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Somarathne RP, Amarasekara DL, Kariyawasam CS, Robertson HA, Mayatt R, Gwaltney SR, Fitzkee NC. Protein Binding Leads to Reduced Stability and Solvated Disorder in the Polystyrene Nanoparticle Corona. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2305684. [PMID: 38247186 PMCID: PMC11209821 DOI: 10.1002/smll.202305684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 01/03/2024] [Indexed: 01/23/2024]
Abstract
Understanding the conformation of proteins in the nanoparticle corona has important implications in how organisms respond to nanoparticle-based drugs. These proteins coat the nanoparticle surface, and their properties will influence the nanoparticle's interaction with cell targets and the immune system. While some coronas are thought to be disordered, two key unanswered questions are the degree of disorder and solvent accessibility. Here, a model is developed for protein corona disorder in polystyrene nanoparticles of varying size. For two different proteins, it is found that binding affinity decreases as nanoparticle size increases. The stoichiometry of binding, along with changes in the hydrodynamic size, supports a highly solvated, disordered protein corona anchored at a small number of attachment sites. The scaling of the stoichiometry versus nanoparticle size is consistent with disordered polymer dimensions. Moreover, it is found that proteins are destabilized less in the presence of larger nanoparticles, and hydrophobic exposure decreases at lower curvatures. The observations hold for proteins on flat polystyrene surfaces, which have the lowest hydrophobic exposure. The model provides an explanation for previous observations of increased amyloid fibrillation rates in the presence of larger nanoparticles, and it may rationalize how cell receptors can recognize protein disorder in therapeutic nanoparticles.
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Affiliation(s)
- Radha P Somarathne
- Department of Chemistry, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Dhanush L Amarasekara
- Department of Chemistry, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Chathuri S Kariyawasam
- Department of Chemistry, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Harley A Robertson
- Department of Chemistry, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Railey Mayatt
- Department of Chemistry, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Steven R Gwaltney
- Department of Chemistry, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, MS, 39762, USA
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2
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Upadhyay V, Lucas A, Patrick C, Mallela KMG. Isothermal titration calorimetry and surface plasmon resonance methods to probe protein-protein interactions. Methods 2024; 225:52-61. [PMID: 38492901 DOI: 10.1016/j.ymeth.2024.03.007] [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: 11/13/2023] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 03/18/2024] Open
Abstract
Isothermal titration calorimetry (ITC) and surface plasmon resonance (SPR) are two commonly used methods to probe biomolecular interactions. ITC can provide information about the binding affinity, stoichiometry, changes in Gibbs free energy, enthalpy, entropy, and heat capacity upon binding. SPR can provide information about the association and dissociation kinetics, binding affinity, and stoichiometry. Both methods can determine the nature of protein-protein interactions and help understand the physicochemical principles underlying complex biochemical pathways and communication networks. This methods article discusses the practical knowledge of how to set up and troubleshoot these two experiments with some examples.
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Affiliation(s)
- Vaibhav Upadhyay
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
| | - Alexandra Lucas
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
| | - Casey Patrick
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
| | - Krishna M G Mallela
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States.
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3
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Takemiya K, Wang S, Liu Y, Murthy N, Goodman MM, Taylor WR. Isothermal titration calorimetry analysis of the binding between the maltodextrin binding protein malE of Staphylococcus aureus with maltodextrins of various lengths. Biochem Biophys Res Commun 2024; 695:149467. [PMID: 38211531 PMCID: PMC10842747 DOI: 10.1016/j.bbrc.2023.149467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/12/2023] [Accepted: 12/30/2023] [Indexed: 01/13/2024]
Abstract
Staphylococcus aureus (S. aureus), a Gram-positive bacterium, causes a wide range of infections, and diagnosis at an early stage is challenging. Targeting the maltodextrin transporter has emerged as a promising strategy for imaging bacteria and has been able to image a wide range of bacteria including S. aureus. However, little is known about the maltodextrin transporter in S. aureus, and this prevents new S. aureus specific ligands for the maltodextrin transporter from being developed. In Gram-positive bacteria, including S. aureus, the first step of maltodextrin transport is the binding of the maltodextrin-binding protein malE to maltodextrins. Thus, understanding the binding affinity and characteristics of malE from S. aureus is important to developing efficient maltodextrin-based imaging probes. We evaluated the affinity of malE of S. aureus to maltodextrins of various lengths. MalE of S. aureus (SAmalE) was expressed in E. coli BL21(DE3) and purified by Ni-NTA resin. The affinities of SAmalE to maltodextrins were evaluated with isothermal titration calorimetry. SAmalE has low affinity to maltose but binds to maltotriose and longer maltodextrins up to maltoheptaose with affinities up to Ka = 9.02 ± 0.49 × 105 M-1. SAmalE binding to maltotriose-maltoheptaose was exothermic and fit a single-binding site model. The van't Hoff enthalpy in the binding reaction of SAmalE with maltotriose was 9.9 ± 1.3 kcal/mol, and the highest affinity of SAmalE was observed with maltotetraose with Ka = 9.02 ± 0.49 × 105 M-1. In the plot of ΔH-T*ΔS, the of Enthalpy-Entropy Compensation effect was observed in binding reaction of SAmalE to maltodextrins. Acarbose and maltotetraiol bind with SAmalE indicating that SAmalE is tolerant of modifications on both the reducing and non-reducing ends of maltodextrins. Our results show that unlike ECmalE and similar to the maltodextrin binding protein of Streptococci, SAmalE primarily binds to maltodextrins via hydrogen bonds. This is distinct from the maltodextrin binding protein of Streptococci, SAmalE that binds to maltotetraiol with high affinity. Understanding the binding characteristics and tolerance to maltodextrins modifications by maltodextrin binding proteins will hopefully provide the basis for developing bacterial species-specific maltodextrin-based imaging probes.
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Affiliation(s)
- Kiyoko Takemiya
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, 1750 Haygood Dr. NE, Atlanta, GA, 30322, USA.
| | - Shelly Wang
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, 1750 Haygood Dr. NE, Atlanta, GA, 30322, USA
| | - Yu Liu
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, 1750 Haygood Dr. NE, Atlanta, GA, 30322, USA
| | - Niren Murthy
- Department of Bioengineering, Stanley Hall 306 University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Mark M Goodman
- Department of Radiology and Imaging Sciences, School of Medicine, Emory University, 1364 Clifton Road NE, Atlanta, GA, 30322, USA; Center for Systems Imaging, Emory University, 1364 Clifton Rd NE, Atlanta, 30322, Georgia
| | - W Robert Taylor
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, 1750 Haygood Dr. NE, Atlanta, GA, 30322, USA; Joseph Maxwell Cleland Atlanta VA Medical Center, 1670 Clairmont Road, Decatur, GA, 30033, USA; Wallace H. Coulter Department of Biomedical Engineering School of Medicine, Emory University, 1750 Haygood Dr. NE, Atlanta, GA, 30322, USA
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4
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Metwally K, Abo-Dya NE, Hamdan AME, Alrashidi MN, Alturki MS, Aly OM, Aljoundi A, Ibrahim M, Soliman MES. Investigation of Simultaneous and Sequential Cooperative Homotropic Inhibitor Binding to the Catalytic Chamber of SARS-CoV-2 RNA-dependent RNA Polymerase (RdRp). Cell Biochem Biophys 2023; 81:697-706. [PMID: 37658974 DOI: 10.1007/s12013-023-01163-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2023] [Indexed: 09/05/2023]
Abstract
In our previous report, the unique architecture of the catalytic chamber of the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), which harbours two distinctive binding sites, was fully characterized at molecular level. The significant differences in the two binding sites BS1 and BS2 in terms of binding pockets motif, as well as the preferential affinities of eight anti-viral drugs to each of the two binding sites were described. Recent Cryogenic Electron Microscopy (Cryo-EM) studies on the RdRp revealed that two suramin molecules, a SARS-CoV-2 inhibitor, bind to RdRp in two different sites with distinctive interaction landscape. Here, we provide the first account of investigating the combined inhibitor binding to both binding sites, and whether the binding of two inhibitors molecules concurrently is "Cooperative binding" or not. It should be noted that the binding of inhibitors to different sites do not necessary constitute mutually independent events, therefore, we investigated two scenarios to better understand cooperativity: simultaneous binding and sequential binding. It has been demonstrated by binding free energy calculations (MM/PBSA) and piecewise linear potential (PLP) interaction energy analysis that the co-binding of two suramin molecules is not cooperative in nature; rather, when compared to individual binding, both molecules adversely affect one another's binding affinities. This observation appeared to be primarily due to RdRp's rigidity, which prevented both ligands from fitting comfortably within the catalytic chamber. Instead, the suramin molecules showed a tendency to change their orientation within the binding pockets in order to maintain their binding to the protein, but at the expense of the ligand internal energies. Although co-binding resulted in the loss of several important key interactions, a few interactions were conserved, and these appear to be crucial in preserving the binding of ligands in the active site. The structural and mechanistic details of this study will be useful for future research on creating and developing RdRp inhibitors against SARS-CoV-2.
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Affiliation(s)
- Kamel Metwally
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Tabuk, Tabuk, 71491, Saudi Arabia.
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig, 44519, Egypt.
| | - Nader E Abo-Dya
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Tabuk, Tabuk, 71491, Saudi Arabia
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig, 44519, Egypt
| | - Ahmed M E Hamdan
- Department of Pharmacy Practice, Faculty of Pharmacy, University of Tabuk, Tabuk, 71491, Saudi Arabia
| | - Maram N Alrashidi
- Pharm D Program, Faculty of Pharmacy, University of Tabuk, Tabuk, 71491, Saudi Arabia
| | - Mansour S Alturki
- Department of Pharmaceutical Chemistry, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, Dammam, 34212, Saudi Arabia
| | - Omar M Aly
- Medicinal Chemistry Department Faculty of Pharmacy Port Said University, Port Said, 42526, Egypt
| | - Aimen Aljoundi
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Mahmoud Ibrahim
- CompChem Lab, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa.
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Broch F, El Hajji L, Pietrancosta N, Gautier A. Engineering of Tunable Allosteric-like Fluorogenic Protein Sensors. ACS Sens 2023; 8:3933-3942. [PMID: 37830919 DOI: 10.1021/acssensors.3c01536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Optical protein sensors that enable detection of relevant biomolecules of interest play central roles in biological research. Coupling fluorescent reporters with protein sensing units has enabled the development of a wide range of biosensors that recognize analytes with high selectivity. In these sensors, analyte recognition induces a conformational change in the protein sensing unit that can modulate the optical signal of the fluorescent reporter. Here, we explore various designs for the creation of tunable allosteric-like fluorogenic protein sensors through incorporation of sensing protein units within the chemogenetic fluorescence-activating and absorption-shifting tag (FAST) that selectively binds and stabilizes the fluorescent state of 4-hydroxybenzylidene rhodanine (HBR) analogs. Conformational coupling allowed us to design analyte-responsive optical protein sensors through allosteric-like modulation of fluorogen binding.
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Affiliation(s)
- Fanny Broch
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
| | - Lina El Hajji
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
| | - Nicolas Pietrancosta
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
- Neuroscience Paris Seine-Institut de Biologie Paris Seine (NPS-IBPS) INSERM, CNRS, Sorbonne Université, 75005 Paris, France
| | - Arnaud Gautier
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
- Institut Universitaire de France, 75231 Paris, France
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6
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Kimata-Ariga Y, Shinkoda R, Abe R. Inter-domain interaction of ferredoxin-NADP+ reductase important for the negative cooperativity by ferredoxin and NADP(H). J Biochem 2023; 174:327-334. [PMID: 37311065 DOI: 10.1093/jb/mvad046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/26/2023] [Accepted: 06/09/2023] [Indexed: 06/15/2023] Open
Abstract
Ferredoxin-NADP+ reductase (FNR) in plants receives electrons from ferredoxin (Fd) and converts NADP+ to NADPH. The affinity between FNR and Fd is weakened by the allosteric binding of NADP(H) on FNR, which is considered as a part of negative cooperativity. We have been investigating the molecular mechanism of this phenomenon and proposed that the NADP(H)-binding signal is transferred to the Fd-binding region across the two domains of FNR, NADP(H)-binding domain and FAD-binding domain. In this study, we analyzed the effect of altering the inter-domain interaction of FNR on the negative cooperativity. Four site-directed FNR mutants at the inter-domain region were prepared, and their NADPH-dependent changes in the Km for Fd and physical binding ability to Fd were investigated. Two mutants, in which an inter-domain hydrogen bond was changed to a disulfide bond (FNR D52C/S208C) and an inter-domain salt bridge was lost (FNR D104N), were shown to suppress the negative cooperativity by using kinetic analysis and Fd-affinity chromatography. These results showed that the inter-domain interaction of FNR is important for the negative cooperativity, suggesting that the allosteric NADP(H)-binding signal is transferred to Fd-binging region by conformational changes involving inter-domain interactions of FNR.
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Affiliation(s)
- Yoko Kimata-Ariga
- Department of Biological Chemistry, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yoshida, Yamaguchi 753-8515, Japan
| | - Rina Shinkoda
- Department of Biological Chemistry, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yoshida, Yamaguchi 753-8515, Japan
| | - Ryuya Abe
- Department of Biological Chemistry, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yoshida, Yamaguchi 753-8515, Japan
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7
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Ashaduzzaman M, Lingkon K, De Silva AJ, Bellizzi JJ. Crystallographic and thermodynamic evidence of negative cooperativity of flavin and tryptophan binding in the flavin-dependent halogenases AbeH and BorH. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554356. [PMID: 37662313 PMCID: PMC10473636 DOI: 10.1101/2023.08.22.554356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The flavin-dependent halogenase AbeH produces 5-chlorotryptophan in the biosynthetic pathway of the chlorinated bisindole alkaloid BE-54017. We report that in vitro, AbeH (assisted by the flavin reductase AbeF) can chlorinate and brominate tryptophan as well as other indole derivatives and substrates with phenyl and quinoline groups. We solved the X-ray crystal structures of AbeH alone and complexed with FAD, as well as crystal structures of the tryptophan-6-halogenase BorH alone, in complex with 6-chlorotryptophan, and in complex with FAD and tryptophan. Partitioning of FAD and tryptophan into different chains of BorH and failure to incorporate tryptophan into AbeH/FAD crystals suggested that flavin and tryptophan binding are negatively coupled in both proteins. ITC and fluorescence quenching experiments confirmed the ability of both AbeH and BorH to form binary complexes with FAD or tryptophan and the inability of tryptophan to bind to AbeH/FAD or BorH/FAD complexes. FAD could not bind to BorH/tryptophan complexes, but FAD appears to displace tryptophan from AbeH/tryptophan complexes in an endothermic entropically-driven process.
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Affiliation(s)
- Md Ashaduzzaman
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo OH 43606
| | - Kazi Lingkon
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo OH 43606
| | - Aravinda J De Silva
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo OH 43606
| | - John J Bellizzi
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo OH 43606
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8
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Somarathne RP, Amarasekara DL, Kariyawasam CS, Robertson HA, Mayatt R, Fitzkee NC. Protein Binding Leads to Reduced Stability and Solvated Disorder in the Polystyrene Nanoparticle Corona. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.06.548033. [PMID: 37461509 PMCID: PMC10350082 DOI: 10.1101/2023.07.06.548033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Understanding the conformation of proteins in the nanoparticle corona has important implications in how organisms respond to nanoparticle-based drugs. These proteins coat the nanoparticle surface, and their properties will influence the nanoparticle's interaction with cell targets and the immune system. While some coronas are thought to be disordered, two key unanswered questions are the degree of disorder and solvent accessibility. Here, using a comprehensive thermodynamic approach, along with supporting spectroscopic experiments, we develop a model for protein corona disorder in polystyrene nanoparticles of varying size. For two different proteins, we find that binding affinity decreases as nanoparticle size increases. The stoichiometry of binding, along with changes in the hydrodynamic size, support a highly solvated, disordered protein corona anchored at a small number of enthalpically-driven attachment sites. The scaling of the stoichiometry vs. nanoparticle size is consistent disordered polymer dimensions. Moreover, we find that proteins are destabilized less severely in the presence of larger nanoparticles, and this is supported by measurements of hydrophobic exposure, which becomes less pronounced at lower curvatures. Our observations hold for flat polystyrene surfaces, which, when controlled for total surface area, have the lowest hydrophobic exposure of all systems. Our model provides an explanation for previous observations of increased amyloid fibrillation rates in the presence of larger nanoparticles, and it may rationalize how cell receptors can recognize protein disorder in therapeutic nanoparticles.
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Affiliation(s)
- Radha P. Somarathne
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762 USA
| | | | | | - Harley A. Robertson
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762 USA
| | - Railey Mayatt
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762 USA
| | - Nicholas C. Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762 USA
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9
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Novo N, Romero-Tamayo S, Marcuello C, Boneta S, Blasco-Machin I, Velázquez-Campoy A, Villanueva R, Moreno-Loshuertos R, Lostao A, Medina M, Ferreira P. Beyond a platform protein for the degradosome assembly: The Apoptosis-Inducing Factor as an efficient nuclease involved in chromatinolysis. PNAS NEXUS 2022; 2:pgac312. [PMID: 36845352 PMCID: PMC9944232 DOI: 10.1093/pnasnexus/pgac312] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022]
Abstract
The Apoptosis-Inducing Factor (AIF) is a moonlighting flavoenzyme involved in the assembly of mitochondrial respiratory complexes in healthy cells, but also able to trigger DNA cleavage and parthanatos. Upon apoptotic-stimuli, AIF redistributes from the mitochondria to the nucleus, where upon association with other proteins such as endonuclease CypA and histone H2AX, it is proposed to organize a DNA-degradosome complex. In this work, we provide evidence for the molecular assembly of this complex as well as for the cooperative effects among its protein components to degrade genomic DNA into large fragments. We have also uncovered that AIF has nuclease activity that is stimulated in the presence of either Mg2+ or Ca2+. Such activity allows AIF by itself and in cooperation with CypA to efficiently degrade genomic DNA. Finally, we have identified TopIB and DEK motifs in AIF as responsible for its nuclease activity. These new findings point, for the first time, to AIF as a nuclease able to digest nuclear dsDNA in dying cells, improving our understanding of its role in promoting apoptosis and opening paths for the development of new therapeutic strategies.
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Affiliation(s)
- Nerea Novo
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza 50009, Spain,Instituto de Biocomputación y Física de Sistemas Complejos, BIFI (GBsC-CSIC Joint Unit), Universidad de Zaragoza, Zaragoza 50018, Spain
| | - Silvia Romero-Tamayo
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza 50009, Spain,Instituto de Biocomputación y Física de Sistemas Complejos, BIFI (GBsC-CSIC Joint Unit), Universidad de Zaragoza, Zaragoza 50018, Spain
| | - Carlos Marcuello
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain,Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain
| | - Sergio Boneta
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza 50009, Spain
| | - Irene Blasco-Machin
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza 50009, Spain
| | - Adrián Velázquez-Campoy
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza 50009, Spain,Instituto de Biocomputación y Física de Sistemas Complejos, BIFI (GBsC-CSIC Joint Unit), Universidad de Zaragoza, Zaragoza 50018, Spain,Aragón Institute for Health Research (IIS Aragón), Zaragoza, Zaragoza 50009, Spain,Biomedical Research Networking Centre for Liver and Digestive Diseases (CIBERehd), Madrid 28029, Spain
| | - Raquel Villanueva
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza 50009, Spain,Instituto de Biocomputación y Física de Sistemas Complejos, BIFI (GBsC-CSIC Joint Unit), Universidad de Zaragoza, Zaragoza 50018, Spain
| | - Raquel Moreno-Loshuertos
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza 50009, Spain,Instituto de Biocomputación y Física de Sistemas Complejos, BIFI (GBsC-CSIC Joint Unit), Universidad de Zaragoza, Zaragoza 50018, Spain
| | - Anabel Lostao
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain,Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain,Fundación ARAID, Aragón, Zaragoza 50018, Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza 50009, Spain,Instituto de Biocomputación y Física de Sistemas Complejos, BIFI (GBsC-CSIC Joint Unit), Universidad de Zaragoza, Zaragoza 50018, Spain
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10
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Inter-Site Cooperativity of Calmodulin N-Terminal Domain and Phosphorylation Synergistically Improve the Affinity and Selectivity for Uranyl. Biomolecules 2022; 12:biom12111703. [DOI: 10.3390/biom12111703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/10/2022] [Accepted: 11/12/2022] [Indexed: 11/19/2022] Open
Abstract
Uranyl–protein interactions participate in uranyl trafficking or toxicity to cells. In addition to their qualitative identification, thermodynamic data are needed to predict predominant mechanisms that they mediate in vivo. We previously showed that uranyl can substitute calcium at the canonical EF-hand binding motif of calmodulin (CaM) site I. Here, we investigate thermodynamic properties of uranyl interaction with site II and with the whole CaM N-terminal domain by spectrofluorimetry and ITC. Site II has an affinity for uranyl about 10 times lower than site I. Uranyl binding at site I is exothermic with a large enthalpic contribution, while for site II, the enthalpic contribution to the Gibbs free energy of binding is about 10 times lower than the entropic term. For the N–terminal domain, macroscopic binding constants for uranyl are two to three orders of magnitude higher than for calcium. A positive cooperative process driven by entropy increases the second uranyl-binding event as compared with the first one, with ΔΔG = −2.0 ± 0.4 kJ mol−1, vs. ΔΔG = −6.1 ± 0.1 kJ mol−1 for calcium. Site I phosphorylation largely increases both site I and site II affinity for uranyl and uranyl-binding cooperativity. Combining site I phosphorylation and site II Thr7Trp mutation leads to picomolar dissociation constants Kd1 = 1.7 ± 0.3 pM and Kd2 = 196 ± 21 pM at pH 7. A structural model obtained by MD simulations suggests a structural role of site I phosphorylation in the affinity modulation.
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11
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Moreno MJ, Loura LMS, Martins J, Salvador A, Velazquez-Campoy A. Analysis of the Equilibrium Distribution of Ligands in Heterogeneous Media–Approaches and Pitfalls. Int J Mol Sci 2022; 23:ijms23179757. [PMID: 36077155 PMCID: PMC9478965 DOI: 10.3390/ijms23179757] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 12/02/2022] Open
Abstract
The equilibrium distribution of small molecules (ligands) between binding agents in heterogeneous media is an important property that determines their activity. Heterogeneous systems containing proteins and lipid membranes are particularly relevant due to their prevalence in biological systems, and their importance to ligand distribution, which, in turn, is crucial to ligand’s availability and biological activity. In this work, we review several approaches and formalisms for the analysis of the equilibrium distribution of ligands in the presence of proteins, lipid membranes, or both. Special attention is given to common pitfalls in the analysis, with the establishment of the validity limits for the distinct approaches. Due to its widespread use, special attention is given to the characterization of ligand binding through the analysis of Stern–Volmer plots of protein fluorescence quenching. Systems of increasing complexity are considered, from proteins with single to multiple binding sites, from ligands interacting with proteins only to biomembranes containing lipid bilayers and membrane proteins. A new formalism is proposed, in which ligand binding is treated as a partition process, while considering the saturation of protein binding sites. This formalism is particularly useful for the characterization of interaction with membrane proteins.
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Affiliation(s)
- Maria João Moreno
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal
- Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
- Correspondence:
| | - Luís M. S. Loura
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal
- Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Jorge Martins
- Centro de Ciências do Mar (CCMAR/CIMAR, LA) and DCBB-FCT, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Armindo Salvador
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal
- CNC—Center for Neuroscience and Cell Biology, 3004-504 Coimbra, Portugal
- Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Adrian Velazquez-Campoy
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Instituto de Investigación Sanitaria de Aragón (IIS Aragon), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas Digestivas (CIBERehd), 28029 Madrid, Spain
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12
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Beyett TS, To C, Heppner DE, Rana JK, Schmoker AM, Jang J, De Clercq DJH, Gomez G, Scott DA, Gray NS, Jänne PA, Eck MJ. Molecular basis for cooperative binding and synergy of ATP-site and allosteric EGFR inhibitors. Nat Commun 2022; 13:2530. [PMID: 35534503 PMCID: PMC9085736 DOI: 10.1038/s41467-022-30258-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/19/2022] [Indexed: 12/22/2022] Open
Abstract
Lung cancer is frequently caused by activating mutations in the epidermal growth factor receptor (EGFR). Allosteric EGFR inhibitors offer promise as the next generation of therapeutics, as they are unaffected by common ATP-site resistance mutations and synergize with the drug osimertinib. Here, we examine combinations of ATP-competitive and allosteric inhibitors to better understand the molecular basis for synergy. We identify a subset of irreversible EGFR inhibitors that display positive binding cooperativity and synergy with the allosteric inhibitor JBJ-04-125-02 in several EGFR variants. Structural analysis of these complexes reveals conformational changes occur mainly in the phosphate-binding loop (P-loop). Mutation of F723 in the P-loop reduces cooperative binding and synergy, supporting a mechanism in which F723-mediated contacts between the P-loop and the allosteric inhibitor are critical for synergy. These structural and mechanistic insights will aid in the identification and development of additional inhibitor combinations with potential clinical value. Acquired drug resistance is common during chemotherapy. Here, the authors describe the structural basis and molecular mechanism by which allosteric and clinically approved, ATP-competitive inhibitors of EGFR synergize to overcome resistance in lung cancer.
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13
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Wani TA, Bakheit AH, Zargar S, Alamery S. Mechanistic competitive binding interaction study between olmutinib and colchicine with model transport protein using spectroscopic and computer simulation approaches. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2022.113794] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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14
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Rajakumara E, Abhishek S, Nitin K, Saniya D, Bajaj P, Schwaneberg U, Davari MD. Structure and Cooperativity in Substrate-Enzyme Interactions: Perspectives on Enzyme Engineering and Inhibitor Design. ACS Chem Biol 2022; 17:266-280. [PMID: 35041385 DOI: 10.1021/acschembio.1c00500] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Enzyme-based synthetic chemistry provides a green way to synthesize industrially important chemical scaffolds and provides incomparable substrate specificity and unmatched stereo-, regio-, and chemoselective product formation. However, using biocatalysts at an industrial scale has its challenges, like their narrow substrate scope, limited stability in large-scale one-pot reactions, and low expression levels. These limitations can be overcome by engineering and fine-tuning these biocatalysts using advanced protein engineering methods. A detailed understanding of the enzyme structure and catalytic mechanism and its structure-function relationship, cooperativity in binding of substrates, and dynamics of substrate-enzyme-cofactor complexes is essential for rational enzyme engineering for a specific purpose. This Review covers all these aspects along with an in-depth categorization of various industrially and pharmaceutically crucial bisubstrate enzymes based on their reaction mechanisms and their active site and substrate/cofactor-binding site structures. As the bisubstrate enzymes constitute around 60% of the known industrially important enzymes, studying their mechanism of actions and structure-activity relationship gives significant insight into deciding the targets for protein engineering for developing industrial biocatalysts. Thus, this Review is focused on providing a comprehensive knowledge of the bisubstrate enzymes' structure, their mechanisms, and protein engineering approaches to develop them into industrial biocatalysts.
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Affiliation(s)
- Eerappa Rajakumara
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Suman Abhishek
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Kulhar Nitin
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Dubey Saniya
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Priyanka Bajaj
- National Institute of Pharmaceutical Education and Research (NIPER), NH-44, Balanagar, Hyderabad 500037, India
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany
| | - Mehdi D. Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
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15
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Greytak AB, Abiodun SL, Burrell JM, Cook EN, Jayaweera NP, Islam MM, Shaker AE. Thermodynamics of nanocrystal–ligand binding through isothermal titration calorimetry. Chem Commun (Camb) 2022; 58:13037-13058. [DOI: 10.1039/d2cc05012a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Manipulations of nanocrystal (NC) surfaces have propelled the applications of colloidal NCs across various fields such as bioimaging, catalysis, electronics, and sensing applications.
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Affiliation(s)
- Andrew B. Greytak
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Sakiru L. Abiodun
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Jennii M. Burrell
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Emily N. Cook
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Nuwanthaka P. Jayaweera
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Md Moinul Islam
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Abdulla E Shaker
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
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16
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de Vink PJ, Koops AA, D'Arrigo G, Cruciani G, Spyrakis F, Brunsveld L. Cooperativity as quantification and optimization paradigm for nuclear receptor modulators. Chem Sci 2022; 13:2744-2752. [PMID: 35340861 PMCID: PMC8890100 DOI: 10.1039/d1sc06426f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/19/2022] [Indexed: 01/01/2023] Open
Abstract
A cooperativity framework describes the formation of nuclear receptor ternary complexes and deconvolutes ligand and cofactor binding into intrinsic affinities and a cooperativity factor, providing a conceptually new understanding of NR modulation.
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Affiliation(s)
- Pim J. de Vink
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P. O. Box 513, 5600MB Eindhoven, The Netherlands
| | - Auke A. Koops
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P. O. Box 513, 5600MB Eindhoven, The Netherlands
| | - Giulia D'Arrigo
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P. O. Box 513, 5600MB Eindhoven, The Netherlands
- Department of Drug Science and Technology, University of Turin, via Giuria 9, 10125 Turin, Italy
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123, Perugia, Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, via Giuria 9, 10125 Turin, Italy
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P. O. Box 513, 5600MB Eindhoven, The Netherlands
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17
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Hóbor F, Hegedüs Z, Ibarra AA, Petrovicz VL, Bartlett GJ, Sessions RB, Wilson AJ, Edwards TA. Understanding p300-transcription factor interactions using sequence variation and hybridization. RSC Chem Biol 2022; 3:592-603. [PMID: 35656479 PMCID: PMC9092470 DOI: 10.1039/d2cb00026a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/10/2022] [Indexed: 11/21/2022] Open
Abstract
The hypoxic response is central to cell function and plays a significant role in the growth and survival of solid tumours. HIF-1 regulates the hypoxic response by activating over 100...
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Affiliation(s)
- Fruzsina Hóbor
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Zsófia Hegedüs
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H-6720 Szeged Hungary
| | - Amaurys Avila Ibarra
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
| | - Vencel L Petrovicz
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H-6720 Szeged Hungary
| | - Gail J Bartlett
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Richard B Sessions
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
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18
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Molecular mechanism of glycolytic flux control intrinsic to human phosphoglycerate kinase. Proc Natl Acad Sci U S A 2021; 118:2112986118. [PMID: 34893542 DOI: 10.1073/pnas.2112986118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2021] [Indexed: 01/17/2023] Open
Abstract
Glycolysis plays a fundamental role in energy production and metabolic homeostasis. The intracellular [adenosine triphosphate]/[adenosine diphosphate] ([ATP]/[ADP]) ratio controls glycolytic flux; however, the regulatory mechanism underlying reactions catalyzed by individual glycolytic enzymes enabling flux adaptation remains incompletely understood. Phosphoglycerate kinase (PGK) catalyzes the reversible phosphotransfer reaction, which directly produces ATP in a near-equilibrium step of glycolysis. Despite extensive studies on the transcriptional regulation of PGK expression, the mechanism in response to changes in the [ATP]/[ADP] ratio remains obscure. Here, we report a protein-level regulation of human PGK (hPGK) by utilizing the switching ligand-binding cooperativities between adenine nucleotides and 3-phosphoglycerate (3PG). This was revealed by nuclear magnetic resonance (NMR) spectroscopy at physiological salt concentrations. MgADP and 3PG bind to hPGK with negative cooperativity, whereas MgAMPPNP (a nonhydrolyzable ATP analog) and 3PG bind to hPGK with positive cooperativity. These opposite cooperativities enable a shift between different ligand-bound states depending on the intracellular [ATP]/[ADP] ratio. Based on these findings, we present an atomic-scale description of the reaction scheme for hPGK under physiological conditions. Our results indicate that hPGK intrinsically modulates its function via ligand-binding cooperativities that are finely tuned to respond to changes in the [ATP]/[ADP] ratio. The alteration of ligand-binding cooperativities could be one of the self-regulatory mechanisms for enzymes in bidirectional pathways, which enables rapid adaptation to changes in the intracellular environment.
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19
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Kimata-Ariga Y, Morihisa R. Functional analyses of plasmodium ferredoxin Asp97Tyr mutant related to artemisinin resistance of human malaria parasites. J Biochem 2021; 170:521-529. [PMID: 34415329 DOI: 10.1093/jb/mvab070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/01/2021] [Indexed: 11/14/2022] Open
Abstract
Mutation of Asp97Tyr in the C-terminal region of ferredoxin (PfFd) in the apicoplast of malaria parasites was recently reported to be strongly related to the parasite's resistance to the frontline antimalarial drug, artemisinin. We previously showed that the aromatic amino acid in the C-terminal region of PfFd is important for the interaction with its electron transfer partner, Fd-NADP+ reductase (PfFNR). Here, the importance of the aromatic-aromatic interaction between PfFd and PfFNR was shown using the kinetic analysis of the electron transfer reaction of site-directed mutants of PfFNR with PfFd. Mutation of Asp97Tyr of PfFd was further shown to increase the affinity with PfFNR by the measurements of the dissociation constant (Kd) using tryptophan fluorescence titration and the Michaelis constant (Km) in the kinetic analysis with PfFNRs. Diaphorase activity of PfFNR was inhibited by D97Y PfFd at lower concentration as compared to wild-type PfFd. Ascorbate radical scavenging activity of PfFd and electron transfer activity to a heterogeneous Fd-dependent enzyme was lower with D97Y PfFd than that of wild-type PfFd. These results showed that D97Y mutant of PfFd binds to PfFNR tighter than wild-type PfFd, and thus may suppress the function of PfFNR which could be associated with the action of artemisinin.
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Affiliation(s)
- Yoko Kimata-Ariga
- Department of Biological Chemistry, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan
| | - Rena Morihisa
- Department of Biological Chemistry, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan
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20
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Choudhury A, Khanppnavar B, Datta S. Crystallographic and biophysical analyses of Pseudomonas aeruginosa ketopantoate reductase: Implications of ligand induced conformational changes in cofactor recognition. Biochimie 2021; 193:103-114. [PMID: 34757166 DOI: 10.1016/j.biochi.2021.10.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 10/15/2021] [Accepted: 10/28/2021] [Indexed: 11/26/2022]
Abstract
Ketopantoate reductases (KPRs) catalyse NADPH-dependent reduction of ketopantoate to pantoate, the rate-limiting step of pantothenate biosynthetic pathway. In our recent study, we showed KPRs are under dynamic evolutionary selection and highlighted the possible role of ordered substrate binding kinetics for cofactor selection. To further delineate this at molecular level, here, we perform X-ray crystallographic and biophysical analyses of KPR in presence of non-canonical cofactor NAD+. In our structure, NAD+ was found to be highly dynamic in catalytic pocket of KPR, which could attain stable conformation only in presence of ketopantoate. Further, isothermal calorimetric (ITC) titrations showed that affinity of KPR for ketopantoate is higher in presence of NADP+ than in presence of NAD+ and lowest in absence of redox cofactors. In sum, our results clearly depict two modes of redox cofactor selections in KPRs, firstly by specific salt bridge interactions with unique phosphate moiety of NADP+ and secondly via ordered sequential heterotrophic cooperative binding of substrate ketopantoate.
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Affiliation(s)
- Arkaprabha Choudhury
- Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology (CSIR-IICB), Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), India
| | - Basavraj Khanppnavar
- Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology (CSIR-IICB), Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), India
| | - Saumen Datta
- Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology (CSIR-IICB), Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), India.
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21
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Chikuma Y, Miyata M, Lee YH, Hase T, Kimata-Ariga Y. Molecular mechanism of negative cooperativity of ferredoxin-NADP+ reductase by ferredoxin and NADP(H): involvement of a salt bridge between Asp60 of ferredoxin and Lys33 of FNR. Biosci Biotechnol Biochem 2021; 85:860-865. [PMID: 33693505 DOI: 10.1093/bbb/zbaa102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/03/2020] [Indexed: 11/13/2022]
Abstract
Ferredoxin-NADP+ reductase (FNR) in plants receives electrons from ferredoxin (Fd) and converts NADP+ to NADPH at the end of the photosynthetic electron transfer chain. We previously showed that the interaction between FNR and Fd was weakened by the allosteric binding of NADP(H) on FNR, which was considered as a part of negative cooperativity. In this study, we investigated the molecular mechanism of this phenomenon using maize FNR and Fd, as the three-dimensional structure of this Fd:FNR complex is available. NMR chemical shift perturbation analysis identified a site (Asp60) on Fd molecule which was selectively affected by NADP(H) binding on FNR. Asp60 of Fd forms a salt bridge with Lys33 of FNR in the complex. Site-specific mutants of FdD60 and FNRK33 suppressed the negative cooperativity (downregulation of the interaction between FNR and Fd by NADPH), indicating that a salt bridge between FdD60 and FNRK33 is involved in this negative cooperativity.
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Affiliation(s)
- Yutaro Chikuma
- Division of Protein chemistry, Institute for Protein Research, Osaka University, Suita, Japan
| | - Masayuki Miyata
- Department of Biological Chemistry, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yoshida, Japan
| | - Young-Ho Lee
- Division of Protein chemistry, Institute for Protein Research, Osaka University, Suita, Japan
| | - Toshiharu Hase
- Division of Protein chemistry, Institute for Protein Research, Osaka University, Suita, Japan
| | - Yoko Kimata-Ariga
- Department of Biological Chemistry, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yoshida, Japan
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22
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Anoz-Carbonell E, Rivero M, Polo V, Velázquez-Campoy A, Medina M. Human riboflavin kinase: Species-specific traits in the biosynthesis of the FMN cofactor. FASEB J 2020; 34:10871-10886. [PMID: 32649804 DOI: 10.1096/fj.202000566r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/26/2020] [Accepted: 06/05/2020] [Indexed: 11/11/2022]
Abstract
Human riboflavin kinase (HsRFK) catalyzes vitamin B2 (riboflavin) phosphorylation to flavin mononucleotide (FMN), obligatory step in flavin cofactor synthesis. HsRFK expression is related to protection from oxidative stress, amyloid-β toxicity, and some malignant cancers progression. Its downregulation alters expression profiles of clock-controlled metabolic-genes and destroys flavins protection on stroke treatments, while its activity reduction links to protein-energy malnutrition and thyroid hormones decrease. We explored specific features of the mechanisms underlying the regulation of HsRFK activity, showing that both reaction products regulate it through competitive inhibition. Fast-kinetic studies show that despite HsRFK binds faster and preferably the reaction substrates, the complex holding both products is kinetically most stable. An intricate ligand binding landscape with all combinations of substrates/products competing with the catalytic complex and exhibiting moderate cooperativity is also presented. These data might contribute to better understanding the molecular bases of pathologies coursing with aberrant HsRFK availability, and envisage that interaction with its client-apoproteins might favor FMN release. Finally, HsRFK parameters differ from those of the so far evaluated bacterial counterparts, reinforcing the idea of species-specific mechanisms in RFK catalysis. These observations support HsRFK as potential therapeutic target because of its key functions, while also envisage bacterial RFK modules as potential antimicrobial targets.
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Affiliation(s)
- Ernesto Anoz-Carbonell
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
| | - Maribel Rivero
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Victor Polo
- Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain.,Departamento de Química Física, Universidad de Zaragoza, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain.,Fundación ARAID, Diputación General de Aragón, Zaragoza, Spain.,Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain.,Biomedical Research Networking Centre for Liver and Digestive Diseases (CIBERehd), Madrid, Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
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23
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Srivastava AP, Mishra N, Prasad RLA, Rajesh P, Knaff DB. Thermodynamics of ferredoxin binding to cyanobacterial nitrate reductase. PHOTOSYNTHESIS RESEARCH 2020; 144:73-84. [PMID: 32222887 DOI: 10.1007/s11120-020-00738-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/20/2020] [Indexed: 06/10/2023]
Abstract
The role of the seven negatively charged amino acids of Synechocystis sp. PCC 6803 ferredoxin (Fd), i.e., Glu29, Glu30, Asp60, Asp65, Asp66, Glu92, and Glu93, predicted to form complex with nitrate reductase (NR), was investigated using site-directed mutagenesis and isothermal titration calorimetry (ITC). These experiments identified four Fd amino acids, i.e., Glu29, Asp60, Glu92, and Glu93, that are essential for the Fd binding and efficient electron transfer to the NR. ITC measurements showed that the most likely stoichiometry for the wild-type NR/wild-type Fd complex is 1:1, a Kd value 4.7 μM for the complex at low ionic strength residues and both the enthalpic and entropic components are associated with complex formation. ITC titrations of wild-type NR with four Fd variants, E29N, D60N, E92Q, and E93N demonstrated that the complex formation, although favorable, was less energetically favorable when compared to complex formation between the two wild-type proteins, suggesting that these negatively charged Fd residues at these positions are important for the effective and productive interaction with wild-type enzyme.
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Affiliation(s)
- Anurag P Srivastava
- Department of Life Sciences, Garden City University, Bangalore, Karnataka, India.
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA.
| | - Neelam Mishra
- Department of Botany, St. Joseph's College, Bangalore, Karnataka, India
| | | | - Preethi Rajesh
- Department of Life Sciences, Garden City University, Bangalore, Karnataka, India.
| | - David B Knaff
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
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Cotrina EY, Gimeno A, Llop J, Jiménez-Barbero J, Quintana J, Valencia G, Cardoso I, Prohens R, Arsequell G. Calorimetric Studies of Binary and Ternary Molecular Interactions between Transthyretin, Aβ Peptides, and Small-Molecule Chaperones toward an Alternative Strategy for Alzheimer's Disease Drug Discovery. J Med Chem 2020; 63:3205-3214. [PMID: 32124607 PMCID: PMC7115756 DOI: 10.1021/acs.jmedchem.9b01970] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
Transthyretin
(TTR) modulates the deposition, processing, and toxicity
of Abeta (Aβ) peptides. We have shown that this effect is enhanced
in mice by treatment with small molecules such as iododiflunisal (IDIF, 4), a good TTR stabilizer. Here, we describe the thermodynamics
of the formation of binary and ternary complexes among TTR, Aβ(1–42)
peptide, and TTR stabilizers using isothermal titration calorimetry
(ITC). A TTR/Aβ(1–42) (1:1)
complex with a dissociation constant of Kd = 0.94 μM is formed; with IDIF
(4), this constant improves up to Kd = 0.32 μM, indicating
the presence of a ternary complex TTR/IDIF/Aβ(1–42).
However, with the drugs diflunisal (1) or Tafamidis (2), an analogous chaperoning effect could not be observed.
Similar phenomena could be recorded with the shorter peptide Aβ(12–28)
(7). We propose the design of a simple assay system for
the search of other chaperones that behave like IDIF and may become
potential candidate drugs for Alzheimer’s disease (AD).
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Affiliation(s)
- Ellen Y Cotrina
- Institut de Quı́mica Avançada de Catalunya (I.Q.A.C.-C.S.I.C.), 08034 Barcelona, Spain
| | - Ana Gimeno
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Spain
| | - Jordi Llop
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), 20014 San Sebastian, Spain
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Spain.,Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 13, 48009 Bilbao, Spain.,Department of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, 48940 Leioa, Bizkaia, Spain
| | - Jordi Quintana
- Research Programme on Biomedical Informatics, Universitat Pompeu Fabra (UPF-IMIM), 08003 Barcelona, Spain
| | - Gregorio Valencia
- Institut de Quı́mica Avançada de Catalunya (I.Q.A.C.-C.S.I.C.), 08034 Barcelona, Spain
| | - Isabel Cardoso
- IBMC-Instituto de Biologia Molecular e Celular, 4200-135 Porto, Portugal.,i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Rafel Prohens
- Unitat de Polimorfisme i Calorimetria, Centres Cientı́fics i Tecnològics, Universitat de Barcelona, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Gemma Arsequell
- Institut de Quı́mica Avançada de Catalunya (I.Q.A.C.-C.S.I.C.), 08034 Barcelona, Spain
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25
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Chaves OA, Acunha TV, Iglesias BA, Jesus CS, Serpa C. Effect of peripheral platinum(II) bipyridyl complexes on the interaction of tetra-cationic porphyrins with human serum albumin. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112466] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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26
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Kimata-Ariga Y, Chikuma Y, Saitoh T, Miyata M, Yanagihara Y, Yamane K, Hase T. NADP(H) allosterically regulates the interaction between ferredoxin and ferredoxin-NADP + reductase. FEBS Open Bio 2019; 9:2126-2136. [PMID: 31665566 PMCID: PMC6886308 DOI: 10.1002/2211-5463.12752] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/21/2019] [Accepted: 10/28/2019] [Indexed: 11/17/2022] Open
Abstract
Ferredoxin‐NADP+ reductase (FNR) in plants receives electrons from ferredoxin (Fd) at the end of the photosynthetic electron transfer chain and converts NADP+ to NADPH. The interaction between Fd and FNR in plants was previously shown to be attenuated by NADP(H). Here, we investigated the molecular mechanism of this phenomenon using maize FNR and Fd, as the three‐dimensional structure of this complex is available. NADPH, NADP+, and 2′5′‐ADP differentially affected the interaction, as revealed through kinetic and physical binding analyses. Site‐directed mutations of FNR which change the affinity for NADPH altered the affinity for Fd in the opposite direction to that for NADPH. We propose that the binding of NADP(H) causes a conformational change of FNR which is transferred to the Fd‐binding region through different domains of FNR, resulting in allosteric changes in the affinity for Fd. The interaction between ferredoxin (Fd) and Fd‐NADP+ reductase (FNR) in plants is attenuated by NADP(H). Site‐directed mutations of FNR which change the affinity for NADPH altered the affinity for Fd in the opposite direction. We propose that the binding of NADP(H) leads to conformational changes of FNR, resulting in allosteric changes in the affinity for Fd.![]()
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Affiliation(s)
- Yoko Kimata-Ariga
- Department of Biological Chemistry, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yoshida, Japan
| | - Yutaro Chikuma
- Laboratory of Regulation of Biological Reactions, Division of Protein Chemistry, Institute for Protein Research, Osaka University, Suita, Japan
| | - Takashi Saitoh
- Division of Pharmaceutics, Hokkaido Pharmaceutical University School of Pharmacy, Sapporo, Japan
| | - Masayuki Miyata
- Department of Biological Chemistry, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yoshida, Japan
| | - Yuetsu Yanagihara
- Department of Biological Chemistry, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yoshida, Japan
| | - Kazukiyo Yamane
- Department of Biological Chemistry, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yoshida, Japan
| | - Toshiharu Hase
- Laboratory of Regulation of Biological Reactions, Division of Protein Chemistry, Institute for Protein Research, Osaka University, Suita, Japan
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27
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Pérez-Amigot D, Taleb V, Boneta S, Anoz-Carbonell E, Sebastián M, Velázquez-Campoy A, Polo V, Martínez-Júlvez M, Medina M. Towards the competent conformation for catalysis in the ferredoxin-NADP + reductase from the Brucella ovis pathogen. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:148058. [PMID: 31394095 DOI: 10.1016/j.bbabio.2019.148058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 07/19/2019] [Accepted: 08/02/2019] [Indexed: 02/02/2023]
Abstract
Brucella ovis encodes a bacterial subclass 1 ferredoxin-NADP(H) reductase (BoFPR) that, by similarity with other FPRs, is expected either to deliver electrons from NADPH to the redox-based metabolism and/or to oxidize NADPH to regulate the soxRS regulon that protects bacteria against oxidative damage. Such potential roles for the pathogen survival under infection conditions make of interest to understand and to act on the BoFPR mechanism. Here, we investigate the NADP+/H interaction and NADPH oxidation by hydride transfer (HT) to BoFPR. Crystal structures of BoFPR in free and in complex with NADP+ hardly differ. The latter shows binding of the NADP+ adenosine moiety, while its redox-reactive nicotinamide protrudes towards the solvent. Nonetheless, pre-steady-state kinetics show formation of a charge-transfer complex (CTC-1) prior to the hydride transfer, as well as conversion of CTC-1 into a second charge-transfer complex (CTC-2) concomitantly with the HT event. Thus, during catalysis nicotinamide and flavin reacting rings stack. Kinetic data also identify the HT itself as the rate limiting step in the reduction of BoFPR by NADPH, as well as product release limiting the overall reaction. Using all-atom molecular dynamics simulations with a thermal effect approach we are able to visualise a potential transient catalytically competent interaction of the reacting rings. Simulations indicate that the architecture of the FAD folded conformation in BoFPR might be key in catalysis, pointing to its adenine as an element to orient the reactive atoms in conformations competent for HT.
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Affiliation(s)
- Daniel Pérez-Amigot
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Víctor Taleb
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Sergio Boneta
- Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain; Departamento de Química Física, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Ernesto Anoz-Carbonell
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - María Sebastián
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain; Aragon Institute for Health Research (IIS-Aragon), Zaragoza 50009, Spain; Biomedical Research Networking Center in Digestive and Hepatic Diseases (CIBERehd), Madrid, Spain; Fundacion ARAID, Government of Aragon, Zaragoza 50018, Spain
| | - Víctor Polo
- Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain; Departamento de Química Física, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Marta Martínez-Júlvez
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain.
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain.
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28
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Abstract
Isothermal titration calorimetry (ITC) has become the preferred experimental technique for characterizing intermolecular interactions between biological molecules. Among the several advantages, the use of natural non-labeled molecules and the determination of the complete thermodynamic profile for the interaction in solution remain as the primary features that have promoted ITC to the forefront of experimental biophysics. The experimental design in ITC may range from studying a simple direct binary macromolecule-ligand interaction to studying the homotropic or heterotropic cooperative effect between ligands when interacting with a given macromolecule. The theory of the binding polynomial has proven to be an appropriate unifying framework for handling the complexities that can be encountered when studying macromolecule-ligand interactions, though it has been deemed troublesome. The goal of this chapter is to provide a quite simple and widely available set of training experiments aimed at mastering the formalism of the binding polynomial applied to isothermal titration calorimetry.
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29
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Sebastián M, Velázquez-Campoy A, Medina M. The RFK catalytic cycle of the pathogen Streptococcus pneumoniae shows species-specific features in prokaryotic FMN synthesis. J Enzyme Inhib Med Chem 2018; 33:842-849. [PMID: 29693467 PMCID: PMC6010069 DOI: 10.1080/14756366.2018.1461857] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 03/31/2018] [Accepted: 04/03/2018] [Indexed: 02/03/2023] Open
Abstract
Emergence of multidrug-resistant bacteria forces us to explore new therapeutic strategies, and proteins involved in key metabolic pathways are promising anti-bacterial targets. Bifunctional flavin-adenine dinucleotide (FAD) synthetases (FADS) are prokaryotic enzymes that synthesise the flavin mononucleotide (FMN) and FAD cofactors. The FADS from the human pathogen Streptococcus pneumoniae (SpnFADS)-causative agent of pneumonia in humans - shows relevant catalytic dissimilarities compared to other FADSs. Here, by integrating thermodynamic and kinetic data, we present a global description of the riboflavin kinase activity of SpnFADS, as well as of the inhibition mechanisms regulating this activity. Our data shed light on biophysical determinants that modulate species-specific conformational changes leading to catalytically competent conformations, as well as binding rates and affinities of substrates versus products. This knowledge paves the way for the development of tools - that taking advantage of the regulatory dissimilarities during FMN biosynthesis in different species - might be used in the discovery of specific anti-pneumococcal drugs.
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Affiliation(s)
- María Sebastián
- Facultad de Ciencias, Departamento de Bioquímica y Biología Molecular y Celular, and Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC-CSIC and BIFI-CSIC Joint Units), Universidad de Zaragoza, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Facultad de Ciencias, Departamento de Bioquímica y Biología Molecular y Celular, and Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC-CSIC and BIFI-CSIC Joint Units), Universidad de Zaragoza, Zaragoza, Spain
- Fundación ARAID, Diputación General de Aragón, Zaragoza, Spain
- Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain
| | - Milagros Medina
- Facultad de Ciencias, Departamento de Bioquímica y Biología Molecular y Celular, and Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC-CSIC and BIFI-CSIC Joint Units), Universidad de Zaragoza, Zaragoza, Spain
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30
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Lamazares E, Vega S, Ferreira P, Medina M, Galano-Frutos JJ, Martínez-Júlvez M, Velázquez-Campoy A, Sancho J. Direct examination of the relevance for folding, binding and electron transfer of a conserved protein folding intermediate. Phys Chem Chem Phys 2018; 19:19021-19031. [PMID: 28702545 DOI: 10.1039/c7cp02606d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Near the minimum free energy basin of proteins where the native ensemble resides, partly unfolded conformations of slightly higher energy can be significantly populated under native conditions. It has been speculated that they play roles in molecular recognition and catalysis, but they might represent contemporary features of the evolutionary process without functional relevance. Obtaining conclusive evidence on these alternatives is difficult because it requires comparing the performance of a given protein when populating and when not populating one such intermediate, in otherwise identical conditions. Wild type apoflavodoxin populates under native conditions a partly unfolded conformation (10% of molecules) whose unstructured region includes the binding sites for the FMN cofactor and for redox partner proteins. We recently engineered a thermostable variant where the intermediate is no longer detectable. Using the wild type and variant, we assess the relevance of the intermediate comparing folding kinetics, cofactor binding kinetics, cofactor affinity, X-ray structure, intrinsic dynamics, redox potential of the apoflavodoxin-cofactor complex (Fld), its affinity for partner protein FNR, and electron transfer rate within the Fld/FNR physiological complex. Our data strongly suggest the intermediate state, conserved in long-chain apoflavodoxins, is not required for the correct assembly of flavodoxin nor does it contribute to shape its electron transfer properties. This analysis can be applied to evaluate other native basin intermediates.
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Affiliation(s)
- Emilio Lamazares
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Sonia Vega
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain
| | - Patricia Ferreira
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Milagros Medina
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Juan J Galano-Frutos
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Marta Martínez-Júlvez
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain and Fundación ARAID, Gobierno de Aragón, Spain and Aragon Health Research Institute (IIS Aragón), Universidad de Zaragoza, Zaragoza, Spain.
| | - Javier Sancho
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain and Aragon Health Research Institute (IIS Aragón), Universidad de Zaragoza, Zaragoza, Spain.
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31
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Domínguez-Martín MA, López-Lozano A, Clavería-Gimeno R, Velázquez-Campoy A, Seidel G, Burkovski A, Díez J, García-Fernández JM. Differential NtcA Responsiveness to 2-Oxoglutarate Underlies the Diversity of C/N Balance Regulation in Prochlorococcus. Front Microbiol 2018; 8:2641. [PMID: 29375510 PMCID: PMC5767323 DOI: 10.3389/fmicb.2017.02641] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 12/19/2017] [Indexed: 11/29/2022] Open
Abstract
Previous studies showed differences in the regulatory response to C/N balance in Prochlorococcus with respect to other cyanobacteria, but no information was available about its causes, or the ecological advantages conferred to thrive in oligotrophic environments. We addressed the changes in key enzymes (glutamine synthetase, isocitrate dehydrogenase) and the ntcA gene (the global nitrogen regulator) involved in C/N metabolism and its regulation, in three model Prochlorococcus strains: MED4, SS120, and MIT9313. We observed a remarkable level of diversity in their response to azaserine, a glutamate synthase inhibitor which increases the concentration of the key metabolite 2-oxoglutarate, used to sense the C/N balance by cyanobacteria. Besides, we studied the binding between the global nitrogen regulator (NtcA) and the promoter of the glnA gene in the same Prochlorococcus strains, and its dependence on the 2-oxoglutarate concentration, by using isothermal titration calorimetry, surface plasmon resonance, and electrophoretic mobility shift. Our results show a reduction in the responsiveness of NtcA to 2-oxoglutarate in Prochlorococcus, especially in the MED4 and SS120 strains. This suggests a trend to streamline the regulation of C/N metabolism in late-branching Prochlorococcus strains (MED4 and SS120), in adaptation to the rather stable conditions found in the oligotrophic ocean gyres where this microorganism is most abundant.
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Affiliation(s)
- María A Domínguez-Martín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Antonio López-Lozano
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Rafael Clavería-Gimeno
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units BIFI-IQFR-CSIC and GBsC-BIFI-CSIC, Universidad de Zaragoza, Zaragoza, Spain.,Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain.,Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units BIFI-IQFR-CSIC and GBsC-BIFI-CSIC, Universidad de Zaragoza, Zaragoza, Spain.,Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain.,Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas, Barcelona, Spain.,Fundación ARAID, Gobierno de Aragón, Zaragoza, Spain
| | - Gerald Seidel
- Professur für Mikrobiologie, Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Andreas Burkovski
- Professur für Mikrobiologie, Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jesús Díez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - José M García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
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32
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Mulo P, Medina M. Interaction and electron transfer between ferredoxin-NADP + oxidoreductase and its partners: structural, functional, and physiological implications. PHOTOSYNTHESIS RESEARCH 2017; 134:265-280. [PMID: 28361449 DOI: 10.1007/s11120-017-0372-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 03/20/2017] [Indexed: 05/25/2023]
Abstract
Ferredoxin-NADP+ reductase (FNR) catalyzes the last step of linear electron transfer in photosynthetic light reactions. The FAD cofactor of FNR accepts two electrons from two independent reduced ferredoxin molecules (Fd) in two sequential steps, first producing neutral semiquinone and then the fully anionic reduced, or hydroquinone, form of the enzyme (FNRhq). FNRhq transfers then both electrons in a single hydride transfer step to NADP+. We are presenting the recent progress in studies focusing on Fd:FNR interaction and subsequent electron transfer processes as well as on interaction of FNR with NADP+/H followed by hydride transfer, both from the structural and functional point of views. We also present the current knowledge about the physiological role(s) of various FNR isoforms present in the chloroplasts of higher plants and the functional impact of subchloroplastic location of FNR. Moreover, open questions and current challenges about the structure, function, and physiology of FNR are discussed.
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Affiliation(s)
- Paula Mulo
- Molecular Plant Biology, University of Turku, 20520, Turku, Finland
| | - Milagros Medina
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, and Institute of Biocomputation and Physics of Complex Systems (Joint Units: BIFI-IQFR and GBsC-CSIC), University of Zaragoza, 50009, Zaragoza, Spain.
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33
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Zhang Z, Oni O, Liu J. New insights into a classic aptamer: binding sites, cooperativity and more sensitive adenosine detection. Nucleic Acids Res 2017; 45:7593-7601. [PMID: 28591844 PMCID: PMC5737652 DOI: 10.1093/nar/gkx517] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 06/01/2017] [Indexed: 11/27/2022] Open
Abstract
The DNA aptamer for adenosine (also for AMP and ATP) is a highly conserved sequence that has recurred in a few selections. It it a widely used model aptamer for biosensor development, and its nuclear magnetic resonance structure shows that each aptamer binds two AMP molecules. In this work, each binding site was individually removed by rational sequence design, while the remaining site still retained a similar binding affinity and specificity as confirmed by isothermal titration calorimetry. The thermodynamic parameters of binding are presented, and its biochemical implications are discussed. The number of binding sites can also be increased, and up to four sites are introduced in a single DNA sequence. Finally, the different sequences are made into fluorescent biosensors based on the structure-switching signaling aptamer design. The one-site aptamer has 3.8-fold higher sensitivity at lower adenosine concentration with a limit of detection of 9.1 μM adenosine, but weaker fluorescence signal at higher adenosine concentrations, consistent with a moderate cooperativity in the original aptamer. This work has offered insights into a classic aptamer for the relationship between the number of binding sites and sensitivity, and a shorter aptamer for improved biosensor design.
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Affiliation(s)
- Zijie Zhang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Olatunji Oni
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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Sebastián M, Serrano A, Velázquez-Campoy A, Medina M. Kinetics and thermodynamics of the protein-ligand interactions in the riboflavin kinase activity of the FAD synthetase from Corynebacterium ammoniagenes. Sci Rep 2017; 7:7281. [PMID: 28779158 PMCID: PMC5544777 DOI: 10.1038/s41598-017-07875-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 07/04/2017] [Indexed: 01/20/2023] Open
Abstract
Enzymes known as bifunctional and bimodular prokaryotic type-I FAD synthetase (FADS) exhibit ATP:riboflavin kinase (RFK) and FMN:ATP adenylyltransferase (FMNAT) activities in their C-terminal and N-terminal modules, respectively, and produce flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). These act as cofactors of a plethora of flavoproteins in all organisms. Therefore, regulation of their production maintains the cellular flavoproteome homeostasis. Here, we focus on regulation of the FMN synthesis in Corynebacterium ammoniagenes (Ca) by the inhibition of its RFK activity by substrates and products of the reaction. We use a truncated CaFADS variant consisting in the isolated C-terminal RFK module, whose RFK activity is similar to that of the full-length enzyme. Inhibition of the RFK activity by the RF substrate is independent of the FMNAT module, and FMN production, in addition to being inhibited by an excess of RF, is also inhibited by both of the reaction products. Pre-steady-state kinetic and thermodynamic studies reveal key aspects to the substrates induced fit to produce the catalytically competent complex. Among them, the role of Mg2+ in the concerted allocation of substrates for catalysis and the ensemble of non-competent complexes that contribute to the regulated inhibition of the RFK activity are particularly relevant.
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Affiliation(s)
- María Sebastián
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, and Institute of Biocomputation and Physics of Complex Systems (Joint Units: BIFI-IQFR and GBsC-CSIC), University of Zaragoza, Zaragoza, Spain
| | - Ana Serrano
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, and Institute of Biocomputation and Physics of Complex Systems (Joint Units: BIFI-IQFR and GBsC-CSIC), University of Zaragoza, Zaragoza, Spain.,Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, Madrid, Spain
| | - Adrián Velázquez-Campoy
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, and Institute of Biocomputation and Physics of Complex Systems (Joint Units: BIFI-IQFR and GBsC-CSIC), University of Zaragoza, Zaragoza, Spain.,ARAID Foundation, Diputación General de Aragón, Zaragoza, Spain.,Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain
| | - Milagros Medina
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, and Institute of Biocomputation and Physics of Complex Systems (Joint Units: BIFI-IQFR and GBsC-CSIC), University of Zaragoza, Zaragoza, Spain.
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Ihms EC, Kleckner IR, Gollnick P, Foster MP. Mechanistic Models Fit to Variable Temperature Calorimetric Data Provide Insights into Cooperativity. Biophys J 2017; 112:1328-1338. [PMID: 28402876 DOI: 10.1016/j.bpj.2017.02.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 02/12/2017] [Accepted: 02/16/2017] [Indexed: 12/22/2022] Open
Abstract
Allostery pervades macromolecular function and drives cooperative binding of ligands to macromolecules. To decipher the mechanisms of cooperative ligand binding it is necessary to define at a microscopic level the structural and thermodynamic consequences of binding of each ligand to its allosterically coupled site(s). However, dynamic sampling of alternative conformations (microstates) in allosteric molecules complicates interpretation of both structural and thermodynamic data. Isothermal titration calorimetry has the potential to directly quantify the thermodynamics of allosteric interactions, but usually falls short of enabling mechanistic insight. This is because 1) its measurements reflect the sum of overlapping caloric processes involving binding-linked population shifts within and between microstates, and 2) data are generally fit with phenomenological binding polynomials that are underdetermined. Nevertheless, temperature-dependent binding data have the potential to resolve overlapping thermodynamic processes, while mechanistically constrained models enable hypothesis testing and identification of informative parameters. We globally fit temperature-dependent isothermal titration calorimetry data for binding of 11 tryptophan ligands to the homo-undecameric trp RNA-binding Attenuation Protein from Bacillus stearothermophilus using nearest-neighbor statistical thermodynamic models. This approach allowed us to distinguish alternative nearest-neighbor interaction models, and quantifies the thermodynamic contribution of neighboring ligands to individual binding sites. We also perform conventional Hill equation modeling and illustrate how comparatively limited it is in quantitative or mechanistic value. This work illustrates the potential of mechanistically constrained global fitting of binding data to yield the microscopic thermodynamic parameters essential for deciphering mechanisms of cooperativity in a wide range of ligand-regulated homo-oligomeric assemblies.
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Affiliation(s)
- Elihu C Ihms
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio
| | - Ian R Kleckner
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio
| | - Paul Gollnick
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Mark P Foster
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio.
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Claveria-Gimeno R, Vega S, Abian O, Velazquez-Campoy A. A look at ligand binding thermodynamics in drug discovery. Expert Opin Drug Discov 2017; 12:363-377. [DOI: 10.1080/17460441.2017.1297418] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Rafael Claveria-Gimeno
- Institute of Biocomputation and Physics of Complex Systems (BIFI), IQFR-CSIC-BIFI and GBsC-CSIC-BIFI Joint Units, Universidad de Zaragoza, Zaragoza, Spain
- Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain
- Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain
| | - Sonia Vega
- Institute of Biocomputation and Physics of Complex Systems (BIFI), IQFR-CSIC-BIFI and GBsC-CSIC-BIFI Joint Units, Universidad de Zaragoza, Zaragoza, Spain
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), IQFR-CSIC-BIFI and GBsC-CSIC-BIFI Joint Units, Universidad de Zaragoza, Zaragoza, Spain
- Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain
- Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain
- Department of Biochemistry and Molecular and Cell Biology, Universidad de Zaragoza, Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), IQFR-CSIC-BIFI and GBsC-CSIC-BIFI Joint Units, Universidad de Zaragoza, Zaragoza, Spain
- Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain
- Department of Biochemistry and Molecular and Cell Biology, Universidad de Zaragoza, Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
- Fundación ARAID, Government of Aragon, Zaragoza, Spain
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37
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On the link between conformational changes, ligand binding and heat capacity. Biochim Biophys Acta Gen Subj 2016; 1860:868-878. [DOI: 10.1016/j.bbagen.2015.10.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/09/2015] [Accepted: 10/10/2015] [Indexed: 10/22/2022]
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A theoretical multiscale treatment of protein-protein electron transfer: The ferredoxin/ferredoxin-NADP(+) reductase and flavodoxin/ferredoxin-NADP(+) reductase systems. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1530-8. [PMID: 26385068 DOI: 10.1016/j.bbabio.2015.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/10/2015] [Accepted: 09/14/2015] [Indexed: 11/21/2022]
Abstract
In the photosynthetic electron transfer (ET) chain, two electrons transfer from photosystem I to the flavin-dependent ferredoxin-NADP(+) reductase (FNR) via two sequential independent ferredoxin (Fd) electron carriers. In some algae and cyanobacteria (as Anabaena), under low iron conditions, flavodoxin (Fld) replaces Fd as single electron carrier. Extensive mutational studies have characterized the protein-protein interaction in FNR/Fd and FNR/Fld complexes. Interestingly, even though Fd and Fld share the interaction site on FNR, individual residues on FNR do not participate to the same extent in the interaction with each of the protein partners, pointing to different electron transfer mechanisms. Despite of extensive mutational studies, only FNR/Fd X-ray structures from Anabaena and maize have been solved; structural data for FNR/Fld remains elusive. Here, we present a multiscale modelling approach including coarse-grained and all-atom protein-protein docking, the QM/MM e-Pathway analysis and electronic coupling calculations, allowing for a molecular and electronic comprehensive analysis of the ET process in both complexes. Our results, consistent with experimental mutational data, reveal the ET in FNR/Fd proceeding through a bridge-mediated mechanism in a dominant protein-protein complex, where transfer of the electron is facilitated by Fd loop-residues 40-49. In FNR/Fld, however, we observe a direct transfer between redox cofactors and less complex specificity than in Fd; more than one orientation in the encounter complex can be efficient in ET.
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Vega S, Abian O, Velazquez-Campoy A. A unified framework based on the binding polynomial for characterizing biological systems by isothermal titration calorimetry. Methods 2014; 76:99-115. [PMID: 25305413 DOI: 10.1016/j.ymeth.2014.09.010] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/26/2014] [Accepted: 09/29/2014] [Indexed: 01/10/2023] Open
Abstract
Isothermal titration calorimetry (ITC) has become the gold-standard technique for studying binding processes due to its high precision and sensitivity, as well as its capability for the simultaneous determination of the association equilibrium constant, the binding enthalpy and the binding stoichiometry. The current widespread use of ITC for biological systems has been facilitated by technical advances and the availability of commercial calorimeters. However, the complexity of data analysis for non-standard models is one of the most significant drawbacks in ITC. Many models for studying macromolecular interactions can be found in the literature, but it looks like each biological system requires specific modeling and data analysis approaches. The aim of this article is to solve this lack of unity and provide a unified methodological framework for studying binding interactions by ITC that can be applied to any experimental system. The apparent complexity of this methodology, based on the binding polynomial, is overcome by its easy generalization to complex systems.
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Affiliation(s)
- Sonia Vega
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit IQFR-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit IQFR-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain; Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain; IIS Aragón, Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain.
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit IQFR-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain; Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Zaragoza, Spain; Fundacion ARAID, Government of Aragon, Spain.
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40
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Keeler C, Poon G, Kuo IY, Ehrlich BE, Hodsdon ME. An explicit formulation approach for the analysis of calcium binding to EF-hand proteins using isothermal titration calorimetry. Biophys J 2014; 105:2843-53. [PMID: 24359756 DOI: 10.1016/j.bpj.2013.11.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 11/08/2013] [Accepted: 11/12/2013] [Indexed: 11/28/2022] Open
Abstract
We present an improved and extended version of a recently proposed mathematical approach for modeling isotherms of ligand-to-macromolecule binding from isothermal titration calorimetry. Our approach uses ordinary differential equations, solved implicitly and numerically as initial value problems, to provide a quantitative description of the fraction bound of each competing member of a complex mixture of macromolecules from the basis of general binding polynomials. This approach greatly simplifies the formulation of complex binding models. In addition to our generalized, model-free approach, we have introduced a mathematical treatment for the case where ligand is present before the onset of the titration, essential for data analysis when complete removal of the binding partner may disrupt the structural and functional characteristics of the macromolecule. Demonstration programs playable on a freely available software platform are provided. Our method is experimentally validated with classic calcium (Ca(2+)) ion-selective potentiometry and isotherms of Ca(2+) binding to a mixture of chelators with and without residual ligand present in the reaction vessel. Finally, we simulate and compare experimental data fits for the binding isotherms of Ca(2+) binding to its canonical binding site (EF-hand domain) of polycystin 2, a Ca(2+)-dependent channel with relevance to polycystic kidney disease.
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Affiliation(s)
- Camille Keeler
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Gregory Poon
- Department of Pharmaceutical Sciences, Washington State University, Pullman, Washington
| | - Ivana Y Kuo
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut
| | - Barbara E Ehrlich
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut
| | - Michael E Hodsdon
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut.
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Ferreira P, Martínez-Júlvez M, Medina M. Electron transferases. Methods Mol Biol 2014; 1146:79-94. [PMID: 24764089 DOI: 10.1007/978-1-4939-0452-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
The flavin isoalloxazine ring in electron transferases functions in a redox capacity, being able to take up electrons from a donor to subsequently deliver them to an acceptor. The main characteristics of these flavoproteins, including their unique ability to mediate obligatory processes of two-electron transfers with those involving single-electron transfer, are here described. To illustrate the versatility of these proteins, the acquired knowledge of the function of the two electron transferases involved in the cyanobacterial photosynthetic electron transfer from photosystem I to NADP(+) is presented. Many aspects of their biochemistry and biophysics have been extensively characterized using site-directed mutagenesis, steady-state and transient kinetics, spectroscopy, calorimetry, X-ray crystallography, electron paramagnetic resonance, and computational methods.
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Affiliation(s)
- Patricia Ferreira
- Department of Biochemistry and Molecular and Cellular Biology, Institute for Biocomputation and Physics of Complex Systems, Zaragoza, Spain
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42
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Herrera I, Winnik MA. Differential binding models for isothermal titration calorimetry: moving beyond the Wiseman isotherm. J Phys Chem B 2013; 117:8659-72. [PMID: 23841823 DOI: 10.1021/jp311812a] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We present a set of model-independent differential equations to analyze isothermal titration calorimetry (ITC) experiments. In contrast with previous approaches that begin with specific assumptions about the number of binding sites and the interactions among them (e.g., sequential, independent, cooperative), our derivation makes more general assumptions, such that a receptor with multiple sites for one type of ligand species (homotropic binding) can be studied with the same analytical expression. Our approach is based on the binding polynomial formalism, and the resulting analytical expressions can be extended to account for any number of binding sites and any type of binding interaction among them. We refer to the set of model-independent differential equations to study ITC experiments as a differential binding model (DBM). To demonstrate the flexibility of our DBM, we present the analytical expressions to study receptors with one or two binding sites. The DBM for a receptor with one site is equivalent to the Wiseman isotherm but with a more intuitive representation that depends on the binding polynomial and the dimensionless parameter c = K·MT, where K is the binding constant and MT the total receptor concentration. In addition, we show how to constrain the general DBM for a receptor with two sites to represent sequential, independent, or cooperative binding interactions between the sites. We use the sequential binding model to study the binding interaction between Gd(III) and citrate anions. In addition, we simulate calorimetry titrations of receptors with positive, negative, and noncooperative interactions between the two binding sites. Finally, we derive a DBM for titrations of receptors with n-independent binding sites.
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Affiliation(s)
- Isaac Herrera
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto ON Canada M5S 3H6
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Chopra S, Palencia A, Virus C, Tripathy A, Temple BR, Velazquez-Campoy A, Cusack S, Reader JS. Plant tumour biocontrol agent employs a tRNA-dependent mechanism to inhibit leucyl-tRNA synthetase. Nat Commun 2013; 4:1417. [PMID: 23361008 DOI: 10.1038/ncomms2421] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 12/20/2012] [Indexed: 11/08/2022] Open
Abstract
Leucyl-tRNA synthetases (LeuRSs) have an essential role in translation and are promising targets for antibiotic development. Agrocin 84 is a LeuRS inhibitor produced by the biocontrol agent Agrobacterium radiobacter K84 that targets pathogenic strains of A. tumefaciens, the causative agent of plant tumours. Agrocin 84 acts as a molecular Trojan horse and is processed inside the pathogen into a toxic moiety (TM84). Here we show using crystal structure, thermodynamic and kinetic analyses, that this natural antibiotic employs a unique and previously undescribed mechanism to inhibit LeuRS. TM84 requires tRNA(Leu) for tight binding to the LeuRS synthetic active site, unlike any previously reported inhibitors. TM84 traps the enzyme-tRNA complex in a novel 'aminoacylation-like' conformation, forming novel interactions with the KMSKS loop and the tRNA 3'-end. Our findings reveal an intriguing tRNA-dependent inhibition mechanism that may confer a distinct evolutionary advantage in vivo and inform future rational antibiotic design.
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Affiliation(s)
- Shaileja Chopra
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, 536 Taylor Hall, CB# 7090, Chapel Hill, North Carolina 27599-7090, USA
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Human cystathionine β-synthase (CBS) contains two classes of binding sites for S-adenosylmethionine (SAM): complex regulation of CBS activity and stability by SAM. Biochem J 2012; 449:109-21. [DOI: 10.1042/bj20120731] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
CBS (cystathionine β-synthase) is a multidomain tetrameric enzyme essential in the regulation of homocysteine metabolism, whose activity is enhanced by the allosteric regulator SAM (S-adenosylmethionine). Missense mutations in CBS are the major cause of inherited HCU (homocystinuria). In the present study we apply a novel approach based on a combination of calorimetric methods, functional assays and kinetic modelling to provide structural and energetic insight into the effects of SAM on the stability and activity of WT (wild-type) CBS and seven HCU-causing mutants. We found two sets of SAM-binding sites in the C-terminal regulatory domain with different structural and energetic features: a high affinity set of two sites, probably involved in kinetic stabilization of the regulatory domain, and a low affinity set of four sites, which are involved in the enzyme activation. We show that the regulatory domain displays a low kinetic stability in WT CBS, which is further decreased in many HCU-causing mutants. We propose that the SAM-induced stabilization may play a key role in modulating steady-state levels of WT and mutant CBS in vivo. Our strategy may be valuable for understanding ligand effects on proteins with a complex architecture and their role in human genetic diseases and for the development of novel pharmacological strategies.
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González B, Garrido F, Ortega R, Martínez-Júlvez M, Revilla-Guarinos A, Pérez-Pertejo Y, Velázquez-Campoy A, Sanz-Aparicio J, Pajares MA. NADP+ binding to the regulatory subunit of methionine adenosyltransferase II increases intersubunit binding affinity in the hetero-trimer. PLoS One 2012. [PMID: 23189196 PMCID: PMC3506619 DOI: 10.1371/journal.pone.0050329] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Mammalian methionine adenosyltransferase II (MAT II) is the only hetero-oligomer in this family of enzymes that synthesize S-adenosylmethionine using methionine and ATP as substrates. Binding of regulatory β subunits and catalytic α2 dimers is known to increase the affinity for methionine, although scarce additional information about this interaction is available. This work reports the use of recombinant α2 and β subunits to produce oligomers showing kinetic parameters comparable to MAT II purified from several tissues. According to isothermal titration calorimetry data and densitometric scanning of the stained hetero-oligomer bands on denatured gels, the composition of these oligomers is that of a hetero-trimer with α2 dimers associated to single β subunits. Additionally, the regulatory subunit is able to bind NADP(+) with a 1:1 stoichiometry, the cofactor enhancing β to α2-dimer binding affinity. Mutants lacking residues involved in NADP(+) binding and N-terminal truncations of the β subunit were able to oligomerize with α2-dimers, although the kinetic properties appeared altered. These data together suggest a role for both parts of the sequence in the regulatory role exerted by the β subunit on catalysis. Moreover, preparation of a structural model for the hetero-oligomer, using the available crystal data, allowed prediction of the regions involved in β to α2-dimer interaction. Finally, the implications that the presence of different N-terminals in the β subunit could have on MAT II behavior are discussed in light of the recent identification of several splicing forms of this subunit in hepatoma cells.
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Affiliation(s)
- Beatriz González
- Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física “Rocasolano” (CSIC), Madrid, Spain
| | - Francisco Garrido
- Instituto de Investigaciones Biomédicas “Alberto Sols” (CSIC-UAM), Madrid, Spain
| | - Rebeca Ortega
- Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física “Rocasolano” (CSIC), Madrid, Spain
| | - Marta Martínez-Júlvez
- Departmento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Biocomputación y Física de Complejos, Unidad Asociada IQFR-BIFI, Mariano Esquillor s/n, Edificio I+D, Campus Rio Ebro, Zaragoza, Spain
| | | | - Yolanda Pérez-Pertejo
- Departamento de Farmacología y Toxicología (INTOXCAL), Universidad de León, Campus de Vegazana s/n, León, Spain
| | - Adrián Velázquez-Campoy
- Departmento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Biocomputación y Física de Complejos, Unidad Asociada IQFR-BIFI, Mariano Esquillor s/n, Edificio I+D, Campus Rio Ebro, Zaragoza, Spain
- Fundacion ARAID, Diputación General de Aragón, Zaragoza, Spain
| | - Julia Sanz-Aparicio
- Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física “Rocasolano” (CSIC), Madrid, Spain
| | - María A. Pajares
- Instituto de Investigaciones Biomédicas “Alberto Sols” (CSIC-UAM), Madrid, Spain
- Molecular Hepatology Group, IdiPAZ, Madrid, Spain
- * E-mail:
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47
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Martinez-Julvez M, Abian O, Vega S, Medina M, Velazquez-Campoy A. Studying the allosteric energy cycle by isothermal titration calorimetry. Methods Mol Biol 2012; 796:53-70. [PMID: 22052485 DOI: 10.1007/978-1-61779-334-9_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Isothermal titration calorimetry (ITC) is a powerful biophysical technique which allows a complete thermodynamic characterization of protein interactions with other molecules. The possibility of dissecting the Gibbs energy of interaction into its enthalpic and entropic contributions, as well as the detailed additional information experimentally accessible on the intermolecular interactions (stoichiometry, cooperativity, heat capacity changes, and coupled equilibria), make ITC a suitable technique for studying allosteric interactions in proteins. Two experimental methodologies for the characterization of allosteric heterotropic ligand interactions by ITC are described in this chapter, illustrated with two proteins with markedly different structural and functional features: a photosynthetic electron transfer protein and a drug target viral protease.
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Affiliation(s)
- Marta Martinez-Julvez
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, Zaragoza, Spain.
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48
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The transient catalytically competent coenzyme allocation into the active site of Anabaena ferredoxin NADP+ -reductase. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 41:117-28. [PMID: 21538059 DOI: 10.1007/s00249-011-0704-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 04/05/2011] [Indexed: 10/18/2022]
Abstract
Ferredoxin-NADP(+) reductase (FNR) catalyses the electron transfer from ferredoxin to NADP(+) via its flavin FAD cofactor. A molecular dynamics theoretical approach is applied here to visualise the transient catalytically competent interaction of Anabaena FNR with its coenzyme, NADP(+). The particular role of some of the residues identified as key in binding and accommodating the 2'P-AMP moiety of the coenzyme is confirmed in molecular terms. Simulations also indicate that the architecture of the active site precisely contributes to the orientation of the N5 of the FAD isoalloxazine ring and the C4 of the coenzyme nicotinamide ring in the conformation of the catalytically competent hydride transfer complex and, therefore, contributes to the efficiency of the process. In particular, the side chain of the C-terminal Y303 in Anabaena FNR appears key to providing the optimum geometry by reducing the stacking probability between the isoalloxazine and nicotinamide rings, thus providing the required co-linearity and distance among the N5 of the flavin cofactor, the C4 of the coenzyme nicotinamide and the hydride that has to be transferred between them. All these factors are highly related to the reaction efficiency, mechanism and reversibility of the process.
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49
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Hansen LD, Fellingham GW, Russell DJ. Simultaneous determination of equilibrium constants and enthalpy changes by titration calorimetry: Methods, instruments, and uncertainties. Anal Biochem 2010; 409:220-9. [PMID: 21073852 DOI: 10.1016/j.ab.2010.11.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 10/28/2010] [Accepted: 11/03/2010] [Indexed: 11/16/2022]
Abstract
Calorimetric methods have been used to determine equilibrium constants since 1937, but no comprehensive review of the various calorimeters and methods has been done previously. This article reports methods for quantitative comparison of the capabilities of calorimeters for simultaneous determination of equilibrium constants and enthalpy changes, for determining optimal experimental conditions, and for assessing the effects of systematic and random errors on the accuracy and precision of equilibrium constants and enthalpy changes determined by this method.
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Affiliation(s)
- Lee D Hansen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA.
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Pulido NO, Salcedo G, Pérez-Hernández G, José-Núñez C, Velázquez-Campoy A, García-Hernández E. Energetic effects of magnesium in the recognition of adenosine nucleotides by the F(1)-ATPase beta subunit. Biochemistry 2010; 49:5258-68. [PMID: 20518490 DOI: 10.1021/bi1006767] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Nucleotide-induced conformational changes of the catalytic beta subunits play a crucial role in the rotary mechanism of F(1)-ATPase. To gain insights into the energetic bases that govern the recognition of nucleotides by the isolated beta subunit from thermophilic Bacillus PS3 (Tbeta), the binding of this monomer to Mg(II)-free and Mg(II)-bound adenosine nucleotides was characterized using high-precision isothermal titration calorimetry. The interactions of Mg(II) with free ATP or ADP were also measured calorimetrically. A model that considers simultaneously the interactions of Tbeta with Mg.ATP or with ATP and in which ATP is able to bind two Mg(II) atoms sequentially was used to determine the formation parameters of the Tbeta-Mg.ATP complex from calorimetric data. This analysis yielded significantly different DeltaH(b) and DeltaS(b) values in relation to those obtained using a single-binding site model, while DeltaG(b) was almost unchanged. Published calorimetric data for the titration of Tbeta with Mg.ADP [Perez-Hernandez, G., et al. (2002) Arch. Biochem. Biophys. 408, 177-183] were reanalyzed with the ternary model to determine the corresponding true binding parameters. Interactions of Tbeta with Mg.ATP, ATP, Mg.ADP, or ADP were enthalpically driven. Larger differences in thermodynamic properties were observed between Tbeta-Mg.ATP and Tbeta-ATP complexes than between Tbeta-Mg.ADP and Tbeta-ADP complexes or between Tbeta-Mg.ATP and Tbeta-Mg.ADP complexes. These binding data, in conjunction with those for the association of Mg(II) with free nucleotides, allowed for a determination of the energetic effects of the metal ion on the recognition of adenosine nucleotides by Tbeta [i.e., Tbeta.AT(D)P + Mg(II) right harpoon over left harpoon Tbeta.AT(D)P-Mg]. Because of a more favorable binding enthalpy, Mg(II) is recognized more avidly by the Tbeta.ATP complex, indicating better stereochemical complementarity than in the Tbeta.ADP complex. Furthermore, a structural-energetic analysis suggests that Tbeta adopts a more closed conformation when it is bound to Mg.ATP than to ATP or Mg.ADP, in agreement with recently published NMR data [Yagi, H., et al. (2009) J. Biol. Chem. 284, 2374-2382]. Using published binding data, a similar analysis of Mg(II) energetic effects was performed for the free energy change of F(1) catalytic sites, in the framework of bi- or tri-site binding models.
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Affiliation(s)
- Nancy O Pulido
- Instituto de Quimica, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Mexico
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