1
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Boral S, Sen S, Kushwaha T, Inampudi KK, De S. Extein residues regulate the catalytic function of Spl DnaX intein enzyme by restricting the near-attack conformations of the active-site residues. Protein Sci 2023; 32:e4699. [PMID: 37313648 PMCID: PMC10288555 DOI: 10.1002/pro.4699] [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: 03/23/2023] [Revised: 05/30/2023] [Accepted: 06/06/2023] [Indexed: 06/15/2023]
Abstract
Intein enzymes catalyze the splicing of their flanking polypeptide chains and have found tremendous biotechnological applications. Their terminal residues form the catalytic core and participate in the splicing reaction. Hence, the neighboring N- and C-terminal extein residues influence the catalytic rate. As these extein residues vary depending on the substrate identity, we tested the influence of 20 amino acids at these sites in the Spl DnaX intein and observed significant variation of spliced product as well as N- and C-terminus cleavage product formation. We investigated the dependence of these reactions on the extein residues by molecular dynamics (MD) simulations on eight extein variants, and found that the conformational sampling of the active-site residues of the intein enzyme differed among these extein variants. We found that the extein variants that sample higher population of near-attack conformers (NACs) of the active-site residues undergo higher product formation in our activity assays. Ground state conformers that closely resemble the transition state are referred to as NACs. Very good correlation was observed between the NAC populations from the MD simulations of eight extein variants and the corresponding product formation from our activity assays. Furthermore, this molecular detail enabled us to elucidate the mechanistic roles of several conserved active-site residues in the splicing reaction. Overall, this study shows that the catalytic power of Spl DnaX intein enzyme, and most likely other inteins, depends on the efficiency of formation of NACs in the ground state, which is further modulated by the extein residues.
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Affiliation(s)
- Soumendu Boral
- School of BioscienceIndian Institute of Technology KharagpurKharagpurIndia
| | - Srijon Sen
- School of BioscienceIndian Institute of Technology KharagpurKharagpurIndia
| | - Tushar Kushwaha
- Department of BiophysicsAll India Institute of Medical SciencesNew DelhiIndia
| | - Krishna K. Inampudi
- Department of BiophysicsAll India Institute of Medical SciencesNew DelhiIndia
| | - Soumya De
- School of BioscienceIndian Institute of Technology KharagpurKharagpurIndia
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2
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SufB intein splicing in Mycobacterium tuberculosis is influenced by two remote conserved N-extein histidines. Biosci Rep 2022; 42:230724. [PMID: 35234249 PMCID: PMC8891592 DOI: 10.1042/bsr20212207] [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: 09/14/2021] [Revised: 01/11/2022] [Accepted: 01/27/2022] [Indexed: 11/24/2022] Open
Abstract
Inteins are auto-processing domains that implement a multistep biochemical reaction termed protein splicing, marked by cleavage and formation of peptide bonds. They excise from a precursor protein, generating a functional protein via covalent bonding of flanking exteins. We report the kinetic study of splicing and cleavage reaction in [Fe–S] cluster assembly protein SufB from Mycobacterium tuberculosis (Mtu). Although it follows a canonical intein splicing pathway, distinct features are added by extein residues present in the active site. Sequence analysis identified two conserved histidines in the N-extein region; His-5 and His-38. Kinetic analyses of His-5Ala and His-38Ala SufB mutants exhibited significant reductions in splicing and cleavage rates relative to the SufB wildtype (WT) precursor protein. Structural analysis and molecular dynamics (MD) simulations suggested that Mtu SufB displays a unique mechanism where two remote histidines work concurrently to facilitate N-terminal cleavage reaction. His-38 is stabilized by the solvent-exposed His-5, and can impact N–S acyl shift by direct interaction with the catalytic Cys1. Development of inteins as biotechnological tools or as pathogen-specific novel antimicrobial targets requires a more complete understanding of such unexpected roles of conserved extein residues in protein splicing.
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3
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Nakayoshi T, Wanita K, Kato K, Kurimoto E, Oda A. Computational analysis of nonenzymatic deamidation of asparagine residues catalysed by acetic acid. Mol Phys 2021. [DOI: 10.1080/00268976.2020.1827176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Tomoki Nakayoshi
- Graduate School of Pharmacy, Meijo University, Nagoya, Japan
- Institute of Medical, Pharmaceutical and Health Science, Kanazawa University, Kanazawa, Japan
| | - Kota Wanita
- Graduate School of Pharmacy, Meijo University, Nagoya, Japan
| | - Koichi Kato
- Graduate School of Pharmacy, Meijo University, Nagoya, Japan
- Department of Pharmacy, Kinjo Gakuin University, Nagoya, Japan
| | - Eiji Kurimoto
- Graduate School of Pharmacy, Meijo University, Nagoya, Japan
| | - Akifumi Oda
- Graduate School of Pharmacy, Meijo University, Nagoya, Japan
- Institute of Medical, Pharmaceutical and Health Science, Kanazawa University, Kanazawa, Japan
- Institute for Protein Research, Suita, Japan
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4
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Panda S, Nanda A, Nasker SS, Sen D, Mehra A, Nayak S. Metal effect on intein splicing: A review. Biochimie 2021; 185:53-67. [PMID: 33727137 DOI: 10.1016/j.biochi.2021.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/04/2021] [Accepted: 03/06/2021] [Indexed: 02/08/2023]
Abstract
Inteins are intervening polypeptides that interrupt the functional domains of several important proteins across the three domains of life. Inteins excise themselves from the precursor protein, ligating concomitant extein residues in a process called protein splicing. Post-translational auto-removal of inteins remain critical for the generation of active proteins. The perspective of inteins in science is a robust field of research, however fundamental studies centralized upon splicing regulatory mechanism are imperative for addressing more intricate issues. Controlled engineering of intein splicing has many applications; intein inhibition can facilitate novel drug design, while activation of intein splicing is exploited in protein purification. This paper provides a comprehensive review of the past and recent advances in the splicing regulation via metal-intein interaction. We compare the behavior of different metal ions on diverse intein systems. Though metals such as Zn, Cu, Pt, Cd, Co, Ni exhibit intein inhibitory effect heterogeneously on different inteins, divalent metal ions such as Ca and Mg fail to do so. The observed diversity in the metal-intein interaction arises mostly due to intein polymorphism and variations in atomic structure of metals. A mechanistic understanding of intein regulation by metals in native as well as synthetically engineered intein systems may yield potent intein inhibitors via direct or indirect approach.
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Affiliation(s)
- Sunita Panda
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, 751024, India
| | - Ananya Nanda
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, 751024, India
| | - Sourya Subhra Nasker
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, 751024, India
| | - Debjani Sen
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, 751024, India
| | - Ashwaria Mehra
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, 751024, India
| | - Sasmita Nayak
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, 751024, India.
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5
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Voice AT, Tresadern G, Twidale RM, van Vlijmen H, Mulholland AJ. Mechanism of covalent binding of ibrutinib to Bruton's tyrosine kinase revealed by QM/MM calculations. Chem Sci 2021; 12:5511-5516. [PMID: 33995994 PMCID: PMC8097726 DOI: 10.1039/d0sc06122k] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Ibrutinib is the first covalent inhibitor of Bruton's tyrosine kinase (BTK) to be used in the treatment of B-cell cancers. Understanding the mechanism of covalent inhibition will aid in the design of safer and more selective covalent inhibitors that target BTK. The mechanism of covalent inhibition in BTK has been uncertain because there is no appropriate residue nearby that can act as a base to deprotonate the cysteine thiol prior to covalent bond formation. We investigate several mechanisms of covalent modification of C481 in BTK by ibrutinib using combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics reaction simulations. The lowest energy pathway involves direct proton transfer from C481 to the acrylamide warhead in ibrutinib, followed by covalent bond formation to form an enol intermediate. There is a subsequent rate-limiting keto-enol tautomerisation step (ΔG ‡ = 10.5 kcal mol-1) to reach the inactivated BTK/ibrutinib complex. Our results represent the first mechanistic study of BTK inactivation by ibrutinib to consider multiple mechanistic pathways. These findings should aid in the design of covalent drugs that target BTK and other similar targets.
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Affiliation(s)
- Angus T Voice
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Gary Tresadern
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V. Turnhoutseweg 30 B-2340 Beerse Belgium
| | - Rebecca M Twidale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Herman van Vlijmen
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V. Turnhoutseweg 30 B-2340 Beerse Belgium
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
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6
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Inteins in Science: Evolution to Application. Microorganisms 2020; 8:microorganisms8122004. [PMID: 33339089 PMCID: PMC7765530 DOI: 10.3390/microorganisms8122004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 12/20/2022] Open
Abstract
Inteins are mobile genetic elements that apply standard enzymatic strategies to excise themselves post-translationally from the precursor protein via protein splicing. Since their discovery in the 1990s, recent advances in intein technology allow for them to be implemented as a modern biotechnological contrivance. Radical improvement in the structure and catalytic framework of cis- and trans-splicing inteins devised the development of engineered inteins that contribute to various efficient downstream techniques. Previous literature indicates that implementation of intein-mediated splicing has been extended to in vivo systems. Besides, the homing endonuclease domain also acts as a versatile biotechnological tool involving genetic manipulation and control of monogenic diseases. This review orients the understanding of inteins by sequentially studying the distribution and evolution pattern of intein, thereby highlighting a role in genetic mobility. Further, we include an in-depth summary of specific applications branching from protein purification using self-cleaving tags to protein modification, post-translational processing and labelling, followed by the development of intein-based biosensors. These engineered inteins offer a disruptive approach towards research avenues like biomaterial construction, metabolic engineering and synthetic biology. Therefore, this linear perspective allows for a more comprehensive understanding of intein function and its diverse applications.
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7
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Hoffmann S, Terhorst TME, Singh RK, Kümmel D, Pietrokovski S, Mootz HD. Biochemical and Structural Characterization of an Unusual and Naturally Split Class 3 Intein. Chembiochem 2020; 22:364-373. [PMID: 32813312 PMCID: PMC7891396 DOI: 10.1002/cbic.202000509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/19/2020] [Indexed: 12/31/2022]
Abstract
Split inteins are indispensable tools for protein engineering because their ligation and cleavage reactions enable unique modifications of the polypeptide backbone. Three different classes of inteins have been identified according to the nature of the covalent intermediates resulting from the acyl rearrangements in the multistep protein‐splicing pathway. Class 3 inteins employ a characteristic internal cysteine for a branched thioester intermediate. A bioinformatic database search of non‐redundant protein sequences revealed the absence of split variants in 1701 class 3 inteins. We have discovered the first reported split class 3 intein in a metagenomics data set and report its biochemical, mechanistic and structural analysis. The AceL NrdHF intein exhibits low sequence conservation with other inteins and marked deviations in residues at conserved key positions, including a variation of the typical class‐3 WCT triplet motif. Nevertheless, functional analysis confirmed the class 3 mechanism of the intein and revealed excellent splicing yields within a few minutes over a wide range of conditions and with barely detectable cleavage side reactions. A high‐resolution crystal structure of the AceL NrdHF precursor and a mutagenesis study explained the importance and roles of several residues at the key positions. Tolerated substitutions in the flanking extein residues and a high affinity between the split intein fragments further underline the intein's future potential as a ligation tool.
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Affiliation(s)
- Simon Hoffmann
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149, Münster, Germany
| | - Tobias M E Terhorst
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149, Münster, Germany
| | - Rohit K Singh
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149, Münster, Germany
| | - Daniel Kümmel
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149, Münster, Germany
| | - Shmuel Pietrokovski
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Henning D Mootz
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149, Münster, Germany
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8
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Fang YT, Li SY, Hu NJ, Yang J, Liu JH, Liu YC. Study on Cecropin B2 Production via Construct Bearing Intein Oligopeptide Cleavage Variants. Molecules 2020; 25:E1005. [PMID: 32102349 PMCID: PMC7070832 DOI: 10.3390/molecules25041005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/19/2020] [Accepted: 02/23/2020] [Indexed: 11/16/2022] Open
Abstract
In this study, genetic engineering was applied to the overexpression of the antimicrobial peptide (AMP) cecropin B2 (cecB2). pTWIN1 vector with a chitin-binding domain (CBD) and an auto-cleavage Ssp DnaB intein (INT) was coupled to the cecB2 to form a fusion protein construct and expressed via Escherichia coli ER2566. The cecB2 was obtained via the INT cleavage reaction, which was highly related to its adjacent amino acids. Three oligopeptide cleavage variants (OCVs), i.e., GRA, CRA, and SRA, were used as the inserts located at the C-terminus of the INT to facilitate the cleavage reaction. SRA showed the most efficient performance in accelerating the INT self-cleavage reaction. In addition, in order to treat the INT as a biocatalyst, a first-order rate equation was applied to fit the INT cleavage reaction. A possible inference was proposed for the INT cleavage promotion with varied OCVs using a molecular dynamics (MD) simulation. The production and purification via the CBD-INT-SRA-cecB2 fusion protein resulted in a cecB2 yield of 58.7 mg/L with antimicrobial activity.
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Affiliation(s)
- Yi-Ting Fang
- Department of Chemical Engineering, National Chung Hsing University, Taichung 40227, Taiwan; (Y.-T.F.); (S.-Y.L.)
| | - Si-Yu Li
- Department of Chemical Engineering, National Chung Hsing University, Taichung 40227, Taiwan; (Y.-T.F.); (S.-Y.L.)
- Innovation and Development Center of Sustainable Agriculture, NCHU, Taichung 40227, Taiwan
| | - Nien-Jen Hu
- Graduate Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan; (N.-J.H.); (J.Y.)
| | - Jie Yang
- Graduate Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan; (N.-J.H.); (J.Y.)
| | - Jyung-Hurng Liu
- Institute of Genomics and Bioinformatics, NCHU, Taichung 40227, Taiwan
- PhD program in Medical Biotechnology, NCHU, Taichung 40227, Taiwan
- Department of Life Sciences, NCHU, Taichung 40227, Taiwan
| | - Yung-Chuan Liu
- Department of Chemical Engineering, National Chung Hsing University, Taichung 40227, Taiwan; (Y.-T.F.); (S.-Y.L.)
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9
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Kick LM, Harteis S, Koch MF, Schneider S. Mechanistic Insights into Cyclic Peptide Generation by DnaE Split-Inteins through Quantitative and Structural Investigation. Chembiochem 2017; 18:2242-2246. [DOI: 10.1002/cbic.201700503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Leonhard M. Kick
- Center for Integrated Protein Science; Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85748 Garching Germany
| | - Sabrina Harteis
- Center for Integrated Protein Science; Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85748 Garching Germany
| | - Maximilian F. Koch
- Center for Integrated Protein Science; Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85748 Garching Germany
| | - Sabine Schneider
- Center for Integrated Protein Science; Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85748 Garching Germany
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10
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Ramsoomair CK, Yakely AE, Urbanski LM, Karanja K, Giaccone ZT, Siegart NM, Wang C, Gomez AV, Reitter JN, Mills KV. Coordination of the third step of protein splicing in two cyanobacterial inteins. FEBS Lett 2017. [PMID: 28649707 DOI: 10.1002/1873-3468.12730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The third step of protein splicing is cyclization of Asn coupled to peptide bond cleavage. In two related cyanobacterial inteins, this step is facilitated by Asn or Gln. For a Synechococcus sp. PCC7002 intein, the isolated third step of protein splicing is more efficient with its native Asn than with substitution to Gln. For a Trichodesmium erythraeum intein, its native Gln facilitates the third step as efficiently as with Asn. Despite these differences, the yield of splicing is not affected, suggesting that the third step is influenced by mechanism-linked conformational changes. A conserved catalytic His and the penultimate residue also play roles in promoting side-chain cyclization.
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Affiliation(s)
| | - Anthony E Yakely
- Department of Chemistry, College of the Holy Cross, Worcester, MA, USA
| | - Laura M Urbanski
- Department of Chemistry, College of the Holy Cross, Worcester, MA, USA
| | - Kevin Karanja
- Department of Chemistry, College of the Holy Cross, Worcester, MA, USA
| | | | - Nicolle M Siegart
- Department of Chemistry, College of the Holy Cross, Worcester, MA, USA
| | - Chunyu Wang
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA.,Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Alvin V Gomez
- Department of Chemistry, College of the Holy Cross, Worcester, MA, USA
| | - Julie N Reitter
- Department of Chemistry, College of the Holy Cross, Worcester, MA, USA
| | - Kenneth V Mills
- Department of Chemistry, College of the Holy Cross, Worcester, MA, USA
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11
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Abstract
The first crystal trans-structure of a naturally occurring split intein has been determined for the Npu (Nostoc punctiforme PCC73102) DnaE split intein. Guided by this structure, the residues NArg50 and CSer35, well conserved in DnaE split inteins, are identified to be critical in the trans-splicing of Npu DnaE split intein. An in vitro splicing assay demonstrates that NArg50 and CSer35 play synergistic roles in modulating its intein activity. The C-terminal CAsn36 exhibits two orientations of its side chain and interacts with both NArg50 and CSer35 through hydrogen bonding. These interactions likely facilitate the cyclization of asparagine in the course of protein splicing. The mutation of either residue reduces intein activity, and correlates with the low activity of the Ssp (Cyanobacterium synechocystis sp. strain PCC6803) DnaE split intein. On the other hand, NArg50 also forms a hydrogen bond with the highly conserved F-block CAsp17, thus influencing the N-S acyl shift during N-terminal cleavage. Sequence alignments show that residues NArg50 and CSer35 are rather conserved in those split inteins that lack a penultimate histidine residue. The conserved non-catalytic residues of split inteins modulate the efficiency of protein trans-splicing by hydrogen-bond interactions with the catalytic residues at the splice junction.
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12
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Abstract
Inteins are nature's escape artists; they facilitate their excision from flanking polypeptides (exteins) concomitant with extein ligation to produce a mature host protein. Splicing requires sequential nucleophilic displacement reactions catalyzed by strategies similar to proteases and asparagine lyases. Inteins require precise reaction coordination rather than rapid turnover or tight substrate binding because they are single turnover enzymes with covalently linked substrates. This has allowed inteins to explore alternative mechanisms with different steps or to use different methods for activation and coordination of the steps. Pressing issues include understanding the underlying details of catalysis and how the splicing steps are controlled.
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Affiliation(s)
- Kenneth V Mills
- From the Department of Chemistry, College of the Holy Cross, Worcester, Massachusetts 01610
| | - Margaret A Johnson
- the Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama 35294, and
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13
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Volkmann G, Mootz HD. Recent progress in intein research: from mechanism to directed evolution and applications. Cell Mol Life Sci 2013; 70:1185-206. [PMID: 22926412 PMCID: PMC11113529 DOI: 10.1007/s00018-012-1120-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 07/23/2012] [Accepted: 08/06/2012] [Indexed: 10/27/2022]
Abstract
Inteins catalyze a post-translational modification known as protein splicing, where the intein removes itself from a precursor protein and concomitantly ligates the flanking protein sequences with a peptide bond. Over the past two decades, inteins have risen from a peculiarity to a rich source of applications in biotechnology, biomedicine, and protein chemistry. In this review, we focus on developments of intein-related research spanning the last 5 years, including the three different splicing mechanisms and their molecular underpinnings, the directed evolution of inteins towards improved splicing in exogenous protein contexts, as well as novel applications of inteins for cell biology and protein engineering, which were made possible by a clearer understanding of the protein splicing mechanism.
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Affiliation(s)
- Gerrit Volkmann
- Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany
| | - Henning D. Mootz
- Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany
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14
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Wallin G, Härd T, Åqvist J. Folding-Reaction Coupling in a Self-Cleaving Protein. J Chem Theory Comput 2012; 8:3871-9. [DOI: 10.1021/ct3001427] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Göran Wallin
- Department of Cell and Molecular
Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Torleif Härd
- Department of Molecular Biology,
Swedish University of Agricultural Sciences (SLU), Box 590, SE-751
24 Uppsala, Sweden
| | - Johan Åqvist
- Department of Cell and Molecular
Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
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15
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Mujika JI, Lopez X, Mulholland AJ. Mechanism of C-terminal intein cleavage in protein splicing from QM/MM molecular dynamics simulations. Org Biomol Chem 2011; 10:1207-18. [PMID: 22179261 DOI: 10.1039/c1ob06444d] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein splicing is a post-translational process in which a biologically inactive protein is activated by the release of a segment denoted as an intein. The process involves four steps. In the third, the scission of the intein takes place after the cyclization of the last amino acid of the segment, an asparagine. Little is known about the chemical reaction necessary for this cyclization. Experiments demonstrate that two histidines (the penultimate amino acid of the intein, and a histidine located 10 amino acids upstream) are relevant in the cyclization of the asparagine. We have investigated the mechanism and determinants of reaction in the GyrA intein focusing on the requirements for asparagine activation for its cyclization. First, the influence that the protonation states of these two histidines have on the orientation of the asparagine side chain is investigated by means of molecular dynamics simulation. Molecular dynamics simulations using the CHARMM27 force field were carried out on the three possible protonation states for each of these two histidines. The results indicate that the only protonation state in which the conformation of the system is suitable for cyclization is when the penultimate histidine is fully protonated (positively charged), and the upstream histidine is in the His(ε) neutral tautomeric form. The free energy profile for the reaction in which the asparagine is activated by a proton transfer to the upstream histidine is presented, computed by hybrid quantum mechanics/molecular mechanics (QM/MM) umbrella sampling molecular dynamics at the SCCDFTB/CHARMM27 level of theory. The calculated free energy barrier for the reaction is 19.0 kcal mol(-1). B3LYP/6-31+G(d) QM/MM single-point calculations give a qualitatively a similar energy profile, although with somewhat higher energy barriers, in good agreement with the value derived from experiment of 25 kcal mol(-1) at 60 °C. QM/MM molecular dynamics simulations of the reactant, activated reactant and intermediate states highlight the importance of the Arg181-Val182-Asp183 segment in catalysing the reaction. Overall, the results indicate that nucleophilic activation of the asparagine for its cyclization by the upstream histidine acting as the base is a plausible mechanism for the C-terminal cleavage in protein splicing.
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Affiliation(s)
- Jon I Mujika
- Kimika Fakultatea, Euskal Herriko Unibertsitatea and Donostia International Physics Center (DIPC, P. K. 1072, 20080, Donostia, Euskadi, Spain.
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16
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Molecular basis for the activation of a catalytic asparagine residue in a self-cleaving bacterial autotransporter. J Mol Biol 2011; 415:128-42. [PMID: 22094314 DOI: 10.1016/j.jmb.2011.10.049] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 10/26/2011] [Accepted: 10/31/2011] [Indexed: 11/23/2022]
Abstract
Autotransporters are secreted proteins produced by pathogenic Gram-negative bacteria. They consist of a membrane-embedded β-domain and an extracellular passenger domain that is sometimes cleaved and released from the cell surface. We solved the structures of three noncleavable mutants of the autotransporter EspP to examine how it promotes asparagine cyclization to cleave its passenger. We found that cyclization is facilitated by multiple factors. The active-site asparagine is sterically constrained to conformations favorable for cyclization, while electrostatic interactions correctly orient the carboxamide group for nucleophilic attack. During molecular dynamics simulations, water molecules were observed to enter the active site and to form hydrogen bonds favorable for increasing the nucleophilicity of the active-site asparagine. When the activated asparagine attacks its main-chain carbonyl carbon, the resulting oxyanion is stabilized by a protonated glutamate. Upon cleavage, this proton could be transferred to the leaving amine group, helping overcome a significant energy barrier. Together, these findings provide insight into factors important for asparagine cyclization, a mechanism broadly used for protein cleavage.
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O'Brien KM, Schufreider AK, McGill MA, O'Brien KM, Reitter JN, Mills KV. Mechanism of protein splicing of the Pyrococcus abyssi lon protease intein. Biochem Biophys Res Commun 2010; 403:457-61. [PMID: 21094142 DOI: 10.1016/j.bbrc.2010.11.055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 11/13/2010] [Indexed: 11/16/2022]
Abstract
Protein splicing is a post-translational process by which an intervening polypeptide, the intein, excises itself from the flanking polypeptides, the exteins, coupled to ligation of the exteins. The lon protease of Pyrococcus abyssi (Pab) is interrupted by an intein. When over-expressed as a fusion protein in Escherichia coli, the Pab lon protease intein can promote efficient protein splicing. Mutations that block individual steps of splicing generally do not lead to unproductive side reactions, suggesting that the intein tightly coordinates the splicing process. The intein can splice, although it has Lys in place of the highly conserved penultimate His, and mutants of the intein in the C-terminal region lead to the accumulation of stable branched-ester intermediate.
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Affiliation(s)
- Kevin M O'Brien
- Department of Chemistry, College of the Holy Cross, Worcester, MA 01610, USA
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Kerrigan AM, Powers TL, Dorval DM, Reitter JN, Mills KV. Protein splicing of the three Pyrococcus abyssi ribonucleotide reductase inteins. Biochem Biophys Res Commun 2009; 387:153-7. [PMID: 19577540 DOI: 10.1016/j.bbrc.2009.06.145] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2009] [Accepted: 06/26/2009] [Indexed: 10/20/2022]
Abstract
An intein is a polypeptide that interrupts the functional domains of a protein, called the exteins. The intein can facilitate its own excision from the exteins, concomitant with the ligation of the exteins, in a process called protein splicing. The alpha subunit of the ribonucleotide reductase of the extreme thermophile Pyrococcus abyssi is interrupted by three inteins in separate insertion sites. Each intein can facilitate protein splicing when over-expressed in Escherichia coli, with affinity domains serving as the exteins. The influence of the N-terminal flanking residue on the efficiency of splicing is specific to each intein. Each intein has a different downstream nucleophilic residue, and cannot tolerate substitution to a residue of lesser or equal nucleophilicity. The influence of the conserved penultimate His also differs between the inteins.
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Affiliation(s)
- Adam M Kerrigan
- Department of Chemistry, College of the Holy Cross, Worcester, MA 01610, USA
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