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Jones SP, Goossen C, Lewis SD, Delaney AM, Gleghorn ML. Not making the cut: Techniques to prevent RNA cleavage in structural studies of RNase-RNA complexes. J Struct Biol X 2022; 6:100066. [PMID: 35340590 PMCID: PMC8943300 DOI: 10.1016/j.yjsbx.2022.100066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/04/2022] [Indexed: 11/16/2022] Open
Abstract
RNases are varied in the RNA structures and sequences they target for cleavage and are an important type of enzyme in cells. Despite the numerous examples of RNases known, and of those with determined three-dimensional structures, relatively few examples exist with the RNase bound to intact cognate RNA substrate prior to cleavage. To better understand RNase structure and sequence specificity for RNA targets, in vitro methods used to assemble these enzyme complexes trapped in a pre-cleaved state have been developed for a number of different RNases. We have surveyed the Protein Data Bank for such structures and in this review detail methodologies that have successfully been used and relate them to the corresponding structures. We also offer ideas and suggestions for future method development. Many strategies within this review can be used in combination with X-ray crystallography, as well as cryo-EM, and other structure-solving techniques. Our hope is that this review will be used as a guide to resolve future yet-to-be-determined RNase-substrate complex structures.
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Affiliation(s)
- Seth P. Jones
- School of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, United States
| | - Christian Goossen
- School of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, United States
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Lothrop St, Pittsburgh, PA 15261, United States
| | - Sean D. Lewis
- School of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, United States
- Mayo Clinic, 200 1st St SW, Rochester, MN 5590, United States
| | - Annie M. Delaney
- School of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, United States
| | - Michael L. Gleghorn
- School of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, United States
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2
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Shao L, Huo Z, Lei N, Yang M, He Z, Zhang Y, Wei Q, Chen C, Xiao M, Wang F, Gu G, Cai F. Reinvestigation of N, N-Diacetylimido-Protected 2-Aminothioglycosides in O-Glycosylation: Intermolecular Hydrogen Bonds Contributing to 1,2-Orthoamide Formation. J Org Chem 2021; 86:13212-13230. [PMID: 34533021 DOI: 10.1021/acs.joc.1c01009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
N,N-Diacetylimido protection of 2-aminoglycosides is an elegant strategy but has had limited applications due to unexpected side reactions in glycosylation. We found that high acid concentrations could diminish the side reactions. We observed intermolecular hydrogen bonding among alcohols and acids could disrupt. Assuming that intermolecular hydrogen bonding accelerates the formation of 1,2-orthoamides and disrupting intermolecular hydrogen bonds could turn to the desired glycosylation, we successfully employed sulfenyl triflate pre-activation in the glycosylation of a broad scope of alcohol acceptors, as well as in a one-pot synthesis of a protected human milk oligosaccharide, lacto-N-neotetraose.
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Affiliation(s)
- Liming Shao
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Zhenni Huo
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Na Lei
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Min Yang
- Center for Analysis and Characterization, School of Physical Science and Technology, ShanghaiTech University, 393 Huaxia Middle Rd., Shanghai 201210, China
| | - Zehuan He
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Yongliang Zhang
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Qinlong Wei
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Changsheng Chen
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Mei Xiao
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Fei Wang
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Guofeng Gu
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Feng Cai
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, 72 Binhai Road, Qingdao 266237, China
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3
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Wang D, Chen W, Huang S, He Y, Liu X, Hu Q, Wei T, Sang H, Gan J, Chen H. Structural basis of Zn(II) induced metal detoxification and antibiotic resistance by histidine kinase CzcS in Pseudomonas aeruginosa. PLoS Pathog 2017; 13:e1006533. [PMID: 28732057 PMCID: PMC5540610 DOI: 10.1371/journal.ppat.1006533] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 08/02/2017] [Accepted: 07/14/2017] [Indexed: 11/19/2022] Open
Abstract
Pseudomonas aeruginosa (P. aeruginosa) is a major opportunistic human pathogen, causing serious nosocomial infections among immunocompromised patients by multi-determinant virulence and high antibiotic resistance. The CzcR-CzcS signal transduction system in P. aeruginosa is primarily involved in metal detoxification and antibiotic resistance through co-regulating cross-resistance between Zn(II) and carbapenem antibiotics. Although the intracellular regulatory pathway is well-established, the mechanism by which extracellular sensor domain of histidine kinase (HK) CzcS responds to Zn(II) stimulus to trigger downstream signal transduction remains unclear. Here we determined the crystal structure of the CzcS sensor domain (CzcS SD) in complex with Zn(II) at 1.7 Å resolution. This is the first three-dimensional structural view of Zn(II)-sensor domain of the two-component system (TCS). The CzcS SD is of α/β-fold in nature, and it senses the Zn(II) stimulus at micromole level in a tetrahedral geometry through its symmetry-related residues (His55 and Asp60) on the dimer interface. Though the CzcS SD resembles the PhoQ-DcuS-CitA (PDC) superfamily member, it interacts with the effector in a novel domain with the N-terminal α-helices rather than the conserved β-sheets pocket. The dimerization of the N-terminal H1 and H1’ α-helices is of primary importance for the activity of HK CzcS. This study provides preliminary insight into the molecular mechanism of Zn(II) sensing and signaling transduction by the HK CzcS, which will be beneficial to understand how the pathogen P. aeruginosa resists to high levels of heavy metals and antimicrobial agents. P. aeruginosa inhabits diverse environments and is one of the most prevalent opportunistic human pathogens of immunocompromised patients. The high antibiotic resistance is a major cause of therapeutic failure in the treatment of P. aeruginosa infections. The opportunistic pathogen P. aeruginosa co-regulates cross-resistance between Zn(II) and carbapenem antibiotics by the CzcR-CzcS signal transduction system. The extracellular Zn(II) stimulus is sensed by the HK CzcS and further triggers metal detoxification and antibiotic resistance through intracellular regulatory pathway. Here, we provide the three-dimensional structure of CzcS SD in complex with the Zn(II). Based on the structure, several key residues for Zn(II) sensing and regulation are identified, and the signal transduction is disclosed to be modulated by the dimerization of N-terminal α-helices in the sensor domain. Our research will provide potential guidance for the treatment of clinical issues caused by co-regulation between heavy metals and antibiotics in P. aeruginosa.
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Affiliation(s)
- Dan Wang
- Coordination Chemistry Institute and the State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, Nanjing, P.R. China
| | - Weizhong Chen
- Coordination Chemistry Institute and the State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, Nanjing, P.R. China
| | - Shanqing Huang
- Coordination Chemistry Institute and the State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, Nanjing, P.R. China
| | - Yafeng He
- Coordination Chemistry Institute and the State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, Nanjing, P.R. China
| | - Xichun Liu
- Coordination Chemistry Institute and the State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, Nanjing, P.R. China
| | - Qingyuan Hu
- Coordination Chemistry Institute and the State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, Nanjing, P.R. China
| | - Tianbiao Wei
- Coordination Chemistry Institute and the State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, Nanjing, P.R. China
| | - Hong Sang
- Jinling Hospital, Department of Dermatology, Medical School of Nanjing University, Nanjing University, Nanjing, P. R. China
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
| | - Hao Chen
- Coordination Chemistry Institute and the State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, Nanjing, P.R. China
- * E-mail:
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4
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Roy RK, Saha S. Studies of regioselectivity of large molecular systems using DFT based reactivity descriptors. ACTA ACUST UNITED AC 2010. [DOI: 10.1039/b811052m] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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5
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Gu J, Wang J, Leszczynski J. Molecular basis of the recognition process: hydrogen-bonding patterns in the guanine primary recognition site of ribonuclease T1. J Phys Chem B 2007; 110:13590-6. [PMID: 16821886 DOI: 10.1021/jp061360x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Investigation of the intrinsic H-bonding pattern of the guanine complex with a sizable segment (from Asn43 to Glu46) of the primary recognition site (PRS) in RNase T1 at the B3LYP/6-311G(d,p) level of theory enables the electronic density characteristics of the H-bonding patterns of the guanine-PRS complexes to be identified. The perfect H-bonding pattern in the guanine recognition site is achieved through the guanine complex interactions with the large segment of the PRS. Two significant short H-bonds, O epsilon 1...HN1 and O epsilon 2...HN2, have been identified. The similar short H-bond distances found in the anionic GC- base pair and in this study suggest that the short hydrogen-bond distances may be characteristic of the multiple H-bonded anionic nucleobases. The H-bonding energy distribution, the geometric analysis of the H-bonding pattern, and the electron structure characteristics of the H-bonds in the guanine PRS of RNase T1 all suggest that the O epsilon 1...HN1 and O epsilon 2...HN2 side-chain H-bonds dominate the binding at the guanine recognition site of RNase T1. Also, the geometry evidence, the electron structure characteristics, and the properties of the bond critical points of the H-bonds reveal that the side-chain H-bonding and the main-chain H-bonding are mutually intensifying. Thus the positive cooperativity between Asn43 to Tyr45 and Glu46 is proposed.
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Affiliation(s)
- Jiande Gu
- Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 203201, People's Republic of China.
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6
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Roos G, Loverix S, Brosens E, Van Belle K, Wyns L, Geerlings P, Messens J. The Activation of Electrophile, Nucleophile and Leaving Group during the Reaction Catalysed by pI258 Arsenate Reductase. Chembiochem 2006; 7:981-9. [PMID: 16607668 DOI: 10.1002/cbic.200500507] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The reduction of arsenate to arsenite by pI258 arsenate reductase (ArsC) combines a nucleophilic displacement reaction with a unique intramolecular disulfide cascade. Within this reaction mechanism, the oxidative equivalents are translocated from the active site to the surface of ArsC. The first reaction step in the reduction of arsenate by pI258 ArsC consists of a nucleophilic displacement reaction carried out by Cys10 on dianionic arsenate. The second step involves the nucleophilic attack of Cys82 on the Cys10-arseno intermediate formed during the first reaction step. The onset of the second step is studied here by using quantum chemical calculations in a density functional theory context. The optimised geometry of the Cys10-arseno adduct in the ArsC catalytic site (sequence motif: Cys10-Thr11-Gly12-Asn13-Ser14-Cys15-Arg16-Ser17) forms the starting point for all subsequent calculations. Thermodynamic data and a hard and soft acids and bases (HSAB) reactivity analysis show a preferential nucleophilic attack on a monoanionic Cys10-arseno adduct, which is stabilised by Ser17. The P-loop active site of pI258 ArsC activates first a hydroxy group and subsequently arsenite as the leaving group, as is clear from an increase in the calculated nucleofugality of these groups upon going from the gas phase to the solvent phase to the enzymatic environment. Furthermore, the enzymatic environment stabilises the thiolate form of the nucleophile Cys82 by 3.3 pH units through the presence of the eight-residue alpha helix flanked by Cys82 and Cys89 (redox helix) and through a hydrogen bond with Thr11. The importance of Thr11 in the pKa regulation of Cys82 was confirmed by the observed decrease in the kcat value of the Thr11Ala mutant as compared to that of wild-type ArsC. During the final reaction step, Cys89 is activated as a nucleophile by structural alterations of the redox helix that functions as a pKa control switch for Cys89; this final step is necessary to expose a Cys82-Cys89 disulfide.
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Affiliation(s)
- Goedele Roos
- Vrije Universiteit Brussel, Algemene Chemie, Pleinlaan 2, 1050, Brussels, Belgium.
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7
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Vanommeslaeghe K, De Proft F, Loverix S, Tourwé D, Geerlings P. Theoretical study revealing the functioning of a novel combination of catalytic motifs in histone deacetylase. Bioorg Med Chem 2005; 13:3987-92. [PMID: 15878665 DOI: 10.1016/j.bmc.2005.04.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2005] [Revised: 03/22/2005] [Accepted: 04/01/2005] [Indexed: 12/20/2022]
Abstract
Histone deacetylases (HDACs) have recently attracted considerable interest as targets in the treatment of cell proliferative diseases such as cancer. In the present work, the chemical properties of the active site of HDAC were theoretically investigated at a high computational level. Evidence was gathered for a novel catalytic mechanism, which differs from a previous proposal in the native protonation state of the His-Asp dyads, and in the deprotonation of water as a distinct step in the mechanism.
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Affiliation(s)
- K Vanommeslaeghe
- General Chemistry Group, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
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8
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Mignon P, Loverix S, Steyaert J, Geerlings P. Influence of the pi-pi interaction on the hydrogen bonding capacity of stacked DNA/RNA bases. Nucleic Acids Res 2005; 33:1779-89. [PMID: 15788750 PMCID: PMC1069514 DOI: 10.1093/nar/gki317] [Citation(s) in RCA: 179] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The interplay between aromatic stacking and hydrogen bonding in nucleobases has been investigated via high-level quantum chemical calculations. The experimentally observed stacking arrangement between consecutive bases in DNA and RNA/DNA double helices is shown to enhance their hydrogen bonding ability as opposed to gas phase optimized complexes. This phenomenon results from more repulsive electrostatic interactions as is demonstrated in a model system of cytosine stacked offset-parallel with substituted benzenes. Therefore, the H-bonding capacity of the N3 and O2 atoms of cytosine increases linearly with the electrostatic repulsion between the stacked rings. The local hardness, a density functional theory-based reactivity descriptor, appears to be a key index associated with the molecular electrostatic potential (MEP) minima around H-bond accepting atoms, and is inversely proportional to the electrostatic interaction between stacked molecules. Finally, the MEP minima on surfaces around the bases in experimental structures of DNA and RNA-DNA double helices show that their hydrogen bonding capacity increases when taking more neighboring (intra-strand) stacking partners into account.
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Affiliation(s)
- Pierre Mignon
- Eenheid Algemene Chemie (ALGC), Faculteit Wetenschappen, Vrije Universiteit BrusselPleinlaan 2, 1050 Brussels, Belgium
| | - Stefan Loverix
- Eenheid Algemene Chemie (ALGC), Faculteit Wetenschappen, Vrije Universiteit BrusselPleinlaan 2, 1050 Brussels, Belgium
- Eenheid van Moleculaire en Cellulaire Interacties, VIB (Vlaams Interuniversitair Instituut Biotechnologie), Faculteit Wetenschappen, Vrije Universiteit BrusselPleinlaan 2, 1050 Brussels, Belgium
| | - Jan Steyaert
- Eenheid van Moleculaire en Cellulaire Interacties, VIB (Vlaams Interuniversitair Instituut Biotechnologie), Faculteit Wetenschappen, Vrije Universiteit BrusselPleinlaan 2, 1050 Brussels, Belgium
| | - Paul Geerlings
- Eenheid Algemene Chemie (ALGC), Faculteit Wetenschappen, Vrije Universiteit BrusselPleinlaan 2, 1050 Brussels, Belgium
- To whom correspondence should be addressed. Tel: +32 2 629 33 14; Fax: +32 2 629 33 17;
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9
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Mignon P, Loverix S, Geerlings P. Interplay between π–π interactions and the H-bonding ability of aromatic nitrogen bases. Chem Phys Lett 2005. [DOI: 10.1016/j.cplett.2004.11.016] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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10
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Saïda F, Odaert B, Uzan M, Bontems F. First structural investigation of the restriction ribonuclease RegB: NMR spectroscopic conditions, 13C/15N double-isotopic labelling and two-dimensional heteronuclear spectra. Protein Expr Purif 2004; 34:158-65. [PMID: 14766312 DOI: 10.1016/j.pep.2003.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2003] [Revised: 11/06/2003] [Indexed: 11/24/2022]
Abstract
The bacteriophage T4 genome-encoded ribonuclease RegB is the unique well-defined restriction endoribonuclease. This protein cleaves with an almost absolute specificity its RNA substrate in the middle of the GGAG tetranucleotide mainly found in the Shine-Dalgarno sequence (required for the prokaryotic initiation of the translation). This protein has no significant homology to any known ribonuclease and its structure has never been investigated. The extreme toxicity of this ribonuclease prevents the expression of large quantities for structural studies. Here, we show that the toxicity of RegB can be bypassed by using the RegB H48A point mutant and explain why resolving the structure of this mutant is relevant. For nuclear magnetic resonance (NMR) purposes, we report the preparation of highly pure (13)C/(15)N double-labelled 1.2mM samples of RegB H48A using a high yield expression procedure in minimal medium (30 mg/L). We also present a set of solution conditions that maintain the concentrated samples of this protein stable for long periods at the NMR-required temperature. Finally, we present the first (1)H/(15)N and (1)H/(13)C two-dimensional NMR spectra of RegB H48A. These spectra show that the protein is folded and that the full structural analysis of RegB by NMR is feasible.
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Affiliation(s)
- Fakhri Saïda
- Laboratoire ICSN-RMN, Institut de Chimie des Substances Naturelles, Ecole polytechnique, route de Saclay, 91128 Palaiseau Cedex, France.
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11
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Roos G, Messens J, Loverix S, Wyns L, Geerlings P. A Computational and Conceptual DFT Study on the Michaelis Complex of pI258 Arsenate Reductase. Structural Aspects and Activation of the Electrophile and Nucleophile. J Phys Chem B 2004. [DOI: 10.1021/jp0486550] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Goedele Roos
- Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050, Brussels, Belgium, and Departement Ultrastructuur, Vlaams interuniversitair Instituut voor Biotechnologie (VIB), Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050, Brussels, Belgium
| | - Joris Messens
- Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050, Brussels, Belgium, and Departement Ultrastructuur, Vlaams interuniversitair Instituut voor Biotechnologie (VIB), Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050, Brussels, Belgium
| | - Stefan Loverix
- Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050, Brussels, Belgium, and Departement Ultrastructuur, Vlaams interuniversitair Instituut voor Biotechnologie (VIB), Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050, Brussels, Belgium
| | - Lode Wyns
- Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050, Brussels, Belgium, and Departement Ultrastructuur, Vlaams interuniversitair Instituut voor Biotechnologie (VIB), Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050, Brussels, Belgium
| | - Paul Geerlings
- Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050, Brussels, Belgium, and Departement Ultrastructuur, Vlaams interuniversitair Instituut voor Biotechnologie (VIB), Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050, Brussels, Belgium
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12
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Mignon P, Loverix S, De Proft F, Geerlings P. Influence of Stacking on Hydrogen Bonding: Quantum Chemical Study on Pyridine−Benzene Model Complexes. J Phys Chem A 2004. [DOI: 10.1021/jp049240h] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pierre Mignon
- Eenheid Algemene Chemie (ALGC) and Eenheid van Moleculaire en Cellulaire Interacties, Vlaams Interuniversitair Instituut Biotechnologie (VIB), Faculteit Wetenschappen, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Stefan Loverix
- Eenheid Algemene Chemie (ALGC) and Eenheid van Moleculaire en Cellulaire Interacties, Vlaams Interuniversitair Instituut Biotechnologie (VIB), Faculteit Wetenschappen, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Frank De Proft
- Eenheid Algemene Chemie (ALGC) and Eenheid van Moleculaire en Cellulaire Interacties, Vlaams Interuniversitair Instituut Biotechnologie (VIB), Faculteit Wetenschappen, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Paul Geerlings
- Eenheid Algemene Chemie (ALGC) and Eenheid van Moleculaire en Cellulaire Interacties, Vlaams Interuniversitair Instituut Biotechnologie (VIB), Faculteit Wetenschappen, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
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13
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Matsuura H, Shimotakahara S, Sakuma C, Tashiro M, Shindo H, Mochizuki K, Yamagishi A, Kojima M, Takahashi K. Thermal unfolding of ribonuclease T1 studied by multi-dimensional NMR spectroscopy. Biol Chem 2004; 385:1157-64. [PMID: 15653428 DOI: 10.1515/bc.2004.149] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Thermal unfolding of ribonculease (RNase) T1 was studied by 1H nuclear Overhauser enhancement spectroscopy (NOESY) and 1H- 15N heteronuclear single-quantum coherence (HSQC) NMR spectroscopy at various temperatures. Native RNase T1 is a single-chain molecule of 104 amino acid residues, and has a single alpha-helix and two beta-sheets, A and B, which consist of two and five strands, respectively. Singular value decomposition analysis based on temperature-dependent HSQC spectra revealed that the thermal unfolding of RNase T1 can be described by a two-state transition model. The midpoint temperature and the change in enthalpy were determined as 54.0 degrees C and 696 kJ/mol, respectively, which are consistent with results obtained by other methods. To analyze the transition profile in more detail, we investigated local structural changes using temperature-dependent NOE intensities. The results indicate that the helical region starts to unfold at lower temperature than some beta-strands (B3, B4, and B5 in beta-sheet B). These beta-strands correspond to the hydrophobic cluster region, which had been expected to be a folding core. This was confirmed by structure calculations using the residual NOEs observed at 56 degrees C. Thus, the two-state transition of RNase T1 appears to involve locally different conformational changes.
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Affiliation(s)
- Hisae Matsuura
- School of Life Science, Tokyo University of Pharmacy and Life Science, Hachioji, Tokyo 192-0392, Japan
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14
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Vanommeslaeghe K, Van Alsenoy C, De Proft F, Martins JC, Tourwé D, Geerlings P. Ab initio study of the binding of Trichostatin A (TSA) in the active site of histone deacetylase like protein (HDLP). Org Biomol Chem 2003; 1:2951-7. [PMID: 12968347 DOI: 10.1039/b304707e] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Histone deacetylase (HDAC) inhibitors have recently attracted considerable interest because of their therapeutic potential for the treatment of cell proliferative diseases. An X-ray structure of a very potent inhibitor, Trichostatin A (TSA), bound to HDLP (an HDAC analogue isolated from Aquifex aeolicus), is available. From this structure, an active site model (322 atoms), relevant for the binding of TSA and structural analogues, has been derived, and TSA has been minimized in this active site at HF 3-21G* level. The resulting conformation is in excellent accordance with the X-ray structure, and indicates a deprotonation of the hydroxamic acid in TSA by His 131. Also, a water molecule was minimized in the active site. In addition to a similar deprotonation, in accordance with a possible catalytic mechanism of HDAC as proposed by Finnin et al. (M. S. Finnin, J. R. Donigian, A. Cohen, V. M. Richon, R. A. Rifkind and P. A. Marks, Nature, 1999, 401, 188-193), a displacement of the resulting OH- ion in the active site was observed. Based on these results, the difference in energy of binding between TSA and water was calculated. The resulting value is realistic in respect to experimental binding affinities. Furthermore, the mechanism of action of the His 131-Asp 166 charge relay system was investigated. Although the Asp residue in this motif is known to substantially increase the basicity of the His residue, no proton transfer from His 131 to Asp 166 was observed on binding of TSA or water. However, in the empty protonated active site, this proton transfer does occur.
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Affiliation(s)
- Kenno Vanommeslaeghe
- Vrije Universiteit Brussel, Organic Chemistry Group, Pleinlaan 2, B-1050 Brussel, Belgium.
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Affiliation(s)
- P Geerlings
- Eenheid Algemene Chemie, Faculteit Wetenschappen, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
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