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Jeliazkov JR, Sljoka A, Kuroda D, Tsuchimura N, Katoh N, Tsumoto K, Gray JJ. Repertoire Analysis of Antibody CDR-H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification. Front Immunol 2018; 9:413. [PMID: 29545810 PMCID: PMC5840193 DOI: 10.3389/fimmu.2018.00413] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 02/14/2018] [Indexed: 12/18/2022] Open
Abstract
Antibodies can rapidly evolve in specific response to antigens. Affinity maturation drives this evolution through cycles of mutation and selection leading to enhanced antibody specificity and affinity. Elucidating the biophysical mechanisms that underlie affinity maturation is fundamental to understanding B-cell immunity. An emergent hypothesis is that affinity maturation reduces the conformational flexibility of the antibody's antigen-binding paratope to minimize entropic losses incurred upon binding. In recent years, computational and experimental approaches have tested this hypothesis on a small number of antibodies, often observing a decrease in the flexibility of the complementarity determining region (CDR) loops that typically comprise the paratope and in particular the CDR-H3 loop, which contributes a plurality of antigen contacts. However, there were a few exceptions and previous studies were limited to a small handful of cases. Here, we determined the structural flexibility of the CDR-H3 loop for thousands of recent homology models of the human peripheral blood cell antibody repertoire using rigidity theory. We found no clear delineation in the flexibility of naïve and antigen-experienced antibodies. To account for possible sources of error, we additionally analyzed hundreds of human and mouse antibodies in the Protein Data Bank through both rigidity theory and B-factor analysis. By both metrics, we observed only a slight decrease in the CDR-H3 loop flexibility when comparing affinity matured antibodies to naïve antibodies, and the decrease was not as drastic as previously reported. Further analysis, incorporating molecular dynamics simulations, revealed a spectrum of changes in flexibility. Our results suggest that rigidification may be just one of many biophysical mechanisms for increasing affinity.
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Affiliation(s)
- Jeliazko R Jeliazkov
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, United States
| | - Adnan Sljoka
- Department of Informatics, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo, Japan
| | - Daisuke Kuroda
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.,Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Nobuyuki Tsuchimura
- Department of Informatics, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo, Japan
| | - Naoki Katoh
- Department of Informatics, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.,Laboratory of Medical Proteomics, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Jeffrey J Gray
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, United States.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States.,Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, United States.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, United States
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52
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Abstract
The immune systems protect our bodies from foreign molecules or antigens, where antibodies play important roles. Antibodies evolve over time upon antigen encounter by somatically mutating their genome sequences. The end result is a series of antibodies that display higher affinities and specificities to specific antigens. This process is called affinity maturation. Recent improvements in computer hardware and modeling algorithms now enable the rational design of protein structures and functions, and several works on computer-aided antibody design have been published. In this chapter, we briefly describe computational methods for antibody affinity maturation, focusing on methods for sampling antibody conformations and for scoring designed antibody variants. We also discuss lessons learned from the successful computer-aided design of antibodies.
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Affiliation(s)
- Daisuke Kuroda
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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53
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Yan Y, Huang SY. Protein-Protein Docking with Improved Shape Complementarity. INTELLIGENT COMPUTING THEORIES AND APPLICATION 2018. [DOI: 10.1007/978-3-319-95930-6_60] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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54
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Entzminger KC, Hyun JM, Pantazes RJ, Patterson-Orazem AC, Qerqez AN, Frye ZP, Hughes RA, Ellington AD, Lieberman RL, Maranas CD, Maynard JA. De novo design of antibody complementarity determining regions binding a FLAG tetra-peptide. Sci Rep 2017; 7:10295. [PMID: 28860479 PMCID: PMC5579192 DOI: 10.1038/s41598-017-10737-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 08/14/2017] [Indexed: 12/30/2022] Open
Abstract
Computational antibody engineering efforts to date have focused on improving binding affinities or biophysical characteristics. De novo design of antibodies binding specific epitopes could greatly accelerate discovery of therapeutics as compared to conventional immunization or synthetic library selection strategies. Here, we employed de novo complementarity determining region (CDR) design to engineer targeted antibody-antigen interactions using previously described in silico methods. CDRs predicted to bind the minimal FLAG peptide (Asp-Tyr-Lys-Asp) were grafted onto a single-chain variable fragment (scFv) acceptor framework. Fifty scFvs comprised of designed heavy and light or just heavy chain CDRs were synthesized and screened for peptide binding by phage ELISA. Roughly half of the designs resulted in detectable scFv expression. Four antibodies, designed entirely in silico, bound the minimal FLAG sequence with high specificity and sensitivity. When reformatted as soluble antigen-binding fragments (Fab), these clones expressed well, were predominantly monomeric and retained peptide specificity. In both formats, the antibodies bind the peptide only when present at the amino-terminus of a carrier protein and even conservative peptide amino acid substitutions resulted in a complete loss of binding. These results support in silico CDR design of antibody specificity as an emerging antibody engineering strategy.
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Affiliation(s)
- Kevin C Entzminger
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Jeong-Min Hyun
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Robert J Pantazes
- Department of Chemical Engineering, Auburn University, Auburn, AL, 36849, USA
| | | | - Ahlam N Qerqez
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Zach P Frye
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Randall A Hughes
- Applied Research Laboratories, University of Texas at Austin, Austin, TX, 78712, USA
| | - Andrew D Ellington
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Raquel L Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Costas D Maranas
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, PA, 16802, USA
| | - Jennifer A Maynard
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA. .,Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA.
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55
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Weitzner BD, Jeliazkov JR, Lyskov S, Marze N, Kuroda D, Frick R, Adolf-Bryfogle J, Biswas N, Dunbrack RL, Gray JJ. Modeling and docking of antibody structures with Rosetta. Nat Protoc 2017; 12:401-416. [PMID: 28125104 DOI: 10.1038/nprot.2016.180] [Citation(s) in RCA: 180] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We describe Rosetta-based computational protocols for predicting the 3D structure of an antibody from sequence (RosettaAntibody) and then docking the antibody to protein antigens (SnugDock). Antibody modeling leverages canonical loop conformations to graft large segments from experimentally determined structures, as well as offering (i) energetic calculations to minimize loops, (ii) docking methodology to refine the VL-VH relative orientation and (iii) de novo prediction of the elusive complementarity determining region (CDR) H3 loop. To alleviate model uncertainty, antibody-antigen docking resamples CDR loop conformations and can use multiple models to represent an ensemble of conformations for the antibody, the antigen or both. These protocols can be run fully automated via the ROSIE web server (http://rosie.rosettacommons.org/) or manually on a computer with user control of individual steps. For best results, the protocol requires roughly 1,000 CPU-hours for antibody modeling and 250 CPU-hours for antibody-antigen docking. Tasks can be completed in under a day by using public supercomputers.
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Affiliation(s)
- Brian D Weitzner
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jeliazko R Jeliazkov
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sergey Lyskov
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Nicholas Marze
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Daisuke Kuroda
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA.,Department of Analytical and Physical Chemistry, Showa University School of Pharmacy, Tokyo, Japan
| | - Rahel Frick
- Centre for Immune Regulation, Department of Biosciences, University of Oslo, Oslo, Norway.,Centre for Immune Regulation, Department of Immunology, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Jared Adolf-Bryfogle
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA.,Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Naireeta Biswas
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Roland L Dunbrack
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Jeffrey J Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA.,Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland, USA.,Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, USA.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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56
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Lei J, Hansen G, Nitsche C, Klein CD, Zhang L, Hilgenfeld R. Crystal structure of Zika virus NS2B-NS3 protease in complex with a boronate inhibitor. Science 2016; 353:503-5. [DOI: 10.1126/science.aag2419] [Citation(s) in RCA: 240] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 06/30/2016] [Indexed: 01/09/2023]
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