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Peng HP, Yang AS. Computational Analysis of Antibody Paratopes for Antibody Sequences in Antibody Libraries. Methods Mol Biol 2023; 2552:437-445. [PMID: 36346607 DOI: 10.1007/978-1-0716-2609-2_24] [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] [Indexed: 06/16/2023]
Abstract
To ensure the functionalities of the antibodies in phage-displayed synthetic antibody libraries, we use computational method to evaluate the designs of the antibody libraries. The computational methodologies developed in our lab for designing antibody library provide rich information on the function of the designed antibody sequences-adequate antibody designs for a specific antigen type should have predicted paratopes for the antigen type. This computational assessment of the designed antibody sequences helps eliminate non-functional designs before proceeding to construct the library designs in the wet lab. As such, only reasonable antibody designs are constructed for antibody discoveries.
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Affiliation(s)
- Hung-Pin Peng
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.
| | - An-Suei Yang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.
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2
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Chang RL, Stanley JA, Robinson MC, Sher JW, Li Z, Chan YA, Omdahl AR, Wattiez R, Godzik A, Matallana-Surget S. Protein structure, amino acid composition and sequence determine proteome vulnerability to oxidation-induced damage. EMBO J 2020; 39:e104523. [PMID: 33073387 PMCID: PMC7705453 DOI: 10.15252/embj.2020104523] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 09/16/2020] [Accepted: 09/22/2020] [Indexed: 02/05/2023] Open
Abstract
Oxidative stress alters cell viability, from microorganism irradiation sensitivity to human aging and neurodegeneration. Deleterious effects of protein carbonylation by reactive oxygen species (ROS) make understanding molecular properties determining ROS susceptibility essential. The radiation‐resistant bacterium Deinococcus radiodurans accumulates less carbonylation than sensitive organisms, making it a key model for deciphering properties governing oxidative stress resistance. We integrated shotgun redox proteomics, structural systems biology, and machine learning to resolve properties determining protein damage by γ‐irradiation in Escherichia coli and D. radiodurans at multiple scales. Local accessibility, charge, and lysine enrichment accurately predict ROS susceptibility. Lysine, methionine, and cysteine usage also contribute to ROS resistance of the D. radiodurans proteome. Our model predicts proteome maintenance machinery, and proteins protecting against ROS are more resistant in D. radiodurans. Our findings substantiate that protein‐intrinsic protection impacts oxidative stress resistance, identifying causal molecular properties.
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Affiliation(s)
- Roger L Chang
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Julian A Stanley
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA
| | - Matthew C Robinson
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA
| | - Joel W Sher
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA
| | - Zhanwen Li
- Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, USA
| | - Yujia A Chan
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Ashton R Omdahl
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Adam Godzik
- Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, USA
| | - Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, UK
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Srinivasan E, Ravikumar S, Venkataramanan S, Purohit R, Rajasekaran R. Molecular mechanics and quantum chemical calculations unveil the combating effect of baicalein on human islet amyloid polypeptide aggregates. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1660778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- E. Srinivasan
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore, India
| | - S. Ravikumar
- Multidisciplinary Center for Biomedical Research, Aarupadai Veedu Medical College and Hospital, Vinayaka Missions Research Foundation, Puducherry, India
| | - S. Venkataramanan
- Department of Diagnostic and Allied Health Science, Faculty of Health and Life Sciences, Management and Science University, Shah Alam, Malaysia
| | - Rituraj Purohit
- Structural Bioinformatics Laboratory, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, India
| | - R. Rajasekaran
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore, India
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Jian JW, Chen HS, Chiu YK, Peng HP, Tung CP, Chen IC, Yu CM, Tsou YL, Kuo WY, Hsu HJ, Yang AS. Effective binding to protein antigens by antibodies from antibody libraries designed with enhanced protein recognition propensities. MAbs 2019; 11:373-387. [PMID: 30526270 PMCID: PMC6380391 DOI: 10.1080/19420862.2018.1550320] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Antibodies provide immune protection by recognizing antigens of diverse chemical properties, but elucidating the amino acid sequence-function relationships underlying the specificity and affinity of antibody-antigen interactions remains challenging. We designed and constructed phage-displayed synthetic antibody libraries with enriched protein antigen-recognition propensities calculated with machine learning predictors, which indicated that the designed single-chain variable fragment variants were encoded with enhanced distributions of complementarity-determining region (CDR) hot spot residues with high protein antigen recognition propensities in comparison with those in the human antibody germline sequences. Antibodies derived directly from the synthetic antibody libraries, without affinity maturation cycles comparable to those in in vivo immune systems, bound to the corresponding protein antigen through diverse conformational or linear epitopes with specificity and affinity comparable to those of the affinity-matured antibodies from in vivo immune systems. The results indicated that more densely populated CDR hot spot residues were sustainable by the antibody structural frameworks and could be accompanied by enhanced functionalities in recognizing protein antigens. Our study results suggest that synthetic antibody libraries, which are not limited by the sequences found in antibodies in nature, could be designed with the guidance of the computational machine learning algorithms that are programmed to predict interaction propensities to molecules of diverse chemical properties, leading to antibodies with optimal characteristics pertinent to their medical applications.
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Affiliation(s)
- Jhih-Wei Jian
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan.,b Institute of Biomedical Informatics, National Yang-Ming University , Taipei , Taiwan.,c Bioinformatics Program, Taiwan International Graduate Program , Institute of Information Science, Academia Sinica , Taipei , Taiwan
| | - Hong-Sen Chen
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Yi-Kai Chiu
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Hung-Pin Peng
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Chao-Ping Tung
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Ing-Chien Chen
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Chung-Ming Yu
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Yueh-Liang Tsou
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Wei-Ying Kuo
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Hung-Ju Hsu
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - An-Suei Yang
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
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Balaraman S, Ramalingam R. The structural and functional reliability of Circulins of
Chassalia parvifolia
for peptide therapeutic scaffolding. J Cell Biochem 2018; 119:3999-4008. [DOI: 10.1002/jcb.26557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 11/30/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Senthilkumar Balaraman
- Bioinformatics Division, School of Bio Sciences and TechnologyVellore Institute of Technology UniversityVelloreTamil NaduIndia
| | - Rajasekaran Ramalingam
- Bioinformatics Division, School of Bio Sciences and TechnologyVellore Institute of Technology UniversityVelloreTamil NaduIndia
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Senthilkumar B, Rajasekaran R. In Silico Template Selection of Short Antimicrobial Peptide Viscotoxin for Improving Its Antimicrobial Efficiency in Development of Potential Therapeutic Drugs. Appl Biochem Biotechnol 2016; 181:898-913. [PMID: 27696138 DOI: 10.1007/s12010-016-2257-7] [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] [Received: 04/26/2016] [Accepted: 09/19/2016] [Indexed: 12/22/2022]
Abstract
Rapid increase in antibiotic resistance has posed a worldwide threat, due to increased mortality, morbidity, and expenditure caused by antibiotic-resistant microbes. Recent development of the antimicrobial peptides like viscotoxin (Vt) has been successfully comprehended as a substitute for classical antibiotics. A structurally stable peptide, Vt can enhance antimicrobial property and can be used for various developmental purposes. Thus, structural stability among the antimicrobial peptides, Vt A1 (3C8P), A2 (1JMN), A3 (1ED0), B (1JMP), and C (1ORL) of Viscus album was computationally analyzed. In specific, the static confirmation of VtA3 showed high number of intramolecular interactions, along with an increase in hydrophobicity than others comparatively. Further, conformational sampling was used to analyze various geometrical parameters such as root mean square deviation, root mean square fluctuation, radius of gyration, and ovality which also revealed the structural stability of VtA3. Moreover, the statistically validated contours of surface area, lipophilicity, and distance constraints of disulfide bonds also supported the priority of VtA3 with respect to stability. Finally, the functional activity of peptides was accessed by computing their free energy of membrane association and membrane interactions, which defined VtA3 as functionally stable. Currently, peptide-based antibiotics and nanoparticles have attracted the pharmaceutical industries for their potential therapeutic applications. Thereby, it is proposed that viscotoxin A3 (1ED0) could be used as a preeminent template for scaffolding potentially efficient antimicrobial peptide-based drugs and nanomaterials in future.
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Affiliation(s)
- B Senthilkumar
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - R Rajasekaran
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India.
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Geometric Simulation Approach for Grading and Assessing the Thermostability of CALBs. Biochem Res Int 2016; 2016:4101059. [PMID: 27123343 PMCID: PMC4830698 DOI: 10.1155/2016/4101059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 03/16/2016] [Indexed: 11/17/2022] Open
Abstract
Candida antarctica lipase B (CALB) is a known stable and highly active enzyme used widely in biodiesel synthesis. In this work, the stability of native (4K6G) and mutant (4K5Q) CALB was studied through various structural parameters using conformational sampling approach. The contours of polar surface area and surface area of mutant CALB were 11357.67 Å(2) and 30007.4 Å(2), respectively, showing an enhanced stability compared to native CALB with a statistically significant P value of < 0.0001. Moreover, simulated thermal denaturation of CALB, a process involving dilution of hydrogen bond, significantly shielded against different intervals of energy application in mutant CALB revealing its augmentation of structural rigidity against native CALB. Finally, computational docking analysis showed an increase in the binding affinity of CALB and its substrate (triglyceride) in mutant CALB with Atomic Contact Energy (ACE) of -91.23 kcal/mol compared to native CALB (ACE of -70.3 kcal/mol). The computational observations proposed that the use of mutant CALB (4K5Q) could serve as a best template for production of biodiesel in the future. Additionally, it can also be used as a template to identify efficient thermostable lipases through further mutations.
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Selection of effective and highly thermostable Bacillus subtilis lipase A template as an industrial biocatalyst-A modern computational approach. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s11515-015-1379-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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