Comparison and Comprehensive Evaluation of 80 Amino Acid Descriptors in Peptide QSAR Modeling. J Chem Inf Model 2021; 61:1718-1731. [DOI: 10.1021/acs.jcim.0c01370] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Peng Zhou
- Center for Informational Biology, University of Electronic Science and Technology of China (UESTC) at Qingshuihe Campus, Chengdu 611731, China
- School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC) at Shahe Campus, Chengdu 610054, China
| | - Qian Liu
- Center for Informational Biology, University of Electronic Science and Technology of China (UESTC) at Qingshuihe Campus, Chengdu 611731, China
- School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC) at Shahe Campus, Chengdu 610054, China
| | - Ting Wu
- School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC) at Shahe Campus, Chengdu 610054, China
| | - Qingqing Miao
- Center for Informational Biology, University of Electronic Science and Technology of China (UESTC) at Qingshuihe Campus, Chengdu 611731, China
- School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC) at Shahe Campus, Chengdu 610054, China
| | - Shuyong Shang
- College of Chemistry and Life Science, Chengdu Normal University, Chengdu 611130, China
| | - Heyi Wang
- Center for Informational Biology, University of Electronic Science and Technology of China (UESTC) at Qingshuihe Campus, Chengdu 611731, China
- School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC) at Shahe Campus, Chengdu 610054, China
| | - Zheng Chen
- Center for Informational Biology, University of Electronic Science and Technology of China (UESTC) at Qingshuihe Campus, Chengdu 611731, China
- School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC) at Shahe Campus, Chengdu 610054, China
| | - Shaozhou Wang
- School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC) at Shahe Campus, Chengdu 610054, China
| | - Heyan Wang
- School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC) at Shahe Campus, Chengdu 610054, China
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13
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Ronan T, Garnett R, Naegle KM. New analysis pipeline for high-throughput domain-peptide affinity experiments improves SH2 interaction data. J Biol Chem 2020; 295:11346-11363. [PMID: 32540967 DOI: 10.1074/jbc.ra120.012503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 06/11/2020] [Indexed: 11/06/2022] Open
Abstract
Protein domain interactions with short linear peptides, such as those of the Src homology 2 (SH2) domain with phosphotyrosine-containing peptide motifs (pTyr), are ubiquitous and important to many biochemical processes of the cell. The desire to map and quantify these interactions has resulted in the development of high-throughput (HTP) quantitative measurement techniques, such as microarray or fluorescence polarization assays. For example, in the last 15 years, experiments have progressed from measuring single interactions to covering 500,000 of the 5.5 million possible SH2-pTyr interactions in the human proteome. However, high variability in affinity measurements and disagreements about positive interactions between published data sets led us here to reevaluate the analysis methods and raw data of published SH2-pTyr HTP experiments. We identified several opportunities for improving the identification of positive and negative interactions and the accuracy of affinity measurements. We implemented model-fitting techniques that are more statistically appropriate for the nonlinear SH2-pTyr interaction data. We also developed a method to account for protein concentration errors due to impurities and degradation or protein inactivity and aggregation. Our revised analysis increases the reported affinity accuracy, reduces the false-negative rate, and increases the amount of useful data by adding reliable true-negative results. We demonstrate improvement in classification of binding versus nonbinding when using machine-learning techniques, suggesting improved coherence in the reanalyzed data sets. We present revised SH2-pTyr affinity results and propose a new analysis pipeline for future HTP measurements of domain-peptide interactions.
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Affiliation(s)
- Tom Ronan
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Roman Garnett
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Kristen M Naegle
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
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14
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Mei S, Li F, Leier A, Marquez-Lago TT, Giam K, Croft NP, Akutsu T, Smith AI, Li J, Rossjohn J, Purcell AW, Song J. A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction. Brief Bioinform 2020; 21:1119-1135. [PMID: 31204427 DOI: 10.1093/bib/bbz051] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/02/2019] [Accepted: 04/03/2019] [Indexed: 12/13/2022] Open
Abstract
Human leukocyte antigen class I (HLA-I) molecules are encoded by major histocompatibility complex (MHC) class I loci in humans. The binding and interaction between HLA-I molecules and intracellular peptides derived from a variety of proteolytic mechanisms play a crucial role in subsequent T-cell recognition of target cells and the specificity of the immune response. In this context, tools that predict the likelihood for a peptide to bind to specific HLA class I allotypes are important for selecting the most promising antigenic targets for immunotherapy. In this article, we comprehensively review a variety of currently available tools for predicting the binding of peptides to a selection of HLA-I allomorphs. Specifically, we compare their calculation methods for the prediction score, employed algorithms, evaluation strategies and software functionalities. In addition, we have evaluated the prediction performance of the reviewed tools based on an independent validation data set, containing 21 101 experimentally verified ligands across 19 HLA-I allotypes. The benchmarking results show that MixMHCpred 2.0.1 achieves the best performance for predicting peptides binding to most of the HLA-I allomorphs studied, while NetMHCpan 4.0 and NetMHCcons 1.1 outperform the other machine learning-based and consensus-based tools, respectively. Importantly, it should be noted that a peptide predicted with a higher binding score for a specific HLA allotype does not necessarily imply it will be immunogenic. That said, peptide-binding predictors are still very useful in that they can help to significantly reduce the large number of epitope candidates that need to be experimentally verified. Several other factors, including susceptibility to proteasome cleavage, peptide transport into the endoplasmic reticulum and T-cell receptor repertoire, also contribute to the immunogenicity of peptide antigens, and some of them can be considered by some predictors. Therefore, integrating features derived from these additional factors together with HLA-binding properties by using machine-learning algorithms may increase the prediction accuracy of immunogenic peptides. As such, we anticipate that this review and benchmarking survey will assist researchers in selecting appropriate prediction tools that best suit their purposes and provide useful guidelines for the development of improved antigen predictors in the future.
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Affiliation(s)
- Shutao Mei
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Fuyi Li
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - André Leier
- Department of Genetics and Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, AL, USA
| | - Tatiana T Marquez-Lago
- Department of Genetics and Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, AL, USA
| | - Kailin Giam
- Department of Immunology, King's College London, London, UK
| | - Nathan P Croft
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Tatsuya Akutsu
- Bioinformatics Centre, Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - A Ian Smith
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC, Australia
| | - Jian Li
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Jamie Rossjohn
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC, Australia
| | - Anthony W Purcell
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Jiangning Song
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC, Australia.,Monash Centre for Data Science, Monash University, Melbourne, VIC, Australia
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15
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Rational Derivation of Osteogenic Peptides from Bone
Morphogenetic Protein-2 Knuckle Epitope by Integrating In
Silico Analysis and In Vitro Assay. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-020-10058-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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16
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Xu B, Chung HY. Quantitative Structure-Activity Relationship Study of Bitter Di-, Tri- and Tetrapeptides Using Integrated Descriptors. Molecules 2019; 24:molecules24152846. [PMID: 31387305 PMCID: PMC6696392 DOI: 10.3390/molecules24152846] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/23/2019] [Accepted: 08/05/2019] [Indexed: 11/16/2022] Open
Abstract
New quantitative structure–activity relationship (QSAR) models for bitter peptides were built with integrated amino acid descriptors. Datasets contained 48 dipeptides, 52 tripeptides and 23 tetrapeptides with their reported bitter taste thresholds. Independent variables consisted of 14 amino acid descriptor sets. A bootstrapping soft shrinkage approach was utilized for variable selection. The importance of a variable was evaluated by both variable selecting frequency and standardized regression coefficient. Results indicated model qualities for di-, tri- and tetrapeptides with R2 and Q2 at 0.950 ± 0.002, 0.941 ± 0.001; 0.770 ± 0.006, 0.742 ± 0.004; and 0.972 ± 0.002, 0.956 ± 0.002, respectively. The hydrophobic C-terminal amino acid was the key determinant for bitterness in dipeptides, followed by the contribution of bulky hydrophobic N-terminal amino acids. For tripeptides, hydrophobicity of C-terminal amino acids and the electronic properties of the amino acids at the second position were important. For tetrapeptides, bulky hydrophobic amino acids at N-terminus, hydrophobicity and partial specific volume of amino acids at the second position, and the electronic properties of amino acids of the remaining two positions were critical. In summary, this study not only constructs reliable models for predicting the bitterness in different groups of peptides, but also facilitates better understanding of their structure-bitterness relationships and provides insights for their future studies.
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Affiliation(s)
- Biyang Xu
- Food and Nutritional Sciences Programme, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Hau Yin Chung
- Food and Nutritional Sciences Programme, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
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17
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Agnew HD, Coppock MB, Idso MN, Lai BT, Liang J, McCarthy-Torrens AM, Warren CM, Heath JR. Protein-Catalyzed Capture Agents. Chem Rev 2019; 119:9950-9970. [PMID: 30838853 DOI: 10.1021/acs.chemrev.8b00660] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein-catalyzed capture agents (PCCs) are synthetic and modular peptide-based affinity agents that are developed through the use of single-generation in situ click chemistry screens against large peptide libraries. In such screens, the target protein, or a synthetic epitope fragment of that protein, provides a template for selectively promoting the noncopper catalyzed azide-alkyne dipolar cycloaddition click reaction between either a library peptide and a known ligand or a library peptide and the synthetic epitope. The development of epitope-targeted PCCs was motivated by the desire to fully generalize pioneering work from the Sharpless and Finn groups in which in situ click screens were used to develop potent, divalent enzymatic inhibitors. In fact, a large degree of generality has now been achieved. Various PCCs have demonstrated utility for selective protein detection, as allosteric or direct inhibitors, as modulators of protein folding, and as tools for in vivo tumor imaging. We provide a historical context for PCCs and place them within the broader scope of biological and synthetic aptamers. The development of PCCs is presented as (i) Generation I PCCs, which are branched ligands engineered through an iterative, nonepitope-targeted process, and (ii) Generation II PCCs, which are typically developed from macrocyclic peptide libraries and are precisely epitope-targeted. We provide statistical comparisons of Generation II PCCs relative to monoclonal antibodies in which the protein target is the same. Finally, we discuss current challenges and future opportunities of PCCs.
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Affiliation(s)
- Heather D Agnew
- Indi Molecular, Inc. , 6162 Bristol Parkway , Culver City , California 90230 , United States
| | - Matthew B Coppock
- Sensors and Electron Devices Directorate , U.S. Army Research Laboratory , Adelphi , Maryland 20783 , United States
| | - Matthew N Idso
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109-5234 , United States
| | - Bert T Lai
- Indi Molecular, Inc. , 6162 Bristol Parkway , Culver City , California 90230 , United States
| | - JingXin Liang
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109-5234 , United States
| | - Amy M McCarthy-Torrens
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109-5234 , United States
| | - Carmen M Warren
- Indi Molecular, Inc. , 6162 Bristol Parkway , Culver City , California 90230 , United States
| | - James R Heath
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109-5234 , United States
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18
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Deng B, Long H, Tang T, Ni X, Chen J, Yang G, Zhang F, Cao R, Cao D, Zeng M, Yi L. Quantitative Structure-Activity Relationship Study of Antioxidant Tripeptides Based on Model Population Analysis. Int J Mol Sci 2019; 20:ijms20040995. [PMID: 30823542 PMCID: PMC6413046 DOI: 10.3390/ijms20040995] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 02/13/2019] [Accepted: 02/18/2019] [Indexed: 11/16/2022] Open
Abstract
Due to their beneficial effects on human health, antioxidant peptides have attracted much attention from researchers. However, the structure-activity relationships of antioxidant peptides have not been fully understood. In this paper, quantitative structure-activity relationships (QSAR) models were built on two datasets, i.e., the ferric thiocyanate (FTC) dataset and ferric-reducing antioxidant power (FRAP) dataset, containing 214 and 172 unique antioxidant tripeptides, respectively. Sixteen amino acid descriptors were used and model population analysis (MPA) was then applied to improve the QSAR models for better prediction performance. The results showed that, by applying MPA, the cross-validated coefficient of determination (Q²) was increased from 0.6170 to 0.7471 for the FTC dataset and from 0.4878 to 0.6088 for the FRAP dataset, respectively. These findings indicate that the integration of different amino acid descriptors provide additional information for model building and MPA can efficiently extract the information for better prediction performance.
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Affiliation(s)
- Baichuan Deng
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Hongrong Long
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Tianyue Tang
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Xiaojun Ni
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Jialuo Chen
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Guangming Yang
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Fan Zhang
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Ruihua Cao
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Dongsheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410083, China.
| | - Maomao Zeng
- State Key Laboratory of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.
| | - Lunzhao Yi
- Yunnan Food Safety Research Institute, Kunming University of Science and Technology, Kunming 650500, China.
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19
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Agyei D, Tsopmo A, Udenigwe CC. Bioinformatics and peptidomics approaches to the discovery and analysis of food-derived bioactive peptides. Anal Bioanal Chem 2018. [PMID: 29516135 DOI: 10.1007/s00216-018-0974-1] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
There are emerging advancements in the strategies used for the discovery and development of food-derived bioactive peptides because of their multiple food and health applications. Bioinformatics and peptidomics are two computational and analytical techniques that have the potential to speed up the development of bioactive peptides from bench to market. Structure-activity relationships observed in peptides form the basis for bioinformatics and in silico prediction of bioactive sequences encrypted in food proteins. Peptidomics, on the other hand, relies on "hyphenated" (liquid chromatography-mass spectrometry-based) techniques for the detection, profiling, and quantitation of peptides. Together, bioinformatics and peptidomics approaches provide a low-cost and effective means of predicting, profiling, and screening bioactive protein hydrolysates and peptides from food. This article discuses the basis, strengths, and limitations of bioinformatics and peptidomics approaches currently used for the discovery and analysis of food-derived bioactive peptides.
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Affiliation(s)
- Dominic Agyei
- Department of Food Science, University of Otago, Dunedin, 9054, New Zealand
| | - Apollinaire Tsopmo
- Food Science and Nutrition Program, Department of Chemistry, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | - Chibuike C Udenigwe
- School of Nutrition Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada. .,Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
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20
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Antunes DA, Abella JR, Devaurs D, Rigo MM, Kavraki LE. Structure-based Methods for Binding Mode and Binding Affinity Prediction for Peptide-MHC Complexes. Curr Top Med Chem 2018; 18:2239-2255. [PMID: 30582480 PMCID: PMC6361695 DOI: 10.2174/1568026619666181224101744] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 11/29/2018] [Accepted: 12/08/2018] [Indexed: 12/26/2022]
Abstract
Understanding the mechanisms involved in the activation of an immune response is essential to many fields in human health, including vaccine development and personalized cancer immunotherapy. A central step in the activation of the adaptive immune response is the recognition, by T-cell lymphocytes, of peptides displayed by a special type of receptor known as Major Histocompatibility Complex (MHC). Considering the key role of MHC receptors in T-cell activation, the computational prediction of peptide binding to MHC has been an important goal for many immunological applications. Sequence- based methods have become the gold standard for peptide-MHC binding affinity prediction, but structure-based methods are expected to provide more general predictions (i.e., predictions applicable to all types of MHC receptors). In addition, structural modeling of peptide-MHC complexes has the potential to uncover yet unknown drivers of T-cell activation, thus allowing for the development of better and safer therapies. In this review, we discuss the use of computational methods for the structural modeling of peptide-MHC complexes (i.e., binding mode prediction) and for the structure-based prediction of binding affinity.
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Affiliation(s)
| | - Jayvee R. Abella
- Computer Science Department, Rice University, Houston, Texas, USA
| | - Didier Devaurs
- Computer Science Department, Rice University, Houston, Texas, USA
| | - Maurício M. Rigo
- School of Medicine, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Lydia E. Kavraki
- Computer Science Department, Rice University, Houston, Texas, USA
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21
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Deng B, Ni X, Zhai Z, Tang T, Tan C, Yan Y, Deng J, Yin Y. New Quantitative Structure-Activity Relationship Model for Angiotensin-Converting Enzyme Inhibitory Dipeptides Based on Integrated Descriptors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:9774-9781. [PMID: 28984136 DOI: 10.1021/acs.jafc.7b03367] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Angiotensin-converting enzyme (ACE) inhibitory peptides derived from food proteins have been widely reported for hypertension treatment. In this paper, a benchmark data set containing 141 unique ACE inhibitory dipeptides was constructed through database mining, and a quantitative structure-activity relationships (QSAR) study was carried out to predict half-inhibitory concentration (IC50) of ACE activity. Sixteen descriptors were tested and the model generated by G-scale descriptor showed the best predictive performance with the coefficient of determination (R2) and cross-validated R2 (Q2) of 0.6692 and 0.6220, respectively. For most other descriptors, R2 were ranging from 0.52 to 0.68 and Q2 were ranging from 0.48 to 0.61. A complex model combining all 16 descriptors was carried out and variable selection was performed in order to further improve the prediction performance. The quality of model using integrated descriptors (R2 0.7340 ± 0.0038, Q2 0.7151 ± 0.0019) was better than that of G-scale. An in-depth study of variable importance showed that the most correlated properties to ACE inhibitory activity were hydrophobicity, steric, and electronic properties and C-terminal amino acids contribute more than N-terminal amino acids. Five novel predicted ACE-inhibitory peptides were synthesized, and their IC50 values were validated through in vitro experiments. The results indicated that the constructed model could give a reliable prediction of ACE-inhibitory activity of peptides, and it may be useful in the design of novel ACE-inhibitory peptides.
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Affiliation(s)
- Baichuan Deng
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
| | - Xiaojun Ni
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
| | - Zhenya Zhai
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
| | - Tianyue Tang
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
| | - Chengquan Tan
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
| | - Yijing Yan
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
| | - Jinping Deng
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
| | - Yulong Yin
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
- National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences , Changsha 410125, Hunan, P.R. China
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22
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Ma Y, Liu R, Lv H, Han J, Zhong D, Zhang X. A computational method for prediction of matrix proteins in endogenous retroviruses. PLoS One 2017; 12:e0176909. [PMID: 28472185 PMCID: PMC5417524 DOI: 10.1371/journal.pone.0176909] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 04/19/2017] [Indexed: 11/18/2022] Open
Abstract
Human endogenous retroviruses (HERVs) encode active retroviral proteins, which may be involved in the progression of cancer and other diseases. Matrix protein (MA), in group-specific antigen genes (gag) of retroviruses, is associated with the virus envelope glycoproteins in most mammalian retroviruses and may be involved in virus particle assembly, transport and budding. However, the amount of annotated MAs in ERVs is still at a low level so far. No computational method to predict the exact start and end coordinates of MAs in gags has been proposed yet. In this paper, a computational method to identify MAs in ERVs is proposed. A divide and conquer technique was designed and applied to the conventional prediction model to acquire better results when dealing with gene sequences with various lengths. Initiation sites and termination sites were predicted separately and then combined according to their intervals. Three different algorithms were applied and compared: weighted support vector machine (WSVM), weighted extreme learning machine (WELM) and random forest (RF). G − mean (geometric mean of sensitivity and specificity) values of initiation sites and termination sites under 5-fold cross validation generated by random forest models are 0.9869 and 0.9755 respectively, highest among the algorithms applied. Our prediction models combine RF & WSVM algorithms to achieve the best prediction results. 98.4% of all the collected ERV sequences with complete MAs (125 in total) could be predicted exactly correct by the models. 94,671 HERV sequences from 118 families were scanned by the model, 104 new putative MAs were predicted in human chromosomes. Distributions of the putative MAs and optimizations of model parameters were also analyzed. The usage of our predicting method was also expanded to other retroviruses and satisfying results were acquired.
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Affiliation(s)
- Yucheng Ma
- School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China
| | - Ruiling Liu
- School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China
- * E-mail: (RLL); (HQL)
| | - Hongqiang Lv
- School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China
- * E-mail: (RLL); (HQL)
| | - Jiuqiang Han
- School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China
| | - Dexing Zhong
- School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China
| | - Xinman Zhang
- School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China
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23
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Liu Z, Lv H, Han J, Liu R. A computational model for predicting transmembrane regions of retroviruses. J Bioinform Comput Biol 2017; 15:1750010. [PMID: 28403667 DOI: 10.1142/s021972001750010x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Transmembrane region (TR) is a conserved region of transmembrane (TM) subunit in envelope (env) glycoprotein of retrovirus. Evidences have shown that TR is responsible for anchoring the env glycoprotein on the lipid bilayer and substitution of the TR for a covalently linked lipid anchor abrogates fusion. However, universal software could not achieve sufficient accuracy as TM in env also has several motifs such as signal peptide, fusion peptide and immunosuppressive domain composed largely of hydrophobic residues. In this paper, a support vector machine-based (SVM) model is proposed to identify TRs in retroviruses. Firstly, physicochemical and evolutionary information properties were extracted as original features. And then, the feature importance was analyzed by minimum Redundancy Maximum Relevance (mRMR) feature selection criterion. Our model achieved an Sn of 0.955, Sp of 0.998, ACC of 0.995, MCC of 0.954 using 10-fold cross-validation on the training dataset. These results suggest that the proposed model can be used to predict TRs in non-annotation retroviruses and 11917, 3344, 2, 289 and 6 new putative TRs were found in HERV, HIV, HTLV, SIV, MLV, respectively.
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Affiliation(s)
- Ze Liu
- 1 School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Hongqiang Lv
- 1 School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Jiuqiang Han
- 1 School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Ruiling Liu
- 1 School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
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24
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Comprehensive comparison of twenty structural characterization scales applied as QSAM of antimicrobial dodecapeptides derived from Bac2A against P. aeruginosa. J Mol Graph Model 2017; 71:88-95. [DOI: 10.1016/j.jmgm.2016.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Revised: 11/02/2016] [Accepted: 11/06/2016] [Indexed: 02/04/2023]
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25
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Jandrlić DR. SVM and SVR-based MHC-binding prediction using a mathematical presentation of peptide sequences. Comput Biol Chem 2016; 65:117-127. [PMID: 27816828 DOI: 10.1016/j.compbiolchem.2016.10.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 09/16/2016] [Accepted: 10/24/2016] [Indexed: 11/16/2022]
Abstract
At present, there are a number of methods for the prediction of T-cell epitopes and major histocompatibility complex (MHC)-binding peptides. Despite numerous methods for predicting T-cell epitopes, there still exist limitations that affect the reliability of prevailing methods. For this reason, the development of models with high accuracy are crucial. An accurate prediction of the peptides that bind to specific major histocompatibility complex class I and II (MHC-I and MHC-II) molecules is important for an understanding of the functioning of the immune system and the development of peptide-based vaccines. Peptide binding is the most selective step in identifying T-cell epitopes. In this paper, we present a new approach to predicting MHC-binding ligands that takes into account new weighting schemes for position-based amino acid frequencies, BLOSUM and VOGG substitution of amino acids, and the physicochemical and molecular properties of amino acids. We have made models for quantitatively and qualitatively predicting MHC-binding ligands. Our models are based on two machine learning methods support vector machine (SVM) and support vector regression (SVR), where our models have used for feature selection, several different encoding and weighting schemes for peptides. The resulting models showed comparable, and in some cases better, performance than the best existing predictors. The obtained results indicate that the physicochemical and molecular properties of amino acids (AA) contribute significantly to the peptide-binding affinity.
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Affiliation(s)
- Davorka R Jandrlić
- University of Belgrade, Faculty of Mechanical Engineering, Kraljice Marije 16, Belgrade, Serbia.
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Cheng X, Mei Y, Ji X, Xue Q, Chen D. Molecular mechanism of the susceptibility difference between HLA-B*27:02/04/05 and HLA-B*27:06/09 to ankylosing spondylitis: substitution analysis, MD simulation, QSAR modelling, and in vitro assay. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2016; 27:409-425. [PMID: 27228481 DOI: 10.1080/1062936x.2016.1179672] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/13/2016] [Indexed: 06/05/2023]
Abstract
The human leukocyte antigen HLA-B27 is directly involved in the disease pathogenesis of ankylosing spondylitis (AS). HLA-B27 has a high degree of genetic polymorphism, with 105 currently known subtypes; the presence of aspartic acid at residue 116 (Asp116) has been found to play an essential role in AS susceptibility. Here, we systematically investigated the molecular mechanism of the susceptibility difference between the AS-associated subtypes HLA-B*27:02/04/05 and AS-unassociated subtypes HLA-B*27:06/09 to AS at sequence, structure, energetic and dynamic levels. In total seven variable residues were identified among the five studied HLA-B27 subtypes, in which Asp116 can be largely stabilized by a spatially vicinal, positively charged His114 through a salt bridge, while five other variable residues seem to have only a marginal effect on AS susceptibility. We also employed a quantitative structure-activity relationship approach to model the statistical correlation between peptide structure and affinity to HLA-B*27:05, a genetic ancestor of all other HLA-B27 subtypes and associated strongly with AS. The built regression predictor was verified rigorously through both internal cross-validation and external blind validation, and was then employed to identify potential HLA-B*27:05 binders from >20,000 cartilage-derived self-peptides. Subsequently, the binding potency of the top five antigenic peptides to HLA-B*27:05 was assayed in vitro using a FACS-based MHC stabilization experiment. Consequently, two (QRVGSDEFK and LRGAGTNEK) out of the five peptides were determined to have high affinity (BL50 = 5.5 and 15.8 nM, respectively) and, as expected, both of them possess positively charged Lys at the C-terminus.
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Affiliation(s)
- X Cheng
- a Department of Nephrology and Rheumatology, Affiliated Sixth People's Hospital , Shanghai Jiao Tong University , Shanghai , China
| | - Y Mei
- a Department of Nephrology and Rheumatology, Affiliated Sixth People's Hospital , Shanghai Jiao Tong University , Shanghai , China
| | - X Ji
- a Department of Nephrology and Rheumatology, Affiliated Sixth People's Hospital , Shanghai Jiao Tong University , Shanghai , China
| | - Q Xue
- a Department of Nephrology and Rheumatology, Affiliated Sixth People's Hospital , Shanghai Jiao Tong University , Shanghai , China
| | - D Chen
- b Department of Orthopaedics, Affiliated Sixth People's Hospital , Shanghai Jiao Tong University , Shanghai , China
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Agyei D, Ongkudon CM, Wei CY, Chan AS, Danquah MK. Bioprocess challenges to the isolation and purification of bioactive peptides. FOOD AND BIOPRODUCTS PROCESSING 2016. [DOI: 10.1016/j.fbp.2016.02.003] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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28
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Nongonierma AB, FitzGerald RJ. Strategies for the discovery, identification and validation of milk protein-derived bioactive peptides. Trends Food Sci Technol 2016. [DOI: 10.1016/j.tifs.2016.01.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Structure–activity relationship of antioxidant dipeptides: Dominant role of Tyr, Trp, Cys and Met residues. J Funct Foods 2016. [DOI: 10.1016/j.jff.2015.12.003] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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30
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Nongonierma AB, FitzGerald RJ. Learnings from quantitative structure–activity relationship (QSAR) studies with respect to food protein-derived bioactive peptides: a review. RSC Adv 2016. [DOI: 10.1039/c6ra12738j] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
QSAR studies may help to better understand structural requirements for peptide bioactivity and therefore to develop potent BAPs.
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Affiliation(s)
- Alice B. Nongonierma
- Department of Life Sciences and Food for Health Ireland (FHI)
- University of Limerick
- Limerick
- Ireland
| | - Richard J. FitzGerald
- Department of Life Sciences and Food for Health Ireland (FHI)
- University of Limerick
- Limerick
- Ireland
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31
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Li B, Zheng X, Hu C, Cao Y. Human Papillomavirus Genome-Wide Identification of T-Cell Epitopes for Peptide Vaccine Development Against Cervical Cancer: An Integration of Computational Analysis and Experimental Assay. J Comput Biol 2015; 22:962-74. [PMID: 26418056 DOI: 10.1089/cmb.2014.0287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Bo Li
- Department of Obstetrics and Gynecology, Anhui Medical University, Hefei, China
| | - Xianfang Zheng
- Department of Obstetrics and Gynecology, Chaohu Hospital of Anhui Medical University, Chaohu, China
| | - Chuancui Hu
- Department of Obstetrics and Gynecology, Chaohu Hospital of Anhui Medical University, Chaohu, China
| | - Yunxia Cao
- Department of Obstetrics and Gynecology, Anhui Medical University, Hefei, China
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Tian M, Fang B, Jiang L, Guo H, Cui J, Ren F. Structure-activity relationship of a series of antioxidant tripeptides derived from β-Lactoglobulin using QSAR modeling. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s13594-015-0226-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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33
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Aguilar-Bonavides C, Sanchez-Arias R, Lanzas C. Accurate prediction of major histocompatibility complex class II epitopes by sparse representation via ℓ 1-minimization. BioData Min 2014; 7:23. [PMID: 25392716 PMCID: PMC4225598 DOI: 10.1186/1756-0381-7-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 10/25/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The major histocompatibility complex (MHC) is responsible for presenting antigens (epitopes) on the surface of antigen-presenting cells (APCs). When pathogen-derived epitopes are presented by MHC class II on an APC surface, T cells may be able to trigger an specific immune response. Prediction of MHC-II epitopes is particularly challenging because the open binding cleft of the MHC-II molecule allows epitopes to bind beyond the peptide binding groove; therefore, the molecule is capable of accommodating peptides of variable length. Among the methods proposed to predict MHC-II epitopes, artificial neural networks (ANNs) and support vector machines (SVMs) are the most effective methods. We propose a novel classification algorithm to predict MHC-II called sparse representation via ℓ 1-minimization. RESULTS We obtained a collection of experimentally confirmed MHC-II epitopes from the Immune Epitope Database and Analysis Resource (IEDB) and applied our ℓ 1-minimization algorithm. To benchmark the performance of our proposed algorithm, we compared our predictions against a SVM classifier. We measured sensitivity, specificity abd accuracy; then we used Receiver Operating Characteristic (ROC) analysis to evaluate the performance of our method. The prediction performance of MHC-II epitopes of the ℓ 1-minimization algorithm was generally comparable and, in some cases, superior to the standard SVM classification method and overcame the lack of robustness of other methods with respect to outliers. While our method consistently favoured DPPS encoding with the alleles tested, SVM showed a slightly better accuracy when "11-factor" encoding was used. CONCLUSIONS ℓ 1-minimization has similar accuracy than SVM, and has additional advantages, such as overcoming the lack of robustness with respect to outliers. With ℓ 1-minimization no model selection dependency is involved.
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Affiliation(s)
- Clemente Aguilar-Bonavides
- National Institute for Mathematical and Biological Synthesis, University of Tennessee, 37996-3410 Knoxville, TN, USA
| | - Reinaldo Sanchez-Arias
- Department of Applied Mathematics, Wentworth Institute of Technology, 02115 Boston, MA, USA
| | - Cristina Lanzas
- National Institute for Mathematical and Biological Synthesis, University of Tennessee, 37996-3410 Knoxville, TN, USA.,Department of Biomedical and Diagnostic Sciences, University of Tennessee, 37996-3410 Knoxville, TN, USA
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34
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To Determine Biologically Important Mutations in Oxytocin. Int J Pept Res Ther 2014. [DOI: 10.1007/s10989-014-9412-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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35
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Lv H, Han J, Liu J, Zheng J, Zhong D, Liu R. ISDTool: A computational model for predicting immunosuppressive domain of HERVs. Comput Biol Chem 2014; 49:45-50. [DOI: 10.1016/j.compbiolchem.2014.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 02/01/2014] [Accepted: 02/04/2014] [Indexed: 11/26/2022]
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36
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Wang L, Dai Z, Zhang H, Bai L, Yuan Z. Quantitative Sequence-Activity Model Analysis of Oligopeptides Coupling an Improved High-Dimension Feature Selection Method with Support Vector Regression. Chem Biol Drug Des 2014; 83:379-91. [DOI: 10.1111/cbdd.12242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 08/31/2013] [Accepted: 09/27/2013] [Indexed: 01/20/2023]
Affiliation(s)
- Lifeng Wang
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization; Hunan Agricultural University; Changsha 410128 China
- College of Plant Protection; Hunan Agricultural University; Changsha 410128 China
| | - Zhijun Dai
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization; Hunan Agricultural University; Changsha 410128 China
- College of Plant Protection; Hunan Agricultural University; Changsha 410128 China
| | - Hongyan Zhang
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization; Hunan Agricultural University; Changsha 410128 China
- College of Plant Protection; Hunan Agricultural University; Changsha 410128 China
| | - Lianyang Bai
- College of Plant Protection; Hunan Agricultural University; Changsha 410128 China
- Hunan Academy of Agricultural Sciences; Changsha 410125 China
| | - Zheming Yuan
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization; Hunan Agricultural University; Changsha 410128 China
- College of Plant Protection; Hunan Agricultural University; Changsha 410128 China
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He P, Wu W, Wang HD, Liao KL, Zhang W, Lv FL, Yang K. Why ligand cross-reactivity is high within peptide recognition domain families? A case study on human c-Src SH3 domain. J Theor Biol 2014; 340:30-7. [DOI: 10.1016/j.jtbi.2013.08.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/26/2013] [Accepted: 08/21/2013] [Indexed: 10/26/2022]
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38
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Evolution of High-Affinity Peptide Probes to Detect the SH3 Domain of Cancer Biomarker BCR–ABL. Int J Pept Res Ther 2013. [DOI: 10.1007/s10989-013-9382-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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39
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Just an additional hydrogen bond can dramatically reduce the catalytic activity of Bacillus subtilis lipase A I12T mutant: An integration of computational modeling and experimental analysis. Comput Biol Med 2013; 43:1882-8. [DOI: 10.1016/j.compbiomed.2013.08.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 08/19/2013] [Accepted: 08/22/2013] [Indexed: 11/22/2022]
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40
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Zhou Y, Ni Z, Chen K, Liu H, Chen L, Lian C, Yan L. Modeling Protein–Peptide Recognition Based on Classical Quantitative Structure–Affinity Relationship Approach: Implication for Proteome-Wide Inference of Peptide-Mediated Interactions. Protein J 2013; 32:568-78. [DOI: 10.1007/s10930-013-9519-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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41
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Tan J, Tian F, Lv Y, Liu W, Zhong L, Liu Y, Yang L. Integration of QSAR modelling and QM/MM analysis to investigate functional food peptides with antihypertensive activity. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.788247] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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42
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Han KQ, Wu G, Lv F. Development of QSAR-Improved Statistical Potential for the Structure-Based Analysis of ProteinPeptide Binding Affinities. Mol Inform 2013; 32:783-92. [DOI: 10.1002/minf.201300064] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 06/21/2013] [Indexed: 12/21/2022]
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43
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Guo T, Yang J, Zeng L, Wang H, Tong Q, Li X. Does there exist an intrinsic relationship between the flexibility and self-assembly of pepfactants? MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.817673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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44
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Stepwise identification of potent antimicrobial peptides from human genome. Biosystems 2013; 113:1-8. [DOI: 10.1016/j.biosystems.2013.03.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 03/18/2013] [Accepted: 03/31/2013] [Indexed: 11/23/2022]
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45
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Tian F, Tan R, Guo T, Zhou P, Yang L. Fast and reliable prediction of domain–peptide binding affinity using coarse-grained structure models. Biosystems 2013; 113:40-9. [DOI: 10.1016/j.biosystems.2013.04.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 04/15/2013] [Accepted: 04/20/2013] [Indexed: 10/26/2022]
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46
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Structural and Affinity Insight into the Sequence-Specific Interaction of Transcription Factors DEC1 and DEC2 with E-box DNA: A Novel Model Peptide Approach. Int J Pept Res Ther 2013. [DOI: 10.1007/s10989-013-9354-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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47
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Wang JH, Liu YL, Ning JH, Yu J, Li XH, Wang FX. Is the structural diversity of tripeptides sufficient for developing functional food additives with satisfactory multiple bioactivities? J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.03.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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48
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Characterization of structure–antioxidant activity relationship of peptides in free radical systems using QSAR models: Key sequence positions and their amino acid properties. J Theor Biol 2013; 318:29-43. [DOI: 10.1016/j.jtbi.2012.10.029] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 10/21/2012] [Accepted: 10/22/2012] [Indexed: 11/22/2022]
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49
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Biomacromolecular quantitative structure–activity relationship (BioQSAR): a proof-of-concept study on the modeling, prediction and interpretation of protein–protein binding affinity. J Comput Aided Mol Des 2013; 27:67-78. [DOI: 10.1007/s10822-012-9625-3] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 12/12/2012] [Indexed: 01/22/2023]
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50
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Saethang T, Hirose O, Kimkong I, Tran VA, Dang XT, Nguyen LAT, Le TKT, Kubo M, Yamada Y, Satou K. EpicCapo: epitope prediction using combined information of amino acid pairwise contact potentials and HLA-peptide contact site information. BMC Bioinformatics 2012; 13:313. [PMID: 23176036 PMCID: PMC3548761 DOI: 10.1186/1471-2105-13-313] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 11/15/2012] [Indexed: 11/10/2022] Open
Abstract
Background Epitope identification is an essential step toward synthetic vaccine development since epitopes play an important role in activating immune response. Classical experimental approaches are laborious and time-consuming, and therefore computational methods for generating epitope candidates have been actively studied. Most of these methods, however, are based on sophisticated nonlinear techniques for achieving higher predictive performance. The use of these techniques tend to diminish their interpretability with respect to binding potential: that is, they do not provide much insight into binding mechanisms. Results We have developed a novel epitope prediction method named EpicCapo and its variants, EpicCapo+ and EpicCapo+REF. Nonapeptides were encoded numerically using a novel peptide-encoding scheme for machine learning algorithms by utilizing 40 amino acid pairwise contact potentials (referred to as AAPPs throughout this paper). The predictive performances of EpicCapo+ and EpicCapo+REF outperformed other state-of-the-art methods without losing interpretability. Interestingly, the most informative AAPPs estimated by our study were those developed by Micheletti and Simons while previous studies utilized two AAPPs developed by Miyazawa & Jernigan and Betancourt & Thirumalai. In addition, we found that all amino acid positions in nonapeptides could effect on performances of the predictive models including non-anchor positions. Finally, EpicCapo+REF was applied to identify candidates of promiscuous epitopes. As a result, 67.1% of the predicted nonapeptides epitopes were consistent with preceding studies based on immunological experiments. Conclusions Our method achieved high performance in testing with benchmark datasets. In addition, our study identified a number of candidates of promiscuous CTL epitopes consistent with previously reported immunological experiments. We speculate that our techniques may be useful in the development of new vaccines. The R implementation of EpicCapo+REF is available at
http://pirun.ku.ac.th/~fsciiok/EpicCapoREF.zip. Datasets are available at
http://pirun.ku.ac.th/~fsciiok/Datasets.zip.
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Affiliation(s)
- Thammakorn Saethang
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan.
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