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Yang K, Wu Z, Zhang K, Weir MD, Xu HHK, Cheng L, Huang X, Zhou W. Unlocking the potential of stimuli-responsive biomaterials for bone regeneration. Front Pharmacol 2024; 15:1437457. [PMID: 39144636 PMCID: PMC11322102 DOI: 10.3389/fphar.2024.1437457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 07/18/2024] [Indexed: 08/16/2024] Open
Abstract
Bone defects caused by tumors, osteoarthritis, and osteoporosis attract great attention. Because of outstanding biocompatibility, osteogenesis promotion, and less secondary infection incidence ratio, stimuli-responsive biomaterials are increasingly used to manage this issue. These biomaterials respond to certain stimuli, changing their mechanical properties, shape, or drug release rate accordingly. Thereafter, the activated materials exert instructive or triggering effects on cells and tissues, match the properties of the original bone tissues, establish tight connection with ambient hard tissue, and provide suitable mechanical strength. In this review, basic definitions of different categories of stimuli-responsive biomaterials are presented. Moreover, possible mechanisms, advanced studies, and pros and cons of each classification are discussed and analyzed. This review aims to provide an outlook on the future developments in stimuli-responsive biomaterials.
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Affiliation(s)
- Ke Yang
- Fujian Key Laboratory of Oral Diseases & Fujian Provincial Engineering Research Center of Oral Biomaterial & Stomatological Key Lab of Fujian College and University, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
- Clinical Research Center for Oral Tissue Deficiency Diseases of Fujian Province, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
| | - Zhuoshu Wu
- Fujian Key Laboratory of Oral Diseases & Fujian Provincial Engineering Research Center of Oral Biomaterial & Stomatological Key Lab of Fujian College and University, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
- Clinical Research Center for Oral Tissue Deficiency Diseases of Fujian Province, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
| | - Keke Zhang
- School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou, China
| | - Michael D. Weir
- Department of Biomaterials and Regenerative Dental Medicine, University of Maryland School of Dentistry, Baltimore, MD, United States
| | - Hockin H. K. Xu
- Department of Biomaterials and Regenerative Dental Medicine, University of Maryland School of Dentistry, Baltimore, MD, United States
| | - Lei Cheng
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China School of Stomatology & Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xiaojing Huang
- Fujian Key Laboratory of Oral Diseases & Fujian Provincial Engineering Research Center of Oral Biomaterial & Stomatological Key Lab of Fujian College and University, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
- Clinical Research Center for Oral Tissue Deficiency Diseases of Fujian Province, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
| | - Wen Zhou
- Fujian Key Laboratory of Oral Diseases & Fujian Provincial Engineering Research Center of Oral Biomaterial & Stomatological Key Lab of Fujian College and University, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
- Clinical Research Center for Oral Tissue Deficiency Diseases of Fujian Province, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
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2
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de Souza J, Vieira AZ, Dos Santos HG, Faoro H. Potential involvement of beta-lactamase homologous proteins in resistance to beta-lactam antibiotics in gram-negative bacteria of the ESKAPEE group. BMC Genomics 2024; 25:508. [PMID: 38778284 PMCID: PMC11112869 DOI: 10.1186/s12864-024-10410-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Enzymatic degradation mediated by beta-lactamases constitutes one of the primary mechanisms of resistance to beta-lactam antibiotics in gram-negative bacteria. This enzyme family comprises four molecular classes, categorized into serine beta-lactamases (Classes A, C, and D) and zinc-dependent metallo-beta-lactamases (Class B). Gram-negative bacteria producing beta-lactamase are of significant concern, particularly due to their prevalence in nosocomial infections. A comprehensive understanding of the evolution and dissemination of this enzyme family is essential for effective control of these pathogens. In this study, we conducted the prospecting, phylogenetic analysis, and in silico analysis of beta-lactamases and homologous proteins identified in 1827 bacterial genomes with phenotypic data on beta-lactam resistance. These genomes were distributed among Klebsiella pneumoniae (45%), Acinetobacter baumannii (31%), Pseudomonas aeruginosa (14%), Escherichia coli (6%), and Enterobacter spp. (4%). Using an HMM profile and searching for conserved domains, we mined 2514, 8733, 5424, and 2957 proteins for molecular classes A, B, C, and D, respectively. This set of proteins encompasses canonical subfamilies of beta-lactamases as well as hypothetical proteins and other functional groups. Canonical beta-lactamases were found to be phylogenetically distant from hypothetical proteins, which, in turn, are closer to other representatives of the penicillin-binding-protein (PBP-like) and metallo-beta-lactamase (MBL) families. The catalytic amino acid residues characteristic of beta-lactamases were identified from the sequence alignment and revealed that motifs are less conserved in homologous groups than in beta-lactamases. After comparing the frequency of protein groups in genomes of resistant strains with those of sensitive ones applying Fisher's exact test and relative risk, it was observed that some groups of homologous proteins to classes B and C are more common in the genomes of resistant strains, particularly to carbapenems. We identified the beta-lactamase-like domain widely distributed in gram-negative species of the ESKAPEE group, which highlights its importance in the context of beta-lactam resistance. Some hypothetical homologous proteins have been shown to potentially possess promiscuous activity against beta-lactam antibiotics, however, they do not appear to expressly determine the resistance phenotype. The selective pressure due to the widespread use of antibiotics may favor the optimization of these functions for specialized resistance enzymes.
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Affiliation(s)
- Joyce de Souza
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Paraná, 81350-010, Brazil
| | - Alexandre Zanatta Vieira
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Paraná, 81350-010, Brazil
| | | | - Helisson Faoro
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Paraná, 81350-010, Brazil.
- Department of Microbiology, Infectious Disease and Immunology, CHU de Quebec Research Center, University Laval, Quebec, QC, G1V 0A6, Canada.
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3
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Xu L, Nawaz MZ, Khalid HR, Waqar-Ul-Haq, Alghamdi HA, Sun J, Zhu D. Modulating the pH profile of vanillin dehydrogenase enzyme from extremophile Bacillus ligniniphilus L1 through computational guided site-directed mutagenesis. Int J Biol Macromol 2024; 263:130359. [PMID: 38387643 DOI: 10.1016/j.ijbiomac.2024.130359] [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: 11/22/2023] [Revised: 02/18/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Vanillin dehydrogenase (VDH) has recently come forward as an important enzyme for the commercial production of vanillic acid from vanillin in a one-step enzymatic process. However, VDH with high alkaline tolerance and efficiency is desirable to meet the biorefinery requirements. In this study, computationally guided site-directed mutagenesis was performed by increasing the positive and negative charges on the surface and near the active site of the VDH from the alkaliphilic marine bacterium Bacillus ligniniphilus L1, respectively. In total, 20 residues including 15 from surface amino acids and 5 near active sites were selected based on computational analysis and were subjected to site-directed mutations. The optimum pH of the two screened mutants including I132R, and T235E from surface residue and near active site mutant was shifted to 9, and 8.6, with a 2.82- and 2.95-fold increase in their activity compared to wild enzyme at pH 9, respectively. A double mutant containing both these mutations i.e., I132R/T235E was produced which showed a shift in optimum pH of VDH from 7.4 to 9, with an increase of 74.91 % in enzyme activity. Therefore, the double mutant of VDH from the L1 strain (I132R/T235E) produced in this study represents a potential candidate for industrial applications.
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Affiliation(s)
- Lingxia Xu
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China; International Joint Laboratory on Synthetic Biology and Biomass Biorefinery, Jiangsu University, Zhenjiang, Jiangsu 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, PR China
| | - Muhammad Zohaib Nawaz
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China; International Joint Laboratory on Synthetic Biology and Biomass Biorefinery, Jiangsu University, Zhenjiang, Jiangsu 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, PR China
| | - Hafiz Rameez Khalid
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China; International Joint Laboratory on Synthetic Biology and Biomass Biorefinery, Jiangsu University, Zhenjiang, Jiangsu 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, PR China
| | - Waqar-Ul-Haq
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China; International Joint Laboratory on Synthetic Biology and Biomass Biorefinery, Jiangsu University, Zhenjiang, Jiangsu 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, PR China
| | - Huda Ahmed Alghamdi
- Department of Biology, College of Sciences, King Khalid University, Abha 61413, Saudi Arabia
| | - Jianzhong Sun
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Daochen Zhu
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China; International Joint Laboratory on Synthetic Biology and Biomass Biorefinery, Jiangsu University, Zhenjiang, Jiangsu 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, PR China.
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4
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Möhler JS, Pickl M, Reiter T, Simić S, Rackl JW, Kroutil W, Wennemers H. Peptide and Enzyme Catalysts Work in Concert in Stereoselective Cascade Reactions-Oxidation followed by Conjugate Addition. Angew Chem Int Ed Engl 2024; 63:e202319457. [PMID: 38235524 DOI: 10.1002/anie.202319457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/19/2024]
Abstract
Enzymes and peptide catalysts consist of the same building blocks but require vastly different environments to operate best. Herein, we show that an enzyme and a peptide catalyst can work together in a single reaction vessel to catalyze a two-step cascade reaction with high chemo- and stereoselectivity. Abundant linear alcohols, nitroolefins, an alcohol oxidase, and a tripeptide catalyst provided chiral γ-nitroaldehydes in aqueous buffer. High yields (up to 92 %) and stereoselectivities (up to 98 % ee) were achieved for the cascade through the rational design of the peptide catalyst and the identification of common reaction conditions.
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Affiliation(s)
- Jasper S Möhler
- Laboratorium für Organische Chemie, D-CHAB, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Mathias Pickl
- University of Graz, Institute of Chemistry NAWI Graz, BioTechMed Graz, Heinrichstraße 28, 8010, Graz, Austria
| | - Tamara Reiter
- University of Graz, Institute of Chemistry NAWI Graz, BioTechMed Graz, Heinrichstraße 28, 8010, Graz, Austria
| | - Stefan Simić
- University of Graz, Institute of Chemistry NAWI Graz, BioTechMed Graz, Heinrichstraße 28, 8010, Graz, Austria
| | - Jonas W Rackl
- Laboratorium für Organische Chemie, D-CHAB, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Wolfgang Kroutil
- University of Graz, Institute of Chemistry NAWI Graz, BioTechMed Graz, Heinrichstraße 28, 8010, Graz, Austria
- Field of Excellence BioHealth-, University of Graz, 8010, Graz, Austria
| | - Helma Wennemers
- Laboratorium für Organische Chemie, D-CHAB, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
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5
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Fan H, Zhang R, Fan K, Gao L, Yan X. Exploring the Specificity of Nanozymes. ACS NANO 2024; 18:2533-2540. [PMID: 38215476 DOI: 10.1021/acsnano.3c07680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2024]
Abstract
Nanozymes, nanomaterials exhibiting enzyme-like activities, have emerged as a prominent interdisciplinary field over the past decade. To date, over 1200 different nanomaterials have been identified as nanozymes, covering four catalytic categories: oxidoreductases, hydrolases, isomerases, and lyases. Catalytic activity and specificity are two pivotal benchmarks for evaluating enzymatic performance. Despite substantial progress being made in quantifying and optimizing the catalytic activity of nanozymes, there is still a lack of in-depth research on the catalytic specificity of nanozymes, preventing the formation of consensual knowledge and impeding a more refined and systematic classification of nanozymes. Recently, debates have emerged regarding whether nanozymes could possess catalytic specificity similar to that of enzymes. This Perspective discusses the specificity of nanozymes by referring to the catalytic specificity of enzymes, highlights the specificity gap between nanozymes and enzymes, and concludes by offering our perspective on future research on the specificity of nanozymes.
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Affiliation(s)
- Huizhen Fan
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ruofei Zhang
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Kelong Fan
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Nanozyme Laboratory in Zhongyuan, Zhengzhou, Henan 451163, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Lizeng Gao
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Nanozyme Laboratory in Zhongyuan, Zhengzhou, Henan 451163, China
| | - Xiyun Yan
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Nanozyme Laboratory in Zhongyuan, Zhengzhou, Henan 451163, China
- University of Chinese Academy of Sciences, Beijing 101408, China
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6
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Buda K, Miton CM, Tokuriki N. Pervasive epistasis exposes intramolecular networks in adaptive enzyme evolution. Nat Commun 2023; 14:8508. [PMID: 38129396 PMCID: PMC10739712 DOI: 10.1038/s41467-023-44333-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
Enzyme evolution is characterized by constant alterations of the intramolecular residue networks supporting their functions. The rewiring of these network interactions can give rise to epistasis. As mutations accumulate, the epistasis observed across diverse genotypes may appear idiosyncratic, that is, exhibit unique effects in different genetic backgrounds. Here, we unveil a quantitative picture of the prevalence and patterns of epistasis in enzyme evolution by analyzing 41 fitness landscapes generated from seven enzymes. We show that >94% of all mutational and epistatic effects appear highly idiosyncratic, which greatly distorted the functional prediction of the evolved enzymes. By examining seemingly idiosyncratic changes in epistasis along adaptive trajectories, we expose several instances of higher-order, intramolecular rewiring. Using complementary structural data, we outline putative molecular mechanisms explaining higher-order epistasis along two enzyme trajectories. Our work emphasizes the prevalence of epistasis and provides an approach to exploring this phenomenon through a molecular lens.
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Affiliation(s)
- Karol Buda
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Charlotte M Miton
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada.
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7
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Chaturvedi SS, Bím D, Christov CZ, Alexandrova AN. From random to rational: improving enzyme design through electric fields, second coordination sphere interactions, and conformational dynamics. Chem Sci 2023; 14:10997-11011. [PMID: 37860658 PMCID: PMC10583697 DOI: 10.1039/d3sc02982d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 09/11/2023] [Indexed: 10/21/2023] Open
Abstract
Enzymes are versatile and efficient biological catalysts that drive numerous cellular processes, motivating the development of enzyme design approaches to tailor catalysts for diverse applications. In this perspective, we investigate the unique properties of natural, evolved, and designed enzymes, recognizing their strengths and shortcomings. We highlight the challenges and limitations of current enzyme design protocols, with a particular focus on their limited consideration of long-range electrostatic and dynamic effects. We then delve deeper into the impact of the protein environment on enzyme catalysis and explore the roles of preorganized electric fields, second coordination sphere interactions, and protein dynamics for enzyme function. Furthermore, we present several case studies illustrating successful enzyme-design efforts incorporating enzyme strategies mentioned above to achieve improved catalytic properties. Finally, we envision the future of enzyme design research, spotlighting the challenges yet to be overcome and the synergy of intrinsic electric fields, second coordination sphere interactions, and conformational dynamics to push the state-of-the-art boundaries.
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Affiliation(s)
- Shobhit S Chaturvedi
- Department of Chemistry and Biochemistry, University of California, Los Angeles California 90095 USA
| | - Daniel Bím
- Department of Chemistry and Biochemistry, University of California, Los Angeles California 90095 USA
| | - Christo Z Christov
- Department of Chemistry, Michigan Technological University Houghton Michigan 49931 USA
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles California 90095 USA
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8
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Dani R, Pawloski W, Chaurasiya DK, Srilatha NS, Agarwal S, Fushman D, Naganathan AN. Conformational Tuning Shapes the Balance between Functional Promiscuity and Specialization in Paralogous Plasmodium Acyl-CoA Binding Proteins. Biochemistry 2023; 62:2982-2996. [PMID: 37788430 PMCID: PMC10774088 DOI: 10.1021/acs.biochem.3c00449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Paralogous proteins confer enhanced fitness to organisms via complex sequence-conformation codes that shape functional divergence, specialization, or promiscuity. Here, we dissect the underlying mechanism of promiscuous binding versus partial subfunctionalization in paralogues by studying structurally identical acyl-CoA binding proteins (ACBPs) from Plasmodium falciparum that serve as promising drug targets due to their high expression during the protozoan proliferative phase. Combining spectroscopic measurements, solution NMR, SPR, and simulations on two of the paralogues, A16 and A749, we show that minor sequence differences shape nearly every local and global conformational feature. A749 displays a broader and heterogeneous native ensemble, weaker thermodynamic coupling and cooperativity, enhanced fluctuations, and a larger binding pocket volume compared to A16. Site-specific tryptophan probes signal a graded reduction in the sampling of substates in the holo form, which is particularly apparent in A749. The paralogues exhibit a spectrum of binding affinities to different acyl-CoAs with A749, the more promiscuous and hence the likely ancestor, binding 1000-fold stronger to lauroyl-CoA under physiological conditions. We thus demonstrate how minor sequence changes modulate the extent of long-range interactions and dynamics, effectively contributing to the molecular evolution of contrasting functional repertoires in paralogues.
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Affiliation(s)
- Rahul Dani
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Westley Pawloski
- Center for Biomolecular Structure & Organization, Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Dhruv Kumar Chaurasiya
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | | | - Sonal Agarwal
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - David Fushman
- Center for Biomolecular Structure & Organization, Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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9
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Shishparenok AN, Gladilina YA, Zhdanov DD. Engineering and Expression Strategies for Optimization of L-Asparaginase Development and Production. Int J Mol Sci 2023; 24:15220. [PMID: 37894901 PMCID: PMC10607044 DOI: 10.3390/ijms242015220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Genetic engineering for heterologous expression has advanced in recent years. Model systems such as Escherichia coli, Bacillus subtilis and Pichia pastoris are often used as host microorganisms for the enzymatic production of L-asparaginase, an enzyme widely used in the clinic for the treatment of leukemia and in bakeries for the reduction of acrylamide. Newly developed recombinant L-asparaginase (L-ASNase) may have a low affinity for asparagine, reduced catalytic activity, low stability, and increased glutaminase activity or immunogenicity. Some successful commercial preparations of L-ASNase are now available. Therefore, obtaining novel L-ASNases with improved properties suitable for food or clinical applications remains a challenge. The combination of rational design and/or directed evolution and heterologous expression has been used to create enzymes with desired characteristics. Computer design, combined with other methods, could make it possible to generate mutant libraries of novel L-ASNases without costly and time-consuming efforts. In this review, we summarize the strategies and approaches for obtaining and developing L-ASNase with improved properties.
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Affiliation(s)
- Anastasiya N. Shishparenok
- Laboratory of Medical Biotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.N.S.); (Y.A.G.)
| | - Yulia A. Gladilina
- Laboratory of Medical Biotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.N.S.); (Y.A.G.)
| | - Dmitry D. Zhdanov
- Laboratory of Medical Biotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.N.S.); (Y.A.G.)
- Department of Biochemistry, Peoples’ Friendship University of Russia named after Patrice Lumumba (RUDN University), Miklukho—Maklaya St. 6, 117198 Moscow, Russia
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10
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Nicoll CR, Massari M, Fraaije MW, Mascotti ML, Mattevi A. Impact of ancestral sequence reconstruction on mechanistic and structural enzymology. Curr Opin Struct Biol 2023; 82:102669. [PMID: 37544113 DOI: 10.1016/j.sbi.2023.102669] [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: 03/29/2023] [Revised: 06/19/2023] [Accepted: 07/10/2023] [Indexed: 08/08/2023]
Abstract
Ancestral sequence reconstruction (ASR) provides insight into the changes within a protein sequence across evolution. More specifically, it can illustrate how specific amino acid changes give rise to different phenotypes within a protein family. Over the last few decades it has established itself as a powerful technique for revealing molecular common denominators that govern enzyme function. Here, we describe the strength of ASR in unveiling catalytic mechanisms and emerging phenotypes for a range of different proteins, also highlighting biotechnological applications the methodology can provide.
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Affiliation(s)
- Callum R Nicoll
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Marta Massari
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Marco W Fraaije
- Molecular Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747, AG Groningen, the Netherlands. https://twitter.com/fraaije1
| | - Maria Laura Mascotti
- Molecular Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747, AG Groningen, the Netherlands; IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de los Andes 950, D5700HHW, San Luis, Argentina
| | - Andrea Mattevi
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy.
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11
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Ferrero E, Di Gregorio E, Ferrero M, Ortolan E, Moon YA, Di Campli A, Pavinato L, Mancini C, Tripathy D, Manes M, Hoxha E, Costanzi C, Pozzi E, Rossi Sebastiano M, Mitro N, Tempia F, Caruso D, Borroni B, Basso M, Sallese M, Brusco A. Spinocerebellar ataxia 38: structure-function analysis shows ELOVL5 G230V is proteotoxic, conformationally altered and a mutational hotspot. Hum Genet 2023; 142:1055-1076. [PMID: 37199746 PMCID: PMC10449689 DOI: 10.1007/s00439-023-02572-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/10/2023] [Indexed: 05/19/2023]
Abstract
Fatty acid elongase ELOVL5 is part of a protein family of multipass transmembrane proteins that reside in the endoplasmic reticulum where they regulate long-chain fatty acid elongation. A missense variant (c.689G>T p.Gly230Val) in ELOVL5 causes Spinocerebellar Ataxia subtype 38 (SCA38), a neurodegenerative disorder characterized by autosomal dominant inheritance, cerebellar Purkinje cell demise and adult-onset ataxia. Having previously showed aberrant accumulation of p.G230V in the Golgi complex, here we further investigated the pathogenic mechanisms triggered by p.G230V, integrating functional studies with bioinformatic analyses of protein sequence and structure. Biochemical analysis showed that p.G230V enzymatic activity was normal. In contrast, SCA38-derived fibroblasts showed reduced expression of ELOVL5, Golgi complex enlargement and increased proteasomal degradation with respect to controls. By heterologous overexpression, p.G230V was significantly more active than wild-type ELOVL5 in triggering the unfolded protein response and in decreasing viability in mouse cortical neurons. By homology modelling, we generated native and p.G230V protein structures whose superposition revealed a shift in Loop 6 in p.G230V that altered a highly conserved intramolecular disulphide bond. The conformation of this bond, connecting Loop 2 and Loop 6, appears to be elongase-specific. Alteration of this intramolecular interaction was also observed when comparing wild-type ELOVL4 and the p.W246G variant which causes SCA34. We demonstrate by sequence and structure analyses that ELOVL5 p.G230V and ELOVL4 p.W246G are position-equivalent missense variants. We conclude that SCA38 is a conformational disease and propose combined loss of function by mislocalization and gain of toxic function by ER/Golgi stress as early events in SCA38 pathogenesis.
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Affiliation(s)
- Enza Ferrero
- Department of Medical Sciences, University of Torino, Via Santena 19, 10126, Turin, Italy
| | - Eleonora Di Gregorio
- Unit of Medical Genetics, Città della Salute e Della Scienza Hospital, Turin, Italy
| | - Marta Ferrero
- Experimental Zooprophylactic Institute of Piedmont, Liguria and Aosta Valley, Turin, Italy
| | - Erika Ortolan
- Department of Medical Sciences, University of Torino, Via Santena 19, 10126, Turin, Italy
| | - Young-Ah Moon
- Department of Molecular Medicine, Inha University College of Medicine, Incheon, South Korea
| | - Antonella Di Campli
- Institute of Protein Biochemistry, Italian National Research Council, Naples, Italy
- Department of Innovative Technologies in Medicine and Dentistry, G. d'Annunzio University of Chieti-Pescara, Chieti, Italy
| | - Lisa Pavinato
- Department of Medical Sciences, University of Torino, Via Santena 19, 10126, Turin, Italy
| | - Cecilia Mancini
- Department of Medical Sciences, University of Torino, Via Santena 19, 10126, Turin, Italy
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, Rome, Italy
| | - Debasmita Tripathy
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Marta Manes
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Eriola Hoxha
- Neuroscience Institute Cavalieri Ottolenghi, Orbassano and Department of Neuroscience, University of Torino, Turin, Italy
| | | | - Elisa Pozzi
- Department of Medical Sciences, University of Torino, Via Santena 19, 10126, Turin, Italy
| | - Matteo Rossi Sebastiano
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy
| | - Nico Mitro
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Filippo Tempia
- Neuroscience Institute Cavalieri Ottolenghi, Orbassano and Department of Neuroscience, University of Torino, Turin, Italy
| | - Donatella Caruso
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Barbara Borroni
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Manuela Basso
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Michele Sallese
- Centre for Advanced Studies and Technology, G. d'Annunzio University of Chieti-Pescara, Chieti, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Via Santena 19, 10126, Turin, Italy.
- Unit of Medical Genetics, Città della Salute e Della Scienza Hospital, Turin, Italy.
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12
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Brown OR, Hullender DA. Biological evolution requires an emergent, self-organizing principle. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023:S0079-6107(23)00058-5. [PMID: 37343790 DOI: 10.1016/j.pbiomolbio.2023.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/16/2023] [Accepted: 06/09/2023] [Indexed: 06/23/2023]
Abstract
In this perspective review, we assess fundamental flaws in Darwinian evolution, including its modern versions. Fixed mutations 'explain' microevolution but not macroevolution including speciation events and the origination of all the major body plans of the Cambrian explosion. Complex, multifactorial change is required for speciation events and inevitably requires self-organization beyond what is accomplished by known mechanisms. The assembly of ribosomes and ATP synthase are specific examples. We propose their origin is a model for what is unexplained in biological evolution. Probability of evolution is modeled in Section 9 and values are absurdly improbable. Speciation and higher taxonomic changes become exponentially less probable as the number of required, genetically-based events increase. Also, the power required of the proposed selection mechanism (survival of the fittest) is nil for any biological advance requiring multiple changes, because they regularly occur in multiple generations (different genomes) and would not be selectively conserved by the concept survival of the fittest (a concept ultimately centered on the individual). Thus, survival of the fittest cannot 'explain' the origin of the millions of current and extinct species. We also focus on the inadequacies of laboratory chemistry to explain the complex, required biological self-organization seen in cells. We propose that a 'bioelectromagnetic' field/principle emerges in living cells. Synthesis by self-organization of massive molecular complexes involves biochemical responses to this emergent field/principle. There are ramifications for philosophy, science, and religion. Physics and mathematics must be more strongly integrated with biology and integration should receive dedicated funding with special emphasis for medical applications; treatment of cancer and genetic diseases are examples.
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Affiliation(s)
- Olen R Brown
- Emeritus of Biomedical Sciences, at the University of Missouri, Columbia, MO, USA.
| | - David A Hullender
- Mechanical and Aerospace Engineering at the University of Texas at Arlington, USA
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13
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Deng J, Cui Q. Second-Shell Residues Contribute to Catalysis by Predominately Preorganizing the Apo State in PafA. J Am Chem Soc 2023; 145:11333-11347. [PMID: 37172218 PMCID: PMC10810092 DOI: 10.1021/jacs.3c02423] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Residues beyond the first coordination shell are often observed to make considerable cumulative contributions in enzymes. Due to typically indirect perturbations of multiple physicochemical properties of the active site, however, their individual and specific roles in enzyme catalysis and disease-causing mutations remain difficult to predict and understand at the molecular level. Here we analyze the contributions of several second-shell residues in phosphate-irrepressible alkaline phosphatase of flavobacterium (PafA), a representative system as one of the most efficient enzymes. By adopting a multifaceted approach that integrates quantum-mechanical/molecular-mechanical free energy computations, molecular-mechanical molecular dynamics simulations, and density functional theory cluster model calculations, we probe the rate-limiting phosphoryl transfer step and structural properties of all relevant enzyme states. In combination with available experimental data, our computational results show that mutations of the studied second-shell residues impact catalytic efficiency mainly by perturbation of the apo state and therefore substrate binding, while they do not affect the ground state or alter the nature of phosphoryl transfer transition state significantly. Several second-shell mutations also modulate the active site hydration level, which in turn influences the energetics of phosphoryl transfer. These mechanistic insights also help inform strategies that may improve the efficiency of enzyme design and engineering by going beyond the current focus on the first coordination shell.
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Affiliation(s)
- Jiahua Deng
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
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14
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Tian J, Garcia AA, Donnan PH, Bridwell-Rabb J. Leveraging a Structural Blueprint to Rationally Engineer the Rieske Oxygenase TsaM. Biochemistry 2023. [PMID: 37188334 DOI: 10.1021/acs.biochem.3c00150] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Rieske nonheme iron oxygenases use two metallocenters, a Rieske-type [2Fe-2S] cluster and a mononuclear iron center, to catalyze oxidation reactions on a broad range of substrates. These enzymes are widely used by microorganisms to degrade environmental pollutants and to build complexity in a myriad of biosynthetic pathways that are industrially interesting. However, despite the value of this chemistry, there is a dearth of understanding regarding the structure-function relationships in this enzyme class, which limits our ability to rationally redesign, optimize, and ultimately exploit the chemistry of these enzymes. Therefore, in this work, by leveraging a combination of available structural information and state-of-the-art protein modeling tools, we show that three "hotspot" regions can be targeted to alter the site selectivity, substrate preference, and substrate scope of the Rieske oxygenase p-toluenesulfonate methyl monooxygenase (TsaM). Through mutation of six to 10 residues distributed between three protein regions, TsaM was engineered to behave as either vanillate monooxygenase (VanA) or dicamba monooxygenase (DdmC). This engineering feat means that TsaM was rationally engineered to catalyze an oxidation reaction at the meta and ortho positions of an aromatic substrate, rather than its favored native para position, and that TsaM was redesigned to perform chemistry on dicamba, a substrate that is not natively accepted by the enzyme. This work thus contributes to unlocking our understanding of structure-function relationships in the Rieske oxygenase enzyme class and expands foundational principles for future engineering of these metalloenzymes.
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Affiliation(s)
- Jiayi Tian
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Patrick H Donnan
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jennifer Bridwell-Rabb
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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15
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Zhou HY, Chen Q, Zhang YF, Chen DD, Yi XN, Chen DS, Cheng XP, Li M, Wang HY, Chen KQ, Liu ZQ, Zheng YG. Improving the catalytic activity of β-glucosidase from Coniophora puteana via semi-rational design for efficient biomass cellulose degradation. Enzyme Microb Technol 2023; 164:110188. [PMID: 36584665 DOI: 10.1016/j.enzmictec.2022.110188] [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: 09/09/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
In order to improve the degradation activity of β-glucosidase (CpBgl) from Coniophora puteana, the structural modification was conducted. The enzyme activity of mutants CpBgl-Q20C and CpBgl-A240S was increased by 65.75% and 58.58%, respectively. These mutants exhibited maximum activity under the same conditions as wild-type CpBgl (65 ℃ and pH 5.0), slightly improved stabilities compared that of the wild-type, and remarkably enhanced activities in the presence of Mn2+ or Fe2+. The Vmax of CpBgl-Q20C and CpBgl-A240S was increased to 138.18 and 125.14 μmol/mg/min, respectively, from 81.34 μmol/mg/min of the wild-type, and the catalysis efficiency (kcat/Km) of CpBgl-Q20C (335.79 min-1/mM) and CpBgl-A240S (281.51 min-1/mM) was significantly improved compared with that of the wild-type (149.12 min-1/mM). When the mutant CpBgl-Q20C were used in the practical degradation of different biomasses, the glucose yields of filter paper, corncob residue, and fungi mycelia residue were increased by 17.68%, 25.10%, and 20.37%, respectively. The spatial locations of the mutation residues in the architecture of CpBgl and their unique roles in the enzyme-substrate binding and catalytic efficiency were probed in this work. These results laid a foundation for evolution of other glycoside hydrolases and the industrial bio-degradation of cellulosic biomass in nature.
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Affiliation(s)
- Hai-Yan Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Qi Chen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Yi-Feng Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Dou-Dou Chen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Xiao-Nan Yi
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - De-Shui Chen
- Zhejiang Huakang Pharmaceutical Co., LTD., 18 Huagong Road, Huabu Town, Kaihua 324302, People's Republic of China
| | - Xin-Ping Cheng
- Zhejiang Huakang Pharmaceutical Co., LTD., 18 Huagong Road, Huabu Town, Kaihua 324302, People's Republic of China
| | - Mian Li
- Zhejiang Huakang Pharmaceutical Co., LTD., 18 Huagong Road, Huabu Town, Kaihua 324302, People's Republic of China
| | - Hong-Yan Wang
- Zhejiang Huakang Pharmaceutical Co., LTD., 18 Huagong Road, Huabu Town, Kaihua 324302, People's Republic of China
| | - Kai-Qian Chen
- Zhejiang Huakang Pharmaceutical Co., LTD., 18 Huagong Road, Huabu Town, Kaihua 324302, People's Republic of China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China.
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
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16
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Standley M, Blay V, Beleva Guthrie V, Kim J, Lyman A, Moya A, Karchin R, Camps M. Experimental and In Silico Analysis of TEM β-Lactamase Adaptive Evolution. ACS Infect Dis 2022; 8:2451-2463. [PMID: 36377311 PMCID: PMC9745794 DOI: 10.1021/acsinfecdis.2c00216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Multiple mutations often have non-additive (epistatic) phenotypic effects. Epistasis is of fundamental biological relevance but is not well understood mechanistically. Adaptive evolution, i.e., the evolution of new biochemical activities, is rich in epistatic interactions. To better understand the principles underlying epistasis during genetic adaptation, we studied the evolution of TEM-1 β-lactamase variants exhibiting cefotaxime resistance. We report the collection of a library of 487 observed evolutionary trajectories for TEM-1 and determine the epistasis status based on cefotaxime resistance phenotype for 206 combinations of 2-3 TEM-1 mutations involving 17 positions under adaptive selective pressure. Gain-of-function (GOF) mutations are gatekeepers for adaptation. To see if GOF phenotypes can be inferred based solely on sequence data, we calculated the enrichment of GOF mutations in the different categories of epistatic pairs. Our results suggest that this is possible because GOF mutations are particularly enriched in sign and reciprocal sign epistasis, which leave a major imprint on the sequence space accessible to evolution. We also used FoldX to explore the relationship between thermodynamic stability and epistasis. We found that mutations in observed evolutionary trajectories tend to destabilize the folded structure of the protein, albeit their cumulative effects are consistently below the protein's free energy of folding. The destabilizing effect is stronger for epistatic pairs, suggesting that modest or local alterations in folding stability can modulate catalysis. Finally, we report a significant relationship between epistasis and the degree to which two protein positions are structurally and dynamically coupled, even in the absence of ligand.
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Affiliation(s)
- Melissa Standley
- Department
of Microbiology and Environmental Toxicology, University of California, Santa
Cruz, California95064, United States
| | - Vincent Blay
- Department
of Microbiology and Environmental Toxicology, University of California, Santa
Cruz, California95064, United States,Institute
for Integrative Systems Biology (I2Sysbio), Universitat de València and Spanish Research Council (CSIC), 46980Valencia, Spain,
| | - Violeta Beleva Guthrie
- Department
of Biomedical Engineering and Institute for Computational Medicine, The Johns Hopkins University, Baltimore, Maryland21218, United States
| | - Jay Kim
- Department
of Microbiology and Environmental Toxicology, University of California, Santa
Cruz, California95064, United States
| | - Audrey Lyman
- Department
of Microbiology and Environmental Toxicology, University of California, Santa
Cruz, California95064, United States
| | - Andrés Moya
- Institute
for Integrative Systems Biology (I2Sysbio), Universitat de València and Spanish Research Council (CSIC), 46980Valencia, Spain,Foundation
for the Promotion of Sanitary and Biomedical Research of Valencia
Region (FISABIO), 46021Valencia, Spain,CIBER
in Epidemiology and Public Health (CIBEResp), 28029Madrid, Spain
| | - Rachel Karchin
- Department
of Biomedical Engineering and Institute for Computational Medicine, The Johns Hopkins University, Baltimore, Maryland21218, United States
| | - Manel Camps
- Department
of Microbiology and Environmental Toxicology, University of California, Santa
Cruz, California95064, United States,
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17
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Hirschi S, Ward TR, Meier WP, Müller DJ, Fotiadis D. Synthetic Biology: Bottom-Up Assembly of Molecular Systems. Chem Rev 2022; 122:16294-16328. [PMID: 36179355 DOI: 10.1021/acs.chemrev.2c00339] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bottom-up assembly of biological and chemical components opens exciting opportunities to engineer artificial vesicular systems for applications with previously unmet requirements. The modular combination of scaffolds and functional building blocks enables the engineering of complex systems with biomimetic or new-to-nature functionalities. Inspired by the compartmentalized organization of cells and organelles, lipid or polymer vesicles are widely used as model membrane systems to investigate the translocation of solutes and the transduction of signals by membrane proteins. The bottom-up assembly and functionalization of such artificial compartments enables full control over their composition and can thus provide specifically optimized environments for synthetic biological processes. This review aims to inspire future endeavors by providing a diverse toolbox of molecular modules, engineering methodologies, and different approaches to assemble artificial vesicular systems. Important technical and practical aspects are addressed and selected applications are presented, highlighting particular achievements and limitations of the bottom-up approach. Complementing the cutting-edge technological achievements, fundamental aspects are also discussed to cater to the inherently diverse background of the target audience, which results from the interdisciplinary nature of synthetic biology. The engineering of proteins as functional modules and the use of lipids and block copolymers as scaffold modules for the assembly of functionalized vesicular systems are explored in detail. Particular emphasis is placed on ensuring the controlled assembly of these components into increasingly complex vesicular systems. Finally, all descriptions are presented in the greater context of engineering valuable synthetic biological systems for applications in biocatalysis, biosensing, bioremediation, or targeted drug delivery.
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Affiliation(s)
- Stephan Hirschi
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Thomas R Ward
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Wolfgang P Meier
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
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18
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Mallik S, Tawfik DS, Levy ED. How gene duplication diversifies the landscape of protein oligomeric state and function. Curr Opin Genet Dev 2022; 76:101966. [PMID: 36007298 PMCID: PMC9548406 DOI: 10.1016/j.gde.2022.101966] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/01/2022] [Accepted: 07/08/2022] [Indexed: 11/29/2022]
Abstract
Oligomeric proteins are central to cellular life and the duplication and divergence of their genes is a key driver of evolutionary innovations. The duplication of a gene coding for an oligomeric protein has numerous possible outcomes, which motivates questions on the relationship between structural and functional divergence. How do protein oligomeric states diversify after gene duplication? In the simple case of duplication of a homo-oligomeric protein gene, what properties can influence the fate of descendant paralogs toward forming independent homomers or maintaining their interaction as a complex? Furthermore, how are functional innovations associated with the diversification of oligomeric states? Here, we review recent literature and present specific examples in an attempt to illustrate and answer these questions.
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Affiliation(s)
- Saurav Mallik
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Dan S Tawfik
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Emmanuel D Levy
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel.
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19
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Santos TCB, Dingjan T, Futerman AH. The sphingolipid anteome: implications for evolution of the sphingolipid metabolic pathway. FEBS Lett 2022; 596:2345-2363. [PMID: 35899376 DOI: 10.1002/1873-3468.14457] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/10/2022] [Accepted: 07/19/2022] [Indexed: 11/09/2022]
Abstract
Modern cell membranes contain a bewildering complexity of lipids, among them sphingolipids (SLs). Advances in mass spectrometry have led to the realization that the number and combinatorial complexity of lipids, including SLs, is much greater than previously appreciated. SLs are generated de novo by four enzymes, namely serine palmitoyltransferase, 3-ketodihydrosphingosine reductase, ceramide synthase and dihydroceramide Δ4-desaturase 1. Some of these enzymes depend on the availability of specific substrates and cofactors, which are themselves supplied by other complex metabolic pathways. The evolution of these four enzymes is poorly understood and likely depends on the co-evolution of the metabolic pathways that supply the other essential reaction components. Here, we introduce the concept of the 'anteome', from the Latin ante ('before') to describe the network of metabolic ('omic') pathways that must have converged in order for these pathways to co-evolve and permit SL synthesis. We also suggest that current origin of life and evolutionary models lack appropriate experimental support to explain the appearance of this complex metabolic pathway and its anteome.
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Affiliation(s)
- Tania C B Santos
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Tamir Dingjan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Anthony H Futerman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
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20
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Srivastava J, Balaji PV. Clues to reaction specificity in
PLP
‐dependent fold type I aminotransferases of monosaccharide biosynthesis. Proteins 2022; 90:1247-1258. [DOI: 10.1002/prot.26305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 01/20/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Jaya Srivastava
- Department of Biosciences and Bioengineering Indian Institute of Technology Bombay Mumbai India
| | - Petety V. Balaji
- Department of Biosciences and Bioengineering Indian Institute of Technology Bombay Mumbai India
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21
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Brissos V, Borges P, Núñez-Franco R, Lucas MF, Frazão C, Monza E, Masgrau L, Cordeiro TN, Martins LO. Distal Mutations Shape Substrate-Binding Sites during Evolution of a Metallo-Oxidase into a Laccase. ACS Catal 2022; 12:5022-5035. [PMID: 36567772 PMCID: PMC9775220 DOI: 10.1021/acscatal.2c00336] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Laccases are in increasing demand as innovative solutions in the biorefinery fields. Here, we combine mutagenesis with structural, kinetic, and in silico analyses to characterize the molecular features that cause the evolution of a hyperthermostable metallo-oxidase from the multicopper oxidase family into a laccase (k cat 273 s-1 for a bulky aromatic substrate). We show that six mutations scattered across the enzyme collectively modulate dynamics to improve the binding and catalysis of a bulky aromatic substrate. The replacement of residues during the early stages of evolution is a stepping stone for altering the shape and size of substrate-binding sites. Binding sites are then fine-tuned through high-order epistasis interactions by inserting distal mutations during later stages of evolution. Allosterically coupled, long-range dynamic networks favor catalytically competent conformational states that are more suitable for recognizing and stabilizing the aromatic substrate. This work provides mechanistic insight into enzymatic and evolutionary molecular mechanisms and spots the importance of iterative experimental and computational analyses to understand local-to-global changes.
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Affiliation(s)
- Vânia Brissos
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal
| | - Patrícia
T. Borges
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal
| | | | | | - Carlos Frazão
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal
| | - Emanuele Monza
- Zymvol
Biomodeling, Carrer Roc
Boronat, 117, 08018 Barcelona, Spain
| | - Laura Masgrau
- Zymvol
Biomodeling, Carrer Roc
Boronat, 117, 08018 Barcelona, Spain,Department
of Chemistry, Universitat Autònoma
de Barcelona, 08193 Bellaterra, Spain
| | - Tiago N. Cordeiro
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal
| | - Lígia O. Martins
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal,
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22
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Mascotti ML. Resurrecting Enzymes by Ancestral Sequence Reconstruction. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2397:111-136. [PMID: 34813062 DOI: 10.1007/978-1-0716-1826-4_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ancestral Sequence Reconstruction (ASR) allows one to infer the sequences of extinct proteins using the phylogeny of extant proteins. It consists of disclosing the evolutionary history-i.e., the phylogeny-of a protein family of interest and then inferring the sequences of its ancestors-i.e., the nodes in the phylogeny. Assisted by gene synthesis, the selected ancestors can be resurrected in the lab and experimentally characterized. The crucial step to succeed with ASR is starting from a reliable phylogeny. At the same time, it is of the utmost importance to have a clear idea on the evolutionary history of the family under study and the events that influenced it. This allows us to implement ASR with well-defined hypotheses and to apply the appropriate experimental methods. In the last years, ASR has become popular to test hypotheses about the origin of functionalities, changes in activities, understanding physicochemical properties of proteins, among others. In this context, the aim of this chapter is to present the ASR approach applied to the reconstruction of enzymes-i.e., proteins with catalytic roles. The spirit of this contribution is to provide a basic, hands-to-work guide for biochemists and biologists who are unfamiliar with molecular phylogenetics.
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Affiliation(s)
- Maria Laura Mascotti
- Molecular Enzymology group, University of Groningen, Groningen, The Netherlands. .,IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina.
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23
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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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24
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Nagar M, Hayden JA, Sagey E, Worthen G, Park M, Sharma AN, Fetter CM, Kuehm OP, Bearne SL. Altering the binding determinant on the interdigitating loop of mandelate racemase shifts specificity towards that of d-tartrate dehydratase. Arch Biochem Biophys 2022; 718:109119. [DOI: 10.1016/j.abb.2022.109119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 11/02/2022]
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25
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Belinskaia DA, Voronina PA, Goncharov NV. Integrative Role of Albumin: Evolutionary, Biochemical and Pathophysiological Aspects. J EVOL BIOCHEM PHYS+ 2021; 57:1419-1448. [PMID: 34955553 PMCID: PMC8685822 DOI: 10.1134/s002209302106020x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/02/2021] [Accepted: 04/02/2021] [Indexed: 12/12/2022]
Abstract
Being one of the main proteins in the human body and many
animal species, albumin plays a crucial role in the transport of
various ions, electrically neutral molecules and in maintaining
the colloidal osmotic pressure of the blood. Albumin is able to
bind almost all known drugs, many nutraceuticals and toxic substances,
determining their pharmaco- and toxicokinetics. However, albumin
is not only the passive but also the active participant of the pharmacokinetic
and toxicokinetic processes possessing a number of enzymatic activities.
Due to the thiol group of Cys34, albumin can serve as a trap for
reactive oxygen and nitrogen species, thus participating in redox
processes. The interaction of the protein with blood cells, blood
vessels, and also with tissue cells outside the vascular bed is
of great importance. The interaction of albumin with endothelial glycocalyx
and vascular endothelial cells largely determines its integrative
role. This review provides information of a historical nature, information
on evolutionary changes, inflammatory and antioxidant properties
of albumin, on its structural and functional modifications and their significance
in the pathogenesis of some diseases.
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Affiliation(s)
- D. A. Belinskaia
- Sechenov Institute of Evolutionary
Physiology and Biochemistry of the Russian Academy of Sciences, St. Petersburg, Russia
| | - P. A. Voronina
- Sechenov Institute of Evolutionary
Physiology and Biochemistry of the Russian Academy of Sciences, St. Petersburg, Russia
| | - N. V. Goncharov
- Sechenov Institute of Evolutionary
Physiology and Biochemistry of the Russian Academy of Sciences, St. Petersburg, Russia
- Research Institute of Hygiene,
Occupational Pathology and Human Ecology, p/o Kuzmolovsky, Vsevolozhsky District, Leningrad
Region, Russia
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26
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Tatsaki E, Anagnostopoulou E, Zantza I, Lazou P, Mikros E, Frillingos S. Identification of New Specificity Determinants in Bacterial Purine Nucleobase Transporters based on an Ancestral Sequence Reconstruction Approach. J Mol Biol 2021; 433:167329. [PMID: 34710398 DOI: 10.1016/j.jmb.2021.167329] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 10/05/2021] [Accepted: 10/19/2021] [Indexed: 11/28/2022]
Abstract
The relation of sequence with specificity in membrane transporters is challenging to explore. Most relevant studies until now rely on comparisons of present-day homologs. In this work, we study a set of closely related transporters by employing an evolutionary, ancestral-reconstruction approach and reveal unexpected new specificity determinants. We analyze a monophyletic group represented by the xanthine-specific XanQ of Escherichia coli in the Nucleobase-Ascorbate Transporter/Nucleobase-Cation Symporter-2 (NAT/NCS2) family. We reconstructed AncXanQ, the putative common ancestor of this clade, expressed it in E. coli K-12, and found that, in contrast to XanQ, it encodes a high-affinity permease for both xanthine and guanine, which also recognizes adenine, hypoxanthine, and a range of analogs. AncXanQ conserves all binding-site residues of XanQ and differs substantially in only five intramembrane residues outside the binding site. We subjected both homologs to rationally designed mutagenesis and present evidence that these five residues are linked with the specificity change. In particular, we reveal Ser377 of XanQ (Gly in AncXanQ) as a major determinant. Replacement of this Ser with Gly enlarges the specificity of XanQ towards an AncXanQ-phenotype. The ortholog from Neisseria meningitidis retaining Gly at this position is also a xanthine/guanine transporter with extended substrate profile like AncXanQ. Molecular Dynamics shows that the S377G replacement tilts transmembrane helix 12 resulting in rearrangement of Phe376 relative to Phe94 in the XanQ binding pocket. This effect may rationalize the enlarged specificity. On the other hand, the specificity effect of S377G can be masked by G27S or other mutations through epistatic interactions.
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Affiliation(s)
- Ekaterini Tatsaki
- Laboratory of Biological Chemistry, Department of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Eleni Anagnostopoulou
- Laboratory of Biological Chemistry, Department of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece. https://twitter.com/EleniAnagn
| | - Iliana Zantza
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece
| | - Panayiota Lazou
- Laboratory of Biological Chemistry, Department of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Emmanuel Mikros
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece
| | - Stathis Frillingos
- Laboratory of Biological Chemistry, Department of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece; Institute of Biosciences, University Research Center of Ioannina, Ioannina, Greece.
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27
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A shared mechanistic pathway for pyridoxal phosphate-dependent arginine oxidases. Proc Natl Acad Sci U S A 2021; 118:2012591118. [PMID: 34580201 DOI: 10.1073/pnas.2012591118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2021] [Indexed: 01/02/2023] Open
Abstract
The mechanism by which molecular oxygen is activated by the organic cofactor pyridoxal phosphate (PLP) for oxidation reactions remains poorly understood. Recent work has identified arginine oxidases that catalyze desaturation or hydroxylation reactions. Here, we investigate a desaturase from the Pseudoalteromonas luteoviolacea indolmycin pathway. Our work, combining X-ray crystallographic, biochemical, spectroscopic, and computational studies, supports a shared mechanism with arginine hydroxylases, involving two rounds of single-electron transfer to oxygen and superoxide rebound at the 4' carbon of the PLP cofactor. The precise positioning of a water molecule in the active site is proposed to control the final reaction outcome. This proposed mechanism provides a unified framework to understand how oxygen can be activated by PLP-dependent enzymes for oxidation of arginine and elucidates a shared mechanistic pathway and intertwined evolutionary history for arginine desaturases and hydroxylases.
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28
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Yan B, Ran X, Jiang Y, Torrence SK, Yuan L, Shao Q, Yang ZJ. Rate-Perturbing Single Amino Acid Mutation for Hydrolases: A Statistical Profiling. J Phys Chem B 2021; 125:10682-10691. [PMID: 34524819 DOI: 10.1021/acs.jpcb.1c05901] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrolases are a critical component for modern chemical, pharmaceutical, and environmental sciences. Identifying mutations that enhance catalytic efficiency presents a roadblock to design and to discover new hydrolases for broad academic and industrial uses. Here, we report the statistical profiling for rate-perturbing mutant hydrolases with a single amino acid substitution. We constructed an integrated structure-kinetics database for hydrolases, IntEnzyDB, which contains 3907 kcats, 4175 KMs, and 2715 Protein Data Bank IDs. IntEnzyDB adopts a relational architecture with a flattened data structure, enabling facile and efficient access to clean and tabulated data for machine learning uses. We conducted statistical analyses on how single amino acids mutations influence the turnover number (i.e., kcat) and efficiency (i.e., kcat/KM), with a particular emphasis on profiling the features for rate-enhancing mutations. The results show that mutation to bulky nonpolar residues with a hydrocarbon chain involves a higher likelihood for rate acceleration than to other types of residues. Linear regression models reveal geometric descriptors of substrate and mutation residues that mediate rate-perturbing outcomes for hydrolases with bulky nonpolar mutations. On the basis of the analyses of the structure-kinetics relationship, we observe that the propensity for rate enhancement is independent of protein sizes. In addition, we observe that distal mutations (i.e., >10 Å from the active site) in hydrolases are significantly more prone to induce efficiency neutrality and avoid efficiency deletion but involve similar propensity for rate enhancement. The studies reveal the statistical features for identifying rate-enhancing mutations in hydrolases, which will potentially guide hydrolase discovery in biocatalysis.
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Affiliation(s)
- Bailu Yan
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Biostatistics, Vanderbilt University, Nashville, Tennessee 37203, United States
| | - Xinchun Ran
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Yaoyukun Jiang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Sarah K Torrence
- Data Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Li Yuan
- Data Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Qianzhen Shao
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Zhongyue J Yang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States.,Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States.,Data Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
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29
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Serum Albumin in Health and Disease: Esterase, Antioxidant, Transporting and Signaling Properties. Int J Mol Sci 2021; 22:ijms221910318. [PMID: 34638659 PMCID: PMC8508759 DOI: 10.3390/ijms221910318] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 12/11/2022] Open
Abstract
Being one of the main proteins in the human body and many animal species, albumin plays a decisive role in the transport of various ions-electrically neutral and charged molecules-and in maintaining the colloidal osmotic pressure of the blood. Albumin is able to bind to almost all known drugs, as well as many nutraceuticals and toxic substances, largely determining their pharmaco- and toxicokinetics. Albumin of humans and respective representatives in cattle and rodents have their own structural features that determine species differences in functional properties. However, albumin is not only passive, but also an active participant of pharmacokinetic and toxicokinetic processes, possessing a number of enzymatic activities. Numerous experiments have shown esterase or pseudoesterase activity of albumin towards a number of endogeneous and exogeneous esters. Due to the free thiol group of Cys34, albumin can serve as a trap for reactive oxygen and nitrogen species, thus participating in redox processes. Glycated albumin makes a significant contribution to the pathogenesis of diabetes and other diseases. The interaction of albumin with blood cells, blood vessels and tissue cells outside the vascular bed is of great importance. Interactions with endothelial glycocalyx and vascular endothelial cells largely determine the integrative role of albumin. This review considers the esterase, antioxidant, transporting and signaling properties of albumin, as well as its structural and functional modifications and their significance in the pathogenesis of certain diseases.
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30
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Galmés MÀ, Nödling AR, Luk L, Świderek K, Moliner V. Combined Theoretical and Experimental Study to Unravel the Differences in Promiscuous Amidase Activity of Two Nonhomologous Enzymes. ACS Catal 2021; 11:8635-8644. [PMID: 35875595 PMCID: PMC9299431 DOI: 10.1021/acscatal.1c02150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
![]()
Convergent evolution has resulted in nonhomologous enzymes that
contain similar active sites that catalyze the same primary and secondary
reactions. Comparing how these enzymes achieve their reaction promiscuity
can yield valuable insights to develop functions from the optimization
of latent activities. In this work, we have focused on the promiscuous
amidase activity in the esterase from Bacillus subtilis (Bs2) and compared with the same activity in the promiscuous lipase
B from Candida antarctica (CALB). The
study, combining multiscale quantum mechanics/molecular mechanics
(QM/MM) simulations, deep machine learning approaches, and experimental
characterization of Bs2 kinetics, confirms the amidase activity of
Bs2 and CALB. The computational results indicate that both enzymes
offer a slightly different reaction environment reflected by electrostatic
effects within the active site, thus resulting in a different reaction
mechanism during the acylation step. A convolutional neural network
(CNN) has been used to understand the conserved amino acids among
the evolved protein family and suggest that Bs2 provides a more robust
protein scaffold to perform future mutagenesis studies. Results derived
from this work will help reveal the origin of enzyme promiscuity,
which will find applications in enzyme (re)design, particularly in
creating a highly active amidase.
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Affiliation(s)
- Miquel À. Galmés
- Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Alexander R. Nödling
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Louis Luk
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Katarzyna Świderek
- Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Vicent Moliner
- Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
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31
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Fröhlich C, Chen JZ, Gholipour S, Erdogan AN, Tokuriki N. Evolution of β-lactamases and enzyme promiscuity. Protein Eng Des Sel 2021; 34:6294778. [PMID: 34100551 DOI: 10.1093/protein/gzab013] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/12/2021] [Accepted: 05/03/2021] [Indexed: 11/14/2022] Open
Abstract
β-Lactamases represent one of the most prevalent resistance mechanisms against β-lactam antibiotics. Beyond their clinical importance, they have also become key models in enzymology and evolutionary biochemistry. A global understanding of their evolution and sequence and functional diversity can therefore aid a wide set of different disciplines. Interestingly, β-lactamases have evolved multiple times from distinct evolutionary origins, with ancestries that reach back billions of years. It is therefore no surprise that these enzymes exhibit diverse structural features and enzymatic mechanisms. In this review, we provide a bird's eye view on the evolution of β-lactamases within the two enzyme superfamilies-i.e. the penicillin-binding protein-like and metallo-β-lactamase superfamily-through phylogenetics. We further discuss potential evolutionary origins of each β-lactamase class by highlighting signs of evolutionary connections in protein functions between β-lactamases and other enzymes, especially cases of enzyme promiscuity.
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Affiliation(s)
- Christopher Fröhlich
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway, Tromsø 9037, Norway
| | - John Z Chen
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Sevan Gholipour
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Ayse N Erdogan
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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32
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Miton CM, Buda K, Tokuriki N. Epistasis and intramolecular networks in protein evolution. Curr Opin Struct Biol 2021; 69:160-168. [PMID: 34077895 DOI: 10.1016/j.sbi.2021.04.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/01/2021] [Accepted: 04/21/2021] [Indexed: 12/01/2022]
Abstract
Proteins are molecular machines composed of complex, highly connected amino acid networks. Their functional optimization requires the reorganization of these intramolecular networks by evolution. In this review, we discuss the mechanisms by which epistasis, that is, the dependence of the effect of a mutation on the genetic background, rewires intramolecular interactions to alter protein function. Deciphering the biophysical basis of epistasis is crucial to our understanding of evolutionary dynamics and the elucidation of sequence-structure-function relationships. We featured recent studies that provide insights into the molecular mechanisms giving rise to epistasis, particularly at the structural level. These studies illustrate the convoluted and fascinating nature of the intramolecular networks co-opted by epistasis during the evolution of protein function.
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Affiliation(s)
- Charlotte M Miton
- Michael Smith Laboratories, University of British Columbia, Vancouver, V6T 1Z4, BC, Canada
| | - Karol Buda
- Michael Smith Laboratories, University of British Columbia, Vancouver, V6T 1Z4, BC, Canada
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, V6T 1Z4, BC, Canada.
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33
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van den Noort M, de Boer M, Poolman B. Stability of Ligand-induced Protein Conformation Influences Affinity in Maltose-binding Protein. J Mol Biol 2021; 433:167036. [PMID: 33957147 DOI: 10.1016/j.jmb.2021.167036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/13/2021] [Accepted: 04/27/2021] [Indexed: 11/18/2022]
Abstract
Our understanding of what determines ligand affinity of proteins is poor, even with high-resolution structures available. Both the non-covalent ligand-protein interactions and the relative free energies of available conformations contribute to the affinity of a protein for a ligand. Distant, non-binding site residues can influence the ligand affinity by altering the free energy difference between a ligand-free and ligand-bound conformation. Our hypothesis is that when different ligands induce distinct ligand-bound conformations, it should be possible to tweak their affinities by changing the free energies of the available conformations. We tested this idea for the maltose-binding protein (MBP) from Escherichia coli. We used single-molecule Förster resonance energy transfer (smFRET) to distinguish several unique ligand-bound conformations of MBP. We engineered mutations, distant from the binding site, to affect the stabilities of different ligand-bound conformations. We show that ligand affinity can indeed be altered in a conformation-dependent manner. Our studies provide a framework for the tuning of ligand affinity, apart from modifying binding site residues.
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Affiliation(s)
- Marco van den Noort
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, the Netherlands
| | - Marijn de Boer
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, the Netherlands
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, the Netherlands.
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34
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Abstract
Very low antibiotic concentrations have been shown to drive the evolution of antimicrobial resistance. While substantial progress has been made to understand the driving role of low concentrations during resistance development for different antimicrobial classes, the importance of β-lactams, the most commonly used antibiotics, is still poorly studied. Our current understanding of how low antibiotic concentrations shape the evolution of contemporary β-lactamases is limited. Using the widespread carbapenemase OXA-48, we tested the long-standing hypothesis that selective compartments with low antibiotic concentrations cause standing genetic diversity that could act as a gateway to developing clinical resistance. Here, we subjected Escherichia coli expressing blaOXA-48, on a clinical plasmid, to experimental evolution at sub-MICs of ceftazidime. We identified and characterized seven single variants of OXA-48. Susceptibility profiles and dose-response curves showed that they increased resistance only marginally. However, in competition experiments at sub-MICs of ceftazidime, they demonstrated strong selectable fitness benefits. Increased resistance was also reflected in elevated catalytic efficiencies toward ceftazidime. These changes are likely caused by enhanced flexibility of the Ω- and β5-β6 loops and fine-tuning of preexisting active site residues. In conclusion, low-level concentrations of β-lactams can drive the evolution of β-lactamases through cryptic phenotypes which may act as stepping-stones toward clinical resistance. IMPORTANCE Very low antibiotic concentrations have been shown to drive the evolution of antimicrobial resistance. While substantial progress has been made to understand the driving role of low concentrations during resistance development for different antimicrobial classes, the importance of β-lactams, the most commonly used antibiotics, is still poorly studied. Here, we shed light on the evolutionary impact of low β-lactam concentrations on the widespread β-lactamase OXA-48. Our data indicate that the exposure to β-lactams at very low concentrations enhances β-lactamase diversity and drives the evolution of β-lactamases by significantly influencing their substrate specificity. Thus, in contrast to high concentrations, low levels of these drugs may substantially contribute to the diversification and divergent evolution of these enzymes, providing a standing genetic diversity that can be selected and mobilized when antibiotic pressure increases.
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35
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Calzini MA, Malico AA, Mitchler MM, Williams GJ. Protein engineering for natural product biosynthesis and synthetic biology applications. Protein Eng Des Sel 2021; 34:gzab015. [PMID: 34137436 PMCID: PMC8209613 DOI: 10.1093/protein/gzab015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 11/14/2022] Open
Abstract
As protein engineering grows more salient, many strategies have emerged to alter protein structure and function, with the goal of redesigning and optimizing natural product biosynthesis. Computational tools, including machine learning and molecular dynamics simulations, have enabled the rational mutagenesis of key catalytic residues for enhanced or altered biocatalysis. Semi-rational, directed evolution and microenvironment engineering strategies have optimized catalysis for native substrates and increased enzyme promiscuity beyond the scope of traditional rational approaches. These advances are made possible using novel high-throughput screens, including designer protein-based biosensors with engineered ligand specificity. Herein, we detail the most recent of these advances, focusing on polyketides, non-ribosomal peptides and isoprenoids, including their native biosynthetic logic to provide clarity for future applications of these technologies for natural product synthetic biology.
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Affiliation(s)
- Miles A Calzini
- Department of Chemistry, NC State University, Raleigh, NC 27695-8204, USA
| | - Alexandra A Malico
- Department of Chemistry, NC State University, Raleigh, NC 27695-8204, USA
| | - Melissa M Mitchler
- Department of Chemistry, NC State University, Raleigh, NC 27695-8204, USA
| | - Gavin J Williams
- Department of Chemistry, NC State University, Raleigh, NC 27695-8204, USA
- Comparative Medicine Institute, NC State University Raleigh, Raleigh, NC 27695-8204, USA
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36
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Bunzel HA, Anderson JLR, Mulholland AJ. Designing better enzymes: Insights from directed evolution. Curr Opin Struct Biol 2021; 67:212-218. [PMID: 33517098 DOI: 10.1016/j.sbi.2020.12.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/03/2020] [Accepted: 12/28/2020] [Indexed: 12/18/2022]
Abstract
De novo enzymes can be created by computational design and directed evolution. Here, we review recent insights into the origins of catalytic power in evolved designer enzymes to pinpoint opportunities for next-generation designs: Evolution precisely organizes active sites, introduces catalytic H-bonding networks, invokes electrostatic catalysis, and creates dynamical networks embedding the active site in a reactive protein scaffold. Such insights foster our fundamental knowledge of enzyme catalysis and fuel the future design of tailor-made enzymes.
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Affiliation(s)
- H Adrian Bunzel
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | | | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
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37
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Tanaka SI, Tsutaki M, Yamamoto S, Mizutani H, Kurahashi R, Hirata A, Takano K. Exploring mutable conserved sites and fatal non-conserved sites by random mutation of esterase from Sulfolobus tokodaii and subtilisin from Thermococcus kodakarensis. Int J Biol Macromol 2020; 170:343-353. [PMID: 33383075 DOI: 10.1016/j.ijbiomac.2020.12.171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 10/22/2022]
Abstract
Homologous proteins differ in their amino acid sequences at several positions. Generally, conserved sites are recognized as not suitable for amino acid substitution, and thus in evolutionary protein engineering, non-conserved sites are often selected as mutation sites. However, there have also been reports of possible mutations in conserved sites. In this study, we explored mutable conserved sites and immutable non-conserved sites by testing random mutations of two thermostable proteins, an esterase from Sulfolobus tokodaii (Sto-Est) and a subtilisin from Thermococcus kodakarensis (Tko-Sub). The subtilisin domain of Tko-Sub needs Ca2+ ions and the propeptide domain for stability, folding and maturation. The results from the two proteins showed that about one-third of the mutable sites were detected in conserved sites and some non-conserved sites lost enzymatic activity at high temperatures due to mutation. Of the conserved sites in Sto-Est, the sites on the loop, on the surface, and far from the active site are more resistant to mutation. In Tko-Sub, the sites flanking Ca2+-binding sites and propeptide were undesirable for mutation. The results presented here serve as an index for selecting mutation sites and contribute to the expansion of available sequence range by introducing mutations at conserved sites.
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Affiliation(s)
- Shun-Ichi Tanaka
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Minami Tsutaki
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Seira Yamamoto
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Hayate Mizutani
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Ryo Kurahashi
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Azumi Hirata
- Department of Anatomy and Cell Biology, Osaka Medical College, Daigaku-machi, Takatsuki, Osaka 569-8686, Japan
| | - Kazufumi Takano
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan.
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38
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Alejaldre L, Lemay-St-Denis C, Perez Lopez C, Sancho Jodar F, Guallar V, Pelletier JN. Known Evolutionary Paths Are Accessible to Engineered ß-Lactamases Having Altered Protein Motions at the Timescale of Catalytic Turnover. Front Mol Biosci 2020; 7:599298. [PMID: 33330628 PMCID: PMC7716773 DOI: 10.3389/fmolb.2020.599298] [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: 08/26/2020] [Accepted: 10/23/2020] [Indexed: 11/26/2022] Open
Abstract
The evolution of new protein functions is dependent upon inherent biophysical features of proteins. Whereas, it has been shown that changes in protein dynamics can occur in the course of directed molecular evolution trajectories and contribute to new function, it is not known whether varying protein dynamics modify the course of evolution. We investigate this question using three related ß-lactamases displaying dynamics that differ broadly at the slow timescale that corresponds to catalytic turnover yet have similar fast dynamics, thermal stability, catalytic, and substrate recognition profiles. Introduction of substitutions E104K and G238S, that are known to have a synergistic effect on function in the parent ß-lactamase, showed similar increases in catalytic efficiency toward cefotaxime in the related ß-lactamases. Molecular simulations using Protein Energy Landscape Exploration reveal that this results from stabilizing the catalytically-productive conformations, demonstrating the dominance of the synergistic effect of the E014K and G238S substitutions in vitro in contexts that vary in terms of sequence and dynamics. Furthermore, three rounds of directed molecular evolution demonstrated that known cefotaximase-enhancing mutations were accessible regardless of the differences in dynamics. Interestingly, specific sequence differences between the related ß-lactamases were shown to have a higher effect in evolutionary outcomes than did differences in dynamics. Overall, these ß-lactamase models show tolerance to protein dynamics at the timescale of catalytic turnover in the evolution of a new function.
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Affiliation(s)
- Lorea Alejaldre
- Biochemistry Department, Université de Montréal, Montréal, QC, Canada
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec City, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC, Canada
| | - Claudèle Lemay-St-Denis
- Biochemistry Department, Université de Montréal, Montréal, QC, Canada
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec City, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC, Canada
| | | | | | - Victor Guallar
- Barcelona Supercomputing Center, Barcelona, Spain
- ICREA: Institució Catalana de Recerca i Estudis Avancats, Barcelona, Spain
| | - Joelle N. Pelletier
- Biochemistry Department, Université de Montréal, Montréal, QC, Canada
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec City, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC, Canada
- Chemistry Department, Université de Montréal, Montréal, QC, Canada
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39
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Yang G, Miton CM, Tokuriki N. A mechanistic view of enzyme evolution. Protein Sci 2020; 29:1724-1747. [PMID: 32557882 PMCID: PMC7380680 DOI: 10.1002/pro.3901] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/14/2020] [Accepted: 06/16/2020] [Indexed: 12/15/2022]
Abstract
New enzyme functions often evolve through the recruitment and optimization of latent promiscuous activities. How do mutations alter the molecular architecture of enzymes to enhance their activities? Can we infer general mechanisms that are common to most enzymes, or does each enzyme require a unique optimization process? The ability to predict the location and type of mutations necessary to enhance an enzyme's activity is critical to protein engineering and rational design. In this review, via the detailed examination of recent studies that have shed new light on the molecular changes underlying the optimization of enzyme function, we provide a mechanistic perspective of enzyme evolution. We first present a global survey of the prevalence of activity-enhancing mutations and their distribution within protein structures. We then delve into the molecular solutions that mediate functional optimization, specifically highlighting several common mechanisms that have been observed across multiple examples. As distinct protein sequences encounter different evolutionary bottlenecks, different mechanisms are likely to emerge along evolutionary trajectories toward improved function. Identifying the specific mechanism(s) that need to be improved upon, and tailoring our engineering efforts to each sequence, may considerably improve our chances to succeed in generating highly efficient catalysts in the future.
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Affiliation(s)
- Gloria Yang
- Michael Smith LaboratoriesUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Charlotte M. Miton
- Michael Smith LaboratoriesUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Nobuhiko Tokuriki
- Michael Smith LaboratoriesUniversity of British ColumbiaVancouverBritish ColumbiaCanada
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