1
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Purohit V, Steussy CN, Rosales AR, Critchelow CJ, Schmidt T, Helquist P, Wiest O, Mesecar A, Cohen AE, Stauffacher CV. pH-dependent reaction triggering in PmHMGR crystals for time-resolved crystallography. Biophys J 2024; 123:622-637. [PMID: 38327055 PMCID: PMC10938121 DOI: 10.1016/j.bpj.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/22/2023] [Accepted: 02/02/2024] [Indexed: 02/09/2024] Open
Abstract
Serial crystallography and time-resolved data collection can readily be employed to investigate the catalytic mechanism of Pseudomonas mevalonii 3-hydroxy-3-methylglutaryl (HMG)-coenzyme-A (CoA) reductase (PmHMGR) by changing the environmental conditions in the crystal and so manipulating the reaction rate. This enzyme uses a complex mechanism to convert mevalonate to HMG-CoA using the co-substrate CoA and cofactor NAD+. The multi-step reaction mechanism involves an exchange of bound NAD+ and large conformational changes by a 50-residue subdomain. The enzymatic reaction can be run in both forward and reverse directions in solution and is catalytically active in the crystal for multiple reaction steps. Initially, the enzyme was found to be inactive in the crystal starting with bound mevalonate, CoA, and NAD+. To observe the reaction from this direction, we examined the effects of crystallization buffer constituents and pH on enzyme turnover, discovering a strong inhibition in the crystallization buffer and a controllable increase in enzyme turnover as a function of pH. The inhibition is dependent on ionic concentration of the crystallization precipitant ammonium sulfate but independent of its ionic composition. Crystallographic studies show that the observed inhibition only affects the oxidation of mevalonate but not the subsequent reactions of the intermediate mevaldehyde. Calculations of the pKa values for the enzyme active site residues suggest that the effect of pH on turnover is due to the changing protonation state of His381. We have now exploited the changes in ionic inhibition in combination with the pH-dependent increase in turnover as a novel approach for triggering the PmHMGR reaction in crystals and capturing information about its intermediate states along the reaction pathway.
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Affiliation(s)
- Vatsal Purohit
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana
| | - Calvin N Steussy
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana
| | - Anthony R Rosales
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana
| | | | - Tim Schmidt
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana
| | - Paul Helquist
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana
| | - Olaf Wiest
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana
| | - Andrew Mesecar
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana; Purdue Institute for Cancer Research, Purdue University, West Lafayette, Indiana; Department of Biochemistry, Purdue University, West Lafayette, Indiana
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California
| | - Cynthia V Stauffacher
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana; Purdue Institute of Inflammation, Immunology and Infectious Diseases, Purdue University, West Lafayette, Indiana; Purdue Institute for Cancer Research, Purdue University, West Lafayette, Indiana.
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2
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Bouzidi NE, Grama SB, Khelef AE, Yang D, Li J. Inhibition of antioxidant enzyme activities enhances carotenogenesis in microalga Dactylococcus dissociatus MT1. Front Bioeng Biotechnol 2022; 10:1014604. [PMID: 36213061 PMCID: PMC9538356 DOI: 10.3389/fbioe.2022.1014604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Microalgal biotechnology has become a promising field of research for the production of valuable, sustainable and environmentally friendly byproducts, especially for carotenoids. Bulk accumulation of secondary carotenoids in microalgae are mostly induced by oxidative stress of cells. In this research, we investigated the effects of antioxidant enzyme activity inhibition on carotenogenesis in a microalga Dactylococcus dissociatus MT1. The activities of four major antioxidant enzyme families, namely superoxide dismutase (SOD), catalases (CAT), glutathione peroxydases (GPX) and ascorbate perxodases (APX), were inhibited by relevant inhibitors during the stressed cultivation of D. dissociatus to observe the effects on carotenogensis. A 91% decrease in activity was observed for CAT, comparing with controls without any inhibitors added, followed by 65%, 61%, and 47% for the enzymes SOD, APX, and GPX, respectively. Concomitantly, it was found that this partial inhibition had substantial influences on the accumulation of carotenoids, with the highest production levels obtained in CAT inhibition conditions and an increase of 2.6 times of carotenoid concentration observed, comparing with control cultivation conditions. We conclude that the modulation of antioxidant enzyme activities could lead to the overproduction of carotenoids in this microalgal cell culture, and we expect that this novel approach of optimizing carotenogenesis processes for D. dissociatus cell cultures could be transferrable to other cell culture systems and might have an important impact on the carotenoid production industry.
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Affiliation(s)
- Nour Elaimane Bouzidi
- Laboratory of Natural Substances, Biomolecules and Biotechnological Applications, University of Oum El Bouaghi, Oum El Bouaghi, Algeria
| | - Samir Borhane Grama
- Laboratory of Natural Substances, Biomolecules and Biotechnological Applications, University of Oum El Bouaghi, Oum El Bouaghi, Algeria
- *Correspondence: Samir Borhane Grama , ; Jian Li ,
| | - Aboubakeur Essedik Khelef
- Laboratory of Natural Substances, Biomolecules and Biotechnological Applications, University of Oum El Bouaghi, Oum El Bouaghi, Algeria
| | - Duanpeng Yang
- College of Chemical and Biological Engineering, Panzhihua University, Panzhihua, China
| | - Jian Li
- College of Chemical and Biological Engineering, Panzhihua University, Panzhihua, China
- *Correspondence: Samir Borhane Grama , ; Jian Li ,
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3
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Koone JC, Dashnaw CM, Gonzalez M, Shaw BF. A method for quantifying how the activity of an enzyme is affected by the net charge of its nearest crowded neighbor. Protein Sci 2022. [PMCID: PMC9601770 DOI: 10.1002/pro.4384] [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] [Indexed: 11/09/2022]
Abstract
The electrostatic effects of protein crowding have not been systematically explored. Rather, protein crowding is generally studied with co‐solvents or crowders that are electrostatically neutral, with no methods to measure how the net charge (Z) of a crowder affects protein function. For example, can the activity of an enzyme be affected electrostatically by the net charge of its neighbor in crowded milieu? This paper reports a method for crowding proteins of different net charge to an enzyme via semi‐random chemical crosslinking. As a proof of concept, RNase A was crowded (at distances ≤ the Debye length) via crosslinking to different heme proteins with Z = +8.50 ± 0.04, Z = +6.39 ± 0.12, or Z = −10.30 ± 1.32. Crosslinking did not disrupt the structure of proteins, according to amide H/D exchange, and did not inhibit RNase A activity. For RNase A, we found that the electrostatic environment of each crowded neighbor had significant effects on rates of RNA hydrolysis. Crowding with cationic cytochrome c led to increases in activity, while crowding with anionic “supercharged” cytochrome c or myoglobin diminished activity. Surprisingly, electrostatic crowding effects were amplified at high ionic strength (I = 0.201 M) and attenuated at low ionic strength (I = 0.011 M). This salt dependence might be caused by a unique set of electric double layers at the dimer interspace (maximum distance of 8 Å, which cannot accommodate four layers). This new method of crowding via crosslinking can be used to search for electrostatic effects in protein crowding.
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Affiliation(s)
- Jordan C. Koone
- Department of Chemistry and Biochemistry Baylor University Waco Texas USA
| | - Chad M. Dashnaw
- Department of Chemistry and Biochemistry Baylor University Waco Texas USA
| | - Mayte Gonzalez
- Department of Chemistry and Biochemistry Baylor University Waco Texas USA
| | - Bryan F. Shaw
- Department of Chemistry and Biochemistry Baylor University Waco Texas USA
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4
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Salt Dependence of DNA Binding Activity of Human Transcription Factor Dlx3. Int J Mol Sci 2022; 23:ijms23169497. [PMID: 36012753 PMCID: PMC9409194 DOI: 10.3390/ijms23169497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/18/2022] [Accepted: 08/21/2022] [Indexed: 11/17/2022] Open
Abstract
Distal-less 3 (Dlx3) is a homeobox-containing transcription factor and plays a crucial role in the development and differentiation process. Human Dlx3 consists of two transactivation domains and a homeobox domain (HD) that selectively binds to the consensus site (5'-TAATT-3') of the DNA duplex. Here, we performed chemical shift perturbation experiments on Dlx3-HD in a complex with a 10-base-paired (10-bp) DNA duplex under various salt conditions. We also acquired the imino proton spectra of the 10-bp DNA to monitor the changes in base-pair stabilities during titration with Dlx3-HD. Our study demonstrates that Dlx3-HD selectively recognizes its consensus DNA sequences through the α3 helix and L1 loop regions with a unique dynamic feature. The dynamic properties of the binding of Dlx3-HD to its consensus DNA sequence can be modulated by varying the salt concentrations. Our study suggested that this unique structural and dynamic feature of Dlx3-HD plays an important role in target DNA recognition, which might be associated with tricho-dento-osseous syndrome.
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5
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Kembaren R, Westphal AH, Kamperman M, Kleijn JM, Borst JW. Charged Polypeptide Tail Boosts the Salt Resistance of Enzyme-Containing Complex Coacervate Micelles. Biomacromolecules 2022; 23:1195-1204. [PMID: 35042326 PMCID: PMC8924873 DOI: 10.1021/acs.biomac.1c01466] [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] [Indexed: 11/28/2022]
Abstract
![]()
Encapsulation of
proteins can have advantages for their protection,
stability, and delivery purposes. One of the options to encapsulate
proteins is to incorporate them in complex coacervate core micelles
(C3Ms). This can easily be achieved by mixing aqueous solutions of
the protein and an oppositely charged neutral-hydrophilic diblock
copolymer. However, protein-containing C3Ms often suffer from salt-inducible
disintegration due to the low charge density of proteins. The aim
of this study is to improve the salt stability of protein-containing
C3Ms by increasing the net charge of the protein by tagging it with
a charged polypeptide. As a model protein, we used CotA laccase and
generated variants with 10, 20, 30, and 40 glutamic acids attached
at the C-terminus of CotA using genetic engineering. Micelles were
obtained by mixing the five CotA variants with poly(N-methyl-2-vinyl-pyridinium)-block-poly(ethylene
oxide) (PM2VP128-b-PEO477)
at pH 10.8. Hydrodynamic radii of the micelles of approximately 31,
27, and 23 nm for native CotA, CotA-E20, and CotA-E40, respectively,
were determined using dynamic light scattering (DLS) and fluorescence
correlation spectroscopy (FCS). The encapsulation efficiency was not
affected using enzymes with a polyglutamic acid tail but resulted
in more micelles with a smaller number of enzyme molecules per micelle.
Furthermore, it was shown that the addition of a polyglutamic acid
tail to CotA indeed resulted in improved salt stability of enzyme-containing
C3Ms. Interestingly, the polyglutamic acid CotA variants showed an
enhanced enzyme activity. This study demonstrates that increasing
the net charge of enzymes through genetic engineering is a promising
strategy to improve the practical applicability of C3Ms as enzyme
delivery systems.
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Affiliation(s)
- Riahna Kembaren
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Laboratory of Biochemistry, Microspectroscopy Research Facility, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Adrie H. Westphal
- Laboratory of Biochemistry, Microspectroscopy Research Facility, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Marleen Kamperman
- Polymer Science, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - J. Mieke Kleijn
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Jan Willem Borst
- Laboratory of Biochemistry, Microspectroscopy Research Facility, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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6
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Systematic modelling incorporating temperature, pressure, and salinity effects on in-situ microbial selective plugging for enhanced oil recovery in a multi-layered system. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2021.108260] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Garnett ER, Raines RT. Emerging biological functions of ribonuclease 1 and angiogenin. Crit Rev Biochem Mol Biol 2021; 57:244-260. [PMID: 34886717 DOI: 10.1080/10409238.2021.2004577] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Pancreatic-type ribonucleases (ptRNases) are a large family of vertebrate-specific secretory endoribonucleases. These enzymes catalyze the degradation of many RNA substrates and thereby mediate a variety of biological functions. Though the homology of ptRNases has informed biochemical characterization and evolutionary analyses, the understanding of their biological roles is incomplete. Here, we review the functions of two ptRNases: RNase 1 and angiogenin. RNase 1, which is an abundant ptRNase with high catalytic activity, has newly discovered roles in inflammation and blood coagulation. Angiogenin, which promotes neovascularization, is now known to play roles in the progression of cancer and amyotrophic lateral sclerosis, as well as in the cellular stress response. Ongoing work is illuminating the biology of these and other ptRNases.
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Affiliation(s)
- Emily R Garnett
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
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8
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Yuan Y, DeBrosse M, Brothers M, Kim S, Sereda A, Ivanov NV, Hussain S, Heikenfeld J. Oil-Membrane Protection of Electrochemical Sensors for Fouling- and pH-Insensitive Detection of Lipophilic Analytes. ACS APPLIED MATERIALS & INTERFACES 2021; 13:53553-53563. [PMID: 34665962 DOI: 10.1021/acsami.1c14175] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
To take full advantage of the reagent- and label-free sensing capabilities of electrochemical sensors, a frequent and remaining challenge is interference and degradation of the sensors due to uncontrolled pH or salinity in the sample solution or foulants from the sample solution. Here, we present an oil-membrane sensor protection technique that allows for the permeation of hydrophobic (lipophilic) analytes into a sealed sensor compartment containing ideal salinity and pH conditions while simultaneously blocking common hydrophilic interferents (proteins, acids, bases, etc.) In this paper, we validate the oil-membrane sensor protection technique by demonstrating continuous cortisol detection via electrochemical aptamer-based (EAB) sensors. The encapsulated EAB cortisol sensor exhibits a 5 min concentration-on rise time and maintains a measurement signal of at least 7 h even in the extreme condition of an acidic solution of pH 3.
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Affiliation(s)
- Yuchan Yuan
- Novel Devices Lab, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Madeleine DeBrosse
- Novel Devices Lab, University of Cincinnati, Cincinnati, Ohio 45221, United States
- 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Michael Brothers
- 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Steve Kim
- 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | | | | | - Saber Hussain
- 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Jason Heikenfeld
- Novel Devices Lab, University of Cincinnati, Cincinnati, Ohio 45221, United States
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9
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Kraj P, Selivanovitch E, Lee B, Douglas T. Polymer Coatings on Virus-like Particle Nanoreactors at Low Ionic Strength-Charge Reversal and Substrate Access. Biomacromolecules 2021; 22:2107-2118. [PMID: 33877799 PMCID: PMC8238134 DOI: 10.1021/acs.biomac.1c00208] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Virus-like particles (VLPs) are a class of biomaterials which serve as platforms for achieving the desired functionality through interior and exterior modifications. Through ionic strength-mediated electrostatic interactions, VLPs have been assembled into hierarchically ordered materials. This work builds on predictive models to prepare polymer-coated VLP clusters at very low ionic strength. Zeta potential measurements showed that the clusters carried a strongly positive charge, a complete charge reversal from the VLP building block. SAXS analysis confirmed polymer adsorption onto the VLP exterior. We then studied the activity of an encapsulated enzyme toward small molecular and macromolecular substrates to determine the effect of each component of the hierarchically assembled material. We found that while encapsulation and polymer coating did not have a large effect on access to the enzyme by its native, small molecular substrate, substrate modification with a macromolecule caused the polymer coating and encapsulation to affect the access to the enzyme.
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Affiliation(s)
- Pawel Kraj
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington 47405, Indiana, United States
| | - Ekaterina Selivanovitch
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington 47405, Indiana, United States
| | - Byeongdu Lee
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne 60439, Illinois, United States
| | - Trevor Douglas
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington 47405, Indiana, United States
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SUGIMOTO Y, FUJIEDA N, KANO K. Electrochemical Consideration of Electrostatic Interaction of Charged Molecules with Partially Overlapped Electric Field: Zwitterions and Proteins. ELECTROCHEMISTRY 2021. [DOI: 10.5796/electrochemistry.21-00030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Yu SUGIMOTO
- Collaborative Research Organization for Micro and Nano Multifunctional Devices NMfD, The University of Tokyo
| | - Nobutaka FUJIEDA
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University
| | - Kenji KANO
- Center for Advanced Science and Innovation, Kyoto University
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11
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Simulation-Based Optimization of Microbial Enhanced Oil Recovery with a Model Integrating Temperature, Pressure, and Salinity Effects. ENERGIES 2021. [DOI: 10.3390/en14041131] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The microbial enhanced oil recovery (MEOR) method is an eco-friendly and economical alternative technology. The technology involves a variety of uncertainties, and its success depends on controlling microbial growth and metabolism. Though a few numerical studies have been carried out to reduce the uncertainties, no attempt has been made to consider temperature, pressure, and salinity in an integrated manner. In this study, a new modeling method incorporating these environmental impacts was proposed, and MEOR analysis was performed. As a result, accurate modeling was possible to prevent overestimating the performance of MEOR. In addition, oil recovery was maximized through sensitivity analysis and optimization based on an integrative model. Finally, applying MEOR to an actual reservoir model showed a 7% increase in oil recovery compared to waterflooding. This result proved the practical applicability of the method.
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12
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Pinthong N, Limudomporn P, Vasuvat J, Adisakwattana P, Rattaprasert P, Chavalitshewinkoon-Petmitr P. Molecular characterization of Plasmodium falciparum DNA-3-methyladenine glycosylase. Malar J 2020; 19:284. [PMID: 32762689 PMCID: PMC7409487 DOI: 10.1186/s12936-020-03355-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/28/2020] [Indexed: 11/10/2022] Open
Abstract
Background The emergence of artemisinin-resistant malaria parasites highlights the need for novel drugs and their targets. Alkylation of purine bases can hinder DNA replication and if unresolved would eventually result in cell death. DNA-3-methyladenine glycosylase (MAG) is responsible for the repair of those alkylated bases. Plasmodium falciparum (Pf) MAG was characterized for its potential for development as an anti-malarial candidate. Methods Native PfMAG from crude extract of chloroquine- and pyrimethamine-resistant P. falciparum K1 strain was partially purified using three chromatographic procedures. From bio-informatics analysis, primers were designed for amplification, insertion into pBAD202/D-TOPO and heterologous expression in Escherichia coli of recombinant PfMAG. Functional and biochemical properties of the recombinant enzyme were characterized. Results PfMAG activity was most prominent in parasite schizont stages, with a specific activity of 147 U/mg (partially purified) protein. K1 PfMAG contained an insertion of AAT (coding for asparagine) compared to 3D7 strain and 16% similarity to the human enzyme. Recombinant PfMAG (74 kDa) was twice as large as the human enzyme, preferred double-stranded DNA substrate, and demonstrated glycosylase activity over a pH range of 4–9, optimal salt concentration of 100–200 mM NaCl but reduced activity at 250 mM NaCl, no requirement for divalent cations, which were inhibitory in a dose-dependent manner. Conclusion PfMAG activity increased with parasite development being highest in the schizont stages. K1 PfMAG contained an indel AAT (asparagine) not present in 3D7 strain and the recombinant enzyme was twice as large as the human enzyme. Recombinant PfMAG had a wide range of optimal pH activity, and was inhibited at high (250 mM) NaCl concentration as well as by divalent cations. The properties of PfMAG provide basic data that should be of assistance in developing anti-malarials against this potential parasite target.
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Affiliation(s)
- Nattapon Pinthong
- Department of Protozoology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Paviga Limudomporn
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Jitlada Vasuvat
- Department of Protozoology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Poom Adisakwattana
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Pongruj Rattaprasert
- Department of Protozoology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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13
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Contreras F, Pramanik S, M. Rozhkova A, N. Zorov I, Korotkova O, P. Sinitsyn A, Schwaneberg U, D. Davari M. Engineering Robust Cellulases for Tailored Lignocellulosic Degradation Cocktails. Int J Mol Sci 2020; 21:E1589. [PMID: 32111065 PMCID: PMC7084875 DOI: 10.3390/ijms21051589] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 12/11/2022] Open
Abstract
Lignocellulosic biomass is a most promising feedstock in the production of second-generation biofuels. Efficient degradation of lignocellulosic biomass requires a synergistic action of several cellulases and hemicellulases. Cellulases depolymerize cellulose, the main polymer of the lignocellulosic biomass, to its building blocks. The production of cellulase cocktails has been widely explored, however, there are still some main challenges that enzymes need to overcome in order to develop a sustainable production of bioethanol. The main challenges include low activity, product inhibition, and the need to perform fine-tuning of a cellulase cocktail for each type of biomass. Protein engineering and directed evolution are powerful technologies to improve enzyme properties such as increased activity, decreased product inhibition, increased thermal stability, improved performance in non-conventional media, and pH stability, which will lead to a production of more efficient cocktails. In this review, we focus on recent advances in cellulase cocktail production, its current challenges, protein engineering as an efficient strategy to engineer cellulases, and our view on future prospects in the generation of tailored cellulases for biofuel production.
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Affiliation(s)
- Francisca Contreras
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Subrata Pramanik
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Aleksandra M. Rozhkova
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, 119071 Moscow, Russia
- Department of Chemistry, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ivan N. Zorov
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, 119071 Moscow, Russia
- Department of Chemistry, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Olga Korotkova
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Arkady P. Sinitsyn
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, 119071 Moscow, Russia
- Department of Chemistry, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52074 Aachen, Germany
| | - Mehdi D. Davari
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
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14
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Biochemical, Thermodynamic and Kinetic Characterization of Glucose Oxidase Purified from Pseudomonas and Actinomyces spp. from Natural Sources. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2019. [DOI: 10.22207/jpam.13.4.60] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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15
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Renders M, Dumbre S, Abramov M, Kestemont D, Margamuljana L, Largy E, Cozens C, Vandenameele J, Pinheiro VB, Toye D, Frère JM, Herdewijn P. Kinetic analysis of N-alkylaryl carboxamide hexitol nucleotides as substrates for evolved polymerases. Nucleic Acids Res 2019; 47:2160-2168. [PMID: 30698800 PMCID: PMC6412122 DOI: 10.1093/nar/gkz008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/21/2018] [Accepted: 01/21/2019] [Indexed: 11/20/2022] Open
Abstract
Six 1′,5′-anhydrohexitol uridine triphosphates were synthesized with aromatic substitutions appended via a carboxamide linker to the 5-position of their bases. An improved method for obtaining such 5-substituted hexitol nucleosides and nucleotides is described. The incorporation profile of the nucleotide analogues into a DNA duplex overhang using recently evolved XNA polymerases is compared. Long, mixed HNA sequences featuring the base modifications are generated. The apparent binding affinity of four of the nucleotides to the enzyme, the rate of the chemical step and of product release, plus the specificity constant for the incorporation of these modified nucleotides into a DNA duplex overhang using the HNA polymerase T6G12_I521L are determined via pre-steady-state kinetics. HNA polymers displaying aromatic functional groups could have significant impact on the isolation of stable and high-affinity binders and catalysts, or on the design of nanomaterials.
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Affiliation(s)
- Marleen Renders
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Rega, Herestraat 49 box 1041, 3000 Leuven, Belgium
| | - Shrinivas Dumbre
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Rega, Herestraat 49 box 1041, 3000 Leuven, Belgium
| | - Mikhail Abramov
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Rega, Herestraat 49 box 1041, 3000 Leuven, Belgium
| | - Donaat Kestemont
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Rega, Herestraat 49 box 1041, 3000 Leuven, Belgium
| | - Lia Margamuljana
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Rega, Herestraat 49 box 1041, 3000 Leuven, Belgium
| | - Eric Largy
- ARNA laboratory, Université de Bordeaux, INSERM U1212, CNRS UMR5320, IECB, 2 rue Robert Escarpit, 33600 Pessac, France
| | - Christopher Cozens
- Structural and Molecular Biology Department, University College London, Gower Street, London WC1E B6T, UK.,Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, United Kingdom
| | - Julie Vandenameele
- Laboratory of Enzymology and Protein Folding/Robotein Platform, Centre for Protein Engineering (CIP), Department of Life Sciences, University of Liège, Quartier Agora, Allée du six Août 13, Bât. B6a, 4000 Liège, Belgium
| | - Vitor B Pinheiro
- Structural and Molecular Biology Department, University College London, Gower Street, London WC1E B6T, UK.,Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, United Kingdom
| | - Dominique Toye
- Chemical engineering laboratory, University of Liège, Allée de la chimie, 3, Bât B6c, 4000 Liège, Belgium
| | - Jean-Marie Frère
- Laboratory of Enzymology and Protein Folding/Robotein Platform, Centre for Protein Engineering (CIP), Department of Life Sciences, University of Liège, Quartier Agora, Allée du six Août 13, Bât. B6a, 4000 Liège, Belgium
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Rega, Herestraat 49 box 1041, 3000 Leuven, Belgium.,Université d'Evry, CNRS-UMR8030/Laboratoire iSSB, CEA, DRF, IG, Genoscope, Université Paris-Saclay, Evry 91000, France
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16
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Pedersen JN, Zhou Y, Guo Z, Pérez B. Genetic and chemical approaches for surface charge engineering of enzymes and their applicability in biocatalysis: A review. Biotechnol Bioeng 2019; 116:1795-1812. [DOI: 10.1002/bit.26979] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 03/10/2019] [Accepted: 03/28/2019] [Indexed: 12/25/2022]
Affiliation(s)
| | - Ye Zhou
- Department of EngineeringAarhus UniversityAarhus Denmark
- Key Laboratory for Molecular Enzymology and Engineering, Ministry of Education, School of Life ScienceJilin UniversityChangchun China
| | - Zheng Guo
- Department of EngineeringAarhus UniversityAarhus Denmark
| | - Bianca Pérez
- AgrotechDanish Technological InstituteAarhus Denmark
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17
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Lee AR, Park CJ, Cheong HK, Ryu KS, Park JW, Kwon MY, Lee J, Kim KK, Choi BS, Lee JH. Solution structure of the Z-DNA binding domain of PKR-like protein kinase from Carassius auratus and quantitative analyses of the intermediate complex during B-Z transition. Nucleic Acids Res 2016; 44:2936-48. [PMID: 26792893 PMCID: PMC4824103 DOI: 10.1093/nar/gkw025] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 12/06/2015] [Accepted: 01/11/2016] [Indexed: 11/23/2022] Open
Abstract
Z-DNA binding proteins (ZBPs) play important roles in RNA editing, innate immune response and viral infection. Structural and biophysical studies show that ZBPs initially form an intermediate complex with B-DNA for B-Z conversion. However, a comprehensive understanding of the mechanism of Z-DNA binding and B-Z transition is still lacking, due to the absence of structural information on the intermediate complex. Here, we report the solution structure of the Zα domain of the ZBP-containing protein kinase from Carassius auratus(caZαPKZ). We quantitatively determined the binding affinity of caZαPKZ for both B-DNA and Z-DNA and characterized its B-Z transition activity, which is modulated by varying the salt concentration. Our results suggest that the intermediate complex formed by caZαPKZ and B-DNA can be used as molecular ruler, to measure the degree to which DNA transitions to the Z isoform.
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Affiliation(s)
- Ae-Ree Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Republic of Korea
| | - Chin-Ju Park
- Division of Liberal Arts and Sciences and Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Hae-Kap Cheong
- Division of Magnetic Resonance, KBSI, Chungbuk 28119, Republic of Korea
| | - Kyoung-Seok Ryu
- Division of Magnetic Resonance, KBSI, Chungbuk 28119, Republic of Korea
| | - Jin-Wan Park
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Republic of Korea Division of Magnetic Resonance, KBSI, Chungbuk 28119, Republic of Korea
| | - Mun-Young Kwon
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Republic of Korea
| | - Janghyun Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Gyeonggi 16419, Republic of Korea
| | - Byong-Seok Choi
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Republic of Korea
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18
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Sugimoto Y, Kitazumi Y, Shirai O, Yamamoto M, Kano K. Understanding of the Effects of Ionic Strength on the Bimolecular Rate Constant between Structurally Identified Redox Enzymes and Charged Substrates Using Numerical Simulations on the Basis of the Poisson–Boltzmann Equation. J Phys Chem B 2016; 120:3122-8. [DOI: 10.1021/acs.jpcb.6b00661] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu Sugimoto
- Division
of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yuki Kitazumi
- Division
of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Osamu Shirai
- Division
of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Masahiro Yamamoto
- Department
of Chemistry, Konan University, 8-9-1 Okamoto, Higashi-Nada, Kobe, Hyogo 658-8501, Japan
| | - Kenji Kano
- Division
of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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19
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Duff MR, Chopra S, Strader MB, Agarwal PK, Howell EE. Tales of Dihydrofolate Binding to R67 Dihydrofolate Reductase. Biochemistry 2015; 55:133-45. [PMID: 26637016 PMCID: PMC5147970 DOI: 10.1021/acs.biochem.5b00981] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Homotetrameric R67 dihydrofolate reductase possesses 222 symmetry and a single active site pore. This situation results in a promiscuous binding site that accommodates either the substrate, dihydrofolate (DHF), or the cofactor, NADPH. NADPH interacts more directly with the protein as it is larger than the substrate. In contrast, the p-aminobenzoyl-glutamate tail of DHF, as monitored by nuclear magnetic resonance and crystallography, is disordered when bound. To explore whether smaller active site volumes (which should decrease the level of tail disorder by confinement effects) alter steady state rates, asymmetric mutations that decreased the half-pore volume by ∼35% were constructed. Only minor effects on k(cat) were observed. To continue exploring the role of tail disorder in catalysis, 1-ethyl-3-[3-(dimethylamino)propyl]carbodiimide-mediated cross-linking between R67 DHFR and folate was performed. A two-folate, one-tetramer complex results in the loss of enzyme activity where two symmetry-related K32 residues in the protein are cross-linked to the carboxylates of two bound folates. The tethered folate could be reduced, although with a ≤30-fold decreased rate, suggesting decreased dynamics and/or suboptimal positioning of the cross-linked folate for catalysis. Computer simulations that restrain the dihydrofolate tail near K32 indicate that cross-linking still allows movement of the p-aminobenzoyl ring, which allows the reaction to occur. Finally, a bis-ethylene-diamine-α,γ-amide folate adduct was synthesized; both negatively charged carboxylates in the glutamate tail were replaced with positively charged amines. The K(i) for this adduct was ∼9-fold higher than for folate. These various results indicate a balance between folate tail disorder, which helps the enzyme bind substrate while dynamics facilitates catalysis.
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Affiliation(s)
- Michael R Duff
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996-0840, United States
| | - Shaileja Chopra
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996-0840, United States
| | - Michael Brad Strader
- Laboratory of Biochemistry and Vascular Biology, Center for Biologics Evaluation and Research, Food and Drug Administration , Silver Spring, Maryland 20993, United States
| | - Pratul K Agarwal
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996-0840, United States.,Computer Science and Mathematics Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Elizabeth E Howell
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996-0840, United States
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20
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Boumaiza M, Jaouen M, Deschemin JC, Ezzine A, Khalaf NB, Vaulont S, Marzouki MN, Sari MA. Expression and purification of a new recombinant camel hepcidin able to promote the degradation of the iron exporter ferroportin1. Protein Expr Purif 2015; 115:11-8. [DOI: 10.1016/j.pep.2015.04.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 04/15/2015] [Accepted: 04/16/2015] [Indexed: 01/03/2023]
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21
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Le CM, Donnay-Moreno C, Bruzac S, Baron R, Nguyen HTM, Bergé JP. Proteolysis of Sardine ( Sardina pilchardus) and Anchovy ( Stolephorus commersonii) by Commercial Enzymes in
Saline Solutions. Food Technol Biotechnol 2015; 53:87-90. [PMID: 27904336 DOI: 10.17113/ftb.53.01.15.3893] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Fish sauce production is a very long process and there is a great interest in shortening it. Among the different strategies to speed up this process, the addition of external proteases could be a solution. This study focuses on the effect of two commercial enzymes (Protamex and Protex 51FP) on the proteolysis of two fish species traditionally converted into fish sauce: sardine and anchovy, by comparison with classical autolysis. Hydrolysis reactions were conducted with fresh fish at a temperature of 30 °C and under different saline conditions (from 0 to 30% NaCl). Hydrolysis degree and liquefaction of the raw material were used to follow the process. As expected, the proteolysis decreased with increasing amount of salt. Regarding the fish species, higher rate of liquefaction and higher hydrolysis degree were obtained with anchovy. Between the two proteases, Protex 51FP gave better results with both fish types. This study demonstrates that the addition of commercial proteases could be helpful for the liquefaction of fish and cleavage of peptide bonds that occur during fish sauce production and thus speed up the production process.
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Affiliation(s)
- Chau Minh Le
- College of Agriculture and Forestry, Thai Nguyen University, Quyet Thang, Thai Nguyen, Vietnam; IFREMER, rue de l'île d'Yeu, BP 21105, FR-44311 Nantes, France
| | | | - Sandrine Bruzac
- IFREMER, rue de l'île d'Yeu, BP 21105, FR-44311 Nantes, France
| | - Régis Baron
- IFREMER, rue de l'île d'Yeu, BP 21105, FR-44311 Nantes, France
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22
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Catalysis by the tumor-suppressor enzymes PTEN and PTEN-L. PLoS One 2015; 10:e0116898. [PMID: 25607987 PMCID: PMC4301912 DOI: 10.1371/journal.pone.0116898] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 12/16/2014] [Indexed: 11/19/2022] Open
Abstract
Phosphatase and tensin homologue deleted from chromosome ten (PTEN) is a lipid phosphatase tumor suppressor that is lost or inactivated in most human tumors. The enzyme catalyzes the hydrolysis of phosphatidylinositol-(3,4,5)-trisphosphate (PIP3) to form phosphatidylinositol-(4,5)-bisphosphate (PIP2) and inorganic phosphate. Here, we report on the first continuous assay for the catalytic activity of PTEN. Using this assay, we demonstrate that human PTEN is activated by the reaction product PIP2, as well as in solutions of low salt concentration. This activation is abrogated in the K13A variant, which has a disruption in a putative binding site for PIP2. We also demonstrate that PTEN-L, which derives from alternative translation of the PTEN mRNA, is activated constitutively. These findings have implications for catalysis by PTEN in physiological environments and could expedite the development of PTEN-based chemotherapeutic agents.
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23
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Zhang L, Jiang L, Liu Y, Yin Q. Ionic strength-modulated catalytic efficiency of a multienzyme cascade nanoconfined on charged hierarchical scaffolds. RSC Adv 2015. [DOI: 10.1039/c5ra04512f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Understanding the effect of ionic strength on the efficiency of this enzyme cascade within charged hierarchical nanospace is not only fundamentally interesting, but also important for translating biochemical pathways to noncellular environments.
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Affiliation(s)
- Ling Zhang
- DSAPM Lab
- PCFM Lab
- GDHPPC Lab and OFCM Institute
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
| | - Li Jiang
- DSAPM Lab
- PCFM Lab
- GDHPPC Lab and OFCM Institute
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
| | - Yuan Liu
- DSAPM Lab
- PCFM Lab
- GDHPPC Lab and OFCM Institute
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
| | - Qihe Yin
- DSAPM Lab
- PCFM Lab
- GDHPPC Lab and OFCM Institute
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
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24
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Kilic MS, Korkut S, Hazer B, Erhan E. Development and operation of gold and cobalt oxide nanoparticles containing polypropylene based enzymatic fuel cell for renewable fuels. Biosens Bioelectron 2014; 61:500-5. [PMID: 24951919 DOI: 10.1016/j.bios.2014.05.068] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 05/09/2014] [Accepted: 05/24/2014] [Indexed: 10/25/2022]
Abstract
Newly synthesized gold and cobalt oxide nanoparticle embedded Polypropylene-g-Polyethylene glycol was used for a compartment-less enzymatic fuel cell. Glucose oxidase and bilirubin oxidase were selected as anodic and cathodic enzymes, respectively. Electrode fabrication and EFC operation parameters were optimized to achieve high power output. Maximum power density of 23.5 µW cm(-2) was generated at a cell voltage of +560 mV vs Ag/AgCl, in 100mM PBS pH 7.4 with the addition of 20mM of synthetic glucose solution. 20 µg of polymer amount with 185 µg of glucose oxidase and 356 µg of bilirubin oxidase was sufficient to get maximum performance. The working electrodes could harvest glucose, produced during photosynthesis reaction of Carpobrotus Acinaciformis plant, and readily found in real domestic wastewater of Zonguldak City in Turkey.
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Affiliation(s)
| | - Seyda Korkut
- Department of Environmental Engineering, Bulent Ecevit University, 67100 Zonguldak, Turkey.
| | - Baki Hazer
- Department of Chemistry, Bulent Ecevit University, 67100 Zonguldak, Turkey
| | - Elif Erhan
- Department of Environmental Engineering, Gebze Institute of Technology, 41400 Gebze, Kocaeli, Turkey
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25
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Bolel P, Datta S, Mahapatra N, Halder M. Exploration of pH-Dependent Behavior of the Anion Receptor Pocket of Subdomain IIA of HSA: Determination of Effective Pocket Charge Using the Debye–Hückel Limiting Law. J Phys Chem B 2013; 118:26-36. [DOI: 10.1021/jp407057f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Priyanka Bolel
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
| | - Shubhashis Datta
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
| | - Niharendu Mahapatra
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
| | - Mintu Halder
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
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26
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Thomas SA, Immormino RM, Bourret RB, Silversmith RE. Nonconserved active site residues modulate CheY autophosphorylation kinetics and phosphodonor preference. Biochemistry 2013; 52:2262-73. [PMID: 23458124 DOI: 10.1021/bi301654m] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
In two-component signal transduction, response regulator proteins contain the catalytic machinery for their own covalent phosphorylation and can catalyze phosphotransfer from a partner sensor kinase or autophosphorylate using various small molecule phosphodonors. Although response regulator autophosphorylation is physiologically relevant and a powerful experimental tool, the kinetic determinants of the autophosphorylation reaction and how those determinants might vary for different response regulators and phosphodonors are largely unknown. We characterized the autophosphorylation kinetics of 21 variants of the model response regulator Escherichia coli CheY that contained substitutions primarily at nonconserved active site positions D + 2 (CheY residue 59) and T + 2 (CheY residue 89), two residues C-terminal to conserved D57 and T87, respectively. Overall, the CheY variants exhibited a >10(5)-fold range of rate constants (kphos/KS) for reaction with phosphoramidate, acetyl phosphate, or monophosphoimidazole, with the great majority of rates enhanced versus that of wild-type CheY. Although phosphodonor preference varied substantially, nearly all the CheY variants reacted faster with phosphoramidate than acetyl phosphate. Correlation between the increased positive charge of the D + 2 and T + 2 side chains and faster rates indicated electrostatic interactions are a kinetic determinant. Moreover, sensitivities of rate constants to ionic strength indicated that both long-range and localized electrostatic interactions influence autophosphorylation kinetics. The increased nonpolar surface area of the D + 2 and T + 2 side chains also correlated with an enhanced autophosphorylation rate, especially for reaction with phosphoramidate and monophosphoimidazole. Computer docking suggested that highly accelerated monophosphoimidazole autophosphorylation rates for CheY variants with a tyrosine at position T + 2 likely reflect structural mimicry of phosphotransfer from the sensor kinase histidyl phosphate.
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Affiliation(s)
- Stephanie A Thomas
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA
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27
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Arai M, Ferreon JC, Wright PE. Quantitative analysis of multisite protein-ligand interactions by NMR: binding of intrinsically disordered p53 transactivation subdomains with the TAZ2 domain of CBP. J Am Chem Soc 2012; 134:3792-803. [PMID: 22280219 DOI: 10.1021/ja209936u] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Determination of affinities and binding sites involved in protein-ligand interactions is essential for understanding molecular mechanisms in biological systems. Here we combine singular value decomposition and global analysis of NMR chemical shift perturbations caused by protein-protein interactions to determine the number and location of binding sites on the protein surface and to measure the binding affinities. Using this method we show that the isolated AD1 and AD2 binding motifs, derived from the intrinsically disordered N-terminal transactivation domain of the tumor suppressor p53, both interact with the TAZ2 domain of the transcriptional coactivator CBP at two binding sites. Simulations of titration curves and line shapes show that a primary dissociation constant as small as 1-10 nM can be accurately estimated by NMR titration methods, provided that the primary and secondary binding processes are coupled. Unexpectedly, the site of binding of AD2 on the hydrophobic surface of TAZ2 overlaps with the binding site for AD1, but AD2 binds TAZ2 more tightly. The results highlight the complexity of interactions between intrinsically disordered proteins and their targets. Furthermore, the association rate of AD2 to TAZ2 is estimated to be 1.7 × 10(10) M(-1) s(-1), approaching the diffusion-controlled limit and indicating that intrinsic disorder plus complementary electrostatics can significantly accelerate protein binding interactions.
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Affiliation(s)
- Munehito Arai
- Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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28
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Optimization of oxidative bioconversions catalyzed by phenylacetone monooxygenase from Thermobifida fusca. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.molcatb.2011.09.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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29
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Abstract
Mammalian pancreatic-type ribonucleases (ptRNases) comprise an enzyme family that is remarkably well suited for therapeutic exploitation. ptRNases are robust and prodigious catalysts of RNA cleavage that can naturally access the cytosol. Instilling cytotoxic activity requires endowing them with the ability to evade a cytosolic inhibitor protein while retaining other key attributes. These efforts have informed our understanding of ptRNase-based cytotoxins, as well as the action of protein-based drugs with cytosolic targets. Here, we address the most pressing problems encountered in the design of cytotoxic ptRNases, along with potential solutions. In addition, we describe assays that can be used to evaluate a successful design in vitro, in cellulo, and in vivo. The emerging information validates the continuing development of ptRNases as chemotherapeutic agents.
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Affiliation(s)
- Jo E Lomax
- Graduate Program in Cellular & Molecular Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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30
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Reengineering rate-limiting, millisecond enzyme motions by introduction of an unnatural amino acid. Biophys J 2011; 101:411-20. [PMID: 21767494 DOI: 10.1016/j.bpj.2011.05.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Revised: 05/18/2011] [Accepted: 05/19/2011] [Indexed: 01/20/2023] Open
Abstract
Rate-limiting millisecond motions in wild-type (WT) Ribonuclease A (RNase A) are modulated by histidine 48. Here, we incorporate an unnatural amino acid, thia-methylimidazole, at this site (H48C-4MI) to investigate the effects of a single residue on protein motions over multiple timescales and on enzyme catalytic turnover. Molecular dynamics simulations reveal that H48C-4MI retains some crucial WT-like hydrogen bonding interactions but the extent of protein-wide correlated motions in the nanosecond regime is decreased relative to WT. NMR Carr-Purcell-Meiboom-Gill relaxation dispersion experiments demonstrate that millisecond conformational motions in H48C-4MI are present over a similar pH range compared to WT. Furthermore, incorporation of this nonnatural amino acid allows retention of WT-like catalytic activity over the full pH range. These studies demonstrate that the complexity of the protein energy landscape during the catalytic cycle can be maintained using unnatural amino acids, which may prove useful in enzyme design efforts.
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31
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CHAVES IZABELLARODRIGUES, DE SOUZA FERREIRA EDERLAN, DA SILVA MARAIZAAPARECIDA, NEVES VALDIRAUGUSTO. POLYPHENOLOXIDASE FROM ATEMOYA FRUIT (ANNONA CHERIMOLA MILL. × ANNONA SQUAMOSA L.). J Food Biochem 2011. [DOI: 10.1111/j.1745-4514.2010.00508.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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Cuchillo CM, Nogués MV, Raines RT. Bovine pancreatic ribonuclease: fifty years of the first enzymatic reaction mechanism. Biochemistry 2011; 50:7835-41. [PMID: 21838247 DOI: 10.1021/bi201075b] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fifty years ago, the group of Tony Mathias and Bob Rabin at University College London deduced the first mechanism for catalysis by an enzyme, ribonuclease [Findlay, D., Herries, D. G., Mathias, A. P., Rabin, B. R., and Ross, C. A. (1961) Nature 190, 781-784]. Here, we celebrate this historic accomplishment by surveying knowledge of enzymology and protein science at that time, facts that led to the formulation of the mechanism, criticisms and alternative mechanisms, data that supported the proposed mechanism, and some of the refinements that have since provided a more precise picture of catalysis of RNA cleavage by ribonucleases. The Mathias and Rabin mechanism has appeared in numerous textbooks, monographs, and reviews and continues to have a profound impact on biochemistry.
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Affiliation(s)
- Claudi M Cuchillo
- Departament de Bioquímica i Biologia Molecular, Unitat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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33
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Ostanina ES, Varlamov VP, Yakovlev GI. Inhibition of lipase activity by low-molecular-weight chitosan. APPL BIOCHEM MICRO+ 2011. [DOI: 10.1134/s0003683808010055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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34
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Beauchamp DL, Khajehpour M. Probing the effect of water-water interactions on enzyme activity with salt gradients: a case-study using ribonuclease t1. J Phys Chem B 2010; 114:16918-28. [PMID: 21114308 DOI: 10.1021/jp107556s] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Water molecules interact with one another via hydrogen bonds. Experimental and theoretical evidence indicates that these hydrogen bonds occur in two modalities--high- and low-angle hydrogen bonding--and that the addition of various solutes to water affects only the number of water molecules participating in a specific type of hydrogen bond interactions, not the nature of the water-water interactions. In this work, we have investigated the effect of each of these hydrogen bonding types upon the activity of the enzyme ribonuclease t1. This was done through perturbation of the water hydrogen bonding distribution by using various salts. Our results indicate that various salts differ in their ability to reduce the enzymatic activity of ribonuclease t1, and this ability is well correlated with the ability of each salt to promote high-angle hydrogen bonding in water. By applying the two-phase model of liquid water (i.e., liquid water being modeled as an equilibrium existing between two phases, LD and HD water), we demonstrate that our results are compatible with the assumption that increasing the population of high-angle hydrogen bonds among water molecules stabilizes the more compact, less active conformations of the enzyme. This indicates that the structures that proteins adopt in water solution depend upon the nature of interactions between water molecules.
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Affiliation(s)
- David L Beauchamp
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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35
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Schreiber G, Haran G, Zhou HX. Fundamental aspects of protein-protein association kinetics. Chem Rev 2010; 109:839-60. [PMID: 19196002 DOI: 10.1021/cr800373w] [Citation(s) in RCA: 555] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- G Schreiber
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel.
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36
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Abstract
Some of the rate theories that are most useful for modeling biological processes are reviewed. By delving into some of the details and subtleties in the development of the theories, the review will hopefully help the reader gain a more than superficial perspective. Examples are presented to illustrate how rate theories can be used to generate insight at the microscopic level into biomolecular behaviors. An attempt is made to clear up a number of misconceptions in the literature regarding popular rate theories, including the appearance of Planck's constant in the transition-state theory and the Smoluchowski result as an upper limit for protein-protein and protein-DNA association rate constants. Future work in combining the implementation of rate theories through computer simulations with experimental probes of rate processes, and in modeling effects of intracellular environments so that theories can be used for generating rate constants for systems biology studies is particularly exciting.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.
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37
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Abstract
Onconase (ONC) is a member of the ribonuclease A superfamily that is toxic to cancer cells in vitro and in vivo. ONC is now in Phase IIIb clinical trials for the treatment of malignant mesothelioma. Internalization of ONC to the cytosol of cancer cells is essential for its cytotoxic activity, despite the apparent absence of a cell-surface receptor protein. Endocytosis and cytotoxicity do, however, appear to correlate with the net positive charge of ribonucleases. To dissect the contribution made by the endogenous arginine and lysine residues of ONC to its cytotoxicity, 22 variants were created in which cationic residues were replaced with alanine. Variants with the same net charge (+2 to +5) as well as equivalent catalytic activity and conformational stability were found to exhibit large (> 10-fold) differences in toxicity for the cells of a human leukemia line. In addition, a more cationic ONC variant could be either much more or much less cytotoxic than a less cationic variant, again depending on the distribution of its cationic residues. The endocytosis of variants with widely divergent cytotoxic activity was quantified by flow cytometry using a small-molecule fluorogenic label, and was found to vary by twofold or less. This small difference in endocytosis did not account for the large difference in cytotoxicity, implicating the distribution of cationic residues as being critical for lipid-bilayer translocation subsequent to endocytosis. This finding has fundamental implications for understanding the interaction of ribonucleases and other proteins with mammalian cells.
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Affiliation(s)
- Rebecca F Turcotte
- Medical Scientist Training Program and Biophysics Graduate Program, University of Wisconsin-Madison, WI, USA
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38
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Finger LD, Blanchard MS, Theimer CA, Sengerová B, Singh P, Chavez V, Liu F, Grasby JA, Shen B. The 3'-flap pocket of human flap endonuclease 1 is critical for substrate binding and catalysis. J Biol Chem 2009; 284:22184-22194. [PMID: 19525235 DOI: 10.1074/jbc.m109.015065] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Flap endonuclease 1 (FEN1) proteins, which are present in all kingdoms of life, catalyze the sequence-independent hydrolysis of the bifurcated nucleic acid intermediates formed during DNA replication and repair. How FEN1s have evolved to preferentially cleave flap structures is of great interest especially in light of studies wherein mice carrying a catalytically deficient FEN1 were predisposed to cancer. Structural studies of FEN1s from phage to human have shown that, although they share similar folds, the FEN1s of higher organisms contain a 3'-extrahelical nucleotide (3'-flap) binding pocket. When presented with 5'-flap substrates having a 3'-flap, archaeal and eukaryotic FEN1s display enhanced reaction rates and cleavage site specificity. To investigate the role of this interaction, a kinetic study of human FEN1 (hFEN1) employing well defined DNA substrates was conducted. The presence of a 3'-flap on substrates reduced Km and increased multiple- and single turnover rates of endonucleolytic hydrolysis at near physiological salt concentrations. Exonucleolytic and fork-gap-endonucleolytic reactions were also stimulated by the presence of a 3'-flap, and the absence of a 3'-flap from a 5'-flap substrate was more detrimental to hFEN1 activity than removal of the 5'-flap or introduction of a hairpin into the 5'-flap structure. hFEN1 reactions were predominantly rate-limited by product release regardless of the presence or absence of a 3'-flap. Furthermore, the identity of the stable enzyme product species was deduced from inhibition studies to be the 5'-phosphorylated product. Together the results indicate that the presence of a 3'-flap is the critical feature for efficient hFEN1 substrate recognition and catalysis.
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Affiliation(s)
| | | | - Carla A Theimer
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222
| | - Blanka Sengerová
- Centre for Chemical Biology, Department of Chemistry Krebs Institute, University of Sheffield, Sheffield, S3 7HF, United Kingdom
| | - Purnima Singh
- Division of Radiation Biology, Duarte, California 91010
| | - Valerie Chavez
- Division of Radiation Biology, Duarte, California 91010; Graduate School of Biological Sciences, City of Hope National Medical Center and Beckman Research Institute, Duarte, California 91010
| | - Fei Liu
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222
| | - Jane A Grasby
- Centre for Chemical Biology, Department of Chemistry Krebs Institute, University of Sheffield, Sheffield, S3 7HF, United Kingdom
| | - Binghui Shen
- Division of Radiation Biology, Duarte, California 91010
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39
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Plantinga MJ, Korennykh AV, Piccirilli JA, Correll CC. Electrostatic interactions guide the active site face of a structure-specific ribonuclease to its RNA substrate. Biochemistry 2008; 47:8912-8. [PMID: 18672906 PMCID: PMC2646754 DOI: 10.1021/bi800592g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
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Restrictocin, a member of the α-sarcin family of site-specific endoribonucleases, uses electrostatic interactions to bind to the ribosome and to RNA oligonucleotides, including the minimal specific substrate, the sarcin/ricin loop (SRL) of 23S−28S rRNA. Restrictocin binds to the SRL by forming a ground-state E:S complex that is stabilized predominantly by Coulomb interactions and depends on neither the sequence nor structure of the RNA, suggesting a nonspecific complex. The 22 cationic residues of restrictocin are dispersed throughout this protein surface, complicating a priori identification of a Coulomb interacting surface. Structural studies have identified an enzyme−substrate interface, which is expected to overlap with the electrostatic E:S interface. Here, we identified restrictocin residues that contribute to binding in the E:S complex by determining the salt dependence [∂ log(k2/K1/2)/∂ log[KCl]] of cleavage of the minimal SRL substrate for eight point mutants within the protein designed to disrupt contacts in the crystallographically defined interface. Relative to the wild-type salt dependence of −4.1, a subset of the mutants clustering near the active site shows significant changes in salt dependence, with differences of magnitude being ≥0.4. This same subset was identified using calculated salt dependencies for each mutant derived from solutions to the nonlinear Poisson−Boltzmann equation. Our findings support a mechanism in which specific residues on the active site face of restrictocin (primarily K110, K111, and K113) contribute to formation of the E:S complex, thereby positioning the SRL substrate for site-specific cleavage. The same restrictocin residues are expected to facilitate targeting of the SRL on the surface of the ribosome.
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Affiliation(s)
- Matthew J Plantinga
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
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40
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Gerasimova YV, Erchenko IA, Shakirov MM, Godovikova TS. Interaction of human serum albumin and its clinically relevant modification with oligoribonucleotides. Bioorg Med Chem Lett 2008; 18:4511-4. [PMID: 18674900 DOI: 10.1016/j.bmcl.2008.07.060] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Revised: 07/10/2008] [Accepted: 07/13/2008] [Indexed: 11/25/2022]
Abstract
Human serum albumin (HSA) was shown to mediate oligoribonucleotide cleavage. Nonenzymatic glycation of HSA decreased the ribonuclease-like activity of the protein. According to (31)P NMR data, both native and glycated albumins induced hydrolysis of RNA molecule through 2',3'-cyclophosphate intermediates. A feasible mechanism of RNA hydrolysis by native albumin and its clinically relevant modification was discussed.
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Affiliation(s)
- Yuliya V Gerasimova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Lavrentyev Ave., 630090 Novosibirsk, Russia
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41
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Ostanina ES, Varlamov VP, Yakovlev GI. Inhibition of lipase activity by low-molecular-weight chitosan. APPL BIOCHEM MICRO+ 2007. [DOI: 10.1134/s0003683807060154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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42
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Lee JE, Bae E, Bingman CA, Phillips GN, Raines RT. Structural basis for catalysis by onconase. J Mol Biol 2007; 375:165-77. [PMID: 18001769 DOI: 10.1016/j.jmb.2007.09.089] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2007] [Accepted: 09/20/2007] [Indexed: 11/18/2022]
Abstract
Onconase (ONC) is a homolog of bovine pancreatic ribonuclease (RNase A) from the frog Rana pipiens. ONC displays antitumoral activity and is in advanced clinical trials for the treatment of cancer. Here, we report the first atomic structures of ONC-nucleic acid complexes: a T89N/E91A ONC-5'-AMP complex at 1.65 A resolution and a wild-type ONC-d(AUGA) complex at 1.90 A resolution. The latter structure and site-directed mutagenesis were used to reveal the atomic basis for substrate recognition and turnover by ONC. The residues in ONC that are proximal to the scissile phosphodiester bond (His10, Lys31, and His97) and uracil nucleobase (Thr35, Asp67, and Phe98) are conserved from RNase A and serve to generate a similar bell-shaped pH versus k(cat)/K(M) profile for RNA cleavage. Glu91 of ONC forms two hydrogen bonds with the guanine nucleobase in d(AUGA), and Thr89 is in close proximity to that nucleobase. Installing a neutral or cationic residue at position 91 or an asparagine residue at position 89 virtually eliminated the 10(2)-fold guanine:adenine preference of ONC. A variant that combined such substitutions, T89N/E91A ONC, actually preferred adenine over guanine. In contrast, installing an arginine residue at position 91 increased the guanine preference and afforded an ONC variant with the highest known k(cat)/K(M) value. These data indicate that ONC discriminates between guanine and adenine by using Coulombic interactions and a network of hydrogen bonds. The structure of the ONC-d(AUGA) complex was also used to probe other aspects of catalysis. For example, the T5R substitution, designed to create a favorable Coulombic interaction between ONC and a phosphoryl group in RNA, increased ribonucleolytic activity by twofold. No variant, however, was more toxic to human cancer cells than wild-type ONC. Together, these findings provide a cynosure for understanding catalysis of RNA cleavage in a system of high medicinal relevance.
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Affiliation(s)
- J Eugene Lee
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
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43
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Gitlin I, Carbeck JD, Whitesides GM. Why are proteins charged? Networks of charge-charge interactions in proteins measured by charge ladders and capillary electrophoresis. Angew Chem Int Ed Engl 2007; 45:3022-60. [PMID: 16619322 DOI: 10.1002/anie.200502530] [Citation(s) in RCA: 196] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Almost all proteins contain charged amino acids. While the function in catalysis or binding of individual charges in the active site can often be identified, it is less clear how to assign function to charges beyond this region. Are they necessary for solubility? For reasons other than solubility? Can manipulating these charges change the properties of proteins? A combination of capillary electrophoresis (CE) and protein charge ladders makes it possible to study the roles of charged residues on the surface of proteins outside the active site. This method involves chemical modification of those residues to generate a large number of derivatives of the protein that differ in charge. CE separates those derivatives into groups with the same number of modified charged groups. By studying the influence of charge on the properties of proteins using charge ladders, it is possible to estimate the net charge and hydrodynamic radius and to infer the role of charged residues in ligand binding and protein folding.
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Affiliation(s)
- Irina Gitlin
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St., Cambridge, MA 02138, USA
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44
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Salis A, Bilanicova D, Ninham BW, Monduzzi M. Hofmeister Effects in Enzymatic Activity: Weak and Strong Electrolyte Influences on the Activity of Candida rugosa Lipase. J Phys Chem B 2007; 111:1149-56. [PMID: 17266269 DOI: 10.1021/jp066346z] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effects of weak and strong electrolytes on the enzymatic activity of Candida rugosa lipase are explored. Weak electrolytes, used as buffers, set the pH, while strong electrolytes regulate the ionic strength. The interplay between pH and ionic strength has been assumed to be the determinant of enzymatic activity. In experiments that probe activities by varying these parameters, there has been little attention focused on the role of specific electrolyte effects. Here we show that both buffers and the choice of background electrolyte ion strongly affect the enzymatic activity of Candida rugosa lipase. The effects here shown are dramatic at high salt concentration; indeed, a 2 M concentration of NaSCN is able to fully inactivate the lipase. By contrast, Na2SO4 acts generally as an activator, whereas NaCl shows a quasi-neutral behavior. Such specific ion effects are well-known and are classified among the "Hofmeister effects". However, there has been little awareness of them, or of their potential for optimization of activities in the enzyme community. Rather than the effects per se, the focus here is on their origin. New insights into mechanism are proposed.
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Affiliation(s)
- Andrea Salis
- Dipartimento di Scienze Chimiche, Università di Cagliari-CSGI Cittadella Monserrato, S.S. 554 Bivio Sestu, 09042 Monserrato, Italy.
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45
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Tanaka H, Bollot G, Mareda J, Litvinchuk S, Tran DH, Sakai N, Matile S. Synthetic pores with sticky π-clamps. Org Biomol Chem 2007; 5:1369-80. [PMID: 17464406 DOI: 10.1039/b702255g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this report, we describe design, synthesis, evaluation and molecular dynamics simulations of synthetic multifunctional pores with pi-acidic naphthalenediimide clamps. Experimental evidence is provided for the formation of unstable but inert, heterogeneous and acid-insensitive dynamic tetrameric pores that are sensitive to base and ionic strength. Blockage experiments reveal that the introduction of aromatic electron donor-acceptor interactions provides access to the selective recognition of pi-basic intercalators within the pore. This breakthrough is important for the application of synthetic pores as multianalyte sensors.
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Affiliation(s)
- Hiroyuki Tanaka
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
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46
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Zhang D, Kovach IM. Deuterium solvent isotope effect and proton-inventory studies of factor Xa-catalyzed reactions. Biochemistry 2006; 45:14175-82. [PMID: 17115712 PMCID: PMC2535812 DOI: 10.1021/bi061218m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Kinetic solvent isotope effects (KSIEs) for the factor Xa (FXa)-catalyzed activation of prothrombin in the presence and absence of factor Va (FVa) and 5.0 x 10(-5) M phospholipid vesicles are slightly inverse, 0.82-0.93, when substrate concentrations are at 0.2 Km. This is consistent with the rate-determining association of the enzyme-prothrombin assembly, rather than the rate-limiting chemical transformation. FVa is known to effect a major conformational change to expose the first scissile bond in prothrombin, which is the likely event triggering a major solvent rearrangement. At prothrombin concentrations > 5 Km, the KSIE is 1.6 +/- 0.3, when FXa is in a 1:1 ratio with FVa but becomes increasingly inverse, 0.30 +/- 0.05 and 0.19 +/- 0.04, when FXa/FVa is 1:4, with an increasing FXa and substrate concentration. The rate-determining step changes with the conditions, but the chemical step is not limiting under any circumstance. This corroborates the proposed predominance of the meizothrombin pathway when FXa is well-saturated with the prothrombin complex. In contrast, the FXa-catalyzed hydrolysis of N-alpha-Z-D-Arg-Gly-Arg-pNA.2HCl (S-2765) and H-D-Ile-L-Pro-L-Arg-pNA.HCl (S-2288) is most consistent with two-proton bridges forming at the transition state between Ser195 OgammaH and His57 N(epsilon)2 and His57 Ndelta1 and Asp102 COObeta- at the active site, with transition-state fractionation factors of phi1 = phi2 = 0.57 +/- 0.07 and phiS = 0.78 +/- 0.16 for solvent rearrangement for S-2765 and phi1 = phi2 = 0.674 +/- 0.001 for S-2288 under enzyme saturation with the substrate at pH 8.40 and 25.0 +/- 0.1 degrees C. The rate-determining step(s) in these reactions is most likely the cleavage of the C-N bond and departure of the leaving group.
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Affiliation(s)
| | - Ildiko M. Kovach
- Corresponding author. Telephone: (202) 319−6550. FAX: (202) 319−5381.
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47
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Gitlin I, Carbeck JD, Whitesides GM. Warum sind Proteine geladen? Netzwerke aus Ladungs-Ladungs-Wechselwirkungen in Proteinen, analysiert über Ladungsleitern und Kapillarelektrophorese. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200502530] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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48
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Korennykh AV, Piccirilli JA, Correll CC. The electrostatic character of the ribosomal surface enables extraordinarily rapid target location by ribotoxins. Nat Struct Mol Biol 2006; 13:436-43. [PMID: 16604082 PMCID: PMC1847776 DOI: 10.1038/nsmb1082] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2005] [Accepted: 03/07/2006] [Indexed: 11/09/2022]
Abstract
Alpha-sarcin ribotoxins comprise a unique family of ribonucleases that cripple the ribosome by catalyzing endoribonucleolytic cleavage of ribosomal RNA at a specific location in the sarcin/ricin loop (SRL). The SRL structure alone is cleaved site-specifically by the ribotoxin, but the ribosomal context enhances the reaction rate by several orders of magnitude. We show that, for the alpha-sarcin-like ribotoxin restrictocin, this catalytic advantage arises from favorable electrostatic interactions with the ribosome. Restrictocin binds at many sites on the ribosomal surface and under certain conditions cleaves the SRL with a second-order rate constant of 1.7 x 10(10) M(-1) s(-1), a value that matches the predicted frequency of random restrictocin-ribosome encounters. The results suggest a mechanism of target location whereby restrictocin encounters ribosomes randomly and diffuses within the ribosomal electrostatic field to the SRL. These studies show a role for electrostatics in protein-ribosome recognition.
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Affiliation(s)
- Alexei V Korennykh
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA
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49
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Wijaya K, Tri Wahyuni E, Yoshioka N, Inoue H. Salt-dependent binding of iron(II) mixed-ligand complexes containing 1,10-phenanthroline and dipyrido[3,2-a:2′,3′-c]phenazine to calf thymus DNA. Biophys Chem 2006; 121:44-50. [PMID: 16442696 DOI: 10.1016/j.bpc.2005.12.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2005] [Revised: 12/21/2005] [Accepted: 12/21/2005] [Indexed: 10/25/2022]
Abstract
The salt-dependent binding of racemic iron(II) mixed-ligand complex containing 1,10-phenanthroline (phen) and dipyrido[3,2-a:2',3'-c]phenazine (dppz), [Fe(phen)2(dppz)]2+ to calf thymus DNA (ct-DNA) has been characterized by UV-VIS spectrophotometric titration. The equilibrium binding constant (Kb) of the iron(II) complex to ct-DNA decreases with the salt concentration in the solution. The slope, SK=(deltalog Kb/deltalog [Na2+]) has been found to be 0.49, suggesting that, in addition to intercalation, considerable electrostatic interaction is also involved in the ct-DNA binding of [Fe(phen)2(dppz)]2+. The calculation of non-electrostatic binding constant (Kt(o)) based on polyelectrolyte theory has revealed that the non-electrostatic contribution to the total binding constant (Kb) increases significantly with the increase in [Na+] and reaches 36% at 0.1 M NaCl. On the other hand, the contribution of the non-electrostatic binding free energy (DeltaGt(o)) to the total binding free energy change (DeltaGo) is considerably large, i.e. 87% at [Na+]=0.1 M, suggesting that the stabilization of the DNA binding is mostly due to the contribution of non-electrostatic process. Moreover, the effect of specific ligand substitutions on DeltaGo has been rigorously evaluated using the quantity DeltaDeltaGt(o), i.e. the difference in DeltaGt(o) relative to that of the parent iron(II) complex, [Fe(phen)3]2+, indicating that each substitution of phen by dip and dppz contributes 7.5 and 17.5 kJ mol(-1), respectively to more favorable ct-DNA binding.
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50
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Bauduin P, Nohmie F, Touraud D, Neueder R, Kunz W, Ninham BW. Hofmeister specific-ion effects on enzyme activity and buffer pH: Horseradish peroxidase in citrate buffer. J Mol Liq 2006. [DOI: 10.1016/j.molliq.2005.03.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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