1
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Fan R, Aranko AS. Catcher/Tag Toolbox: Biomolecular Click-Reactions For Protein Engineering Beyond Genetics. Chembiochem 2024; 25:e202300600. [PMID: 37851860 DOI: 10.1002/cbic.202300600] [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: 08/28/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 10/20/2023]
Abstract
Manipulating protein architectures beyond genetic control has attracted widespread attention. Catcher/Tag systems enable highly specific conjugation of proteins in vivo and in vitro via an isopeptide-bond. They provide efficient, robust, and irreversible strategies for protein conjugation and are simple yet powerful tools for a variety of applications in enzyme industry, vaccines, biomaterials, and cellular applications. Here we summarize recent development of the Catcher/Tag toolbox with a particular emphasis on the design of Catcher/Tag pairs targeted for specific applications. We cover the current limitations of the Catcher/Tag systems and discuss the pH sensitivity of the reactions. Finally, we conclude some of the future directions in the development of this versatile protein conjugation method and envision that improved control over inducing the ligation reaction will further broaden the range of applications.
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Affiliation(s)
- Ruxia Fan
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, 02150, Espoo, Finland
| | - A Sesilja Aranko
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, 02150, Espoo, Finland
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2
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Young PG, Paynter JM, Wardega JK, Middleditch MJ, Payne LS, Baker EN, Squire CJ. Domain structure and cross-linking in a giant adhesin from the Mobiluncus mulieris bacterium. Acta Crystallogr D Struct Biol 2023; 79:971-979. [PMID: 37860959 PMCID: PMC10619420 DOI: 10.1107/s2059798323007507] [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: 06/16/2023] [Accepted: 08/27/2023] [Indexed: 10/21/2023] Open
Abstract
Cell-surface proteins known as adhesins enable bacteria to colonize particular environments, and in Gram-positive bacteria often contain autocatalytically formed covalent intramolecular cross-links. While investigating the prevalence of such cross-links, a remarkable example was discovered in Mobiluncus mulieris, a pathogen associated with bacterial vaginosis. This organism encodes a putative adhesin of 7651 residues. Crystallography and mass spectrometry of two selected domains, and AlphaFold structure prediction of the remainder of the protein, were used to show that this adhesin belongs to the family of thioester, isopeptide and ester-bond-containing proteins (TIE proteins). It has an N-terminal domain homologous to thioester adhesion domains, followed by 51 immunoglobulin (Ig)-like domains containing ester- or isopeptide-bond cross-links. The energetic cost to the M. mulieris bacterium in retaining such a large adhesin as a single gene or protein construct suggests a critical role in pathogenicity and/or persistence.
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Affiliation(s)
- Paul G. Young
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, c/o The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Jacob M. Paynter
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Julia K. Wardega
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Martin J. Middleditch
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Leo S. Payne
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Edward N. Baker
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, c/o The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Christopher J. Squire
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, c/o The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
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3
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Nikkel DJ, Wetmore SD. Distinctive Formation of a DNA-Protein Cross-Link during the Repair of DNA Oxidative Damage: Insights into Human Disease from MD Simulations and QM/MM Calculations. J Am Chem Soc 2023. [PMID: 37285289 DOI: 10.1021/jacs.3c01773] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Reactive oxygen species damage DNA and result in health issues. The major damage product, 8-oxo-7,8-dihydroguanine (8oG), is repaired by human adenine DNA glycosylase homologue (MUTYH). Although MUTYH misfunction is associated with a genetic disorder called MUTYH-associated polyposis (MAP) and MUTYH is a potential target for cancer drugs, the catalytic mechanism required to develop disease treatments is debated in the literature. This study uses molecular dynamics simulations and quantum mechanics/molecular mechanics techniques initiated from DNA-protein complexes that represent different stages of the repair pathway to map the catalytic mechanism of the wild-type MUTYH bacterial homologue (MutY). This multipronged computational approach characterizes a DNA-protein cross-linking mechanism that is consistent with all previous experimental data and is a distinct pathway across the broad class of monofunctional glycosylase repair enzymes. In addition to clarifying how the cross-link is formed, accommodated by the enzyme, and hydrolyzed for product release, our calculations rationalize why cross-link formation is favored over immediate glycosidic bond hydrolysis, the accepted mechanism for all other monofunctional DNA glycosylases to date. Calculations on the Y126F mutant MutY highlight critical roles for active site residues throughout the reaction, while investigation of the N146S mutant rationalizes the connection between the analogous N224S MUTYH mutation and MAP. In addition to furthering our knowledge of the chemistry associated with a devastating disorder, the structural information gained about the distinctive MutY mechanism compared to other repair enzymes represents an important step for the development of specific and potent small-molecule inhibitors as cancer therapeutics.
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Affiliation(s)
- Dylan J Nikkel
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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4
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Fan R, Hakanpää J, Elfving K, Taberman H, Linder MB, Aranko AS. Biomolecular Click Reactions Using a Minimal pH-Activated Catcher/Tag Pair for Producing Native-Sized Spider-Silk Proteins. Angew Chem Int Ed Engl 2023; 62:e202216371. [PMID: 36695475 DOI: 10.1002/anie.202216371] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 01/26/2023]
Abstract
A type of protein/peptide pair known as Catcher/Tag pair spontaneously forms an intermolecular isopeptide bond which can be applied for biomolecular click reactions. Covalent protein conjugation using Catcher/Tag pairs has turned out to be a valuable tool in biotechnology and biomedicines, but it is essential to increase the current toolbox of orthogonal Catcher/Tag pairs to expand the range of applications further, for example, for controlled multiple-fragment ligation. We report here the engineering of novel Catcher/Tag pairs for protein ligation, aided by a crystal structure of a minimal CnaB domain from Lactobacillus plantarum. We show that a newly engineered pair, called SilkCatcher/Tag enables efficient pH-inducible protein ligation in addition to being compatible with the widely used SpyCatcher/Tag pair. Finally, we demonstrate the use of the SilkCatcher/Tag pair in the production of native-sized highly repetitive spider-silk-like proteins with >90 % purity, which is not possible by traditional recombinant production methods.
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Affiliation(s)
- Ruxia Fan
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, 02150, Espoo, Finland
| | - Johanna Hakanpää
- Deutsches Elektronen Synchrotron (DESY), Photon Science, Notkestrasse 85, 22607, Hamburg, Germany.,Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22603, Hamburg, Germany
| | - Karoliina Elfving
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, 02150, Espoo, Finland
| | - Helena Taberman
- Deutsches Elektronen Synchrotron (DESY), Photon Science, Notkestrasse 85, 22607, Hamburg, Germany
| | - Markus B Linder
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, 02150, Espoo, Finland
| | - A Sesilja Aranko
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, 02150, Espoo, Finland
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5
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Moghimianavval H, Patel C, Mohapatra S, Hwang SW, Kayikcioglu T, Bashirzadeh Y, Liu AP, Ha T. Engineering Functional Membrane-Membrane Interfaces by InterSpy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2202104. [PMID: 35618485 PMCID: PMC9789529 DOI: 10.1002/smll.202202104] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/26/2022] [Indexed: 06/15/2023]
Abstract
Engineering synthetic interfaces between membranes has potential applications in designing non-native cellular communication pathways and creating synthetic tissues. Here, InterSpy is introduced as a synthetic biology tool consisting of a heterodimeric protein engineered to form and maintain membrane-membrane interfaces between apposing synthetic as well as cell membranes through the SpyTag/SpyCatcher interaction. The inclusion of split fluorescent protein fragments in InterSpy allows tracking of the formation of a membrane-membrane interface and reconstitution of functional fluorescent protein in the space between apposing membranes. First, InterSpy is demonstrated by testing split protein designs using a mammalian cell-free expression (CFE) system. By utilizing co-translational helix insertion, cell-free synthesized InterSpy fragments are incorporated into the membrane of liposomes and supported lipid bilayers with the desired topology. Functional reconstitution of split fluorescent protein between the membranes is strictly dependent on SpyTag/SpyCatcher. Finally, InterSpy is demonstrated in mammalian cells by detecting fluorescence reconstitution of split protein at the membrane-membrane interface between two cells each expressing a component of InterSpy. InterSpy demonstrates the power of CFE systems in the functional reconstitution of synthetic membrane interfaces via proximity-inducing proteins. This technology may also prove useful where cell-cell contacts and communication are recreated in a controlled manner using minimal components.
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Affiliation(s)
- Hossein Moghimianavval
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Chintan Patel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sonisilpa Mohapatra
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sung-Won Hwang
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Tunc Kayikcioglu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Yashar Bashirzadeh
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Allen P. Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Baltimore, MD 21205, USA
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6
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Cox N, Charlier C, Vijayaraj R, De La Mare M, Barbe S, André I, Lippens G, Montanier CY. The covalent complex of Jo-In results from a long-lived, non-covalent intermediate state with near-native structure. Biochem Biophys Res Commun 2021; 589:223-228. [PMID: 34929445 DOI: 10.1016/j.bbrc.2021.12.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 11/30/2022]
Abstract
Covalent protein complexes have been used to assemble enzymes in large scaffolds for biotechnology purposes. Although the catalytic mechanism of the covalent linking of such proteins is well known, the recognition and overall structural mechanisms driving the association are far less understood but could help further functional engineering of these complexes. Here, we study the Jo-In complex by NMR spectroscopy and molecular modelling. We characterize a transient non-covalent complex, with structural elements close to those in the final covalent complex. Using site specific mutagenesis, we further show that this non-covalent association is essential for the covalent complex to form.
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Affiliation(s)
- Neil Cox
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France
| | - Cyril Charlier
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France
| | - Ramadoss Vijayaraj
- Toulouse White Biotechnology, UMS INRA 1337, UMS CNRS 3582, Institut National des Sciences Appliquées de Toulouse, 31077, Toulouse, France
| | - Marion De La Mare
- Toulouse White Biotechnology, UMS INRA 1337, UMS CNRS 3582, Institut National des Sciences Appliquées de Toulouse, 31077, Toulouse, France
| | - Sophie Barbe
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France
| | - Isabelle André
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France
| | - Guy Lippens
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France.
| | - Cédric Y Montanier
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France.
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7
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Abstract
Intramolecular isopeptide bonds, formed autocatalytically between Lys and Asn/Asp side chains, are widely present in the immunoglobulin-like domains of Gram-positive bacterial adhesins, including Group A Streptococcus, and confer considerable mechanical and chemical stability. These properties make them attractive for applications in biotechnology. Here, we detail the practical considerations that are involved in engineering isopeptide bonds into Ig-like proteins, including the choice of a site where bond-forming residues could be introduced and the appropriate methodology for mutagenesis. We specify how to determine whether an isopeptide bond has formed, what strategies can be adopted to overcome problems, and how to monitor the stability of the engineered protein.
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8
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Liu Y, Li L, Yu F, Luo Y, Liang W, Yang Q, Wang R, Li M, Tang J, Gu Q, Luo Z, Chen M. Genome-wide analysis revealed the virulence attenuation mechanism of the fish-derived oral attenuated Streptococcus iniae vaccine strain YM011. FISH & SHELLFISH IMMUNOLOGY 2020; 106:546-554. [PMID: 32781206 DOI: 10.1016/j.fsi.2020.07.046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/13/2020] [Accepted: 07/21/2020] [Indexed: 06/11/2023]
Abstract
Streptococcus iniae has become one the most serious aquatic pathogens causing invasive diseases in farmed marine and freshwater fish worldwide, and orally attenuated vaccine is still the best option in protecting these invasive diseases. In this study, the safety, stability, immunogenicity of the S. iniae attenuated strain YM011 were evaluated, and comprehensively analyzed its virulence weakening mechanism at whole genome level. The results shown that attenuated S. iniae strain YM011 completely lost its pathogenicity to tilapia and had good immunogenicity with relative percent survival being 93.25% at 15 days and 90.31% at 30 days via IP injection, respectively, and 76.81% at 15 days and 56.69% at 30 days via oral gavage, respectively. Back-passage safety assay indicated that YM011 did not cause diseases or death in tilapia after 100 generations of serial passaging. Comparative genome-wide sequencing shown that YM011 had a 0.4 M large inversion fragment compared with its parental strain virulent strain GX005, which encoded 372 genes including drug resistance genes pbp2A and tet, as well as known virulence factors including hemolysin transport system gene, recA, and mutator family transposase. The attenuated S. iniae strain YM011 is an ideal attenuated oral vaccine candidate with good immunogenicity, safety and stability. Abnormal expression of important drug resistance genes as well as known virulence factors due to inversion of a 0.4 M large fragment is the leading mechanism underlying its attenuated virulence.
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Affiliation(s)
- Yu Liu
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Liping Li
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Fangzhao Yu
- Zhuhai Modern Agriculture Development Center, Zhuhai, 519000, China
| | - Yongju Luo
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Wanwen Liang
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Qiong Yang
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Rui Wang
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Min Li
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Jiayou Tang
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Qunhong Gu
- Zhuhai Modern Agriculture Development Center, Zhuhai, 519000, China
| | - Zhiping Luo
- Zhuhai Modern Agriculture Development Center, Zhuhai, 519000, China
| | - Ming Chen
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China.
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9
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Peyret H, Ponndorf D, Meshcheriakova Y, Richardson J, Lomonossoff GP. Covalent protein display on Hepatitis B core-like particles in plants through the in vivo use of the SpyTag/SpyCatcher system. Sci Rep 2020; 10:17095. [PMID: 33051543 PMCID: PMC7555512 DOI: 10.1038/s41598-020-74105-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 09/21/2020] [Indexed: 01/07/2023] Open
Abstract
Virus-like particles (VLPs) can be used as nano-carriers and antigen-display systems in vaccine development and therapeutic applications. Conjugation of peptides or whole proteins to VLPs can be achieved using different methods such as the SpyTag/SpyCatcher system. Here we investigate the conjugation of tandem Hepatitis B core (tHBcAg) VLPs and the model antigen GFP in vivo in Nicotiana benthamiana. We show that tHBcAg VLPs could be successfully conjugated with GFP in the cytosol and ER without altering VLP formation or GFP fluorescence. Conjugation in the cytosol was more efficient when SpyCatcher was displayed on tHBcAg VLPs instead of being fused to GFP. This effect was even more obvious in the ER, showing that it is optimal to display SpyCatcher on the tHBcAg VLPs and SpyTag on the binding partner. To test transferability of the GFP results to other antigens, we successfully conjugated tHBcAg VLPs to the HIV capsid protein P24 in the cytosol. This work presents an efficient strategy which can lead to time and cost saving post-translational, covalent conjugation of recombinant proteins in plants.
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Affiliation(s)
- Hadrien Peyret
- Department of Biological Chemistry, John Innes Centre, Norwich, NR4 7UH, UK.
| | - Daniel Ponndorf
- Department of Biological Chemistry, John Innes Centre, Norwich, NR4 7UH, UK
| | | | - Jake Richardson
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, NR4 7UH, UK
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10
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Sharma S, Subramani S, Popa I. Does protein unfolding play a functional role in vivo? FEBS J 2020; 288:1742-1758. [PMID: 32761965 DOI: 10.1111/febs.15508] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/09/2020] [Accepted: 08/03/2020] [Indexed: 12/21/2022]
Abstract
Unfolding and refolding of multidomain proteins under force have yet to be recognized as a major mechanism of function for proteins in vivo. In this review, we discuss the inherent properties of multidomain proteins under a force vector from a structural and functional perspective. We then characterize three main systems where multidomain proteins could play major roles through mechanical unfolding: muscular contraction, cellular mechanotransduction, and bacterial adhesion. We analyze how key multidomain proteins for each system can produce a gain-of-function from the perspective of a fine-tuned quantized response, a molecular battery, delivery of mechanical work through refolding, elasticity tuning, protection and exposure of cryptic sites, and binding-induced mechanical changes. Understanding how mechanical unfolding and refolding affect function will have important implications in designing mechano-active drugs against conditions such as muscular dystrophy, cancer, or novel antibiotics.
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Affiliation(s)
- Sabita Sharma
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Smrithika Subramani
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Ionel Popa
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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11
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Enjalbert T, De La Mare M, Roblin P, Badruna L, Vernet T, Dumon C, Montanier CY. Characterisation of the Effect of the Spatial Organisation of Hemicellulases on the Hydrolysis of Plant Biomass Polymer. Int J Mol Sci 2020; 21:ijms21124360. [PMID: 32575393 PMCID: PMC7353053 DOI: 10.3390/ijms21124360] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/15/2020] [Accepted: 06/15/2020] [Indexed: 01/21/2023] Open
Abstract
Synergism between enzymes is of crucial importance in cell metabolism. This synergism occurs often through a spatial organisation favouring proximity and substrate channelling. In this context, we developed a strategy for evaluating the impact of the geometry between two enzymes involved in nature in the recycling of the carbon derived from plant cell wall polymers. By using an innovative covalent association process using two protein fragments, Jo and In, we produced two bi-modular chimeric complexes connecting a xylanase and a xylosidase, involved in the deconstruction of xylose-based plant cell wall polymer. We first show that the intrinsic activity of the individual enzymes was preserved. Small Angle X-rays Scattering (SAXS) analysis of the complexes highlighted two different spatial organisations in solution, affecting both the distance between the enzymes (53 Å and 28 Å) and the distance between the catalytic pockets (94 Å and 75 Å). Reducing sugar and HPAEC-PAD analysis revealed different behaviour regarding the hydrolysis of Beechwood xylan. After 24 h of hydrolysis, one complex was able to release a higher amount of reducing sugar compare to the free enzymes (i.e., 15,640 and 14,549 µM of equivalent xylose, respectively). However, more interestingly, the two complexes were able to release variable percentages of xylooligosaccharides compared to the free enzymes. The structure of the complexes revealed some putative steric hindrance, which impacted both enzymatic efficiency and the product profile. This report shows that controlling the spatial geometry between two enzymes would help to better investigate synergism effect within complex multi-enzymatic machinery and control the final product.
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Affiliation(s)
- Thomas Enjalbert
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France; (T.E.); (L.B.); (C.D.)
| | - Marion De La Mare
- Toulouse White Biotechnology, UMS INRA 1337, UMS CNRS 3582, Institut National des Sciences Appliquées de Toulouse, 31077 Toulouse, France;
| | - Pierre Roblin
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, 31077 Toulouse, France;
| | - Louise Badruna
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France; (T.E.); (L.B.); (C.D.)
| | - Thierry Vernet
- Institut de Biologie Structurale, Univ., Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France;
| | - Claire Dumon
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France; (T.E.); (L.B.); (C.D.)
| | - Cédric Y. Montanier
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France; (T.E.); (L.B.); (C.D.)
- Correspondence: ; Tel.: +33-(0)5-61-55-97-13
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12
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Zhang F, Zhang W. Encrypting Chemical Reactivity in Protein Sequences toward
Information‐Coded
Reactions
†. CHINESE J CHEM 2020. [DOI: 10.1002/cjoc.202000083] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Fan Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 China
| | - Wen‐Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 China
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13
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Bonnet J, Cartannaz J, Tourcier G, Contreras-Martel C, Kleman JP, Morlot C, Vernet T, Di Guilmi AM. Autocatalytic association of proteins by covalent bond formation: a Bio Molecular Welding toolbox derived from a bacterial adhesin. Sci Rep 2017; 7:43564. [PMID: 28252635 PMCID: PMC5333627 DOI: 10.1038/srep43564] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 01/25/2017] [Indexed: 11/26/2022] Open
Abstract
Unusual intramolecular cross-links present in adhesins from Gram-positive bacteria have been used to develop a generic process amenable to biotechnology applications. Based on the crystal structure of RrgA, the Streptococcus pneumoniae pilus adhesin, we provide evidence that two engineered protein fragments retain their ability to associate covalently with high specificity, in vivo and in vitro, once isolated from the parent protein. We determined the optimal conditions for the assembly of the complex and we solved its crystal structure at 2 Å. Furthermore, we demonstrate biotechnological applications related to antibody production, nanoassembly and cell-surface labeling based on this process we named Bio Molecular Welding.
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Affiliation(s)
- J Bonnet
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - J Cartannaz
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - G Tourcier
- Institut de Biosciences et Biotechnologies de Grenoble (BIG), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - C Contreras-Martel
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - J P Kleman
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - C Morlot
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - T Vernet
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - A M Di Guilmi
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
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14
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Kwon H, Young PG, Squire CJ, Baker EN. Engineering a Lys-Asn isopeptide bond into an immunoglobulin-like protein domain enhances its stability. Sci Rep 2017; 7:42753. [PMID: 28202898 PMCID: PMC5311914 DOI: 10.1038/srep42753] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 01/11/2017] [Indexed: 11/15/2022] Open
Abstract
The overall stability of globular protein structures is marginal, a balance between large numbers of stabilizing non-covalent interactions and a destabilizing entropic term. Higher stability can be engineered by introduction of disulfide bonds, provided the redox environment is controlled. The discovery of stabilizing isopeptide bond crosslinks, formed spontaneously between lysine and asparagine (or aspartic acid) side chains in certain bacterial cell-surface proteins suggests that such bonds could be introduced by protein engineering as an alternative protein stabilization strategy. We report the first example of an isopeptide bond engineered de novo into an immunoglobulin-like protein, the minor pilin FctB from Streptococcus pyogenes. Four mutations were sufficient; lysine, asparagine and glutamic acid residues were introduced for the bond-forming reaction, with a fourth Val/Phe mutation to help steer the lysine side chain into position. The spontaneously-formed isopeptide bond was confirmed by mass spectrometry and X-ray crystallography, and was shown to increase the thermal stability by 10 °C compared with the wild type protein. This novel method for increasing the stability of IgG-like proteins has potential to be adopted by the field of antibody engineering, which share similar β-clasp Ig-type domains.
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Affiliation(s)
- Hanna Kwon
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Paul G Young
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Christopher J Squire
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Edward N Baker
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
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15
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Chaurasia P, Pratap S, von Ossowski I, Palva A, Krishnan V. New insights about pilus formation in gut-adapted Lactobacillus rhamnosus GG from the crystal structure of the SpaA backbone-pilin subunit. Sci Rep 2016; 6:28664. [PMID: 27349405 PMCID: PMC4923907 DOI: 10.1038/srep28664] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 06/08/2016] [Indexed: 12/11/2022] Open
Abstract
Thus far, all solved structures of pilin-proteins comprising sortase-assembled pili are from pathogenic genera and species. Here, we present the first crystal structure of a pilin subunit (SpaA) from a non-pathogen host (Lactobacillus rhamnosus GG). SpaA consists of two tandem CnaB-type domains, each with an isopeptide bond and E-box motif. Intriguingly, while the isopeptide bond in the N-terminal domain forms between lysine and asparagine, the one in the C-terminal domain atypically involves aspartate. We also solved crystal structures of mutant proteins where residues implicated in forming isopeptide bonds were replaced. Expectedly, the E-box-substituted E139A mutant lacks an isopeptide bond in the N-terminal domain. However, the C-terminal E269A substitution gave two structures; one of both domains with their isopeptide bonds present, and another of only the N-terminal domain, but with an unformed isopeptide bond and significant conformational changes. This latter crystal structure has never been observed for any other Gram-positive pilin. Notably, the C-terminal isopeptide bond still forms in D295N-substituted SpaA, irrespective of E269 being present or absent. Although E-box mutations affect SpaA proteolytic and thermal stability, a cumulative effect perturbing normal pilus polymerization was unobserved. A model showing the polymerized arrangement of SpaA within the SpaCBA pilus is proposed.
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Affiliation(s)
- Priyanka Chaurasia
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad-121 001, India.,Department of Biotechnology, Manipal University, Karnataka, 576104, India
| | - Shivendra Pratap
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad-121 001, India
| | | | - Airi Palva
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Vengadesan Krishnan
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad-121 001, India
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16
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Secrets of a covalent interaction for biomaterials and biotechnology: SpyTag and SpyCatcher. Curr Opin Chem Biol 2015; 29:94-9. [DOI: 10.1016/j.cbpa.2015.10.002] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 10/01/2015] [Indexed: 01/20/2023]
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17
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Self-generated covalent cross-links in the cell-surface adhesins of Gram-positive bacteria. Biochem Soc Trans 2015; 43:787-94. [DOI: 10.1042/bst20150066] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The ability of bacteria to adhere to other cells or to surfaces depends on long, thin adhesive structures that are anchored to their cell walls. These structures include extended protein oligomers known as pili and single, multi-domain polypeptides, mostly based on multiple tandem Ig-like domains. Recent structural studies have revealed the widespread presence of covalent cross-links, not previously seen within proteins, which stabilize these domains. The cross-links discovered so far are either isopeptide bonds that link lysine side chains to the side chains of asparagine or aspartic acid residues or ester bonds between threonine and glutamine side chains. These bonds appear to be formed by spontaneous intramolecular reactions as the proteins fold and are strategically placed so as to impart considerable mechanical strength.
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18
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Zhang Z, Xu L, Wang G, Shao C, Jiang L. The development and validation of a pseudoatoms approach for combined quantum mechanics and molecular mechanics calculations of polypeptide. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.05.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Veggiani G, Zakeri B, Howarth M. Superglue from bacteria: unbreakable bridges for protein nanotechnology. Trends Biotechnol 2014; 32:506-12. [PMID: 25168413 DOI: 10.1016/j.tibtech.2014.08.001] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/13/2014] [Accepted: 08/04/2014] [Indexed: 11/28/2022]
Abstract
Biotechnology is often limited by weak interactions. We suggest that an ideal interaction between proteins would be covalent, specific, require addition of only a peptide tag to the protein of interest, and form under a wide range of conditions. Here we summarize peptide tags that are able to form spontaneous amide bonds, based on harnessing reactions of adhesion proteins from the bacterium Streptococcus pyogenes. These include the irreversible peptide-protein interaction of SpyTag with SpyCatcher, as well as irreversible peptide-peptide interactions via SpyLigase. We describe existing applications, including polymerization to enhance cancer cell capture, assembly of living biomaterial, access to diverse protein shapes, and improved enzyme resilience. We also indicate future opportunities for resisting biological force and extending the scope of protein nanotechnology.
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Affiliation(s)
- Gianluca Veggiani
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Bijan Zakeri
- MIT Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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20
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The inhibitory effect of helenalin on telomerase activity is attributed to the alkylation of the CYS445 residue: Evidence from QM/MM simulations. J Mol Graph Model 2014; 51:97-103. [DOI: 10.1016/j.jmgm.2014.04.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 03/16/2014] [Accepted: 04/28/2014] [Indexed: 01/18/2023]
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21
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Kang HJ, Paterson NG, Kim CU, Middleditch M, Chang C, Ton-That H, Baker EN. A slow-forming isopeptide bond in the structure of the major pilin SpaD from Corynebacterium diphtheriae has implications for pilus assembly. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:1190-201. [PMID: 24816089 PMCID: PMC4014117 DOI: 10.1107/s1399004714001400] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 01/20/2014] [Indexed: 12/04/2022]
Abstract
The Gram-positive organism Corynebacterium diphtheriae, the cause of diphtheria in humans, expresses pili on its surface which it uses for adhesion and colonization of its host. These pili are covalent protein polymers composed of three types of pilin subunit that are assembled by specific sortase enzymes. A structural analysis of the major pilin SpaD, which forms the polymeric backbone of one of the three types of pilus expressed by C. diphtheriae, is reported. Mass-spectral and crystallographic analysis shows that SpaD contains three internal Lys-Asn isopeptide bonds. One of these, shown by mass spectrometry to be located in the N-terminal D1 domain of the protein, only forms slowly, implying an energy barrier to bond formation. Two crystal structures, of the full-length three-domain protein at 2.5 Å resolution and of a two-domain (D2-D3) construct at 1.87 Å resolution, show that each of the three Ig-like domains contains a single Lys-Asn isopeptide-bond cross-link, assumed to give mechanical stability as in other such pili. Additional stabilizing features include a disulfide bond in the D3 domain and a calcium-binding loop in D2. The N-terminal D1 domain is more flexible than the others and, by analogy with other major pilins of this type, the slow formation of its isopeptide bond can be attributed to its location adjacent to the lysine used in sortase-mediated polymerization during pilus assembly.
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Affiliation(s)
- Hae Joo Kang
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Neil G. Paterson
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Chae Un Kim
- Cornell High Energy Synchrotron Source and Macromolecular Diffraction Facility at CHESS (MacCHESS), Cornell University, Ithaca, NY 14853, USA
| | - Martin Middleditch
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Chungyu Chang
- Department of Microbiology and Molecular Genetics, University of Texas–Houston Medical School, Houston, TX 77030, USA
| | - Hung Ton-That
- Department of Microbiology and Molecular Genetics, University of Texas–Houston Medical School, Houston, TX 77030, USA
| | - Edward N. Baker
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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22
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Yet more intramolecular cross-links in Gram-positive surface proteins. Proc Natl Acad Sci U S A 2014; 111:1229-30. [PMID: 24425773 DOI: 10.1073/pnas.1322482111] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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23
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Shi T, Han Y, Li W, Zhao Y, Liu Y, Huang Z, Lu S, Zhang J. Exploring the desumoylation process of SENP1: a study combined MD simulations with QM/MM calculations on SENP1-SUMO1-RanGAP1. J Chem Inf Model 2013; 53:2360-8. [PMID: 23930863 DOI: 10.1021/ci4002487] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The small ubiquitin-related modifier (SUMO)-specific protease (SENP) processes SUMOs to mature forms and deconjugates them from various modified substrates. Loss of the equilibrium from desumoylation catalyzed by abnormal SENP1 is associated with cancers and transcription factor activity. In spite of the significant role of SENP1, the molecular basis of its desumoylation remains unclear. Here, MD simulations and QM/MM methods are combined to investigate the catalytic mechanism of desumoylation. The results showed that substrate SUMO1-RanGAP1 fitted into the catalytic pocket of SENP1 by the break of internal hydrophobic interactions and the isomerization of isopeptide from trans to cis. After that, the nucleophilic sulfur anion of Cys603 in SENP1 attacked the carbonyl carbon of Gly97 of SUMO1 to trigger the reaction, and then a tetrahedral intermediate and an acyl-enzyme intermediate were generated in turn, leading to the final release of enzyme SENP1 and two products, free SUMO1 and RanGAP1. In the process, nucleophilic attack was identified as the rate-determining step with a potential energy barrier of 20.2 kcal/mol. These results are in agreement with experimental data from mutagenesis and other experiments. Our findings elucidate the catalytic mechanism of SENP1 with its substrate and may provide a better understanding of SENP desumoylation. In particular, we have identified key residues in SENP1 needed for desumoylation that might be beneficial for the design of novel inhibitors of SENP1-related diseases.
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Affiliation(s)
- Ting Shi
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao-Tong University School of Medicine , Shanghai 200025, China
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24
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Wang B, Xiao S, Edwards S, Gräter F. Isopeptide bonds mechanically stabilize spy0128 in bacterial pili. Biophys J 2013; 104:2051-7. [PMID: 23663848 PMCID: PMC3647160 DOI: 10.1016/j.bpj.2013.04.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 03/26/2013] [Accepted: 04/02/2013] [Indexed: 01/20/2023] Open
Abstract
Pili on the surface of Streptococcus pyogenes play a crucial role in adhesion to and colonization in human cells. The major pilin subunit, Spy0128, features intramolecular covalent isopeptide bonds that autocatalytically form between the side chains of lysine and asparagine residues and are regarded as important factors in conveying structural stability. In support of this notion, single-molecule force spectroscopy experiments with Spy0128 recently demonstrated the inextensibility of these bonds under mechanical load. However, the molecular determinants of their apparent absolute durability remain unknown. Here, we studied the impact of the isopeptide bond in the Spy0128 C-terminal domain on the mechanical properties of this subunit using force-probe molecular dynamics simulations and force distribution analysis. Even in the presence of the covalent cross-link, the pili β-sandwich domain undergoes partial unfolding, albeit at ∼50% higher rupture forces and with the ability to rapidly refold on the nanosecond timescale. We find that the isopeptide bond is located right at the point of stress concentration in the protein, leading to relative, yet not absolute, mechanical stabilization by the additional cross-link. Our findings indicate how the isopeptide bond enhances the mechanical stability and refolding capability at the molecular level, ensuring that the domain remains predominantly in a potentially adhesive conformation.
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Affiliation(s)
- Bo Wang
- CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai, China
| | - Shijun Xiao
- CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai, China
| | - Scott A. Edwards
- CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai, China
- College of Physics and Technology, Shenzhen University, Guangdong, China
| | - Frauke Gräter
- CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai, China
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
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25
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Wu P, Chaudret R, Hu X, Yang W. Noncovalent Interaction Analysis in Fluctuating Environments. J Chem Theory Comput 2013; 9:2226-2234. [PMID: 23894230 DOI: 10.1021/ct4001087] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Noncovalent interactions play a central role in many chemical and biological systems. In a previous study, Johnson et al developed a NonCovalent Interaction (NCI) index to characterize and visualize different types of weak interactions. To apply the NCI analysis to fluctuating environments as in solution phase, we here develop a new Averaged NonCovalent Interaction (i.e., aNCI) index along with a fluctuation index to characterize magnitude of interactions and fluctuations. We applied aNCI for various systems including solute-solvent and ligand-protein noncovalent interactions. For water and benzene molecules in aqueous solution, solvation structures and the specific hydrogen bond patterns were visualized clearly. For the Cl-+CH3Cl SN2 reaction in aqueous solution, charge reorganization influences over solvation structure along SN2 reaction were revealed. For ligand-protein systems, aNCI can recover several key fluctuating hydrogen bond patterns that have potential applications for drug design. Therefore, aNCI, as a complementary approach to the original NCI method, can extract and visualize noncovalent interactions from thermal noise in fluctuating environments.
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Affiliation(s)
- Pan Wu
- Department of Chemistry, Duke University, Durham, NC 27708
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26
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Heim KP, Crowley PJ, Brady LJ. An intramolecular interaction involving the N terminus of a streptococcal adhesin affects its conformation and adhesive function. J Biol Chem 2013; 288:13762-74. [PMID: 23539625 DOI: 10.1074/jbc.m113.459974] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND P1 is an adhesin on the surface of Streptococcus mutans. RESULTS Destroying the high affinity interaction between the N and C termini of S. mutans P1 creates a non-adherent phenotype. CONCLUSION The N terminus facilitates proper folding, function, and stability within recombinant P1. SIGNIFICANCE The relationship between folding, maturation, and cell surface assembly is critical to understanding the P1 mechanism of action. The adhesin P1 is localized on the surface of the oral pathogen Streptococcus mutans and facilitates an interaction with the glycoprotein complex salivary agglutinin that is comprised primarily of the scavenger receptor gp340. Recent crystal structures of P1 display an unusual structure in which the protein folds back upon itself to form an elongated hybrid helical stalk with a globular head at the apex and a globular C-terminal region at the base. The N terminus of P1 has not yet been characterized. In this report we describe the contribution of an interaction between the N-terminal and C-terminal portions of the protein that is required for proper function of P1 on the surface of S. mutans. Utilizing recombinant N-terminal and C-terminal fragments, we employed isothermal titration calorimetry and native gel electrophoresis to demonstrate that these fragments form a high affinity and stable complex in solution. Furthermore, circular dichroism and surface plasmon resonance measurements indicated that the N-terminal fragment contributes to the folding and increases the functionality of the C-terminal fragment in trans. Finally, we utilized circular dichroism, surface plasmon resonance, and differential scanning calorimetry to show that an N-terminal 106-amino acid segment within P1 contributes to the proper folding and function of the full-length recombinant molecule and increases the stability of its elongated hybrid helical stalk.
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Affiliation(s)
- Kyle P Heim
- Department of Oral Biology, University of Florida, Gainesville, Florida 32610, USA
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27
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Paasche A, Schirmeister T, Engels B. Benchmark Study for the Cysteine-Histidine Proton Transfer Reaction in a Protein Environment: Gas Phase, COSMO, QM/MM Approaches. J Chem Theory Comput 2013; 9:1765-77. [PMID: 26587634 DOI: 10.1021/ct301082y] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Proton transfer reactions are of crucial interest for the investigation of proteins. We have investigated the accuracy of commonly used quantum chemical methods for the description of proton transfer reactions in different environments (gas phase, COSMO, QM/MM) using the proton transfer between the catalytic dyad residues cysteine 145 and histidine 41 of SARS coronavirus main protease as a case study. The test includes thermodynamic, kinetic, and structural properties. The study comprises computationally demanding ab initio approaches (HF, CC2, MP2, SCS-CC2, SCS-MP2, CCSD(T)), popular density functional theories (BLYP, B3LYP, M06-2X), and semiempirical methods (MNDO/d, AM1, RM1, PM3, PM6). The approximated coupled cluster approach LCCSD(T) is taken as a reference method. We find that the robustness of the tested methods with respect to the environment correlates well with the level of theory. As an example HF, CC2, MP2, and their SCS variants show similar errors for gas phase, COSMO, or QM/MM computations. In contrast for semiempirical methods, the errors strongly diversify if one goes from gas phase to COSMO or QM/MM. Particular problems are observed for the recent semiempirical methods PM6 and RM1, which show the best performance for gas phase calculations but possess larger errors in conjunction with COSMO. Finally, a combination of SCS-MP2 and B3LYP or M06-2X allows reliable estimates about remaining errors.
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Affiliation(s)
- Alexander Paasche
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Emil-Fischer-Str. 42, 97074 Würzburg, Germany
| | - Tanja Schirmeister
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Bernd Engels
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Emil-Fischer-Str. 42, 97074 Würzburg, Germany
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28
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Abe H, Wakabayashi R, Yonemura H, Yamada S, Goto M, Kamiya N. Split Spy0128 as a Potent Scaffold for Protein Cross-Linking and Immobilization. Bioconjug Chem 2013; 24:242-50. [DOI: 10.1021/bc300606b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hiroki Abe
- Department
of Applied Chemistry, Graduate School of Engineering,
and ‡Center for Future
Chemistry, Kyushu University, 744 Motooka, Fukuoka 819-0395,
Japan
| | - Rie Wakabayashi
- Department
of Applied Chemistry, Graduate School of Engineering,
and ‡Center for Future
Chemistry, Kyushu University, 744 Motooka, Fukuoka 819-0395,
Japan
| | - Hiroaki Yonemura
- Department
of Applied Chemistry, Graduate School of Engineering,
and ‡Center for Future
Chemistry, Kyushu University, 744 Motooka, Fukuoka 819-0395,
Japan
| | - Sunao Yamada
- Department
of Applied Chemistry, Graduate School of Engineering,
and ‡Center for Future
Chemistry, Kyushu University, 744 Motooka, Fukuoka 819-0395,
Japan
| | - Masahiro Goto
- Department
of Applied Chemistry, Graduate School of Engineering,
and ‡Center for Future
Chemistry, Kyushu University, 744 Motooka, Fukuoka 819-0395,
Japan
| | - Noriho Kamiya
- Department
of Applied Chemistry, Graduate School of Engineering,
and ‡Center for Future
Chemistry, Kyushu University, 744 Motooka, Fukuoka 819-0395,
Japan
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29
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Rinderspacher BC, Andzelm JW, Lambeth RH. DFT study of metal-complex structural variation on tensile force profiles. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.09.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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30
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Theoretical study of catalytic mechanism for single-site water oxidation process. Proc Natl Acad Sci U S A 2012; 109:15669-72. [PMID: 22615356 DOI: 10.1073/pnas.1118344109] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Water oxidation is a linchpin in solar fuels formation, and catalysis by single-site ruthenium complexes has generated significant interest in this area. Combining several theoretical tools, we have studied the entire catalytic cycle of water oxidation for a single-site catalyst starting with [Ru(II)(tpy)(bpm)(OH(2))](2+) (i.e., [Ru(II)-OH(2)](2+); tpy is 2,2':6',2''-terpyridine and bpm is 2,2'-bypyrimidine) as a representative example of a new class of single-site catalysts. The redox potentials and pK(a) calculations for the first two proton-coupled electron transfers (PCETs) from [Ru(II)-OH(2)](2+) to [Ru(IV) = O](2+) and the following electron-transfer process to [Ru(V) = O](3+) suggest that these processes can proceed readily in acidic or weakly basic conditions. The subsequent water splitting process involves two water molecules, [Ru(V) = O](3+) to generate [Ru(III)-OOH](2+), and H(3)O(+) with a low activation barrier (~10 kcal/mol). After the key O-O bond forming step in the single-site Ru catalysis, another PECT process oxidizes [Ru(III)-OOH](2+) to [Ru(IV)-OO](2+) when the pH is lower than 3.7. Two possible forms of [Ru(IV)-OO](2+), open and closed, can exist and interconvert with a low activation barrier (< 7 kcal/mol) due to strong spin-orbital coupling effects. In Pathway 1 at pH = 1.0, oxygen release is rate-limiting with an activation barrier ~12 kcal/mol while the electron-transfer step from [Ru(IV)-OO](2+) to [Ru(V)-OO](3+) becomes rate-determining at pH = 0 (Pathway 2) with Ce(IV) as oxidant. The results of these theoretical studies with atomistic details have revealed subtle details of reaction mechanisms at several stages during the catalytic cycle. This understanding is helpful in the design of new catalysts for water oxidation.
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31
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Kang HJ, Baker EN. Structure and assembly of Gram-positive bacterial pili: unique covalent polymers. Curr Opin Struct Biol 2012; 22:200-7. [DOI: 10.1016/j.sbi.2012.01.009] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2011] [Accepted: 01/24/2012] [Indexed: 11/28/2022]
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32
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Wu P, Cisneros GA, Hu H, Chaudret R, Hu X, Yang W. Catalytic mechanism of 4-oxalocrotonate tautomerase: significances of protein-protein interactions on proton transfer pathways. J Phys Chem B 2012; 116:6889-97. [PMID: 22417185 DOI: 10.1021/jp212643j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
4-Oxalocrotonate tautomerase (4-OT), a member of tautomerase superfamily, is an essential enzyme in the degradative metabolism pathway occurring in the Krebs cycle. The proton transfer process catalyzed by 4-OT has been explored previously using both experimental and theoretical methods; however, the elaborate catalytic mechanism of 4-OT still remains unsettled. By combining classical molecular mechanics with quantum mechanics, our results demonstrate that the native hexametric 4-OT enzyme, including six protein monomers, must be employed to simulate the proton transfer process in 4-OT due to protein-protein steric and electrostatic interactions. As a consequence, only three out of the six active sites in the 4-OT hexamer are observed to be occupied by three 2-oxo-4-hexenedioates (2o4hex), i.e., half-of-the-sites occupation. This agrees with experimental observations on negative cooperative effect between two adjacent substrates. Two sequential proton transfers occur: one proton from the C3 position of 2o4hex is initially transferred to the nitrogen atom of the general base, Pro1. Subsequently, the same proton is shuttled back to the position C5 of 2o4hex to complete the proton transfer process in 4-OT. During the catalytic reaction, conformational changes (i.e., 1-carboxyl group rotation) of 2o4hex may occur in the 4-OT dimer model but cannot proceed in the hexametric structure. We further explained that the docking process of 2o4hex can influence the specific reactant conformations and an alternative substrate (2-hydroxymuconate) may serve as reactant under a different reaction mechanism than 2o4hex.
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Affiliation(s)
- Pan Wu
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
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Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin. Proc Natl Acad Sci U S A 2012; 109:E690-7. [PMID: 22366317 DOI: 10.1073/pnas.1115485109] [Citation(s) in RCA: 1017] [Impact Index Per Article: 84.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Protein interactions with peptides generally have low thermodynamic and mechanical stability. Streptococcus pyogenes fibronectin-binding protein FbaB contains a domain with a spontaneous isopeptide bond between Lys and Asp. By splitting this domain and rational engineering of the fragments, we obtained a peptide (SpyTag) which formed an amide bond to its protein partner (SpyCatcher) in minutes. Reaction occurred in high yield simply upon mixing and amidst diverse conditions of pH, temperature, and buffer. SpyTag could be fused at either terminus or internally and reacted specifically at the mammalian cell surface. Peptide binding was not reversed by boiling or competing peptide. Single-molecule dynamic force spectroscopy showed that SpyTag did not separate from SpyCatcher until the force exceeded 1 nN, where covalent bonds snap. The robust reaction conditions and irreversible linkage of SpyTag shed light on spontaneous isopeptide bond formation and should provide a targetable lock in cells and a stable module for new protein architectures.
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Borden WT. Current Applications of Computational Chemistry in JACS—Molecules, Mechanisms, and Materials. J Am Chem Soc 2011; 133:14841-3. [DOI: 10.1021/ja206656w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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