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Liu C, Zhang K, Zhang S, Li X, Sun H, Ma L. Maggot Kinase and Natural Thrombolytic Proteins. ACS OMEGA 2024; 9:21768-21779. [PMID: 38799322 PMCID: PMC11112594 DOI: 10.1021/acsomega.4c01663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/22/2024] [Accepted: 04/25/2024] [Indexed: 05/29/2024]
Abstract
Thrombolytic enzymes constitute a class of proteases with antithrombotic functions. Derived from natural products and abundant in nature, certain thrombolytic enzymes, such as urokinase, earthworm kinase, and streptokinase, have been widely used in the clinical treatment of vascular embolic diseases. Fly maggots, characterized by their easy growth and low cost, are a traditional Chinese medicine recorded in the Compendium of Materia Medica. These maggots can also be used as raw material for the extraction and preparation of thrombolytic enzymes (maggot kinase). In this review, we assembled global research reports on natural thrombolytic enzymes through a literature search and reviewed the functions and structures of natural thrombolytic enzymes to provide a reference for natural thrombophilic drug screening and development.
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Affiliation(s)
- Can Liu
- Key
Laboratory for Northern Urban Agriculture of Ministry of Agriculture
and Rural Affairs of China, Beijing University
of Agriculture, Beijing 102206, PR China
| | - Kaixin Zhang
- Key
Laboratory for Northern Urban Agriculture of Ministry of Agriculture
and Rural Affairs of China, Beijing University
of Agriculture, Beijing 102206, PR China
| | - Shihao Zhang
- Key
Laboratory for Northern Urban Agriculture of Ministry of Agriculture
and Rural Affairs of China, Beijing University
of Agriculture, Beijing 102206, PR China
| | - Xin Li
- Key
Laboratory for Northern Urban Agriculture of Ministry of Agriculture
and Rural Affairs of China, Beijing University
of Agriculture, Beijing 102206, PR China
| | - Huiting Sun
- Key
Laboratory for Northern Urban Agriculture of Ministry of Agriculture
and Rural Affairs of China, Beijing University
of Agriculture, Beijing 102206, PR China
| | - Lanqing Ma
- Key
Laboratory for Northern Urban Agriculture of Ministry of Agriculture
and Rural Affairs of China, Beijing University
of Agriculture, Beijing 102206, PR China
- Beijing
Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, PR China
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2
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Casadevall G, Pierce C, Guan B, Iglesias-Fernandez J, Lim HY, Greenberg LR, Walsh ME, Shi K, Gordon W, Aihara H, Evans RL, Kazlauskas R, Osuna S. Designing Efficient Enzymes: Eight Predicted Mutations Convert a Hydroxynitrile Lyase into an Efficient Esterase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.23.554512. [PMID: 37662272 PMCID: PMC10473745 DOI: 10.1101/2023.08.23.554512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Hydroxynitrile lyase from rubber tree (HbHNL) shares 45% identical amino acid residues with the homologous esterase from tobacco, SABP2, but the two enzymes catalyze different reactions. The x-ray structures reveal a serine-histidine-aspartate catalytic triad in both enzymes along with several differing amino acid residues within the active site. Previous exchange of three amino acid residues in the active site of HbHNL with the corresponding amino acid residue in SABP2 (T11G-E79H-K236M) created variant HNL3, which showed low esterase activity toward p-nitrophenyl acetate. Further structure comparison reveals additional differences surrounding the active site. HbHNL contains an improperly positioned oxyanion hole residue and differing solvation of the catalytic aspartate. We hypothesized that correcting these structural differences would impart good esterase activity on the corresponding HbHNL variant. To predict the amino acid substitutions needed to correct the structure, we calculated shortest path maps for both HbHNL and SABP2, which reveal correlated movements of amino acids in the two enzymes. Replacing four amino acid residues (C81L-N104T-V106F-G176S) whose movements are connected to the movements of the catalytic residues yielded variant HNL7TV (stabilizing substitution H103V was also added), which showed an esterase catalytic efficiency comparable to that of SABP2. The x-ray structure of an intermediate variant, HNL6V, showed an altered solvation of the catalytic aspartate and a partially corrected oxyanion hole. This dramatic increase in catalytic efficiency demonstrates the ability of shortest path maps to predict which residues outside the active site contribute to catalytic activity.
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Affiliation(s)
- Guillem Casadevall
- Institut de Química Computacional i Catálisi and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
| | - Colin Pierce
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Bo Guan
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Javier Iglesias-Fernandez
- Institut de Química Computacional i Catálisi and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
| | - Huey-Yee Lim
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Lauren R Greenberg
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Meghan E Walsh
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Ke Shi
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Wendy Gordon
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Hideki Aihara
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Robert L Evans
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Romas Kazlauskas
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Sílvia Osuna
- Institut de Química Computacional i Catálisi and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
- ICREA, Barcelona, Spain
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3
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Falkenberg F, Voß L, Bott M, Bongaerts J, Siegert P. New robust subtilisins from halotolerant and halophilic Bacillaceae. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12553-w. [PMID: 37160606 DOI: 10.1007/s00253-023-12553-w] [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: 03/21/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/11/2023]
Abstract
The aim of the present study was the characterisation of three true subtilisins and one phylogenetically intermediate subtilisin from halotolerant and halophilic microorganisms. Considering the currently growing enzyme market for efficient and novel biocatalysts, data mining is a promising source for novel, as yet uncharacterised enzymes, especially from halophilic or halotolerant Bacillaceae, which offer great potential to meet industrial needs. Both halophilic bacteria Pontibacillus marinus DSM 16465T and Alkalibacillus haloalkaliphilus DSM 5271T and both halotolerant bacteria Metabacillus indicus DSM 16189 and Litchfieldia alkalitelluris DSM 16976T served as a source for the four new subtilisins SPPM, SPAH, SPMI and SPLA. The protease genes were cloned and expressed in Bacillus subtilis DB104. Purification to apparent homogeneity was achieved by ethanol precipitation, desalting and ion-exchange chromatography. Enzyme activity could be observed between pH 5.0-12.0 with an optimum for SPPM, SPMI and SPLA around pH 9.0 and for SPAH at pH 10.0. The optimal temperature for SPMI and SPLA was 70 °C and for SPPM and SPAH 55 °C and 50 °C, respectively. All proteases showed high stability towards 5% (w/v) SDS and were active even at NaCl concentrations of 5 M. The four proteases demonstrate potential for future biotechnological applications. KEY POINTS: • Halophilic and halotolerant Bacillaceae are a valuable source of new subtilisins. • Four new subtilisins were biochemically characterised in detail. • The four proteases show potential for future biotechnological applications.
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Affiliation(s)
- Fabian Falkenberg
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428, Jülich, Germany
| | - Leonie Voß
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428, Jülich, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Johannes Bongaerts
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428, Jülich, Germany
| | - Petra Siegert
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428, Jülich, Germany.
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4
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Garrido‐González JJ, Sánchez‐Santos E, Habib A, Cuevas Ferreras ÁV, Sanz F, Morán JR, Fuentes de Arriba ÁL. Transesterification of Non‐Activated Esters Promoted by Small Molecules Mimicking the Active Site of Hydrolases. Angew Chem Int Ed Engl 2022; 61:e202206072. [PMID: 35580193 PMCID: PMC9544131 DOI: 10.1002/anie.202206072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Indexed: 11/05/2022]
Abstract
The synthesis of small molecules able to mimic the active site of hydrolytic enzymes has been largely pursued in recent decades. The high reaction rates and specificity shown by natural hydrolases present an attractive target, and yet the preparation of suitable small‐molecule mimics remains challenging, requiring activated substrates to achieve productive outcomes. Here we present small synthetic artificial enzymes which mimic the catalytic site and the oxyanion hole of chymotrypsin and N‐terminal hydrolases and are able to perform, for the first time, the transesterification of a non‐activated ester such as ethyl acetate with methanol under mild and neutral reaction conditions.
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Affiliation(s)
- José J. Garrido‐González
- Organic Chemistry Department University of Salamanca Plaza de los Caídos s/n 37008 Salamanca Spain
| | - Estela Sánchez‐Santos
- Organic Chemistry Department University of Salamanca Plaza de los Caídos s/n 37008 Salamanca Spain
| | - Asmaa Habib
- Organic Chemistry Department University of Salamanca Plaza de los Caídos s/n 37008 Salamanca Spain
| | - Ángel V. Cuevas Ferreras
- Organic Chemistry Department University of Salamanca Plaza de los Caídos s/n 37008 Salamanca Spain
| | - Francisca Sanz
- X-Ray Diffraction Analysis Department University of Salamanca Plaza de los Caídos s/n 37008 Salamanca Spain
| | - Joaquín R. Morán
- Organic Chemistry Department University of Salamanca Plaza de los Caídos s/n 37008 Salamanca Spain
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5
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Falkenberg F, Rahba J, Fischer D, Bott M, Bongaerts J, Siegert P. Biochemical characterization of a novel oxidatively stable, halotolerant, and high-alkaline subtilisin from Alkalihalobacillus okhensis Kh10-101 T. FEBS Open Bio 2022; 12:1729-1746. [PMID: 35727859 PMCID: PMC9527586 DOI: 10.1002/2211-5463.13457] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/13/2022] [Accepted: 06/20/2022] [Indexed: 12/14/2022] Open
Abstract
Halophilic and halotolerant microorganisms represent a promising source of salt-tolerant enzymes suitable for various biotechnological applications where high salt concentrations would otherwise limit enzymatic activity. Considering the current growing enzyme market and the need for more efficient and new biocatalysts, the present study aimed at the characterization of a high-alkaline subtilisin from Alkalihalobacillus okhensis Kh10-101T . The protease gene was cloned and expressed in Bacillus subtilis DB104. The recombinant protease SPAO with 269 amino acids belongs to the subfamily of high-alkaline subtilisins. The biochemical characteristics of purified SPAO were analyzed in comparison with subtilisin Carlsberg, Savinase, and BPN'. SPAO, a monomer with a molecular mass of 27.1 kDa, was active over a wide range of pH 6.0-12.0 and temperature 20-80 °C, optimally at pH 9.0-9.5 and 55 °C. The protease is highly oxidatively stable to hydrogen peroxide and retained 58% of residual activity when incubated at 10 °C with 5% (v/v) H2 O2 for 1 h while stimulated at 1% (v/v) H2 O2 . Furthermore, SPAO was very stable and active at NaCl concentrations up to 5.0 m. This study demonstrates the potential of SPAO for biotechnological applications in the future.
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Affiliation(s)
- Fabian Falkenberg
- Institute of Nano‐ and BiotechnologiesAachen University of Applied SciencesJülichGermany
| | - Jade Rahba
- Institute of Nano‐ and BiotechnologiesAachen University of Applied SciencesJülichGermany
| | - David Fischer
- Institute of Nano‐ and BiotechnologiesAachen University of Applied SciencesJülichGermany
| | - Michael Bott
- Institute of Bio‐ and GeosciencesIBG‐1: Biotechnology, Forschungszentrum JülichGermany
| | - Johannes Bongaerts
- Institute of Nano‐ and BiotechnologiesAachen University of Applied SciencesJülichGermany
| | - Petra Siegert
- Institute of Nano‐ and BiotechnologiesAachen University of Applied SciencesJülichGermany
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6
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Garrido‐González JJ, Sánchez‐Santos E, Habib A, Cuevas Ferreras ÁV, Sanz F, Morán JR, Fuentes de Arriba ÁL. Transesterification of Non‐Activated Esters Promoted by Small Molecules Mimicking the Active Site of Hydrolases. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- José J. Garrido‐González
- Organic Chemistry Department University of Salamanca Plaza de los Caídos s/n 37008 Salamanca Spain
| | - Estela Sánchez‐Santos
- Organic Chemistry Department University of Salamanca Plaza de los Caídos s/n 37008 Salamanca Spain
| | - Asmaa Habib
- Organic Chemistry Department University of Salamanca Plaza de los Caídos s/n 37008 Salamanca Spain
| | - Ángel V. Cuevas Ferreras
- Organic Chemistry Department University of Salamanca Plaza de los Caídos s/n 37008 Salamanca Spain
| | - Francisca Sanz
- X-Ray Diffraction Analysis Department University of Salamanca Plaza de los Caídos s/n 37008 Salamanca Spain
| | - Joaquín R. Morán
- Organic Chemistry Department University of Salamanca Plaza de los Caídos s/n 37008 Salamanca Spain
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7
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Asadi M, Oanca G, Warshel A. Effect of Environmental Factors on the Catalytic Activity of Intramembrane Serine Protease. J Am Chem Soc 2022; 144:1251-1257. [PMID: 35023734 DOI: 10.1021/jacs.1c10494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The cleavage of protein inside cell membranes regulates pathological pathways and is a subject of major interest. Thus, the nature of the coupling between the physical environment and the function of such proteins has recently attracted significant experimental and theoretical efforts. However, it is difficult to determine the nature of this coupling uniquely by experimental and theoretical studies unless one can separate the chemical and the environmental factors. This work describes calculations of the activation barriers of the intramembrane rhomboid protease in neutral and charged lipid bilayers and in detergent micelle, trying to explore the environmental effect. The calculations of the chemical barrier are done using the empirical valence bond (EVB) method. Additionally, the renormalization method captures the energetics and dynamical effects of the conformational change. The simulations indicate that the physical environment around the rhomboid protease is not a major factor in changing the chemical catalysis and that the conformational and substrate dynamics do not exhibit long-time coupling. General issues about the action of membrane-embedded enzymes are also considered.
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Affiliation(s)
- Mojgan Asadi
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States
| | - Gabriel Oanca
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States
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8
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Abstract
At the heart of drug design is the discovery of molecules that bind with high affinity to their drug targets. Biotin forms the strongest known noncovalent ligand-protein interactions with avidin and streptavidin, achieving femtomolar and picomolar affinities, respectively. This is made even more exceptional because biotin achieves this with a meagre molecular weight of 240 Da. Surprisingly, the approaches by which biotin achieves this are not in the standard repertoire of current medicinal chemistry practice. Biotin's biggest lesson is the importance of nonclassical H-bonds in protein-ligand complexes. Most of biotin's affinity stems from its flexible valeric acid side chain that forms CH-π, CH-O, and classical H-bonds with the lipophilic region of the binding pocket. Biotin also utilizes an oxyanion hole, a sulfur-centered H-bond, and water solvation in the bound state to achieve its potency. The facets and advantages of biotin's approach to binding should be more widely adopted in drug design.
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Affiliation(s)
- Darryl B McConnell
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
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9
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Garrido González JJ, Boya Del Teso I, Fuentes de Arriba AL, Sanz F, Martín Del Valle EM, Morán JR, Alcazar V. An Adjustable Cleft Based on an 8-sulfonamide-2-naphthoic Acid with Oxyanion Hole Geometry. Chemistry 2021; 27:14605-14609. [PMID: 34396599 DOI: 10.1002/chem.202102137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Indexed: 11/11/2022]
Abstract
Cleft type receptors showing the oxyanion hole motif have been prepared in a straightforward synthesis starting from the commercial 3,7-dihidroxy-2-naphthoic acid. The double H-bond donor pattern is achieved by the introduction of a sulfonamide group in the C-8 position of naphthalene and a carboxamide at the C-2 position. This cleft, whose geometry resembles that of an oxyanion hole, is able to adjust to different guests, as shown by the analysis of the X- ray crystal structures of associates with methanol or acetic acid. Combination of hydrogen bonds and charge-transfer interactions led to further stabilization of the complexes, in which the electron-rich aromatic ring of the receptor was close in space to the electron-deficient dinitroaromatic guests. Modelling studies and bidimensional NMR experiments have been carried out to provide additional information.
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Affiliation(s)
| | - Irene Boya Del Teso
- Universidad de Salamanca, Organic Chemistry, Plaza de los Caídos, 37008, España, 37008, Salamanca, SPAIN
| | | | - Francisca Sanz
- Universidad de Salamanca, Servicio de Rayos X, Plaza de los Caídos, 37008, España, 37008, Salamanca, SPAIN
| | - Eva María Martín Del Valle
- Universidad de Salamanca, Chemical Engineering, Plaza de los Caídos, 37008, España, 37008, Salamanca, SPAIN
| | - Joaquín R Morán
- Universidad de Salamanca, Organic Chemistry, Plaza de los Caídos, 37008, España, 37008, Salamanca, SPAIN
| | - Victoria Alcazar
- Polytechnic University of Madrid: Universidad Politecnica de Madrid, Department of Chemical and Environmental Engineering, José Gutiérrez Abascal 2, E-28006, Madrid, SPAIN
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10
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Ramzy A, Kieffer TJ. Altered islet prohormone processing: A cause or consequence of diabetes? Physiol Rev 2021; 102:155-208. [PMID: 34280055 DOI: 10.1152/physrev.00008.2021] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Peptide hormones are first produced as larger precursor prohormones that require endoproteolytic cleavage to liberate the mature hormones. A structurally conserved but functionally distinct family of nine prohormone convertase enzymes (PCs) are responsible for cleavage of protein precursors of which PC1/3 and PC2 are known to be exclusive to neuroendocrine cells and responsible for prohormone cleavage. Differential expression of PCs within tissues define prohormone processing; whereas glucagon is the major product liberated from proglucagon via PC2 in pancreatic α-cells, proglucagon is preferentially processed by PC1/3 in intestinal L cells to produce glucagon-like peptides 1 and 2 (GLP-1, GLP-2). Beyond our understanding of processing of islet prohormones in healthy islets, there is convincing evidence that proinsulin, proIAPP, and proglucagon processing is altered during prediabetes and diabetes. There is predictive value of elevated circulating proinsulin or proinsulin : C-peptide ratio for progression to type 2 diabetes and elevated proinsulin or proinsulin : C-peptide is predictive for development of type 1 diabetes in at risk groups. After onset of diabetes, patients have elevated circulating proinsulin and proIAPP and proinsulin may be an autoantigen in type 1 diabetes. Further, preclinical studies reveal that α-cells have altered proglucagon processing during diabetes leading to increased GLP-1 production. We conclude that despite strong associative data, current evidence is inconclusive on the potential causal role of impaired prohormone processing in diabetes, and suggest that future work should focus on resolving the question of whether altered prohormone processing is a causal driver or merely a consequence of diabetes pathology.
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Affiliation(s)
- Adam Ramzy
- Laboratory of Molecular and Cellular Medicine, Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Timothy J Kieffer
- Laboratory of Molecular and Cellular Medicine, Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.,Department of Surgery, University of British Columbia, Vancouver, BC, Canada.,School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
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11
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Paiva P, Medina FE, Viegas M, Ferreira P, Neves RPP, Sousa JPM, Ramos MJ, Fernandes PA. Animal Fatty Acid Synthase: A Chemical Nanofactory. Chem Rev 2021; 121:9502-9553. [PMID: 34156235 DOI: 10.1021/acs.chemrev.1c00147] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fatty acids are crucial molecules for most living beings, very well spread and conserved across species. These molecules play a role in energy storage, cell membrane architecture, and cell signaling, the latter through their derivative metabolites. De novo synthesis of fatty acids is a complex chemical process that can be achieved either by a metabolic pathway built by a sequence of individual enzymes, such as in most bacteria, or by a single, large multi-enzyme, which incorporates all the chemical capabilities of the metabolic pathway, such as in animals and fungi, and in some bacteria. Here we focus on the multi-enzymes, specifically in the animal fatty acid synthase (FAS). We start by providing a historical overview of this vast field of research. We follow by describing the extraordinary architecture of animal FAS, a homodimeric multi-enzyme with seven different active sites per dimer, including a carrier protein that carries the intermediates from one active site to the next. We then delve into this multi-enzyme's detailed chemistry and critically discuss the current knowledge on the chemical mechanism of each of the steps necessary to synthesize a single fatty acid molecule with atomic detail. In line with this, we discuss the potential and achieved FAS applications in biotechnology, as biosynthetic machines, and compare them with their homologous polyketide synthases, which are also finding wide applications in the same field. Finally, we discuss some open questions on the architecture of FAS, such as their peculiar substrate-shuttling arm, and describe possible reasons for the emergence of large megasynthases during evolution, questions that have fascinated biochemists from long ago but are still far from answered and understood.
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Affiliation(s)
- Pedro Paiva
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Fabiola E Medina
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Autopista Concepción-Talcahuano, 7100 Talcahuano, Chile
| | - Matilde Viegas
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro Ferreira
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Rui P P Neves
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - João P M Sousa
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J Ramos
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A Fernandes
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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12
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Ahsan M, Pindi C, Senapati S. Hydrogen bonding catalysis by water in epoxide ring opening reaction. J Mol Graph Model 2021; 105:107894. [PMID: 33725641 DOI: 10.1016/j.jmgm.2021.107894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/22/2021] [Accepted: 03/01/2021] [Indexed: 11/19/2022]
Abstract
Water can act as catalyst is perhaps the most intriguing property reported of this molecule in the last decade. However, despite being an integral part of many enzyme structures, the role of water in catalyzing enzymatic reactions remains sparsely studied. In a recent study, we have shown that the epoxide ring opening in aspartate proteases follows a two-step process involving water. In this work, we attempt to unravel the electronic basis of the co-catalytic role of water in the epoxide ring opening reaction by employing high-level quantum mechanical calculations at M06-2X/6-31+G(d,p) level of accuracy. Our computed electron density and its reduced gradient show that water anchor the reactant molecules through strong H-bond bridges. In addition, the strong ionizing power of water allows better charge delocalization to stabilize the transition states and oxyanion intermediate. Electrostatic analyses suggest greater charge transfer from the aspartates to the epoxide in the transition state, which is found to be exergonic in nature rendering a low-barrier reaction compared to a control system where water was omitted in the reaction field. This elucidated mechanism at electronic level could promote further research to search for the co-catalytic role of water in other enzymes.
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Affiliation(s)
- Mohd Ahsan
- Department of Biotechnology and BJM School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Chinmai Pindi
- Department of Biotechnology and BJM School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Sanjib Senapati
- Department of Biotechnology and BJM School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India.
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13
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Affiliation(s)
- Mark Aldren M. Feliciano
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Brian Gold
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
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14
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Kries H, Bloch JS, Bunzel HA, Pinkas DM, Hilvert D. Contribution of Oxyanion Stabilization to Kemp Eliminase Efficiency. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00575] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Hajo Kries
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Joël S. Bloch
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - H. Adrian Bunzel
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Daniel M. Pinkas
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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15
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Nutho B, Mulholland AJ, Rungrotmongkol T. The reaction mechanism of Zika virus NS2B/NS3 serine protease inhibition by dipeptidyl aldehyde: a QM/MM study. Phys Chem Chem Phys 2019; 21:14945-14956. [PMID: 31236554 DOI: 10.1039/c9cp02377a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Zika virus (ZIKV) infection has become a global public health problem, associated with microcephaly in newborns and Guillain-Barré syndrome in adults. Currently, there are no commercially available anti-ZIKV drugs. The viral protease NS2B/NS3, which is involved in viral replication and maturation, is a potential drug target. Peptidomimetic aldehyde inhibitors bind covalently to the catalytic S135 of the NS3 protease. Here, we apply hybrid quantum mechanics/molecular mechanics (QM/MM) free-energy simulations at the PDDG-PM3/ff14SB level to investigate the inhibition mechanism of the ZIKV protease by a dipeptidyl aldehyde inhibitor (acyl-KR-aldehyde). The results show that proton transfer from the catalytic S135 to H51 occurs in concert with nucleophilic addition on the aldehyde warhead by S135. The anionic covalent complex between the dipeptidyl aldehyde and the ZIKV protease is analogous to the tetrahedral intermediate for substrate hydrolysis. Spontaneous protonation by H51 forms the hemiacetal. In addition, we use correlated ab initio QM/MM potential energy path calculations at levels up to LCCSD(T)/(aug)-cc-pVTZ to obtain accurate potential energy profiles of the reaction, which also support a concerted mechanism. These results provide detailed insight into the mechanism of ZIKV protease inhibition by a peptidyl aldehyde inhibitor, which will guide in the design of inhibitors.
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Affiliation(s)
- Bodee Nutho
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
| | - Thanyada Rungrotmongkol
- Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand. and Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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16
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Paiva P, Sousa SF, Fernandes PA, João Ramos M. Human Fatty Acid Synthase: A Computational Study of the Transfer of the Acyl Moieties from MAT to the ACP Domain. ChemCatChem 2019. [DOI: 10.1002/cctc.201900548] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Pedro Paiva
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica Faculdade de CiênciasUniversidade do Porto Rua do Campo Alegre s/n 4169-007 Porto Portugal
| | - Sérgio F. Sousa
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica Faculdade de CiênciasUniversidade do Porto Rua do Campo Alegre s/n 4169-007 Porto Portugal
- UCIBIO@REQUIMTE, BioSIM – Departamento de Biomedicina Faculdade de MedicinaUniversidade do Porto Alameda Prof. Hernâni Monteiro 4200-319 Porto Portugal
| | - Pedro A. Fernandes
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica Faculdade de CiênciasUniversidade do Porto Rua do Campo Alegre s/n 4169-007 Porto Portugal
| | - Maria João Ramos
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica Faculdade de CiênciasUniversidade do Porto Rua do Campo Alegre s/n 4169-007 Porto Portugal
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17
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Anti-inflammatory activity of a serine protease produced from Bacillus pumilus SG2. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Schmidt M, Toplak A, Rozeboom HJ, Wijma HJ, Quaedflieg PJLM, van Maarseveen JH, Janssen DB, Nuijens T. Design of a substrate-tailored peptiligase variant for the efficient synthesis of thymosin-α 1. Org Biomol Chem 2019; 16:609-618. [PMID: 29300408 DOI: 10.1039/c7ob02812a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The synthesis of thymosin-α1, an acetylated 28 amino acid long therapeutic peptide, via conventional chemical methods is exceptionally challenging. The enzymatic coupling of unprotected peptide segments in water offers great potential for a more efficient synthesis of peptides that are difficult to synthesize. Based on the design of a highly engineered peptide ligase, we developed a fully convergent chemo-enzymatic peptide synthesis (CEPS) process for the production of thymosin-α1via a 14-mer + 14-mer segment condensation strategy. Using structure-inspired enzyme engineering, the thiol-subtilisin variant peptiligase was tailored to recognize the respective 14-mer thymosin-α1 segments in order to create a clearly improved biocatalyst, termed thymoligase. Thymoligase catalyzes peptide bond formation between both segments with a very high efficiency (>94% yield) and is expected to be well applicable to many other ligations in which residues with similar characteristics (e.g. Arg and Glu) are present in the respective positions P1 and P1'. The crystal structure of thymoligase was determined and shown to be in good agreement with the model used for the engineering studies. The combination of the solid phase peptide synthesis (SPPS) of the 14-mer segments and their thymoligase-catalyzed ligation on a gram scale resulted in a significantly increased, two-fold higher overall yield (55%) of thymosin-α1 compared to those typical of existing industrial processes.
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Affiliation(s)
- Marcel Schmidt
- EnzyPep B.V., Brightlands Campus, Urmonderbaan 22, 6167 RD Geleen, The Netherlands.
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19
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Windsor IW, Gold B, Raines RT. An n→ π* Interaction in the Bound Substrate of Aspartic Proteases Replicates the Oxyanion Hole. ACS Catal 2019; 9:1464-1471. [PMID: 31093467 DOI: 10.1021/acscatal.8b04142] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aspartic proteases regulate many biological processes and are prominent targets for therapeutic intervention. Structural studies have captured intermediates along the reaction pathway, including the Michaelis complex and tetrahedral intermediate. Using a Ramachandran analysis of these structures, we discovered that residues occupying the P1 and P1' positions (which flank the scissile peptide bond) adopt the dihedral angle of an inverse γ-turn and polyproline type-II helix, respectively. Computational analyses reveal that the polyproline type-II helix engenders an n→π* interaction in which the oxygen of the scissile peptide bond is the donor. This interaction stabilizes the negative charge that develops in the tetrahedral intermediate, much like the oxyanion hole of serine proteases. The inverse γ-turn serves to twist the scissile peptide bond, vacating the carbonyl π* orbital and facilitating its hydration. These previously unappreciated interactions entail a form of substrate-assisted catalysis and offer opportunities for drug design.
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Affiliation(s)
- Ian W. Windsor
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Brian Gold
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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20
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Chakraborty J, Nemeria NS, Farinas E, Jordan F. Catalysis of transthiolacylation in the active centers of dihydrolipoamide acyltransacetylase components of 2-oxo acid dehydrogenase complexes. FEBS Open Bio 2018; 8:880-896. [PMID: 29928569 PMCID: PMC5986005 DOI: 10.1002/2211-5463.12431] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 03/29/2018] [Accepted: 04/09/2018] [Indexed: 11/25/2022] Open
Abstract
The Escherichia coli 2‐oxoglutarate dehydrogenase complex (OGDHc) comprises multiple copies of three enzymes—E1o, E2o, and E3—and transthioesterification takes place within the catalytic domain of E2o. The succinyl group from the thiol ester of S8‐succinyldihydrolipoyl‐E2o is transferred to the thiol group of coenzyme A (CoA), forming the all‐important succinyl‐CoA. Here, we report mechanistic studies of enzymatic transthioesterification on OGDHc. Evidence is provided for the importance of His375 and Asp374 in E2o for the succinyl transfer reaction. The magnitude of the rate acceleration provided by these residues (54‐fold from each with alanine substitution) suggests a role in stabilization of the symmetrical tetrahedral oxyanionic intermediate by formation of two hydrogen bonds, rather than in acid–base catalysis. Further evidence ruling out a role in acid–base catalysis is provided by site‐saturation mutagenesis studies at His375 (His375Trp substitution with little penalty) and substitutions to other potential hydrogen bond participants at Asp374. Taking into account that the rate constant for reductive succinylation of the E2o lipoyl domain (LDo) by E1o and 2‐oxoglutarate (99 s−1) was approximately twofold larger than the rate constant for kcat of 48 s−1 for the overall reaction (NADH production), it could be concluded that succinyl transfer to CoA and release of succinyl‐CoA, rather than reductive succinylation, is the rate‐limiting step. The results suggest a revised mechanism of catalysis for acyl transfer in the superfamily of 2‐oxo acid dehydrogenase complexes, thus provide fundamental information regarding acyl‐CoA formation, so important for several biological processes including post‐translational succinylation of protein lysines. Enzymes 2‐oxoglutarate dehydrogenase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/2/4/2.html); dihydrolipoamide succinyltransferase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/3/1/61.html); dihydrolipoamide dehydrogenase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/8/1/4.html); pyruvate dehydrogenase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/2/4/1.html); dihydrolipoamide acetyltransferase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/3/1/12.html).
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Affiliation(s)
- Joydeep Chakraborty
- Department of Chemistry and Environmental Science New Jersey Institute of Technology Newark NJ USA
| | | | - Edgardo Farinas
- Department of Chemistry and Environmental Science New Jersey Institute of Technology Newark NJ USA
| | - Frank Jordan
- Department of Chemistry Rutgers University Newark NJ USA
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21
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Paiva P, Sousa SF, Ramos MJ, Fernandes PA. Understanding the Catalytic Machinery and the Reaction Pathway of the Malonyl-Acetyl Transferase Domain of Human Fatty Acid Synthase. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00577] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pedro Paiva
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Sérgio F. Sousa
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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22
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Abdul Halim MF, Rodriguez R, Stoltzfus JD, Duggin IG, Pohlschroder M. Conserved residues are critical for Haloferax volcanii archaeosortase catalytic activity: Implications for convergent evolution of the catalytic mechanisms of non-homologous sortases from archaea and bacteria. Mol Microbiol 2018; 108:276-287. [PMID: 29465796 DOI: 10.1111/mmi.13935] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2018] [Indexed: 11/29/2022]
Abstract
Proper protein anchoring is key to the biogenesis of prokaryotic cell surfaces, dynamic, resilient structures that play crucial roles in various cell processes. A novel surface protein anchoring mechanism in Haloferax volcanii depends upon the peptidase archaeosortase A (ArtA) processing C-termini of substrates containing C-terminal tripartite structures and anchoring mature substrates to the cell membrane via intercalation of lipid-modified C-terminal amino acid residues. While this membrane protein lacks clear homology to soluble sortase transpeptidases of Gram-positive bacteria, which also process C-termini of substrates whose C-terminal tripartite structures resemble those of ArtA substrates, archaeosortases do contain conserved cysteine, arginine and arginine/histidine/asparagine residues, reminiscent of His-Cys-Arg residues of sortase catalytic sites. The study presented here shows that ArtAWT -GFP expressed in trans complements ΔartA growth and motility phenotypes, while alanine substitution mutants, Cys173 (C173A), Arg214 (R214A) or Arg253 (R253A), and the serine substitution mutant for Cys173 (C173S), fail to complement these phenotypes. Consistent with sortase active site replacement mutants, ArtAC173A -GFP, ArtAC173S -GFP and ArtAR214A -GFP cannot process substrates, while replacement of the third residue, ArtAR253A -GFP retains some processing activity. These findings support the view that similarities between certain aspects of the structures and functions of the sortases and archaeosortases are the result of convergent evolution.
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Affiliation(s)
| | - Ronald Rodriguez
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Iain G Duggin
- The ithree Institute, University of Technology Sydney, Sydney, NSW, 2007, Australia
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23
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Lima MCP, Seabra GM. Reaction mechanism of the dengue virus serine protease: a QM/MM study. Phys Chem Chem Phys 2018; 18:30288-30296. [PMID: 27341353 DOI: 10.1039/c6cp03209e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dengue virus (DENV) is the causative agent of the viral infection dengue fever. In spite of all the efforts made to prevent the spread of the disease, once it is contracted, there is no specific treatment for dengue and the WHO guidelines are limited to rest and symptomatic treatment. In its reproductive cycle, DENV utilizes the NS2B-NS3pro, a serine protease, to cleave the viral polyprotein into its constituents. This enzyme is essential for the virus lifecycle, and presents an attractive target for the development of specific dengue treatments. Here we used a hybrid Quantum Mechanics and Molecular Mechanics (QM/MM) Molecular Dynamics approach and Umbrella Sampling to study the first step (acylation) of the reaction catalyzed by NS2B-NS3pro, using the Pairwise Distance Directed Gaussian PM3 (PDDG/PM3) semi-empirical Hamiltonian for the QM subsystem, and Amber ff99SB for the MM subsystem. Our results indicate that the nucleophilic attack on the substrate by Ser135 occurs in a stepwise manner, in which a proton transfer to His51 first activates Ser135, which only later attacks the substrate. The rate-determining step is the Ser135 activation, with a barrier of 24.1 kcal mol-1. Water molecules completing the oxyanion hole stabilize the negative charge formed on the carbonyl oxygen of the substrate. The final step in the process is a proton transfer from His51 to the substrate's nitrogen, which happens with a lower barrier of 5.1 kcal mol-1, and leads directly to the breakage of the peptide bond.
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Affiliation(s)
- M C P Lima
- Departamento de Química Fundamental, Centro de Ciências Exatas e da Natureza, Universidade Federal de Pernambuco, Av. Jornalista Anibal Fernandes, s/no, Cidade Universitária - Recife, PE - CEP 50.740-560, Brazil.
| | - G M Seabra
- Departamento de Química Fundamental, Centro de Ciências Exatas e da Natureza, Universidade Federal de Pernambuco, Av. Jornalista Anibal Fernandes, s/no, Cidade Universitária - Recife, PE - CEP 50.740-560, Brazil.
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24
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Rubio OH, Mazo SD, Monleón LM, Simón L, Temprano ÁG, Morán JR. A cleft type receptor which combines an oxyanion hole with electrostatic interactions. Org Biomol Chem 2017; 15:4571-4578. [PMID: 28497821 DOI: 10.1039/c7ob00679a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A receptor for carboxylic acids which combines an oxyanion-hole structure with electrostatic forces has been prepared. X-ray diffraction studies have been carried out to evaluate the geometry of both the free receptor and its associated species with several carboxylic acids and many different arrangements have been discovered for the H-bond pattern in the associated species.
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Affiliation(s)
- Omayra H Rubio
- Organic Chemistry Department, University of Salamanca, Plaza de los Caídos, 1-5, E-37008, Salamanca, Spain.
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25
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Arutyunova E, Smithers CC, Corradi V, Espiritu AC, Young HS, Tieleman DP, Lemieux MJ. Probing catalytic rate enhancement during intramembrane proteolysis. Biol Chem 2016; 397:907-19. [DOI: 10.1515/hsz-2016-0124] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 04/06/2016] [Indexed: 11/15/2022]
Abstract
Abstract
Rhomboids are ubiquitous intramembrane serine proteases involved in various signaling pathways. While the high-resolution structures of the Escherichia coli rhomboid GlpG with various inhibitors revealed an active site comprised of a serine-histidine dyad and an extensive oxyanion hole, the molecular details of rhomboid catalysis were unclear because substrates are unknown for most of the family members. Here we used the only known physiological pair of AarA rhomboid with its psTatA substrate to decipher the contribution of catalytically important residues to the reaction rate enhancement. An MD-refined homology model of AarA was used to identify residues important for catalysis. We demonstrated that the AarA active site geometry is strict and intolerant to alterations. We probed the roles of H83 and N87 oxyanion hole residues and determined that substitution of H83 either abolished AarA activity or reduced the transition state stabilization energy (ΔΔG‡) by 3.1 kcal/mol; substitution of N87 decreased ΔΔG‡ by 1.6–3.9 kcal/mol. Substitution M154, a residue conserved in most rhomboids that stabilizes the catalytic general base, to tyrosine, provided insight into the mechanism of nucleophile generation for the catalytic dyad. This study provides a quantitative evaluation of the role of several residues important for hydrolytic efficiency and oxyanion stabilization during intramembrane proteolysis.
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26
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Huang X, Xue J, Lin M, Zhu Y. Use of an Improved Matching Algorithm to Select Scaffolds for Enzyme Design Based on a Complex Active Site Model. PLoS One 2016; 11:e0156559. [PMID: 27243223 PMCID: PMC4887040 DOI: 10.1371/journal.pone.0156559] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/16/2016] [Indexed: 11/24/2022] Open
Abstract
Active site preorganization helps native enzymes electrostatically stabilize the transition state better than the ground state for their primary substrates and achieve significant rate enhancement. In this report, we hypothesize that a complex active site model for active site preorganization modeling should help to create preorganized active site design and afford higher starting activities towards target reactions. Our matching algorithm ProdaMatch was improved by invoking effective pruning strategies and the native active sites for ten scaffolds in a benchmark test set were reproduced. The root-mean squared deviations between the matched transition states and those in the crystal structures were < 1.0 Å for the ten scaffolds, and the repacking calculation results showed that 91% of the hydrogen bonds within the active sites are recovered, indicating that the active sites can be preorganized based on the predicted positions of transition states. The application of the complex active site model for de novo enzyme design was evaluated by scaffold selection using a classic catalytic triad motif for the hydrolysis of p-nitrophenyl acetate. Eighty scaffolds were identified from a scaffold library with 1,491 proteins and four scaffolds were native esterase. Furthermore, enzyme design for complicated substrates was investigated for the hydrolysis of cephalexin using scaffold selection based on two different catalytic motifs. Only three scaffolds were identified from the scaffold library by virtue of the classic catalytic triad-based motif. In contrast, 40 scaffolds were identified using a more flexible, but still preorganized catalytic motif, where one scaffold corresponded to the α-amino acid ester hydrolase that catalyzes the hydrolysis and synthesis of cephalexin. Thus, the complex active site modeling approach for de novo enzyme design with the aid of the improved ProdaMatch program is a promising approach for the creation of active sites with high catalytic efficiencies towards target reactions.
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Affiliation(s)
- Xiaoqiang Huang
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, P.R. China
| | - Jing Xue
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, P.R. China
| | - Min Lin
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, P.R. China
| | - Yushan Zhu
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, P.R. China
- * E-mail:
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27
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Temprano ÁG, Monleón LM, Rubio OH, Rubio LS, Pérez AB, Sanz F, Morán JR. A highly selective receptor for zwitterionic proline. Org Biomol Chem 2016; 14:1325-31. [DOI: 10.1039/c5ob02387d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enantioselective extraction of zwitterionic proline from water to chloroform has been achieved with a chiral apolar chromane receptor.
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Affiliation(s)
- Álvaro G. Temprano
- Organic Chemistry Department
- Plaza de los Caidos 1-5
- University of Salamanca
- 37008 Salamanca
- Spain
| | - Laura M. Monleón
- Organic Chemistry Department
- Plaza de los Caidos 1-5
- University of Salamanca
- 37008 Salamanca
- Spain
| | - Omayra H. Rubio
- Organic Chemistry Department
- Plaza de los Caidos 1-5
- University of Salamanca
- 37008 Salamanca
- Spain
| | - Luis Simón Rubio
- Organic Chemistry Department
- Plaza de los Caidos 1-5
- University of Salamanca
- 37008 Salamanca
- Spain
| | - Asunción B. Pérez
- Organic Chemistry Department
- Paseo Belen no. 7
- University of Valladolid
- 47011 Valladolid
- Spain
| | - Francisca Sanz
- X-Ray Diffraction Service
- Plaza de los Caidos 1-5
- University of Salamanca
- 37008 Salamanca
- Spain
| | - Joaquín R. Morán
- Organic Chemistry Department
- Plaza de los Caidos 1-5
- University of Salamanca
- 37008 Salamanca
- Spain
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28
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Herrero FG, Rubio OH, Monleón LM, Fuentes de Arriba ÁL, Rubio LS, Morán JR. A molecular receptor for zwitterionic phenylalanine. Org Biomol Chem 2016; 14:3906-12. [DOI: 10.1039/c6ob00490c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Extraction of zwitterionic phenylalanine from water to chloroform has been achieved with a chiral apolar benzofuran receptor.
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Affiliation(s)
| | - Omayra H. Rubio
- Organic Chemistry Department
- University of Salamanca
- 37008 Salamanca
- Spain
| | - Laura M. Monleón
- Organic Chemistry Department
- University of Salamanca
- 37008 Salamanca
- Spain
| | | | - Luís Simón Rubio
- Engineering Chemistry Department
- University of Salamanca
- 37008 Salamanca
- Spain
| | - Joaquín R. Morán
- Organic Chemistry Department
- University of Salamanca
- 37008 Salamanca
- Spain
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29
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High resolution structure of an M23 peptidase with a substrate analogue. Sci Rep 2015; 5:14833. [PMID: 26437833 PMCID: PMC4594094 DOI: 10.1038/srep14833] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/09/2015] [Indexed: 12/02/2022] Open
Abstract
LytM is a Staphylococcus aureus autolysin and a homologue of the S. simulans lysostaphin. Both enzymes are members of M23 metallopeptidase family (MEROPS) comprising primarily bacterial peptidoglycan hydrolases. LytM occurs naturally in a latent form, but can be activated by cleavage of an inhibitory N-terminal proregion. Here, we present a 1.45 Å crystal structure of LytM catalytic domain with a transition state analogue, tetraglycine phosphinate, bound in the active site. In the electron density, the active site of the peptidase, the phosphinate and the “diglycine” fragment on the P1′ side of the transition state analogue are very well defined. The density is much poorer or even absent for the P1 side of the ligand. The structure is consistent with the involvement of His260 and/or His291 in the activation of the water nucleophile and suggests a possible catalytic role for Tyr204, which we confirmed by mutagenesis. Possible mechanisms of catalysis and the structural basis of substrate specificity are discussed based on the structure analysis.
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30
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Yao J, Guo H, Chaiprasongsuk M, Zhao N, Chen F, Yang X, Guo H. Substrate-Assisted Catalysis in the Reaction Catalyzed by Salicylic Acid Binding Protein 2 (SABP2), a Potential Mechanism of Substrate Discrimination for Some Promiscuous Enzymes. Biochemistry 2015; 54:5366-75. [PMID: 26244568 DOI: 10.1021/acs.biochem.5b00638] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although one of an enzyme's hallmarks is the high specificity for their natural substrates, substrate promiscuity has been reported more frequently. It is known that promiscuous enzymes generally show different catalytic efficiencies to different substrates, but our understanding of the origin of such differences is still lacking. Here we report the results of quantum mechanical/molecular mechanical simulations and an experimental study of salicylic acid binding protein 2 (SABP2). SABP2 has promiscuous esterase activity toward a series of substrates but shows a high activity toward its natural substrate, methyl salicylate (MeSA). Our results demonstrate that this enzyme may use substrate-assisted catalysis involving the hydroxyl group from MeSA to enhance the activity and achieve substrate discrimination.
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Affiliation(s)
- Jianzhuang Yao
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37830, United States
| | - Haobo Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37830, United States
| | - Minta Chaiprasongsuk
- Department of Plant Sciences, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Nan Zhao
- Department of Plant Sciences, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Hong Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37830, United States
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31
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The use of ene adducts to study and engineer enoyl-thioester reductases. Nat Chem Biol 2015; 11:398-400. [DOI: 10.1038/nchembio.1794] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 03/09/2015] [Indexed: 11/08/2022]
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32
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Abdizadeh H, Guven G, Atilgan AR, Atilgan C. Perturbation response scanning specifies key regions in subtilisin serine protease for both function and stability. J Enzyme Inhib Med Chem 2015; 30:867-73. [DOI: 10.3109/14756366.2014.979345] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Haleh Abdizadeh
- Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla, Istanbul, Turkey
| | - Gokce Guven
- Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla, Istanbul, Turkey
| | - Ali Rana Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla, Istanbul, Turkey
| | - Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla, Istanbul, Turkey
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33
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Wilschanski M, Abbasi M, Blanco E, Lindberg I, Yourshaw M, Zangen D, Berger I, Shteyer E, Pappo O, Bar-Oz B, Martín MG, Elpeleg O. A novel familial mutation in the PCSK1 gene that alters the oxyanion hole residue of proprotein convertase 1/3 and impairs its enzymatic activity. PLoS One 2014; 9:e108878. [PMID: 25272002 PMCID: PMC4182778 DOI: 10.1371/journal.pone.0108878] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 08/26/2014] [Indexed: 02/06/2023] Open
Abstract
Four siblings presented with congenital diarrhea and various endocrinopathies. Exome sequencing and homozygosity mapping identified five regions, comprising 337 protein-coding genes that were shared by three affected siblings. Exome sequencing identified a novel homozygous N309K mutation in the proprotein convertase subtilisin/kexin type 1 (PCSK1) gene, encoding the neuroendocrine convertase 1 precursor (PC1/3) which was recently reported as a cause of Congenital Diarrhea Disorder (CDD). The PCSK1 mutation affected the oxyanion hole transition state-stabilizing amino acid within the active site, which is critical for appropriate proprotein maturation and enzyme activity. Unexpectedly, the N309K mutant protein exhibited normal, though slowed, prodomain removal and was secreted from both HEK293 and Neuro2A cells. However, the secreted enzyme showed no catalytic activity, and was not processed into the 66 kDa form. We conclude that the N309K enzyme is able to cleave its own propeptide but is catalytically inert against in trans substrates, and that this variant accounts for the enteric and systemic endocrinopathies seen in this large consanguineous kindred.
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Affiliation(s)
- Michael Wilschanski
- Gastroenterology Unit, Division of Pediatrics, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Montaser Abbasi
- Gastroenterology Unit, Division of Pediatrics, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Elias Blanco
- Department of Anatomy and Neurobiology, University of Maryland-Baltimore, Baltimore, Maryland, United States of America
- Department of Pediatrics, Division of Gastroenterology and Nutrition, Mattel Children's Hospital and the David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Iris Lindberg
- Department of Anatomy and Neurobiology, University of Maryland-Baltimore, Baltimore, Maryland, United States of America
| | - Michael Yourshaw
- Department of Pediatrics, Division of Gastroenterology and Nutrition, Mattel Children's Hospital and the David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - David Zangen
- Endocrinology Unit, Division of Pediatrics, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Itai Berger
- Neurology Unit, Division of Pediatrics, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Eyal Shteyer
- Gastroenterology Unit, Division of Pediatrics, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Orit Pappo
- Department of Pathology, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Benjamin Bar-Oz
- Department of Neonatology, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Martin G. Martín
- Department of Pediatrics, Division of Gastroenterology and Nutrition, Mattel Children's Hospital and the David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Orly Elpeleg
- Monique and Jacques Roboh Department of Genetic Research, Hadassah Hebrew University Hospital, Jerusalem, Israel
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Investigating the role of a backbone to substrate hydrogen bond in OMP decarboxylase using a site-specific amide to ester substitution. Proc Natl Acad Sci U S A 2014; 111:15066-71. [PMID: 25275007 DOI: 10.1073/pnas.1411772111] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hydrogen bonds between backbone amide groups of enzymes and their substrates are often observed, but their importance in substrate binding and/or catalysis is not easy to investigate experimentally. We describe the generation and kinetic characterization of a backbone amide to ester substitution in the orotidine 5'-monophosphate (OMP) decarboxylase from Methanobacter thermoautotrophicum (MtOMPDC) to determine the importance of a backbone amide-substrate hydrogen bond. The MtOMPDC-catalyzed reaction is characterized by a rate enhancement (∼10(17)) that is among the largest for enzyme-catalyzed reactions. The reaction proceeds through a vinyl anion intermediate that may be stabilized by hydrogen bonding interaction between the backbone amide of a conserved active site serine residue (Ser-127) and oxygen (O4) of the pyrimidine moiety and/or electrostatic interactions with the conserved general acidic lysine (Lys-72). In vitro translation in conjunction with amber suppression using an orthogonal amber tRNA charged with L-glycerate ((HO)S) was used to generate the ester backbone substitution (S127(HO)S). With 5-fluoro OMP (FOMP) as substrate, the amide to ester substitution increased the value of Km by ∼1.5-fold and decreased the value of kcat by ∼50-fold. We conclude that (i) the hydrogen bond between the backbone amide of Ser-127 and O4 of the pyrimidine moiety contributes a modest factor (∼10(2)) to the 10(17) rate enhancement and (ii) the stabilization of the anionic intermediate is accomplished by electrostatic interactions, including its proximity of Lys-72. These conclusions are in good agreement with predictions obtained from hybrid quantum mechanical/molecular mechanical calculations.
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35
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Legler PM, Boisvert SM, Compton JR, Millard CB. Development of organophosphate hydrolase activity in a bacterial homolog of human cholinesterase. Front Chem 2014; 2:46. [PMID: 25077141 PMCID: PMC4100338 DOI: 10.3389/fchem.2014.00046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 06/19/2014] [Indexed: 01/10/2023] Open
Abstract
We applied a combination of rational design and directed evolution (DE) to Bacillus subtilis p-nitrobenzyl esterase (pNBE) with the goal of enhancing organophosphorus acid anhydride hydrolase (OPAAH) activity. DE started with a designed variant, pNBE A107H, carrying a histidine homologous with human butyrylcholinesterase G117H to find complementary mutations that further enhance its OPAAH activity. Five sites were selected (G105, G106, A107, A190, and A400) within a 6.7 Å radius of the nucleophilic serine Oγ. All 95 variants were screened for esterase activity with a set of five substrates: pNP-acetate, pNP-butyrate, acetylthiocholine, butyrylthiocholine, or benzoylthiocholine. A microscale assay for OPAAH activity was developed for screening DE libraries. Reductions in esterase activity were generally concomitant with enhancements in OPAAH activity. One variant, A107K, showed an unexpected 7-fold increase in its k cat/K m for benzoylthiocholine, demonstrating that it is also possible to enhance the cholinesterase activity of pNBE. Moreover, DE resulted in at least three variants with modestly enhanced OPAAH activity compared to wild type pNBE. A107H/A190C showed a 50-fold increase in paraoxonase activity and underwent a slow time- and temperature-dependent change affecting the hydrolysis of OPAA and ester substrates. Structural analysis suggests that pNBE may represent a precursor leading to human cholinesterase and carboxylesterase 1 through extension of two vestigial specificity loops; a preliminary attempt to transfer the Ω-loop of BChE into pNBE is described. Unlike butyrylcholinesterase and pNBE, introducing a G143H mutation (equivalent to G117H) did not confer detectable OP hydrolase activity on human carboxylesterase 1 (hCE1). We discuss the use of pNBE as a surrogate scaffold for the mammalian esterases, and the importance of the oxyanion-hole residues for enhancing the OPAAH activity of selected serine hydrolases.
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Affiliation(s)
- Patricia M. Legler
- Naval Research Laboratory, Center for Bio/Molecular Science and EngineeringWashington, DC, USA
| | | | | | - Charles B. Millard
- United States Army Medical Research and Materiel CommandFort Detrick, MD, USA
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36
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Tsurumura T, Tsuge H. Substrate selectivity of bacterial monoacylglycerol lipase based on crystal structure. ACTA ACUST UNITED AC 2014; 15:83-9. [DOI: 10.1007/s10969-014-9181-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Accepted: 05/22/2014] [Indexed: 01/09/2023]
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37
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Lichtor PA, Miller SJ. Experimental lineage and functional analysis of a remotely directed peptide epoxidation catalyst. J Am Chem Soc 2014; 136:5301-8. [PMID: 24690108 PMCID: PMC4333582 DOI: 10.1021/ja410567a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
![]()
We
describe mechanistic investigations of a catalyst (1)
that leads to selective epoxidation of farnesol at the 6,7-position,
remote from the hydroxyl directing group. The experimental lineage
of peptide 1 and a number of resin-bound peptide analogues
were examined to reveal the importance of four N-terminal residues.
We examined the selectivity of truncated analogues to find that a
trimer is sufficient to furnish the remote selectivity. Both 1D and
2D 1H NMR studies were used to determine possible catalyst
conformations, culminating in proposed models showing possible interactions
of farnesol with a protected Thr side chain and backbone NH. The models
were used to rationalize the selectivity of a modified catalyst (17) for the 6,7-position relative to an ether moiety in two
related substrates.
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Affiliation(s)
- Phillip A Lichtor
- Department of Chemistry, Yale University , P.O. Box 208107, New Haven, Connecticut 06520, United States
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38
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Jang KP, Hutson GE, Johnston RC, McCusker EO, Cheong PHY, Scheidt KA. Asymmetric homoenolate additions to acyl phosphonates through rational design of a tailored N-heterocyclic carbene catalyst. J Am Chem Soc 2013; 136:76-9. [PMID: 24299299 DOI: 10.1021/ja410932t] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A highly selective NHC-catalyzed synthesis of γ-butyrolactones from the fusion of enals and α-ketophosphonates has been developed. Computational modeling of competing transition states guided a rational design strategy to achieve enhanced levels of enantioselectivity with a new tailored C1-symmetric biaryl-saturated imidazolium-derived NHC catalyst.
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Affiliation(s)
- Ki Po Jang
- Department of Chemistry, Center for Molecular Innovation and Drug Discovery, Chemistry of Life Processes Institute, Northwestern University , Silverman Hall, Evanston, Illinois 60208, United States
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39
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Untangling structure-function relationships in the rhomboid family of intramembrane proteases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2862-72. [PMID: 24099005 DOI: 10.1016/j.bbamem.2013.05.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 04/04/2013] [Accepted: 05/04/2013] [Indexed: 12/30/2022]
Abstract
Rhomboid proteases are a family of integral membrane proteins that have been implicated in critical regulatory roles in a wide array of cellular processes and signaling events. The determination of crystal structures of the prokaryotic rhomboid GlpG from Escherichia coli and Haemophilus influenzae has ushered in an era of unprecedented understanding into molecular aspects of intramembrane proteolysis by this fascinating class of protein. A combination of structural studies by X-ray crystallography, and biophysical and spectroscopic analyses, combined with traditional enzymatic and functional analysis has revealed fundamental aspects of rhomboid structure, substrate recognition and the catalytic mechanism. This review summarizes these remarkable advances by examining evidence for the proposed catalytic mechanism derived from inhibitor co-crystal structures, conflicting models of rhomboid-substrate interaction, and recent work on the structure and function of rhomboid cytosolic domains. In addition to exploring progress on aspects of rhomboid structure, areas for future research and unaddressed questions are emphasized and highlighted. This article is part of a Special Issue entitled: Intramembrane Proteases.
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40
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Blomberg R, Kries H, Pinkas DM, Mittl PRE, Grütter MG, Privett HK, Mayo SL, Hilvert D. Precision is essential for efficient catalysis in an evolved Kemp eliminase. Nature 2013; 503:418-21. [DOI: 10.1038/nature12623] [Citation(s) in RCA: 235] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 08/30/2013] [Indexed: 11/09/2022]
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41
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Syrén PO. The solution of nitrogen inversion in amidases. FEBS J 2013; 280:3069-83. [DOI: 10.1111/febs.12241] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 03/06/2013] [Accepted: 03/08/2013] [Indexed: 01/06/2023]
Affiliation(s)
- Per-Olof Syrén
- Institute of Technical Biochemistry; University of Stuttgart; Germany
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42
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Yang H, Wong MW. Oxyanion Hole Stabilization by C–H···O Interaction in a Transition State—A Three-Point Interaction Model for Cinchona Alkaloid-Catalyzed Asymmetric Methanolysis of meso-Cyclic Anhydrides. J Am Chem Soc 2013; 135:5808-18. [DOI: 10.1021/ja4005893] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hui Yang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Ming Wah Wong
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
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43
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Abstract
Linus Pauling proposed that the large rate accelerations for enzymes are caused by the high specificity of the protein catalyst for binding the reaction transition state. The observation that stable analogues of the transition states for enzymatic reactions often act as tight-binding inhibitors provided early support for this simple and elegant proposal. We review experimental results that support the proposal that Pauling's model provides a satisfactory explanation for the rate accelerations for many heterolytic enzymatic reactions through high-energy reaction intermediates, such as proton transfer and decarboxylation. Specificity in transition state binding is obtained when the total intrinsic binding energy of the substrate is significantly larger than the binding energy observed at the Michaelis complex. The results of recent studies that aimed to characterize the specificity in binding of the enolate oxygen at the transition state for the 1,3-isomerization reaction catalyzed by ketosteroid isomerase are reviewed. Interactions between pig heart succinyl-coenzyme A:3-oxoacid coenzyme A transferase (SCOT) and the nonreacting portions of coenzyme A (CoA) are responsible for a rate increase of 3 × 10(12)-fold, which is close to the estimated total 5 × 10(13)-fold enzymatic rate acceleration. Studies that partition the interactions between SCOT and CoA into their contributing parts are reviewed. Interactions of the protein with the substrate phosphodianion group provide an ~12 kcal/mol stabilization of the transition state for the reactions catalyzed by triosephosphate isomerase, orotidine 5'-monophosphate decarboxylase, and α-glycerol phosphate dehydrogenase. The interactions of these enzymes with the substrate piece phosphite dianion provide a 6-8 kcal/mol stabilization of the transition state for reaction of the appropriate truncated substrate. Enzyme activation by phosphite dianion reflects the higher dianion affinity for binding to the enzyme-transition state complex compared with that of the free enzyme. Evidence is presented that supports a model in which the binding energy of the phosphite dianion piece, or the phosphodianion group of the whole substrate, is utilized to drive an enzyme conformational change from an inactive open form E(O) to an active closed form E(C), by closure of a phosphodianion gripper loop. Members of the enolase and haloalkanoic acid dehalogenase superfamilies use variable capping domains to interact with nonreacting portions of the substrate and sequester the substrate from interaction with bulk solvent. Interactions of this capping domain with the phenyl group of mandelate have been shown to activate mandelate racemase for catalysis of deprotonation of α-carbonyl carbon. We propose that an important function of these capping domains is to utilize the binding interactions with nonreacting portions of the substrate to activate the enzyme for catalysis.
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Affiliation(s)
- Tina L. Amyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000
| | - John P. Richard
- To whom correspondence should be addressed: Tel: (716) 645 4232; Fax: (716) 645 6963;
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44
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Schwenteit J, Bogdanović X, Fridjonsson OH, Aevarsson A, Bornscheuer UT, Hinrichs W, Gudmundsdottir BK. Toxoid construction of AsaP1, a lethal toxic aspzincin metalloendopeptidase of Aeromonas salmonicida subsp. achromogenes, and studies of its activity and processing. Vet Microbiol 2013; 162:687-694. [PMID: 23031341 DOI: 10.1016/j.vetmic.2012.09.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 09/11/2012] [Accepted: 09/12/2012] [Indexed: 11/25/2022]
Abstract
AsaP1 is a toxic aspzincin metalloendopeptidase secreted by the fish pathogen Aeromonas salmonicida subsp. achromogenes. The protease is highly immunogenic and antibodies against AsaP1 evoke a passive protection against infection with A. salmonicida subsp. achromogenes. The protease is expressed as 37 kDa pre-pro-protein and processed to an active enzyme of 19kDa in A. salmonicida subsp. achromogenes. Recombinant expression of AsaP1(rec) in E. coli results in a protease of 22 kDa that is not secreted. AsaP1(rec) induces comparable pathological changes in Atlantic salmon (Salmo salar L.) to native AsaP1(wt). The aim of the study was to construct AsaP1 toxoids by exchanging catalytically important amino acids in the active site region of the protease. Four different AsaP1 mutants (AsaP1(E294A), AsaP1(E294Q), AsaP1(Y309A), and AsaP1(Y309F)) were successfully constructed by one step site directed mutagenesis, expressed in E. coli BL21 C43 as pre-pro-proteins and purified by His-tag affinity chromatography and gel filtration. Three of the resulting mutants (AsaP1(E294A), AsaP1(E294Q), and AsaP1(Y309A)) were not caseinolytic active and are detected as unprocessed pre-pro-proteins of 37 kDa. Caseinolytic active AsaP1(rec) and a mutant with reduced activity, AsaP1(Y309F), were processed to a size of 22 kDa. Furthermore, AsaP1(rec) is able to process the inactive mutants to the mature size of 22 kDa, allowing the conclusion that AsaP1 is autocatalytically processed. All four mutants AsaP1(E294A), AsaP1(E294Q), AsaP1(Y309A) and AsaP1(Y309F) are non-toxic in fish but induce a specific anti-AsaP1 antibody response in Arctic charr (Salvelinus alpinus L.) and are therefore true toxoids and possible vaccine additives.
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Affiliation(s)
- Johanna Schwenteit
- Institute for Experimental Pathology, University of Iceland, Keldur v/Vesturlandsveg, IS-112 Reykjavík, Iceland; Institute of Biochemistry, Department of Biotechnology and Enzyme Catalysis, Greifswald University, Felix Hausdorff-Str. 4, 17487 Greifswald, Germany.
| | - Xenia Bogdanović
- Department of Structural Biology, Greifswald University, Felix Hausdorff-Str. 4, 17487 Greifswald, Germany.
| | | | | | - Uwe T Bornscheuer
- Institute of Biochemistry, Department of Biotechnology and Enzyme Catalysis, Greifswald University, Felix Hausdorff-Str. 4, 17487 Greifswald, Germany.
| | - Winfried Hinrichs
- Department of Structural Biology, Greifswald University, Felix Hausdorff-Str. 4, 17487 Greifswald, Germany.
| | - Bjarnheidur K Gudmundsdottir
- Institute for Experimental Pathology, University of Iceland, Keldur v/Vesturlandsveg, IS-112 Reykjavík, Iceland.
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45
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Herschlag D, Natarajan A. Fundamental challenges in mechanistic enzymology: progress toward understanding the rate enhancements of enzymes. Biochemistry 2013; 52:2050-67. [PMID: 23488725 DOI: 10.1021/bi4000113] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzymes are remarkable catalysts that lie at the heart of biology, accelerating chemical reactions to an astounding extent with extraordinary specificity. Enormous progress in understanding the chemical basis of enzymatic transformations and the basic mechanisms underlying rate enhancements over the past decades is apparent. Nevertheless, it has been difficult to achieve a quantitative understanding of how the underlying mechanisms account for the energetics of catalysis, because of the complexity of enzyme systems and the absence of underlying energetic additivity. We review case studies from our own work that illustrate the power of precisely defined and clearly articulated questions when dealing with such complex and multifaceted systems, and we also use this approach to evaluate our current ability to design enzymes. We close by highlighting a series of questions that help frame some of what remains to be understood, and we encourage the reader to define additional questions and directions that will deepen and broaden our understanding of enzymes and their catalysis.
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Affiliation(s)
- Daniel Herschlag
- Department of Biochemistry, Stanford University School of Medicine , Stanford, California 94305, United States
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46
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Richter F, Blomberg R, Khare SD, Kiss G, Kuzin AP, Smith AJT, Gallaher J, Pianowski Z, Helgeson RC, Grjasnow A, Xiao R, Seetharaman J, Su M, Vorobiev S, Lew S, Forouhar F, Kornhaber GJ, Hunt JF, Montelione GT, Tong L, Houk KN, Hilvert D, Baker D. Computational design of catalytic dyads and oxyanion holes for ester hydrolysis. J Am Chem Soc 2012; 134:16197-206. [PMID: 22871159 DOI: 10.1021/ja3037367] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleophilic catalysis is a general strategy for accelerating ester and amide hydrolysis. In natural active sites, nucleophilic elements such as catalytic dyads and triads are usually paired with oxyanion holes for substrate activation, but it is difficult to parse out the independent contributions of these elements or to understand how they emerged in the course of evolution. Here we explore the minimal requirements for esterase activity by computationally designing artificial catalysts using catalytic dyads and oxyanion holes. We found much higher success rates using designed oxyanion holes formed by backbone NH groups rather than by side chains or bridging water molecules and obtained four active designs in different scaffolds by combining this motif with a Cys-His dyad. Following active site optimization, the most active of the variants exhibited a catalytic efficiency (k(cat)/K(M)) of 400 M(-1) s(-1) for the cleavage of a p-nitrophenyl ester. Kinetic experiments indicate that the active site cysteines are rapidly acylated as programmed by design, but the subsequent slow hydrolysis of the acyl-enzyme intermediate limits overall catalytic efficiency. Moreover, the Cys-His dyads are not properly formed in crystal structures of the designed enzymes. These results highlight the challenges that computational design must overcome to achieve high levels of activity.
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Affiliation(s)
- Florian Richter
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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47
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Tangprasittipap A, Chouwdee S, Phiwsaiya K, Laiphrom S, Senapin S, Flegel TW, Sritunyalucksana K. Structure and expression of a shrimp prohormone convertase 2. Gen Comp Endocrinol 2012; 178:185-93. [PMID: 22634957 DOI: 10.1016/j.ygcen.2012.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 05/01/2012] [Accepted: 05/10/2012] [Indexed: 11/17/2022]
Abstract
Although many crustacean neuroendocrine hormones have been reported, the enzymes responsible for post-translational modification of neuroendocrine hormones have rarely been characterized. A prohormone convertase 2 (PC2)-like enzyme has been isolated from the optic lobe of the giant tiger shrimp, Penaeus monodon and referred as PmPC2. The full length cDNA sequence of PmPC2 has been identified and found to resemble evolutionarily conserved PC2 enzymes of vertebrates and invertebrates. PmPC2 was expressed in all larval developmental stages and in neuroendrocrine cells in the adult optic lobe. Its expression was found to be negatively related with shrimp body weight by qPCR (P<0.05). Immunohistochemistry results using an anti-rPmPC2 antibody with adult shrimp revealed high staining intensity in specific neurosecretory cells including the sinus gland, the organ of Hanström (also referred to as the medullar terminalis X-organ) and the organ of Bellonci (also referred to as the sensory or X-organ). By using the yeast two hybrid technique, PmPC2 was found to bind with P. monodon hyperglycemic hormone (Pem-CHH1) that plays an important role in glucose metabolism. Since PmPC2 is a subtilisin-like serine proteinase, it is expected to cleave the synthetic substrate, pyr-RTKR-MCA, but the expressed recombinant catalytic domain of PmPC2 (rPmPC2-cat) showed no enzymatic activity as expected. In vivo injection of dsRNA-PmPC2 resulted in reduced transcripts for both PmPC2 and Pem-CHH1 on day 3 post injection, but there was no accompanying reduction of glucose level in the hemolymph. Taken together, PmPC2 localization, expression and activity suggest that it has a function(s) in the shrimp neuroendrocrine system and that it may not only activate Pem-CHH1 but also affect its expression. However, there is no obvious explanation for the negative correlation between PmPC2 expression level and shrimp body weight.
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Affiliation(s)
- Amornrat Tangprasittipap
- Shrimp-Virus Interaction Laboratory (ASVI), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand
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48
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Rivera-Cancel G, Sanders JM, Hay AG. Kinetics of hydrolysis and mutational analysis of N,N-diethyl-m-toluamide hydrolase from Pseudomonas putida DTB. FEBS J 2012; 279:1044-53. [PMID: 22251573 DOI: 10.1111/j.1742-4658.2012.08495.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The initial step in the biodegradation pathway of N,N-diethyl-m-toluamide (DEET) in Pseudomonas putida strain DTB is catalyzed by DEET hydrolase (DthA), which hydrolyzes the amide bond to yield 3-methylbenzoic acid and diethylamine. In order to extend our understanding of DthA, the enzyme was purified and characterized. The enzyme is most active at pH 7.9, and is probably a tetramer in its native state. The kinetic parameters of the wild-type enzyme are K(m) = 10.2 ± 0.8 μm, k(cat) = 5.53 ± 0.09 s(-1) , and k(cat) /K(m) = (5.4 ± 0.4) × 10(5) m(-1) ·s(-1) . Mild substrate inhibition was observed with DEET concentrations over 500 μm. A homology model of DthA was used to guide mutational analysis of the active site, confirming that the catalytic triad is formed by Ser166, Ap292, and His320. The oxyanion hole is formed by the side chain OH of Tyr84 and the backbone amide of Trp167, with the Tyr84 OH being essential for enzyme activity. The DthA model also revealed a hydrophobic substrate-binding pocket comprosed of Trp167, Met170, and Trp214. W167A and M170A mutations decreased enzymatic activity and exacerbated substrate inhibition, whereas Trp214, which probably plays a role in substrate recognition, was essential for enzymatic activity. The pH rate profile of DthA was fitted to two ionizable groups (pK(a1) = 6.1 and pK(a2) = 9.9) that probably correspond to Nε of His320 and the OH of Tyr84, respectively. In addition to catalyzing the hydrolysis of DEET, DthA hydrolyzed a variety of esters and amides.
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Simón L, Goodman JM. Hydrogen-bond stabilization in oxyanion holes: grand jeté to three dimensions. Org Biomol Chem 2012; 10:1905-13. [PMID: 22273994 DOI: 10.1039/c2ob06717j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We recently reported crystallographic evidence that the hydrogen bonds which can stabilize oxygen-centered negative charge within enzyme oxyanion holes are rarely found in the place they should be expected on the basis of the analysis of small-molecule crystal structures. We investigated this phenomenon using calculations on simplified active site models. A recent paper suggested that several aspects of the analysis required further exploration. In this paper we: (i) review the results of our crystallographic study; (ii) report molecular dynamics studies which investigate the effect of protein movement; (iii) report ONIOM calculations which trace the reaction coordinate for an oxyanion hole reaction in the presence of a complete enzyme active site. These results show that the limitations of gas phase calculations on simplified models do not invalidate our comparison of competing active site geometries. These new results reaffirm the conclusion that oxyanion holes are not usually stabilized by planar arrangements of H-bonds, and that this sub-optimal transition state stabilization leads to better overall catalysis.
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Affiliation(s)
- Luis Simón
- Facultad de Ciencias Químicas, Universidad de Salamanca, Plaza de los Caídos 1-5, Salamanca, E37004, Spain.
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Schwans JP, Sunden F, Gonzalez A, Tsai Y, Herschlag D. Evaluating the catalytic contribution from the oxyanion hole in ketosteroid isomerase. J Am Chem Soc 2011; 133:20052-5. [PMID: 22053826 PMCID: PMC3241876 DOI: 10.1021/ja208050t] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Prior site-directed mutagenesis studies in bacterial ketosteroid isomerase (KSI) reported that substitution of both oxyanion hole hydrogen bond donors gives a 10(5)- to 10(8)-fold rate reduction, suggesting that the oxyanion hole may provide the major contribution to KSI catalysis. But these seemingly conservative mutations replaced the oxyanion hole hydrogen bond donors with hydrophobic side chains that could lead to suboptimal solvation of the incipient oxyanion in the mutants, thereby potentially exaggerating the apparent energetic benefit of the hydrogen bonds relative to water-mediated hydrogen bonds in solution. We determined the functional and structural consequences of substituting the oxyanion hole hydrogen bond donors and several residues surrounding the oxyanion hole with smaller residues in an attempt to create a local site that would provide interactions more analogous to those in aqueous solution. These more drastic mutations created an active-site cavity estimated to be ~650 Å(3) and sufficient for occupancy by 15-17 water molecules and led to a rate decrease of only ~10(3)-fold for KSI from two different species, a much smaller effect than that observed from more traditional conservative mutations. The results underscore the strong context dependence of hydrogen bond energetics and suggest that the oxyanion hole provides an important, but moderate, catalytic contribution relative to the interactions in the corresponding solution reaction.
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Affiliation(s)
- Jason P. Schwans
- Department of Biochemistry, Stanford University, Stanford, CA 94305
| | - Fanny Sunden
- Department of Biochemistry, Stanford University, Stanford, CA 94305
| | - Ana Gonzalez
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025
| | - Yingssu Tsai
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA 94305
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025
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