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Nur A, Lai JY, Ch'ng ACW, Choong YS, Wan Isa WYH, Lim TS. A review of in vitro stochastic and non-stochastic affinity maturation strategies for phage display derived monoclonal antibodies. Int J Biol Macromol 2024; 277:134217. [PMID: 39069045 DOI: 10.1016/j.ijbiomac.2024.134217] [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: 05/15/2024] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 07/30/2024]
Abstract
Monoclonal antibodies identified using display technologies like phage display occasionally suffers from a lack of affinity making it unsuitable for application. This drawback is circumvented with the application of affinity maturation. Affinity maturation is an essential step in the natural evolution of antibodies in the immune system. The evolution of molecular based methods has seen the development of various mutagenesis approaches. This allows for the natural evolutionary process during somatic hypermutation to be replicated in the laboratories for affinity maturation to fine-tune the affinity and selectivity of antibodies. In this review, we will discuss affinity maturation strategies for mAbs generated through phage display systems. The review will highlight various in vitro stochastic and non-stochastic affinity maturation approaches that includes but are not limited to random mutagenesis, site-directed mutagenesis, and gene synthesis.
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Affiliation(s)
- Alia Nur
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Wan Yus Haniff Wan Isa
- School of Medical Sciences, Department of Medicine, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia.
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Mészáros Z, Kulik N, Petrásková L, Bojarová P, Texidó M, Planas A, Křen V, Slámová K. Three-Step Enzymatic Remodeling of Chitin into Bioactive Chitooligomers. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:15613-15623. [PMID: 38978453 PMCID: PMC11261597 DOI: 10.1021/acs.jafc.4c03077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/10/2024]
Abstract
Here we describe a complex enzymatic approach to the efficient transformation of abundant waste chitin, a byproduct of the food industry, into valuable chitooligomers with a degree of polymerization (DP) ranging from 6 to 11. This method involves a three-step process: initial hydrolysis of chitin using engineered variants of a novel fungal chitinase from Talaromyces flavus to generate low-DP chitooligomers, followed by an extension to the desired DP using the high-yielding Y445N variant of β-N-acetylhexosaminidase from Aspergillus oryzae, achieving yields of up to 57%. Subsequently, enzymatic deacetylation of chitooligomers with DP 6 and 7 was accomplished using peptidoglycan deacetylase from Bacillus subtilis BsPdaC. The innovative enzymatic procedure demonstrates a sustainable and feasible route for converting waste chitin into unavailable bioactive chitooligomers potentially applicable as natural pesticides in ecological and sustainable agriculture.
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Affiliation(s)
- Zuzana Mészáros
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14200, Prague 4, Czech Republic
| | - Natalia Kulik
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14200, Prague 4, Czech Republic
| | - Lucie Petrásková
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14200, Prague 4, Czech Republic
| | - Pavla Bojarová
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14200, Prague 4, Czech Republic
| | - Mònica Texidó
- Laboratory
of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, ES 08017 Barcelona, Spain
| | - Antoni Planas
- Laboratory
of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, ES 08017 Barcelona, Spain
| | - Vladimír Křen
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14200, Prague 4, Czech Republic
| | - Kristýna Slámová
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14200, Prague 4, Czech Republic
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Tanaka Y, Uchihashi T, Nakamura A. Product inhibition slow down the moving velocity of processive chitinase and sliding-intermediate state blocks re-binding of product. Arch Biochem Biophys 2024; 752:109854. [PMID: 38081338 DOI: 10.1016/j.abb.2023.109854] [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: 10/09/2023] [Revised: 11/23/2023] [Accepted: 12/06/2023] [Indexed: 12/18/2023]
Abstract
Processive movement is the key reaction for crystalline polymer degradation by enzyme. Product release is an important phenomenon in resetting the moving cycle, but how it affects chitinase kinetics was unknown. Therefore, we investigated the effect of diacetyl chitobiose (C2) on the biochemical activity and movement of chitinase A from Serratia marcescens (SmChiA). The apparent inhibition constant of C2 on crystalline chitin degradation of SmChiA was 159 μM. The binding position of C2 obtained by X-ray crystallography was at subsite +1, +2 and Trp275 interact with C2 at subsite +1. This binding state is consistent with the competitive inhibition obtained by biochemical analysis. The apparent inhibition constant of C2 on the moving velocity of high-speed (HS) AFM observations was 330 μM, which is close to the biochemical results, indicating that the main factor in crystalline chitin degradation is also the decrease in degradation activity due to inhibition of processive movement. The Trp275 is a key residue for making a sliding intermediate complex. SmChiA W275A showed weaker activity and affinity than WT against crystalline chitin because it is less processive than WT. In addition, biochemical apparent inhibition constant for C2 of SmChiA W275A was 45.6 μM. W275A mutant showed stronger C2 inhibition than WT even though the C2 binding affinity is weaker than WT. This result indicated that Trp275 is important for the interaction at subsite +1, but also important for making sliding intermediate complex and physically block the rebinding of C2 on the catalytic site for crystalline chitin degradation.
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Affiliation(s)
- Yoshiko Tanaka
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya,Suruga-ku, Shizuoka, 422-8529, Japan
| | - Takayuki Uchihashi
- Department of Physics, Nagoya University, Aichi, 464-8602, Japan; Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Higashiyama 5-1, Myodaiji, Okazaki, 444-0864, Japan
| | - Akihiko Nakamura
- Department of Applied Life Sciences, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan; Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan; Shizuoka Institute for the Study of Marine Biology and Chemistry, Shizuoka, Shizuoka, 422-8529, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama Myodaijicho, Okazaki, Aichi, 444-8787, Japan.
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4
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Cadet XF, Gelly JC, van Noord A, Cadet F, Acevedo-Rocha CG. Learning Strategies in Protein Directed Evolution. Methods Mol Biol 2022; 2461:225-275. [PMID: 35727454 DOI: 10.1007/978-1-0716-2152-3_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Synthetic biology is a fast-evolving research field that combines biology and engineering principles to develop new biological systems for medical, pharmacological, and industrial applications. Synthetic biologists use iterative "design, build, test, and learn" cycles to efficiently engineer genetic systems that are reliable, reproducible, and predictable. Protein engineering by directed evolution can benefit from such a systematic engineering approach for various reasons. Learning can be carried out before starting, throughout or after finalizing a directed evolution project. Computational tools, bioinformatics, and scanning mutagenesis methods can be excellent starting points, while molecular dynamics simulations and other strategies can guide engineering efforts. Similarly, studying protein intermediates along evolutionary pathways offers fascinating insights into the molecular mechanisms shaped by evolution. The learning step of the cycle is not only crucial for proteins or enzymes that are not suitable for high-throughput screening or selection systems, but it is also valuable for any platform that can generate a large amount of data that can be aided by machine learning algorithms. The main challenge in protein engineering is to predict the effect of a single mutation on one functional parameter-to say nothing of several mutations on multiple parameters. This is largely due to nonadditive mutational interactions, known as epistatic effects-beneficial mutations present in a genetic background may not be beneficial in another genetic background. In this work, we provide an overview of experimental and computational strategies that can guide the user to learn protein function at different stages in a directed evolution project. We also discuss how epistatic effects can influence the success of directed evolution projects. Since machine learning is gaining momentum in protein engineering and the field is becoming more interdisciplinary thanks to collaboration between mathematicians, computational scientists, engineers, molecular biologists, and chemists, we provide a general workflow that familiarizes nonexperts with the basic concepts, dataset requirements, learning approaches, model capabilities and performance metrics of this intriguing area. Finally, we also provide some practical recommendations on how machine learning can harness epistatic effects for engineering proteins in an "outside-the-box" way.
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Affiliation(s)
- Xavier F Cadet
- PEACCEL, Artificial Intelligence Department, Paris, France
| | - Jean Christophe Gelly
- Laboratoire d'Excellence GR-Ex, Paris, France
- BIGR, DSIMB, UMR_S1134, INSERM, University of Paris & University of Reunion, Paris, France
| | | | - Frédéric Cadet
- Laboratoire d'Excellence GR-Ex, Paris, France
- BIGR, DSIMB, UMR_S1134, INSERM, University of Paris & University of Reunion, Paris, France
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Ando J, Kawagoe H, Nakamura A, Iino R, Fujita K. Label-free monitoring of crystalline chitin hydrolysis by chitinase based on Raman spectroscopy. Analyst 2021; 146:4087-4094. [PMID: 34060547 DOI: 10.1039/d1an00581b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrate a method for label-free monitoring of hydrolytic activity of crystalline-chitin-degrading enzyme, chitinase, by means of Raman spectroscopy. We found that crystalline chitin exhibited a characteristic Raman peak at 2995 cm-1, which did not appear in the reaction product, N,N'-diacetylchitobiose. We used this Raman peak as a marker of crystalline chitin degradation to monitor the hydrolytic activity of chitinase. When the crystalline chitin suspension and chitinase were mixed together, the peak intensity of crystalline chitin at 2995 cm-1 was linearly decreased depending on incubation time. The decrease in peak intensity was inversely correlated with the increase in the amount of released N,N'-diacetylchitobiose, which was measured by conventional colorimetric assay with alkaline ferricyanide. Our result, presented here, provides a new method for simple, in situ, and label-free monitoring of enzymatic activity of chitinase.
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Affiliation(s)
- Jun Ando
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan. and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan and Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa 240-0193, Japan
| | - Hiroyuki Kawagoe
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Akihiko Nakamura
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan and Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa 240-0193, Japan and Department of Applied Life Sciences, Shizuoka University, Shizuoka, Shizuoka 422-8529, Japan
| | - Ryota Iino
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan and Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa 240-0193, Japan
| | - Katsumasa Fujita
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan. and Advanced Photonics and Biosensing Open Innovation Laboratory, AIST-Osaka University, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan and Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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