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Wegener D, Pérez-Bitrián A, Limberg N, Wiesner A, Hoffmann KF, Hasenstab-Riedel S. A Highly Sterically Encumbered Boron Lewis Acid Enabled by a Organotellurium-based Ligand. Chemistry 2024:e202401231. [PMID: 38625061 DOI: 10.1002/chem.202401231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/17/2024]
Abstract
Lewis acidic boron compounds are ubiquitous in chemistry due to their numerous applications, yet tuning and optimizing their properties towards different purposes is still a challenging field of research. In this work, the boron Lewis acid B[OTeF3(C6F5)2]3 was synthesized by reaction of the teflate derivative HOTeF3(C6F5)2 with BCl3 or BCl3·SMe2. This new compound presents a remarkably high thermal stability up to 300 °C, as well as one of the most sterically encumbered boron centres known in the literature. Theoretical and experimental methods revealed that B[OTeF3(C6F5)2]3 exhibits a comparable Lewis acidity to that of the well-known B(C6F5)3 and around 85% of the Lewis acidity of the related B(OTeF5)3. The affinity of B[OTeF3(C6F5)2]3 towards pyridine was accessed by Isothermal Titration Calorimetry (ITC) and compared to that of B(OTeF5)3 and B(C6F5)3. The ligand-transfer reactivity of this new boron compound towards different fluorides was demonstrated by the formation of an anionic Au(III) complex and a hypervalent iodine(III) species.
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Affiliation(s)
- Daniel Wegener
- Freie Universität Berlin, Institut für Chemie und Biochemie, GERMANY
| | | | - Niklas Limberg
- Freie Universität Berlin, Institut für Chemie und Biochemie, GERMANY
| | - Anja Wiesner
- Freie Universität Berlin, Institut für Chemie und Biochemie, GERMANY
| | - Kurt F Hoffmann
- Freie Universität Berlin, Institut für Chemie und Biochemie, GERMANY
| | - Sebastian Hasenstab-Riedel
- FU Berlin: Freie Universitat Berlin, Institut fuer Chemie und Biochemie - Anorganische Chemie, Fabeckstrasse 34-36, 14195, Berlin, GERMANY
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2
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Ramsey KM, Barrick D. Unraveling paralog-specific Notch signaling through thermodynamics of ternary complex formation and transcriptional activation of chimeric receptors. Protein Sci 2024; 33:e4947. [PMID: 38511488 PMCID: PMC10962485 DOI: 10.1002/pro.4947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/07/2024] [Accepted: 02/11/2024] [Indexed: 03/22/2024]
Abstract
Notch signaling in humans is mediated by four paralogous receptors that share conserved architectures and possess overlapping, yet non-redundant functions. The receptors share a canonical activation pathway wherein upon extracellular ligand binding, the Notch intracellular domain (NICD) is cleaved from the membrane and translocates to the nucleus where its N-terminal RBP-j-associated molecule (RAM) region and ankyrin repeat (ANK) domain bind transcription factor CSL and recruit co-activator Mastermind-like-1 (MAML1) to activate transcription. However, different paralogs can lead to distinct outcomes. To better understand paralog-specific differences in Notch signaling, we performed a thermodynamic analysis of the Notch transcriptional activation complexes for all four Notch paralogs using isothermal titration calorimetry. Using chimeric constructs, we find that the RAM region is the primary determinant of stability of binary RAMANK:CSL complexes, and that the ANK regions are largely the determinants of MAML1 binding to pre-formed RAMANK:CSL complexes. Free energies of these binding reactions (ΔGRA and ΔGMAML) vary among the four Notch paralogs, although variations for Notch2, 3, and 4 offset in the free energy of the ternary complex (ΔGTC, where ΔGTC = ΔGRA + ΔGMAML). To probe how these affinity differences affect Notch signaling, we performed transcriptional activation assays with the paralogous and chimeric NICDs, and analyzed the results with an independent multiplicative model that quantifies contributions of the paralogous RAM, ANK, and C-terminal regions (CTR) to activation. This analysis shows that transcription activation correlates with ΔGTC, but that activation is further modified by CTR identity in a paralog-specific way.
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Affiliation(s)
- Kristen M. Ramsey
- T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Doug Barrick
- T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
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3
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Li L, Tian J, Huang K, Xue X, Chen J, Guan F, Zhang T, Sun Y, He C, Zeng X, Su S. Metal-Binding Protein TaGlo1 Improves Fungal Resistance to Arsenite (As III) and Methylarsenite (MAs III) in Paddy Soil. Environ Sci Technol 2024. [PMID: 38557082 DOI: 10.1021/acs.est.3c11043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Trivalent arsenicals such as arsenite (AsIII) and methylarsenite (MAsIII) are thought to be ubiquitous in flooded paddy soils and have higher toxicity than pentavalent forms. Fungi are widely prevalent in the rice rhizosphere, and the latter is considered a hotspot for As uptake. However, few studies have focused on alleviating As toxicity in paddy soils using fungi. In this study, we investigated the mechanism by which the protein TaGlo1, derived from the As-resistant fungal strain Trichoderma asperellum SM-12F1, mitigates AsIII and MAsIII toxicity in paddy soils. Taglo1 gene expression in Escherichia coli BL21 conferred strong resistance to AsIII and MAsIII, while purified TaGlo1 showed a high affinity for AsIII and MAsIII. Three cysteine residues (Cys13, Cys18, and Cys71) play crucial roles in binding with AsIII, while only two (Cys13 and Cys18) play crucial roles for MAsIII binding. TaGlo1 had a stronger binding strength for MAsIII than AsIII. Importantly, up to 90.2% of the homologous TaGlo1 proteins originate from fungi by GenBank searching. In the rhizospheres of 14 Chinese paddy soils, Taglo1 was widely distributed and its gene abundance increased with porewater As. This study highlights the potential of fungi to mitigate As toxicity and availability in the soil-rice continuum and suggests future microbial strategies for bioremediation.
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Affiliation(s)
- Lijuan Li
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences/Key Laboratory of Agricultural Environment, MARA, Beijing 100081, P. R. China
| | - Jian Tian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Ke Huang
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Ximei Xue
- Institute of Urban Environment, Key Laboratory of Urban Environment and Health, Chinese Academy of Sciences, Xiamen 361021, P. R. China
| | - Jian Chen
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida 33199, United States
| | - Feifei Guan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Tuo Zhang
- School of Environmental and Life Science, Nanning Normal University, Nanning 530100, P. R. China
| | - Yifei Sun
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences/Key Laboratory of Agricultural Environment, MARA, Beijing 100081, P. R. China
| | - Chao He
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences/Key Laboratory of Agricultural Environment, MARA, Beijing 100081, P. R. China
| | - Xibai Zeng
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences/Key Laboratory of Agricultural Environment, MARA, Beijing 100081, P. R. China
| | - Shiming Su
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences/Key Laboratory of Agricultural Environment, MARA, Beijing 100081, P. R. China
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Au CW, Manfield I, Webb ME, Paci E, Turnbull WB, Ross JF. The Mutagenic Plasticity of the Cholera Toxin B-Subunit Surface Residues: Stability and Affinity. Toxins (Basel) 2024; 16:133. [PMID: 38535799 PMCID: PMC10974167 DOI: 10.3390/toxins16030133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/24/2024] [Accepted: 02/27/2024] [Indexed: 04/01/2024] Open
Abstract
Mastering selective molecule trafficking across human cell membranes poses a formidable challenge in healthcare biotechnology while offering the prospect of breakthroughs in drug delivery, gene therapy, and diagnostic imaging. The cholera toxin B-subunit (CTB) has the potential to be a useful cargo transporter for these applications. CTB is a robust protein that is amenable to reengineering for diverse applications; however, protein redesign has mostly focused on modifications of the N- and C-termini of the protein. Exploiting the full power of rational redesign requires a detailed understanding of the contributions of the surface residues to protein stability and binding activity. Here, we employed Rosetta-based computational saturation scans on 58 surface residues of CTB, including the GM1 binding site, to analyze both ligand-bound and ligand-free structures to decipher mutational effects on protein stability and GM1 affinity. Complimentary experimental results from differential scanning fluorimetry and isothermal titration calorimetry provided melting temperatures and GM1 binding affinities for 40 alanine mutants among these positions. The results showed that CTB can accommodate diverse mutations while maintaining its stability and ligand binding affinity. These mutations could potentially allow modification of the oligosaccharide binding specificity to change its cellular targeting, alter the B-subunit intracellular routing, or impact its shelf-life and in vivo half-life through changes to protein stability. We anticipate that the mutational space maps presented here will serve as a cornerstone for future CTB redesigns, paving the way for the development of innovative biotechnological tools.
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Affiliation(s)
- Cheuk W. Au
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Iain Manfield
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Michael E. Webb
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
| | - Emanuele Paci
- Dipartimento di Fisica e Astronomia “Augusto Righi”, Viale Berti Pichat 6/2, 40127 Bologna, Italy
| | - W. Bruce Turnbull
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
| | - James F. Ross
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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5
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Lv X, Li W, Zhang M, Wang R, Chang J. Investigation of steric hindrance effect on the interactions between four alkaloids and HSA by isothermal titration calorimetry and molecular docking. J Mol Recognit 2024; 37:e3075. [PMID: 38191989 DOI: 10.1002/jmr.3075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/24/2023] [Accepted: 12/24/2023] [Indexed: 01/10/2024]
Abstract
The binding of four alkaloids with human serum albumin (HSA) was investigated by isothermal titration calorimetry (ITC), spectroscopy and molecular docking techniques. The findings demonstrated that theophylline or caffeine can bind to HAS, respectively. The number of binding sites and binding constants are obtained. The binding mode is a static quenching process. The effects of steric hindrance, temperature, salt concentration and buffer solution on the binding indicated that theophylline and HSA have higher binding affinity than caffeine. The fluorescence and ITC results showed that the interaction between HSA and theophylline or caffeine is an entropy-driven spontaneous exothermic process. The hydrophobic force was the primary driving factor. The experimental results were consistent with the molecular docking data. Based on the molecular structures of the four alkaloids, steric hindrance might be a major factor in the binding between HSA and these four alkaloids. This study elucidates the mechanism of interactions between four alkaloids and HSA.
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Affiliation(s)
- Xinluan Lv
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou, China
- Pingyuan Laboratory (Zhengzhou University), Zhengzho, China
| | - Wenjin Li
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou, China
- Pingyuan Laboratory (Zhengzhou University), Zhengzho, China
| | - Miao Zhang
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou, China
- Pingyuan Laboratory (Zhengzhou University), Zhengzho, China
| | - Ruiyong Wang
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou, China
- Pingyuan Laboratory (Zhengzhou University), Zhengzho, China
| | - Junbiao Chang
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou, China
- Pingyuan Laboratory (Zhengzhou University), Zhengzho, China
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6
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Nele V, D'Aria F, Campani V, Silvestri T, Biondi M, Giancola C, De Rosa G. Unravelling the role of lipid composition on liposome-protein interactions. J Liposome Res 2024; 34:88-96. [PMID: 37337884 DOI: 10.1080/08982104.2023.2224449] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 06/06/2023] [Indexed: 06/21/2023]
Abstract
Upon in vivo administration of nanoparticles, a protein corona forms on their surface and affects their half-life in circulation, biodistribution properties, and stability; in turn, the composition of the protein corona depends on the physico-chemical properties of the nanoparticles. We have previously observed lipid composition-dependent in vitro and in vivo microRNA delivery from lipid nanoparticles. Here, we carried out an extensive physico-chemical characterisation to understand the role of the lipid composition on the in vivo fate of lipid-based nanoparticles. We used a combination of differential scanning calorimetry (DSC), membrane deformability measurements, isothermal titration calorimetry (ITC), and dynamic light scattering (DLS) to probe the interactions between the nanoparticle surface and bovine serum albumin (BSA) as a model protein. The lipid composition influenced membrane deformability, improved lipid intermixing, and affected the formation of lipid domains while BSA binding to the liposome surface was affected by the PEGylated lipid content and the presence of cholesterol. These findings highlight the importance of the lipid composition on the protein-liposome interaction and provide important insights for the design of lipid-based nanoparticles for drug delivery applications.
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Affiliation(s)
- Valeria Nele
- BioNanoMed Drug Delivery Group, Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Federica D'Aria
- Biophysics Laboratory, Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Virginia Campani
- BioNanoMed Drug Delivery Group, Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Teresa Silvestri
- BioNanoMed Drug Delivery Group, Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Marco Biondi
- BioNanoMed Drug Delivery Group, Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Concetta Giancola
- Biophysics Laboratory, Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Giuseppe De Rosa
- BioNanoMed Drug Delivery Group, Department of Pharmacy, University of Naples Federico II, Naples, Italy
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7
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Zhang Z, Rondon-Cordero HM, Das C. Crystal structure of bacterial ubiquitin ADP-ribosyltransferase CteC reveals a substrate-recruiting insertion. J Biol Chem 2024; 300:105604. [PMID: 38159861 PMCID: PMC10810742 DOI: 10.1016/j.jbc.2023.105604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024] Open
Abstract
ADP-ribosylation is a post-translational modification involved in regulation of diverse cellular pathways. Interestingly, many pathogens have been identified to utilize ADP-ribosylation as a way for host manipulation. A recent study found that CteC, an effector from the bacterial pathogen Chromobacterium violaceum, hinders host ubiquitin (Ub) signaling pathways via installing mono-ADP-ribosylation on threonine 66 of Ub. However, the molecular basis of substrate recognition by CteC is not well understood. In this article, we probed the substrate specificity of this effector at protein and residue levels. We also determined the crystal structure of CteC in complex with NAD+, which revealed a canonical mono-ADP-ribosyltransferase fold with an additional insertion domain. The AlphaFold-predicted model differed significantly from the experimentally determined structure, even in regions not used in crystal packing. Biochemical and biophysical studies indicated unique features of the NAD+ binding pocket, while showing selectivity distinction between Ub and structurally close Ub-like modifiers and the role of the insertion domain in substrate recognition. Together, this study provides insights into the enzymatic specificities and the key structural features of a novel bacterial ADP-ribosyltransferase involved in host-pathogen interaction.
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Affiliation(s)
- Zhengrui Zhang
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
| | | | - Chittaranjan Das
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA.
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8
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Joshi J, McCauley MJ, Morse M, Muccio MR, Kanlong JG, Rocha MS, Rouzina I, Musier-Forsyth K, Williams MC. Mechanism of DNA Intercalation by Chloroquine Provides Insights into Toxicity. Int J Mol Sci 2024; 25:1410. [PMID: 38338688 PMCID: PMC10855526 DOI: 10.3390/ijms25031410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 01/18/2024] [Accepted: 01/20/2024] [Indexed: 02/12/2024] Open
Abstract
Chloroquine has been used as a potent antimalarial, anticancer drug, and prophylactic. While chloroquine is known to interact with DNA, the details of DNA-ligand interactions have remained unclear. Here we characterize chloroquine-double-stranded DNA binding with four complementary approaches, including optical tweezers, atomic force microscopy, duplex DNA melting measurements, and isothermal titration calorimetry. We show that chloroquine intercalates into double stranded DNA (dsDNA) with a KD ~ 200 µM, and this binding is entropically driven. We propose that chloroquine-induced dsDNA intercalation, which happens in the same concentration range as its observed toxic effects on cells, is responsible for the drug's cytotoxicity.
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Affiliation(s)
- Joha Joshi
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (J.J.); (M.J.M.); (M.M.)
| | - Micah J. McCauley
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (J.J.); (M.J.M.); (M.M.)
| | - Michael Morse
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (J.J.); (M.J.M.); (M.M.)
| | - Michael R. Muccio
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA; (M.R.M.); (J.G.K.); (I.R.); (K.M.-F.)
| | - Joseph G. Kanlong
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA; (M.R.M.); (J.G.K.); (I.R.); (K.M.-F.)
| | - Márcio S. Rocha
- Department of Physics, Universidade Federal de Viçosa, Viçosa CEP 36570-900, MG, Brazil;
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA; (M.R.M.); (J.G.K.); (I.R.); (K.M.-F.)
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA; (M.R.M.); (J.G.K.); (I.R.); (K.M.-F.)
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (J.J.); (M.J.M.); (M.M.)
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9
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Maroju PA, Ganesan R, Ray Dutta J. Probing the Effects of Antimicrobial-Lysozyme Derivatization on Enzymatic Degradation of Poly(ε-caprolactone) Film and Fiber. Macromol Biosci 2023; 23:e2300296. [PMID: 37555590 DOI: 10.1002/mabi.202300296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 08/03/2023] [Indexed: 08/10/2023]
Abstract
Surface derivatization is essential for incorporating unique functionalities into biodegradable polymers. Nonetheless, its precise effects on enzymatic biodegradation still lack comprehensive understanding. In this study, a facile solution-based method is employed to surface derivatize poly(ε-caprolactone) films and electrospun fibers with lysozyme, aiming to impart antimicrobial properties and examine the impact on enzymatic degradation. The derivatized films and fibers have shown high antibacterial efficacy against Escherichia coli and Staphylococcus aureus. Through gravimetric analysis, it is observed that the degradation rate experiences a slight decrease upon lysozyme derivatization. However, this reduction is effectively countered by the inclusion of Tween-20, as affirmed by isothermal titration calorimetry. Comparing films and fibers, the latter undergoes degradation at a more accelerated pace, coupled with a rapid decline in molecular weight. This study provides valuable insights into the factors influencing the degradation of surface-derivatized biopolymers through electrospinning, offering a simple strategy to mitigate biomaterial-associated infections.
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Affiliation(s)
- Pranay Amruth Maroju
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal District, Hyderabad, Telangana, 500078, India
| | - Ramakrishnan Ganesan
- Department of Chemistry, Birla Institute of Technology and Science (BITS), Pilani, Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal District, Hyderabad, Telangana, 500078, India
| | - Jayati Ray Dutta
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal District, Hyderabad, Telangana, 500078, India
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10
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Jarrard TR, Brock E, Hansen LD, Kenealey JD. Measuring β-galactosidase activity in opaque dairy solutions under optimum conditions for galactooligosaccharide synthesis by isothermal titration calorimetry. J Dairy Sci 2023; 106:8312-8320. [PMID: 37641293 DOI: 10.3168/jds.2023-23400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/15/2023] [Indexed: 08/31/2023]
Abstract
The dairy industry uses enzymes to make cheese, alter product flavor, and eliminate lactose. The activities of these enzymes have been measured in clear buffered solutions, but because of the limitations of spectrophotometric methods, enzyme activities have not been measured in opaque or colored dairy products where they are used. Isothermal titration calorimetry (ITC) can be used to determine reaction kinetics in opaque and colored solutions by measuring the heat rate (thermal power) from enzyme-catalyzed reactions as a function of time. This study used ITC to measure β-galactosidase activity in opaque solutions of milk, sweet whey, sweet whey permeate, acid whey, and acid whey permeate with 2 β-galactosidase (Enzyme Commission number 3.2.1.23) isozymes derived from Aspergillus oryzae and Kluyveromyces lactis. The components of the dairy fluids alter the enzyme kinetics and reaction thermodynamics, and the reactions catalyzed by the 2 homologues differ as shown by differing thermodynamic profiles. The study demonstrates that ITC can be used to measure enzyme activity in opaque and colored dairy fluids and identify reactions by their thermodynamic properties.
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Affiliation(s)
- T R Jarrard
- Department of Nutrition, Dietetics and Food Science, Brigham Young University, Provo, UT 84602
| | - E Brock
- Department of Nutrition, Dietetics and Food Science, Brigham Young University, Provo, UT 84602
| | - L D Hansen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - J D Kenealey
- Department of Nutrition, Dietetics and Food Science, Brigham Young University, Provo, UT 84602.
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11
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Huang PJJ, Evans NM, Lu C, Li AZ, Dieckmann T, Liu J. Cross-Binding of Adenosine by Aptamers Selected Using Theophylline. Chembiochem 2023; 24:e202300566. [PMID: 37747943 DOI: 10.1002/cbic.202300566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 09/27/2023]
Abstract
We recently reported that some adenosine binding aptamers can also bind caffeine and theophylline with around 20-fold lower affinities. This discovery led to the current work to examine the cross-binding of adenosine to theophylline aptamers. For the DNA aptamer for theophylline, cross-binding to adenosine was observed, and the affinity was 18 to 38-fold lower for adenosine based on assays using isothermal titration calorimetry and ThT fluorescence spectroscopy. The binding complexes were characterized using NMR spectroscopy, and both adenosine and theophylline showed an overall similar binding structure to the DNA theophylline aptamer, although small differences were also observed. In contrast, the RNA aptamer did not show binding to adenosine, although both aptamers have very similar relative selectivity for various methylxanthines including caffeine. After a negative selection, a few new aptamers with completely different primary sequences for theophylline were obtained and they did not show binding to adenosine. Thus, there are many ways for aptamers to bind theophylline and some can have cross-binding to adenosine. In biology, theophylline, caffeine, and adenosine can bind to the same protein receptors to regulate sleep, and their binding to the same DNA motifs may suggest an early role of nucleic acids in similar regulatory functions.
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2 L 3G1, Canada
- Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2 L 3G1, Canada
| | - Natasha M Evans
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2 L 3G1, Canada
| | - Chang Lu
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2 L 3G1, Canada
| | - Albert Zehan Li
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2 L 3G1, Canada
| | - Thorsten Dieckmann
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2 L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2 L 3G1, Canada
- Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2 L 3G1, Canada
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12
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Juhász Á, Gombár G, Várkonyi EF, Wojnicki M, Ungor D, Csapó E. Thermodynamic Characterization of the Interaction of Biofunctionalized Gold Nanoclusters with Serum Albumin Using Two- and Three-Dimensional Methods. Int J Mol Sci 2023; 24:16760. [PMID: 38069083 PMCID: PMC10706308 DOI: 10.3390/ijms242316760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Fluorescent gold nanoclusters have been successfully used as fluorescent markers for imaging of cells and tissues, and their potential role in drug delivery monitoring is coming to the fore. In addition, the development of biosensors using structure-tunable fluorescent nanoclusters is also a prominent research field. In the case of these sensor applications, the typical goal is the selective identification of, e.g., metal ions, small molecules having neuroactive or antioxidant effects, or proteins. During these application-oriented developments, in general, there is not enough time to systematically examine the interaction between nanoclusters and relevant biomolecules/proteins from a thermodynamic viewpoint. In this way, the primary motivation of this article is to carry out a series of tests to partially fill this scientific gap. Besides the well-known fluorescent probes, the mentioned interactions were investigated using such unique measurement methods as surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC). These two-dimensional (at the solid/liquid interface) and three-dimensional (in the bulk phase) measuring techniques provide a unique opportunity for the thermodynamic characterization of the interaction between different gold nanoclusters containing various surface functionalizing ligands and bovine serum albumin (BSA).
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Affiliation(s)
- Ádám Juhász
- Interdisciplinary Excellence Center, Department of Physical Chemistry and Materials Science, University of Szeged, H-6720 Rerrich B. sqr. 1, 6720 Szeged, Hungary (E.F.V.); (D.U.)
- MTA-SZTE Lendület “Momentum” Noble Metal Nanostructures Research Group, University of Szeged, H-6720 Rerrich B. sqr. 1, 6720 Szeged, Hungary
| | - Gyöngyi Gombár
- Interdisciplinary Excellence Center, Department of Physical Chemistry and Materials Science, University of Szeged, H-6720 Rerrich B. sqr. 1, 6720 Szeged, Hungary (E.F.V.); (D.U.)
- MTA-SZTE Lendület “Momentum” Noble Metal Nanostructures Research Group, University of Szeged, H-6720 Rerrich B. sqr. 1, 6720 Szeged, Hungary
| | - Egon F. Várkonyi
- Interdisciplinary Excellence Center, Department of Physical Chemistry and Materials Science, University of Szeged, H-6720 Rerrich B. sqr. 1, 6720 Szeged, Hungary (E.F.V.); (D.U.)
| | - Marek Wojnicki
- Faculty of Non-Ferrous Metals, AGH University of Science and Technology, Mickiewicza Ave. 30, 30-059 Krakow, Poland;
| | - Ditta Ungor
- Interdisciplinary Excellence Center, Department of Physical Chemistry and Materials Science, University of Szeged, H-6720 Rerrich B. sqr. 1, 6720 Szeged, Hungary (E.F.V.); (D.U.)
| | - Edit Csapó
- Interdisciplinary Excellence Center, Department of Physical Chemistry and Materials Science, University of Szeged, H-6720 Rerrich B. sqr. 1, 6720 Szeged, Hungary (E.F.V.); (D.U.)
- MTA-SZTE Lendület “Momentum” Noble Metal Nanostructures Research Group, University of Szeged, H-6720 Rerrich B. sqr. 1, 6720 Szeged, Hungary
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13
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Zhang R, Gao Y, Chen L, Li D, Ge G. Tunable Gas-Gas Reactions through Nanobubble Pathway. Chemphyschem 2023; 24:e202300429. [PMID: 37534533 DOI: 10.1002/cphc.202300429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/26/2023] [Accepted: 08/02/2023] [Indexed: 08/04/2023]
Abstract
Combustible gas-gas reactions usually do not occur spontaneously upon mixing without ignition or other triggers to lower the activation energy barrier. Nanobubbles, however, could provide such a possibility in solution under ambient conditions due to high inner pressure and catalytic radicals within their boundary layers. Herein, a tunable gas-gas reaction strategy via bulk nanobubble pathway is developed by tuning the interface charge of one type of bulk nanobubble and promoting its fusion and reaction with another, where the reaction-accompanied size and number concentration change of the bulk nanobubbles and the corresponding thermal effect clearly confirm the occurrence of the nanobubble-based H2 /O2 combustion. In addition, abundant radicals can be detected during the reaction, which is considered to be critical to ignite the gas reaction during the fusion of nanobubbles in water at room temperature. Therefore, the nanobubble-based gas-gas reactions provide a safe and efficient pathway to produce energy and synthesize new matter inaccessible under mild or ambient conditions.
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Affiliation(s)
- Ruiyi Zhang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Ya Gao
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Lan Chen
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, P. R. China
| | - Dexing Li
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, P. R. China
| | - Guanglu Ge
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, P. R. China
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14
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Zhou S, Meng L, Lin Y, Dong X, Dong M. Exploring the Interactions of Soybean 7S Globulin with Gallic Acid, Chlorogenic Acid and (-)-Epigallocatechin Gallate. Foods 2023; 12:4013. [PMID: 37959132 PMCID: PMC10649178 DOI: 10.3390/foods12214013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
In this study, the noncovalent interaction mechanisms between soybean 7S globulin and three polyphenols (gallic acid (GA), chlorogenic acid (CA) and (-)-epigallocatechin gallate (EGCG)) were explored and compared using various techniques. Fluorescence experiments showed that GA and EGCG had strong static quenching effects on 7S fluorescence, and that of CA was the result of multiple mechanisms. The interactions caused changes to the secondary and tertiary structure of 7S, and the surface hydrophobicity was decreased. Thermodynamic experiments showed that the combinations of polyphenols with 7S were exothermic processes. Hydrogen bonds and van der Waals forces were the primary driving forces promoting the binding of EGCG and CA to 7S. The combination of GA was mainly affected by electrostatic interaction. The results showed that the structure and molecular weight of polyphenols play an important role in their interactions. This work is helpful for developing products containing polyphenols and soybean protein.
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Affiliation(s)
- Siduo Zhou
- Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China;
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ling Meng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- School of Public Health, Shandong First Medical University, Shandong Academy of Medical Sciences, 6699 Qingdao Road, Jinan 250117, China
| | - Yanfei Lin
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xueqian Dong
- Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China;
| | - Mingsheng Dong
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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15
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Sethi O, Singh M, Sood AK, Kang TS. Water Induced Alterations in Self-Assembly of a Bio-Surfactant in Deep Eutectic Solvent for Enhanced Enzyme Activity. Chemphyschem 2023; 24:e202300293. [PMID: 37431953 DOI: 10.1002/cphc.202300293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/08/2023] [Accepted: 07/11/2023] [Indexed: 07/12/2023]
Abstract
Deep eutectic solvents (DESs) meet important requirements for green solvent technology, including non-toxicity, biodegradability, sustainability, and affordability. Despite possessing low cohesive energy density than water, DESs have been found to support the self-assembly of amphiphiles. It is very much pertinent to examine the effect of water on self-assembly of surfactants in DESs as the presence of water alters the inherent structure of DES, which is expected to affect the characteristic properties of self-assembly. Following this, we have investigated the self-assembly of amino-acid based surfactant, Sodium N-lauroyl sarcosinate (SLS), in DES-water mixtures (10, 30 and 50 w/w% of water) and explored the catalytic activity of Cytochrome-c (Cyt-c) in the formed colloidal systems. Investigations using surface tension, fluorescence, dynamic light scattering (DLS), and isothermal titration calorimetry (ITC) have shown that DES-water mixtures promote the aggregation of SLS, resulting in the lower critical aggregation concentration (cac ∼1.5-6-fold) of the surfactant as compared to water. The nanoclustering of DES at low water content and it's complete de-structuring at high water content affects the self-assembly in a contrasting manner governed by different set of interactions. Further, Cyt-c dispersed in DES-water colloidal solutions demonstrated 5-fold higher peroxidase activity than that observed in phosphate buffer.
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Affiliation(s)
- Omish Sethi
- Department of Chemistry, UGC Centre for Advance Studies-II, Guru Nanak Dev University, Amritsar, 143005, Punjab, India
| | - Manpreet Singh
- Department of Chemistry, UGC Centre for Advance Studies-II, Guru Nanak Dev University, Amritsar, 143005, Punjab, India
| | - Ashwani Kumar Sood
- Department of Chemistry, UGC Centre for Advance Studies-II, Guru Nanak Dev University, Amritsar, 143005, Punjab, India
| | - Tejwant Singh Kang
- Department of Chemistry, UGC Centre for Advance Studies-II, Guru Nanak Dev University, Amritsar, 143005, Punjab, India
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16
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Watson PR, Stollmaier JG, Christianson DW. Crystal structure of histone deacetylase 6 complexed with (R)-lipoic acid, an essential cofactor in central carbon metabolism. J Biol Chem 2023; 299:105228. [PMID: 37703993 PMCID: PMC10622836 DOI: 10.1016/j.jbc.2023.105228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/28/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023] Open
Abstract
The enzyme cofactor (R)-lipoic acid plays a critical role in central carbon metabolism due to its catalytic function in the generation of acetyl-CoA, which links glycolysis with the tricarboxylic acid cycle. This cofactor is also essential for the generation of succinyl CoA within the tricarboxylic acid cycle. However, the biological functions of (R)-lipoic acid extend beyond metabolism owing to its facile redox chemistry. Most recently, the reduced form of (R)-lipoic acid, (R)-dihydrolipoic acid, has been shown to inhibit histone deacetylases (HDACs) with selectivity for the inhibition of HDAC6. Here, we report the 2.4 Å-resolution X-ray crystal structure of the complex between (R)-dihydrolipoic acid and HDAC6 catalytic domain 2 from Danio rerio, and we report a dissociation constant (KD) of 350 nM for this complex as determined by isothermal titration calorimetry. The crystal structure illuminates key affinity determinants in the enzyme active site, including thiolate-Zn2+ coordination and S-π interactions in the F583-F643 aromatic crevice. This study provides the first visualization of the connection between HDAC function and the biological response to oxidative stress: the dithiol moiety of (R)-dihydrolipoic acid can serve as a redox-regulated pharmacophore capable of simultaneously targeting the catalytic Zn2+ ion and the aromatic crevice in the active site of HDAC6.
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Affiliation(s)
- Paris R Watson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Juana Goulart Stollmaier
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States.
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17
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Bonarek P, Mularczyk D, Loch JI, Kurpiewska K, Dziedzicka-Wasylewska M. β-Lactoglobulin variants as potential carriers of pramoxine: Comprehensive structural and biophysical studies. J Mol Recognit 2023; 36:e3052. [PMID: 37610054 DOI: 10.1002/jmr.3052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/24/2023] [Accepted: 08/07/2023] [Indexed: 08/24/2023]
Abstract
β-Lactoglobulin (BLG) is a member of the lipocalin family. As other proteins from this group, BLG can be modified to bind specifically compounds of medical interests. The aim of this study was to evaluate the role of two mutations, L39Y and L58F, in the binding of topical anesthetic pramoxine (PRM) to β-lactoglobulin. Circular dichroism spectroscopy, isothermal titration calorimetry (ITC), and X-ray crystallography were used to understand the mechanisms of BLG-PRM interactions. Studies were performed for three new BLG mutants: L39Y, L58F, and L39Y/L58F. ITC measurements indicated a significant increase in the affinity to the PRM of variants L58F and L39Y. Measurements taken for the double mutant L39Y/L58F showed the additivity of two mutations leading to about 80-fold increase in the affinity to PRM in comparison to natural protein BLG from bovine milk. The determined crystal structures revealed that pramoxine is accommodated in the β-barrel interior of BLG mutants and stabilized by hydrophobic interactions. The observed additive effect of two mutations on drug binding opens the possibility for further designing of new BLG variants with high affinity to selected drugs.
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Affiliation(s)
- Piotr Bonarek
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Physical Biochemistry, Jagiellonian University, Kraków, Poland
| | - Dorota Mularczyk
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Physical Biochemistry, Jagiellonian University, Kraków, Poland
| | - Joanna I Loch
- Faculty of Chemistry, Department of Crystal Chemistry and Crystal Physics, Jagiellonian University, Kraków, Poland
| | - Katarzyna Kurpiewska
- Faculty of Chemistry, Department of Crystal Chemistry and Crystal Physics, Jagiellonian University, Kraków, Poland
| | - Marta Dziedzicka-Wasylewska
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Physical Biochemistry, Jagiellonian University, Kraków, Poland
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18
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Bekker GJ, Numoto N, Kawasaki M, Hayashi T, Yabuno S, Kozono Y, Shimizu T, Kozono H, Ito N, Oda M, Kamiya N. Elucidation of binding mechanism, affinity, and complex structure between mWT1 tumor-associated antigen peptide and HLA-A*24:02. Protein Sci 2023; 32:e4775. [PMID: 37661929 PMCID: PMC10510467 DOI: 10.1002/pro.4775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 08/02/2023] [Accepted: 08/29/2023] [Indexed: 09/05/2023]
Abstract
We have applied our advanced computational and experimental methodologies to investigate the complex structure and binding mechanism of a modified Wilms' Tumor 1 (mWT1) protein epitope to the understudied Asian-dominant allele HLA-A*24:02 (HLA-A24) in aqueous solution. We have applied our developed multicanonical molecular dynamics (McMD)-based dynamic docking method to analyze the binding pathway and mechanism, which we verified by comparing the highest probability structures from simulation with our experimentally solved x-ray crystal structure. Subsequent path sampling MD simulations elucidated the atomic details of the binding process and indicated that first an encounter complex is formed between the N-terminal's positive charge of the 9-residue mWT1 fragment peptide and a cluster of negative residues on the surface of HLA-A24, with the major histocompatibility complex (MHC) molecule preferring a predominantly closed conformation. The peptide first binds to this closed MHC conformation, forming an encounter complex, after which the binding site opens due to increased entropy of the binding site, allowing the peptide to bind to form the native complex structure. Further sequence and structure analyses also suggest that although the peptide loading complex would help with stabilizing the MHC molecule, the binding depends in a large part on the intrinsic affinity between the MHC molecule and the antigen peptide. Finally, our computational tools and analyses can be of great benefit to study the binding mechanism of different MHC types to their antigens, where it could also be useful in the development of higher affinity variant peptides and for personalized medicine.
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Affiliation(s)
- Gert-Jan Bekker
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Nobutaka Numoto
- Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Maki Kawasaki
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Kyoto, Japan
| | - Takahiro Hayashi
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Kyoto, Japan
| | - Saaya Yabuno
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Kyoto, Japan
| | - Yuko Kozono
- Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, Japan
| | - Takeyuki Shimizu
- Department of Immunology, Kochi Medical School, Kochi University, Nankoku-shi, Kochi, Japan
| | - Haruo Kozono
- Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, Japan
| | - Nobutoshi Ito
- Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Masayuki Oda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Kyoto, Japan
| | - Narutoshi Kamiya
- Graduate School of Information Science, University of Hyogo, Kobe, Hyogo, Japan
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19
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Adnan M, DasGupta D, Anwar S, Shamsi A, Siddiqui AJ, Snoussi M, Bardakci F, Patel M, Hassan MI. Mechanistic insights into MARK4 inhibition by galantamine toward therapeutic targeting of Alzheimer's disease. Front Pharmacol 2023; 14:1276179. [PMID: 37795023 PMCID: PMC10546050 DOI: 10.3389/fphar.2023.1276179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 09/04/2023] [Indexed: 10/06/2023] Open
Abstract
Introduction: Hyperphosphorylation of tau is an important event in Alzheimer's disease (AD) pathogenesis, leading to the generation of "neurofibrillary tangles," a histopathological hallmark associated with the onset of AD and related tauopathies. Microtubule-affinity regulating kinase 4 (MARK4) is an evolutionarily conserved Ser-Thr (S/T) kinase that phosphorylates tau and microtubule-associated proteins, thus playing a critical role in AD pathology. The uncontrolled neuronal migration is attributed to overexpressed MARK4, leading to disruption in microtubule dynamics. Inhibiting MARK4 is an attractive strategy in AD therapeutics. Methods: Molecular docking was performed to see the interactions between MARK4 and galantamine (GLT). Furthermore, 250 ns molecular dynamic studies were performed to investigate the stability and conformational dynamics of the MARK4-GLT complex. We performed fluorescence binding and isothermal titration calorimetry studies to measure the binding affinity between GLT and MARK4. Finally, an enzyme inhibition assay was performed to measure the MARK4 activity in the presence and absence of GLT. Results: We showed that GLT, an acetylcholinesterase inhibitor, binds to the active site cavity of MARK4 with an appreciable binding affinity. Molecular dynamic simulation for 250 ns demonstrated the stability and conformational dynamics of the MARK4-GLT complex. Fluorescence binding and isothermal titration calorimetry studies suggested a strong binding affinity. We further show that GLT inhibits the kinase activity of MARK4 significantly (IC50 = 5.87 µM). Conclusion: These results suggest that GLT is a potential inhibitor of MARK4 and could be a promising therapeutic target for AD. GLT's inhibition of MARK4 provides newer insights into the mechanism of GLT's action, which is already used to improve cognition in AD patients.
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Affiliation(s)
- Mohd Adnan
- Department of Biology, College of Science, University of Ha’il, Ha’il, Saudi Arabia
| | - Debarati DasGupta
- College of Pharmacy, University of Michigan, Ann Arbor, MI, United States
| | - Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, New Delhi, India
| | - Anas Shamsi
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Arif Jamal Siddiqui
- Department of Biology, College of Science, University of Ha’il, Ha’il, Saudi Arabia
| | - Mejdi Snoussi
- Department of Biology, College of Science, University of Ha’il, Ha’il, Saudi Arabia
| | - Fevzi Bardakci
- Department of Biology, College of Science, University of Ha’il, Ha’il, Saudi Arabia
| | - Mitesh Patel
- Research and Development Cell, Department of Biotechnology, Parul Institute of Applied Sciences, Parul University, Vadodara, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, New Delhi, India
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20
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Barry CJ, Pillay CS, Rohwer JM. Modelling the Decamerisation Cycle of PRDX1 and the Inhibition-like Effect on Its Peroxidase Activity. Antioxidants (Basel) 2023; 12:1707. [PMID: 37760010 PMCID: PMC10525498 DOI: 10.3390/antiox12091707] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/25/2023] [Accepted: 08/26/2023] [Indexed: 09/29/2023] Open
Abstract
Peroxiredoxins play central roles in the detoxification of reactive oxygen species and have been modelled across multiple organisms using a variety of kinetic methods. However, the peroxiredoxin dimer-to-decamer transition has been underappreciated in these studies despite the 100-fold difference in activity between these forms. This is due to the lack of available kinetics and a theoretical framework for modelling this process. Using published isothermal titration calorimetry data, we obtained association and dissociation rate constants of 0.050 µM-4·s-1 and 0.055 s-1, respectively, for the dimer-decamer transition of human PRDX1. We developed an approach that greatly reduces the number of reactions and species needed to model the peroxiredoxin decamer oxidation cycle. Using these data, we simulated horse radish peroxidase competition and NADPH-oxidation linked assays and found that the dimer-decamer transition had an inhibition-like effect on peroxidase activity. Further, we incorporated this dimer-decamer topology and kinetics into a published and validated in vivo model of PRDX2 in the erythrocyte and found that it almost perfectly reconciled experimental and simulated responses of PRDX2 oxidation state to hydrogen peroxide insult. By accounting for the dimer-decamer transition of peroxiredoxins, we were able to resolve several discrepancies between experimental data and available kinetic models.
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Affiliation(s)
- Christopher J. Barry
- Laboratory for Molecular Systems Biology, Department of Biochemistry, Stellenbosch University, Stellenbosch 7600, South Africa;
| | - Ché S. Pillay
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg 3201, South Africa;
| | - Johann M. Rohwer
- Laboratory for Molecular Systems Biology, Department of Biochemistry, Stellenbosch University, Stellenbosch 7600, South Africa;
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21
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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 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] [What about the content of this article? (0)] [Affiliation(s)] [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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22
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Watson PR, Stollmaier JG, Christianson DW. Crystal Structure of Histone Deacetylase 6 Complexed with ( R )-Lipoic Acid, an Essential Cofactor in Central Carbon Metabolism. bioRxiv 2023:2023.08.08.552419. [PMID: 37609266 PMCID: PMC10441330 DOI: 10.1101/2023.08.08.552419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The enzyme cofactor ( R )-lipoic acid plays a critical role in central carbon metabolism due to its catalytic function in the generation of acetyl-CoA, which links glycolysis with the tricarboxylic acid cycle. This cofactor is also essential for the generation of succinyl CoA within the tricarboxylic acid cycle. However, the biological functions of ( R )-lipoic acid extend beyond metabolism owing to its facile redox chemistry. Most recently, the reduced form of ( R )-lipoic acid, ( R )-dihydrolipoic acid, has been shown to inhibit histone deacetylases (HDACs) with selectivity for the inhibition of HDAC6. Here, we report the 2.4 Å-resolution X-ray crystal structure of the HDAC6-( R )-dihydrolipoic acid complex, and we report a dissociation constant (K D ) of 350 nM for this complex as determined by isothermal titration calorimetry. The crystal structure illuminates key affinity determinants in the enzyme active site, including thiolate-Zn 2+ coordination and S-π interactions in the F583-F643 aromatic crevice. This study provides the first visualization of the connection between HDAC function and the biological response to oxidative stress: the dithiol moiety of ( R )-dihydrolipoic acid can serve as a redox-regulated pharmacophore capable of simultaneously targeting the catalytic Zn 2+ ion and the aromatic crevice in the active site of HDAC6.
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Affiliation(s)
- Paris R. Watson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104-6323, United States
| | - Juana Goulart Stollmaier
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104-6323, United States
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104-6323, United States
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23
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Masternak M, Koch A, Laulumaa S, Tapken D, Hollmann M, Jørgensen FS, Kastrup JS. Differences between the GluD1 and GluD2 receptors revealed by GluD1 X-ray crystallography, binding studies and molecular dynamics. FEBS J 2023; 290:3781-3801. [PMID: 36128700 DOI: 10.1111/febs.16631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 07/29/2022] [Accepted: 09/20/2022] [Indexed: 08/03/2023]
Abstract
Ionotropic glutamate receptors are ligand-gated ion channels essential for fast excitatory neurotransmission in the brain. In contrast to most other members of the iGluR family, the subfamily of delta receptors, GluD1 and GluD2, does not bind glutamate but glycine/D-serine. GluD1 is widely expressed in the brain and the inner ear, where it is required for high-frequency hearing. Furthermore, it has been associated with schizophrenia, autism and depression. X-ray structures of the ligand-binding domain (LBD) of GluD2 have been published; however, no high-resolution structure is available for the ligand-binding domain of GluD1 (GluD1-LBD). Here, we report the X-ray crystal structure of the GluD1-LBD in its apo form at 2.57 Å resolution. Using isothermal titration calorimetry, we show that D-serine binds to the GluD1-LBD in an exothermic manner with a Kd of 160 μm, which is approximately five-fold greater than at GluD2. Furthermore, we identify Glu822 as a critical determinant of receptor activation in GluD1 A654T. In contrast to studies on the GluD2 lurcher mutant A654T, we did not observe any effect of 1 mm D-serine on the spontaneous currents at mouse GluD1 A654T by electrophysiological recordings of Xenopus laevis oocytes as previously also reported by others. These results point towards differences in the structure and dynamics between GluD1 and GluD2. Molecular dynamics simulations were employed to address this observation, suggesting that the apo structure of GluD1 is less flexible than the apo structure of GluD2 and that Pro725 in GluD1 may affect the interlobe closure of the ligand-binding domain of GluD1.
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Affiliation(s)
- Magdalena Masternak
- Department of Drug Design and Pharmacology, University of Copenhagen, Denmark
| | - Angela Koch
- Department of Biochemistry I - Receptor Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Germany
- Institute of Neural and Sensory Physiology, Medical Faculty, Heinrich Heine University Düsseldorf, Germany
| | - Saara Laulumaa
- Department of Drug Design and Pharmacology, University of Copenhagen, Denmark
| | - Daniel Tapken
- Department of Biochemistry I - Receptor Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Germany
| | - Michael Hollmann
- Department of Biochemistry I - Receptor Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Germany
| | - Flemming Steen Jørgensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Denmark
- Research Cluster on Personalised Medicine, Copenhagen, Denmark
| | - Jette Sandholm Kastrup
- Department of Drug Design and Pharmacology, University of Copenhagen, Denmark
- Research Cluster on Molecular Neuroprotection, Copenhagen, Denmark
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24
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Devi Tulsiyan K, Rani Prusty M, Biswal HS. Effect of Choline Amino Acid-Based Ionic Liquids on Stability and Structure of Hemoglobin. Chemphyschem 2023; 24:e202300201. [PMID: 37272734 DOI: 10.1002/cphc.202300201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/05/2023] [Accepted: 06/05/2023] [Indexed: 06/06/2023]
Abstract
Ionic liquids (ILs) can stabilize or destabilize proteins, which motivates us to examine their effect on hemoglobin. The native state of hemoglobin (Hb) is disrupted at different physical conditions such as pressure, temperature, and solvents. Herein, we have monitored the stability of Hb in a nontoxic and biocompatible IL, i. e., choline amino acid-based Ils (ChAAILs), using various spectroscopic techniques like UV-Vis and fluorescence spectroscopy, circular dichroism (CD), and isothermal titration calorimetry (ITC) measurements. It was observed that Hb stays neither in its native state nor in its fully denatured state; rather, it achieves an intermediate state in the presence of ChAAILs. The research on the intermediate state of Hb is still unexplored. Research has been pursued to find a suitable ligand or IL that can stabilize the intermediate state of Hb. In that context, ChAAILs are among the best choices. Molecular docking studies unravel the binding of ChAAILs with Hb. The obtained binding energies of the docked complex are -7.2 kcal/mol and -8.7 kcal/mol for binding of Hb with [Chl][Gly] and [Chl][Met], respectively, which was in line with the ITC results. The quantum chemical calculations show that H-bond plays a significant role for the interaction between Hb and ChAAILs.
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Affiliation(s)
- Kiran Devi Tulsiyan
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Jatni, Khurda, Bhubaneswar, 752050, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Mallika Rani Prusty
- School of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Berhampur, Odisha, 760010, India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Jatni, Khurda, Bhubaneswar, 752050, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
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25
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Sillanpää M, Engström MT, Tähtinen P, Green RJ, Käpylä J, Näreaho A, Karonen M. Tannins Can Have Direct Interactions with Anthelmintics: Investigations by Isothermal Titration Calorimetry. Molecules 2023; 28:5261. [PMID: 37446937 DOI: 10.3390/molecules28135261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/28/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
Plant tannins are known for their anthelmintic and antiparasitic activities and have been increasingly studied to battle the ever-growing problem of anthelmintic resistance. While tannins have been shown to exhibit these activities on their own, one approach would be to use them as complementary nutrients alongside commercial anthelmintics. So far, research on the interactions between tannins and anthelmintics is limited, and few studies have reported both synergistic and antagonistic effects depending on the type of tannin and the method used. These interactions could either strengthen or weaken the efficacy of commercial anthelmintics, especially if tannin-rich diets are combined with anthelmintics used as oral drenches. To study these interactions, a series of hydrolysable tannins (HTs) was selected, and their direct interactions with thiabendazole (TBZ) were evaluated by isothermal titration calorimetry (ITC), which allowed the detection of the exothermic interaction but also the roles and significances of different structural features of HTs in these interactions. Our results show that HTs can have a direct interaction with the benzimidazole anthelmintic TBZ and that the interaction is strengthened by increasing the number of free galloyl groups and the overall molecular flexibility of HTs.
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Affiliation(s)
- Mimosa Sillanpää
- Department of Chemistry, University of Turku, FI-20014 Turku, Finland
| | - Marica T Engström
- Department of Chemistry, University of Turku, FI-20014 Turku, Finland
| | - Petri Tähtinen
- Department of Chemistry, University of Turku, FI-20014 Turku, Finland
| | - Rebecca J Green
- School of Chemistry, Food and Pharmacy, University of Reading, Whiteknights, P.O. Box 224, Reading RG6 6AP, UK
| | - Jarmo Käpylä
- Department of Life Technologies, University of Turku, FI-20014 Turku, Finland
| | - Anu Näreaho
- Department of Veterinary Biosciences, University of Helsinki, FI-00014 Helsinki, Finland
| | - Maarit Karonen
- Department of Chemistry, University of Turku, FI-20014 Turku, Finland
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Araujo-Abad S, Rizzuti B, Villamarin-Ortiz A, Pantoja-Uceda D, Moreno-Gonzalez CM, Abian O, Velazquez-Campoy A, Neira JL, Romero CDJ. New insights into cancer: MDM2 binds to the citrullinating enzyme PADI4. Protein Sci 2023:e4723. [PMID: 37409874 PMCID: PMC10364586 DOI: 10.1002/pro.4723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/07/2023]
Abstract
PADI4 is one of the human isoforms of a family of enzymes implicated in the conversion of arginine to citrulline. MDM2 is an E3 ubiquitin ligase which is crucial for down-regulation of degradation of the tumor suppressor gene p53. Given the relationship between both PADI4 and MDM2 with p53-signaling pathways, we hypothesized they may interact directly, and this interaction could be relevant in the context of cancer. Here, we showed their association in the nucleus and cytosol in several cancer cell lines. Furthermore, binding was hampered in the presence of GSK484, an enzymatic PADI4 inhibitor, suggesting that MDM2 could bind to the active site of PADI4, as confirmed by in silico experiments. In vitro and in silico studies showed that the isolated N-terminal region of MDM2, N-MDM2, interacted with PADI4, and residues Thr26, Val28, Phe91 and Lys98 were more affected by the presence of the enzyme. Moreover, the dissociation constant between N-MDM2 and PADI4 was comparable to the IC50 of GSK484 from in cellulo experiments. The interaction between MDM2 and PADI4 might imply MDM2 citrullination, with potential therapeutic relevance for improving cancer treatment, due to the generation of new antigens. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Salomé Araujo-Abad
- IDIBE, Universidad Miguel Hernández, Elche (Alicante), Spain
- Centro de Biotecnología, Universidad Nacional de Loja, Avda, Pío Jaramillo Alvarado s/n, Loja, Loja, Ecuador
| | - Bruno Rizzuti
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) - Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain
- CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, Rende, Italy
| | | | | | | | - Olga Abian
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) - Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
| | - Adrián Velazquez-Campoy
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) - Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
| | - José L Neira
- IDIBE, Universidad Miguel Hernández, Elche (Alicante), Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) - Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain
| | - Camino de Juan Romero
- IDIBE, Universidad Miguel Hernández, Elche (Alicante), Spain
- Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, 03203, Elche (Alicante), Spain
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27
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Komives EA. Dynamic allostery in thrombin-a review. Front Mol Biosci 2023; 10:1200465. [PMID: 37457835 PMCID: PMC10339233 DOI: 10.3389/fmolb.2023.1200465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023] Open
Abstract
Thrombin is a serine protease that catalyzes a large number of different reactions including proteolytic cleave of fibrinogen to make the fibrin clot (procoagulant activity), of the protease activated receptors (for cell signaling) and of protein C generating activated protein C (anticoagulant activity). Thrombin has an effector binding site called the anion binding exosite 1 that is allosterically coupled to the active site. In this review, we survey results from thermodynamic characterization of the allosteric coupling as well as hydrogen-deuterium exchange mass spectrometry to reveal which parts of the thrombin structure are changed upon effector binding and/or mutagenesis, and finally NMR spectroscopy to characterize the different timescales of motions elicited by the effectors. We also relate the experimental work to computational network analysis of the thrombin-thrombomodulin complex.
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28
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Seeba NN, Risti R, Lõokene A. Lipoprotein Lipase Activity Does Not Differ in the Serum Environment of Vegans and Omnivores. Nutrients 2023; 15:2755. [PMID: 37375658 DOI: 10.3390/nu15122755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Although vegan diets have been reported to be associated with a reduced risk of cardiovascular disease, it was not known whether this might be partly due to vegan diets' effects on plasma triglyceride metabolism. This study aimed to investigate if there are differences in the activity of lipoprotein lipase (LPL), an enzyme that functions at the vascular endothelium and is responsible for triglyceride breakdown, in sera obtained from vegans and omnivores. LPL activity was assessed using isothermal titration calorimetry, which allows measurements in undiluted serum samples, mimicking physiological conditions. Fasted sera from 31 healthy participants (12F 2M vegans, 11F 6M omnivores) were analyzed. The results indicated no significant differences in average LPL activity between the vegan and omnivore groups. Interestingly, despite similar triglyceride levels, there were considerable variations in LPL activity and total very-low-density lipoprotein triglyceride breakdowns between individuals within both groups. Biomarker analysis showed that vegans had lower total cholesterol and LDL-C levels compared to omnivores. These findings suggest that the lipid-related benefits of a vegan diet, in terms of atherogenic risk, may primarily stem from cholesterol reduction rather than affecting serum as a medium for LPL-mediated triglyceride breakdown. In healthy individuals, lipid-related changes in serum composition in response to a vegan diet are likely overshadowed by genetic or other lifestyle factors.
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Affiliation(s)
- Natjan-Naatan Seeba
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia
| | - Robert Risti
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia
| | - Aivar Lõokene
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia
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29
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Andaç C, Çağlar S, Denizli A, Andaç M. Isothermal Titration Calorimetry binding properties of Cibacron Blue F3GA in complex with Human Serum Albumin. J Mol Recognit 2023:e3040. [PMID: 37219027 DOI: 10.1002/jmr.3040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/24/2023]
Abstract
Binding interactions between cibacron blue-F3GA (CB-F3GA) and human serum albumin (HSA, at physiologically ten-fold lower concentration) was studied by isothermal titration calorimetry (ITC) and in-silico docking computations. ITC experiments revealed two separate binding sites on HSA with different binding affinities for CB-F3GA. The high-affinity binding site (PBS-II) on HSA binds CB-F3GA at nanomolar scale (KD1 =118±107 nM) with favorable binding enthalpy (ΔHo 1 = - 6.47±0.44 kcal/mol) and entropy (-TΔSo 1 = -2.98 kcal/mol) energies. CB-F3GA binds to the low-affinity binding site (PBS-I) at μM scale (KD2 = 31.20±18.40 μM) with favorable binding enthalpy (ΔHo 1 = - 5.03±3.86x10-2 kcal/mol) and entropy (-TΔSo 1 = -1.12 kcal/mol) energies. ITC binding data strongly suggest that CB-F3GA binding to PBS-II site increases the formation of dimeric-HSA clusters (N1 = 2.43 ± 0.50), while binding to PBS-I leads to tetrameric-HSA clusters (N2 = 4.61 ± 0.90). These results suggest that a higher degree of HSA aggregation upon drug binding may be expected under physiological conditions, a notion that should be further investigated for the delivery and toxicity of drug.HSA interactions. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Cenk Andaç
- Department of Medical Pharmacology, School of Medicine, Yeditepe University, Istanbul, Turkey
| | - Sena Çağlar
- Department of Analytical Chemistry, School of Pharmacy, Istanbul University, Istanbul, Turkey
| | - Adil Denizli
- Biochemistry Division, Department of Chemistry, Hacettepe University, Ankara, Turkey
| | - Müge Andaç
- Environmental Engineering Department, Hacettepe University, Ankara, Turkey
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30
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Kerep R, Šeba T, Borko V, Weitner T, Keser T, Lauc G, Gabričević M. Potential Clinically Relevant Effects of Sialylation on Human Serum AAG-Drug Interactions Assessed by Isothermal Titration Calorimetry: Insight into Pharmacoglycomics? Int J Mol Sci 2023; 24:8472. [PMID: 37239819 PMCID: PMC10218007 DOI: 10.3390/ijms24108472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/18/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
Human serum alpha-1 acid glycoprotein is an acute-phase plasma protein involved in the binding and transport of many drugs, especially basic and lipophilic substances. It has been reported that the sialic acid groups that terminate the N-glycan chains of alpha-1 acid glycoprotein change in response to certain health conditions and may have a major impact on drug binding to alpha-1 acid glycoprotein. The interaction between native or desialylated alpha-1 acid glycoprotein and four representative drugs-clindamycin, diltiazem, lidocaine, and warfarin-was quantitatively evaluated using isothermal titration calorimetry. The calorimetry assay used here is a convenient and widely used approach to directly measure the amount of heat released or absorbed during the association processes of biomolecules in solution and to quantitatively estimate the thermodynamics of the interaction. The results showed that the binding of drugs with alpha-1 acid glycoprotein were enthalpy-driven exothermic interactions, and the binding affinity was in the range of 10-5-10-6 M. Desialylated alpha-1 acid glycoprotein showed significantly different binding with diltiazem, lidocaine, and warfarin compared with native alpha-1 acid glycoprotein, whereas clindamycin showed no significant difference. Therefore, a different degree of sialylation may result in different binding affinities, and the clinical significance of changes in sialylation or glycosylation of alpha-1 acid glycoprotein in general should not be neglected.
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Affiliation(s)
- Robert Kerep
- Department of General and Inorganic Chemistry, Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia
| | - Tino Šeba
- Department of General and Inorganic Chemistry, Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia
| | - Valentina Borko
- Department of General and Inorganic Chemistry, Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia
| | - Tin Weitner
- Department of General and Inorganic Chemistry, Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia
| | - Toma Keser
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia
| | - Gordan Lauc
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia
| | - Mario Gabričević
- Department of General and Inorganic Chemistry, Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia
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31
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Medvedíková M, Ranc V, Vančo J, Trávníček Z, Anzenbacher P. Highly Cytotoxic Copper(II) Mixed-Ligand Quinolinonato Complexes: Pharmacokinetic Properties and Interactions with Drug Metabolizing Cytochromes P450. Pharmaceutics 2023; 15:pharmaceutics15041314. [PMID: 37111801 PMCID: PMC10146558 DOI: 10.3390/pharmaceutics15041314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/13/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
The effects of two anticancer active copper(II) mixed-ligand complexes of the type [Cu(qui)(mphen)]Y·H2O, where Hqui = 2-phenyl-3-hydroxy- 1H-quinolin-4-one, mphen = bathophenanthroline, and Y = NO3 (complex 1) or BF4 (complex 2) on the activities of different isoenzymes of cytochrome P450 (CYP) have been evaluated. The screening revealed significant inhibitory effects of the complexes on CYP3A4/5 (IC50 values were 2.46 and 4.88 μM), CYP2C9 (IC50 values were 16.34 and 37.25 μM), and CYP2C19 (IC50 values were 61.21 and 77.07 μM). Further, the analysis of mechanisms of action uncovered a non-competitive type of inhibition for both the studied compounds. Consequent studies of pharmacokinetic properties proved good stability of both the complexes in phosphate buffer saline (>96% stability) and human plasma (>91% stability) after 2 h of incubation. Both compounds are moderately metabolised by human liver microsomes (<30% after 1 h of incubation), and over 90% of the complexes bind to plasma proteins. The obtained results showed the potential of complexes 1 and 2 to interact with major metabolic pathways of drugs and, as a consequence of this finding, their apparent incompatibility in combination therapy with most chemotherapeutic agents.
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Affiliation(s)
- Martina Medvedíková
- Department of Pharmacology, Faculty of Medicine and Dentistry, Palacký University in Olomouc, Hněvotínská 3, 779 00 Olomouc, Czech Republic
- Institute of Molecular and Translation Medicine, Faculty of Medicine and Dentistry, Palacký University in Olomouc, Hněvotínská 5, 779 00 Olomouc, Czech Republic
| | - Václav Ranc
- Institute of Molecular and Translation Medicine, Faculty of Medicine and Dentistry, Palacký University in Olomouc, Hněvotínská 5, 779 00 Olomouc, Czech Republic
| | - Ján Vančo
- Regional Centre of Advanced Technologies and Materials (RCPTM), Czech Advanced Technology and Research Institute (CATRIN), Palacký University in Olomouc, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
| | - Zdeněk Trávníček
- Regional Centre of Advanced Technologies and Materials (RCPTM), Czech Advanced Technology and Research Institute (CATRIN), Palacký University in Olomouc, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
| | - Pavel Anzenbacher
- Department of Pharmacology, Faculty of Medicine and Dentistry, Palacký University in Olomouc, Hněvotínská 3, 779 00 Olomouc, Czech Republic
- Institute of Molecular and Translation Medicine, Faculty of Medicine and Dentistry, Palacký University in Olomouc, Hněvotínská 5, 779 00 Olomouc, Czech Republic
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32
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Díaz Casas A, Cordoba JJ, Ferrer BJ, Balakrishnan S, Wurm JE, Pastrana‐Ríos B, Chazin WJ. Binding by calmodulin is coupled to transient unfolding of the third FF domain of Prp40A. Protein Sci 2023; 32:e4606. [PMID: 36810829 PMCID: PMC10022492 DOI: 10.1002/pro.4606] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/16/2023] [Accepted: 02/18/2023] [Indexed: 02/24/2023]
Abstract
Human pre-mRNA processing protein 40 homolog A (hPrp40A) is a splicing factor that interacts with the Huntington's disease protein huntingtin (Htt). Evidence has accumulated that both Htt and hPrp40A are modulated by the intracellular Ca2+ sensor calmodulin (CaM). Here we report characterization of the interaction of human CM with the third FF domain (FF3 ) of hPrp40A using calorimetric, fluorescence and structural approaches. Homology modeling, differential scanning calorimetry and small angle X-ray scattering (SAXS) data show FF3 forms a folded globular domain. CaM was found to bind FF3 in a Ca2+ -dependent manner with a 1:1 stoichiometry and a dissociation constant (Kd ) of 25 ± 3 μM at 25°C. NMR studies showed that both domains of CaM are engaged in binding and SAXS analysis of the FF3 -CaM complex revealed CaM occupies an extended configuration. Analysis of the FF3 sequence showed that the anchors for CaM binding must be buried in its hydrophobic core, suggesting that binding to CaM requires unfolding of FF3 . Trp anchors were proposed based on sequence analysis and confirmed by intrinsic Trp fluorescence of FF3 upon binding of CaM and substantial reductions in affinity for Trp-Ala FF3 mutants. The consensus model of the complex showed that binding to CaM binding occurs to an extended, non-globular state of the FF3 , consistent with coupling to transient unfolding of the domain. The implications of these results are discussed in the context of the complex interplay of Ca2+ signaling and Ca2+ sensor proteins in modulating Prp40A-Htt function.
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Affiliation(s)
- A. Díaz Casas
- Department of BiochemistryVanderbilt UniversityNashvilleTennesseeUSA
- Center for Structural BiologyVanderbilt UniversityNashvilleTennesseeUSA
- Present address:
Department of Natural SciencesPontifical Catholic University of Puerto RicoPoncePuerto RicoUSA
| | - J. J. Cordoba
- Department of BiochemistryVanderbilt UniversityNashvilleTennesseeUSA
- Center for Structural BiologyVanderbilt UniversityNashvilleTennesseeUSA
- Chemical and Physical Biology Graduate ProgramVanderbilt UniversityNashvilleTennesseeUSA
| | - B. J. Ferrer
- Department of BiochemistryVanderbilt UniversityNashvilleTennesseeUSA
- Center for Structural BiologyVanderbilt UniversityNashvilleTennesseeUSA
- Chemical and Physical Biology Graduate ProgramVanderbilt UniversityNashvilleTennesseeUSA
| | - S. Balakrishnan
- Department of BiochemistryVanderbilt UniversityNashvilleTennesseeUSA
- Center for Structural BiologyVanderbilt UniversityNashvilleTennesseeUSA
| | - J. E. Wurm
- Chemical and Physical Biology Graduate ProgramVanderbilt UniversityNashvilleTennesseeUSA
| | - B. Pastrana‐Ríos
- Department of ChemistryUniversity of Puerto Rico, Mayagüez CampusMayagüezPuerto RicoUSA
| | - W. J. Chazin
- Department of BiochemistryVanderbilt UniversityNashvilleTennesseeUSA
- Center for Structural BiologyVanderbilt UniversityNashvilleTennesseeUSA
- Chemical and Physical Biology Graduate ProgramVanderbilt UniversityNashvilleTennesseeUSA
- Department of ChemistryVanderbilt UniversityNashvilleTennesseeUSA
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33
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Elimelech O, Oded M, Harries D, Banin U. Spontaneous Patterning of Binary Ligand Mixtures on CdSe Nanocrystals: From Random to Janus Packing. ACS Nano 2023; 17:5852-5860. [PMID: 36893308 PMCID: PMC10061916 DOI: 10.1021/acsnano.2c12676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
Binary compositions of surface ligands are known to improve the colloidal stability and fluorescence quantum yield of nanocrystals (NCs), due to ligand-ligand interactions and surface organization. Herein, we follow the thermodynamics of a ligand exchange reaction of CdSe NCs with alkylthiol mixtures. The effects of ligand polarity and length difference on ligand packing were investigated using isothermal titration calorimetry (ITC). The thermodynamic signature of the formation of mixed ligand shells was observed. Correlating the experimental results with thermodynamic mixing models has allowed us to calculate the interchain interactions and to infer the final ligand shell configuration. Our findings demonstrate that, in contrast to macroscopic surfaces, the small dimensions of the NCs and the subsequent increased interfacial region between dissimilar ligands allow the formation of a myriad of clustering patterns, controlled by the interligand interactions. This work provides a fundamental understanding of the parameters determining the ligand shell structure and should help guide smart surface design toward NC-based applications.
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Affiliation(s)
- Orian Elimelech
- The
Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Meirav Oded
- The
Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Daniel Harries
- The
Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- The
Fritz Haber Center, The Hebrew University
of Jerusalem, Jerusalem 9190401, Israel
| | - Uri Banin
- The
Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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34
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Mariño-Ocampo N, Rodríguez DF, Guerra Díaz D, Zúñiga-Núñez D, Duarte Y, Fuentealba D, Zacconi FC. Direct Oral FXa Inhibitors Binding to Human Serum Albumin: Spectroscopic, Calorimetric, and Computational Studies. Int J Mol Sci 2023; 24:ijms24054900. [PMID: 36902328 PMCID: PMC10002493 DOI: 10.3390/ijms24054900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/26/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
Direct FXa inhibitors are an important class of bioactive molecules (rivaroxaban, apixaban, edoxaban, and betrixaban) applied for thromboprophylaxis in diverse cardiovascular pathologies. The interaction of active compounds with human serum albumin (HSA), the most abundant protein in blood plasma, is a key research area and provides crucial information about drugs' pharmacokinetics and pharmacodynamic properties. This research focuses on the study of the interactions between HSA and four commercially available direct oral FXa inhibitors, applying methodologies including steady-state and time-resolved fluorescence, isothermal titration calorimetry (ITC), and molecular dynamics. The HSA complexation of FXa inhibitors was found to occur via static quenching, and the complex formation in the ground states affects the fluorescence of HSA, with a moderate binding constant of 104 M-1. However, the ITC studies reported significantly different binding constants (103 M-1) compared with the results obtained through spectrophotometric methods. The suspected binding mode is supported by molecular dynamics simulations, where the predominant interactions were hydrogen bonds and hydrophobic interactions (mainly π-π stacking interactions between the phenyl ring of FXa inhibitors and the indole moiety of Trp214). Finally, the possible implications of the obtained results regarding pathologies such as hypoalbuminemia are briefly discussed.
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Affiliation(s)
- Nory Mariño-Ocampo
- Escuela de Química, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Diego F. Rodríguez
- Escuela de Química, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Daniel Guerra Díaz
- Escuela de Química, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Daniel Zúñiga-Núñez
- Escuela de Química, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Yorley Duarte
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370035, Chile
| | - Denis Fuentealba
- Escuela de Química, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Correspondence: (D.F.); (F.C.Z.)
| | - Flavia C. Zacconi
- Escuela de Química, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Centro de Investigaciones en Nanotecnología y Materiales Avanzados, CIEN-UC, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Center for Nanomedicine, Diagnostic & Drug Development (ND3), Universidad de Talca, Talca 3460000, Chile
- Correspondence: (D.F.); (F.C.Z.)
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35
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Liang X, Kong Y, Sun H, Zhao R, Jiao L, Zhang W, Liu B. Study on the Interaction Mechanism of Methoxy Polyethylene Glycol Maleimide with Sweet Potato β-Amylase. Molecules 2023; 28. [PMID: 36903434 DOI: 10.3390/molecules28052188] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/02/2023] Open
Abstract
In this study, sweet potato β-amylase (SPA) was modified by methoxy polyethylene glycol maleimide (molecular weight 5000, Mal-mPEG5000) to obtain the Mal-mPEG5000-SPA modified β-amylase and the interaction mechanism between SPA and Mal-mPEG5000 was investigated. the changes in the functional groups of different amide bands and modifications in the secondary structure of enzyme protein were analyzed using infrared spectroscopy and circular dichroism spectroscopy. The addition of Mal-mPEG5000 transformed the random curl in the SPA secondary structure into a helix structure, forming a folded structure. The Mal-mPEG5000 improved the thermal stability of SPA and protected the structure of the protein from breaking by the surrounding. The thermodynamic analysis further implied that the intermolecular forces between SPA and Mal-mPEG5000 were hydrophobic interactions and hydrogen bonds due to the positive values of ΔHθ and ΔSθ. Furthermore, the calorie titration data showed that the binding stoichiometry for the complexation of Mal-mPEG5000 to SPA was 1.26, and the binding constant was 1.256 × 107 mol/L. The binding reaction resulted from negative enthalpy, indicating that the interaction of SPA and Mal-mPEG5000 was induced by the van der Waals force and hydrogen bonding. The UV results showed the formation of non-luminescent material during the interaction, the Fluorescence results confirmed that the mechanism between SPA and Mal-mPEG5000 was static quenching. According to the fluorescence quenching measurement, the binding constant (KA) values were 4.65 × 104 L·mol-1 (298K), 5.56 × 104 L·mol-1 (308K), and 6.91 × 104 L·mol-1 (318K), respectively.
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36
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Gopalswamy M, Zheng C, Gaussmann S, Kooshapur H, Hambruch E, Schliebs W, Erdmann R, Antes I, Sattler M. Distinct conformational and energetic features define the specific recognition of (di)aromatic peptide motifs by PEX14. Biol Chem 2023; 404:179-194. [PMID: 36437542 DOI: 10.1515/hsz-2022-0177] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 11/04/2022] [Indexed: 11/29/2022]
Abstract
The cycling import receptor PEX5 and its membrane-located binding partner PEX14 are key constituents of the peroxisomal import machinery. Upon recognition of newly synthesized cargo proteins carrying a peroxisomal targeting signal type 1 (PTS1) in the cytosol, the PEX5/cargo complex docks at the peroxisomal membrane by binding to PEX14. The PEX14 N-terminal domain (NTD) recognizes (di)aromatic peptides, mostly corresponding to Wxxx(F/Y)-motifs, with nano-to micromolar affinity. Human PEX5 possesses eight of these conserved motifs distributed within its 320-residue disordered N-terminal region. Here, we combine biophysical (ITC, NMR, CD), biochemical and computational methods to characterize the recognition of these (di)aromatic peptides motifs and identify key features that are recognized by PEX14. Notably, the eight motifs present in human PEX5 exhibit distinct affinities and energetic contributions for the interaction with the PEX14 NTD. Computational docking and analysis of the interactions of the (di)aromatic motifs identify the specific amino acids features that stabilize a helical conformation of the peptide ligands and mediate interactions with PEX14 NTD. We propose a refined consensus motif ExWΦxE(F/Y)Φ for high affinity binding to the PEX14 NTD and discuss conservation of the (di)aromatic peptide recognition by PEX14 in other species.
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Affiliation(s)
- Mohanraj Gopalswamy
- Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, D-85747 Garching, Germany.,Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Center Munich, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Chen Zheng
- TUM School of Life Sciences, Technical University of Munich, Emil-Erlenmeyer-Forum 8, D-85354 Freising, Germany.,TUM Center for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, D-85748 Garching, Germany
| | - Stefan Gaussmann
- Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, D-85747 Garching, Germany.,Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Center Munich, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Hamed Kooshapur
- Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, D-85747 Garching, Germany.,Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Center Munich, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Eva Hambruch
- Institute of Biochemistry and Pathobiochemistry, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Wolfgang Schliebs
- Institute of Biochemistry and Pathobiochemistry, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Ralf Erdmann
- Institute of Biochemistry and Pathobiochemistry, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Iris Antes
- TUM School of Life Sciences, Technical University of Munich, Emil-Erlenmeyer-Forum 8, D-85354 Freising, Germany.,TUM Center for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, D-85748 Garching, Germany
| | - Michael Sattler
- Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, D-85747 Garching, Germany.,Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Center Munich, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
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37
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Fakih R, Goldstein RH, Kozlov G, Gehring K. Burst kinetics and CNNM binding are evolutionarily conserved properties of phosphatases of regenerating liver. J Biol Chem 2023; 299:103055. [PMID: 36822330 PMCID: PMC10040874 DOI: 10.1016/j.jbc.2023.103055] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/17/2023] [Accepted: 02/18/2023] [Indexed: 02/25/2023] Open
Abstract
Phosphatases of regenerating liver (PRL or PTP4A) are a family of enigmatic protein phosphatases implicated in cell growth and metabolism. Despite their relevance in metastatic cancer, much remains unknown about the PRL family. They act as pseudophosphatases to regulate the CNNM family of magnesium transporters yet also have enzymatic activity on unknown substrates. In mammals, PRLs are mostly found trapped in an intermediate state that regulates their pseudophosphatase activity. Phosphocysteine, which is formed as an intermediate in the phosphatase catalytic cycle, is inefficiently hydrolyzed leading to burst enzyme kinetics and turnover numbers of less than one per hour. In flies, PRLs have recently been shown to have neuroprotective and neurodevelopmental roles raising the question whether they act as phosphatases, pseudophosphatases, or both. Here, we characterize the evolutionary development of PRLs and ask whether their unique structural and functional properties are conserved. We purified recombinant PRL proteins from 15 phylogenetically diverse organisms and characterized their catalytic activities and ability to bind CNNM proteins. We observed PRLs from humans to amoebae form a stable phosphocysteine intermediate and exhibit burst kinetics. Isothermal titration calorimetry experiments confirmed that the PRL-CNNM interaction is broadly conserved with nanomolar affinity in vertebrates. Lastly, we determined the crystal structure of the Drosophila melanogaster PRL-CNNM complex and identified mutants that specifically impair either phosphatase activity or CNNM binding. Our results reveal the unique properties of PRLs are conserved throughout the animal kingdom and open the door to using model organisms to dissect PRL function in cell signaling.
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Affiliation(s)
- Rayan Fakih
- Department of Biochemistry, Centre for Structural Biology, McGill University, Montreal, Quebec, Canada
| | - Robert H Goldstein
- Department of Biochemistry, Centre for Structural Biology, McGill University, Montreal, Quebec, Canada
| | - Guennadi Kozlov
- Department of Biochemistry, Centre for Structural Biology, McGill University, Montreal, Quebec, Canada
| | - Kalle Gehring
- Department of Biochemistry, Centre for Structural Biology, McGill University, Montreal, Quebec, Canada.
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38
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Khatun M, Jana GC, Nayim S, Dhal A, Patra A, Hossain M. Evaluation of the size effect of hydrophobic ring substitution on 9-O position of berberine on DNA binding. J Biomol Struct Dyn 2023; 41:14299-14307. [PMID: 38073529 DOI: 10.1080/07391102.2023.2180436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/08/2023] [Indexed: 02/25/2023]
Abstract
The interaction of deoxyribonucleic acid (DNA) with medicinally significant small molecules has long piqued the interest of researchers because its applications are directly related to the discovery of new classes of drugs. Keeping this in mind, here we report berberine derivatives and their interaction with calf thymus DNA (CT-DNA). In this report we discussed on the structural perspectives and thermodynamic characteristics of the interaction of four 9-O-substituted berberines (BRDR1 to BRDR4) with CT-DNA. The binding affinity of BRDR-DNA complexes increased with increasing the cycloalkane ring size of the substitution except BRDR2. The binding constant value obtained from UV-Visible spectral analysis was 1.12 × 106 for BRDR1, 0.37 × 106 for BRDR2, 1.72 × 106 for BRDR3 and 3.20 × 106 for BRDR4. Ferrocyanide quenching experiments revealed unequivocally that the analogues except BRDR2 had a partly intercalative binding to DNA. From the ITC experiment it was found that the bindings of BRDR1, BRDR3 and BRDR4 to DNA was favoured by negative enthalpy and positive entropy while BRDR2 was driven by positive enthalpy and positive entropy. In all cases the hydrophobic interaction plays a crucial role. Thus, the complete multispectroscopic and thermodynamic binding studies may be useful for new drug design and development.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Munira Khatun
- Department of Chemistry, Vidyasagar University, Midnapore, West Bengal, India
| | - Gopal Chandra Jana
- Department of Chemistry, Vidyasagar University, Midnapore, West Bengal, India
| | - Sk Nayim
- Department of Chemistry, Vidyasagar University, Midnapore, West Bengal, India
| | - Asima Dhal
- Department of Chemistry, Vidyasagar University, Midnapore, West Bengal, India
| | - Anirudha Patra
- Department of Chemistry, Vidyasagar University, Midnapore, West Bengal, India
| | - Maidul Hossain
- Department of Chemistry, Vidyasagar University, Midnapore, West Bengal, India
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39
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Gong Y, Li J, Li J, Wang L, Fan L. In Vitro Inhibitory Effects of Polyphenols from Flos sophorae immaturus on α-Glucosidase: Action Mechanism, Isothermal Titration Calorimetry and Molecular Docking Analysis. Foods 2023; 12. [PMID: 36832790 DOI: 10.3390/foods12040715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
Flos sophorae immaturus (FSI) is considered to be a natural hypoglycemic product with the potential for a-glucosidase inhibitory activity. In this work, the polyphenols with α-glucosidase inhibition in FSI were identified, and then their potential mechanisms were investigated by omission assay, interaction, type of inhibition, fluorescence spectroscopy, circular dichroism, isothermal titration calorimetry and molecular docking analysis. The results showed that five polyphenols, namely rutin, quercetin, hyperoside, quercitrin and kaempferol, were identified as a-glucosidase inhibitors with IC50 values of 57, 0.21, 12.77, 25.37 and 0.55 mg/mL, respectively. Quercetin plays a considerable a-glucosidase inhibition role in FSI. Furthermore, the combination of quercetin with kaempferol generated a subadditive effect, and the combination of quercetin with rutin, hyperoside and quercitrin exhibited an interference effect. The results of inhibition kinetics, fluorescence spectroscopy, isothermal titration calorimetry and molecular docking analysis showed that the five polyphenols were mixed inhibitors and significantly burst the fluorescence intensity of α-glucosidase. Moreover, the isothermal titration calorimetry and molecular docking analysis showed that the binding to α-glucosidase was a spontaneous heat-trapping process, with hydrophobic interactions and hydrogen bonding being the key drivers. In general, rutin, quercetin, hyperoside, quercitrin and kaempferol in FSI are potential α-glucosidase inhibitors.
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40
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Abhishek S, Deeksha W, Rajakumara E. Mechanistic insights into allosteric regulation of methylated DNA and histone H3 recognition by SRA and SET domains of SUVH5 and the basis for di-methylation of lysine residue. FEBS J 2023; 290:1060-1077. [PMID: 36128736 DOI: 10.1111/febs.16633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 08/22/2022] [Accepted: 09/20/2022] [Indexed: 12/01/2022]
Abstract
Su-(var)3-9 homologue 5 (SUVH5), a member of SUVH family of histone lysine methyltransferase (HKMT) in Arabidopsis, is involved in epigenetic regulation of chromatin by recognizing 5-methyl-cytosine (5mC), in both CpG and non-CpG DNA context, through SRA domain and simultaneously performing the di-methylation of lysine 9 of histone H3 (H3K9) through SET domain. Here, we establish that the SET domain of SUVH5 allosterically restricts the SRA domain to the 5mC containing strand(s) of fully methylated CpG, hemi-methylated CpG and methylated CpHpH DNA. In addition, SET domain enhances the binding affinity of the SRA-SET dual domains to fully-mCpG but not to hemi-mCpG. Also, the recognition of methylated DNA by the SRA positively influences the recognition of H3K9 by the SET domain. Our further studies revealed that the SET domain recognizes the "A(R/K)KST" motif present in H3K9 and in other histone H2A variants. Further, computational analyses and quantum mechanics/molecular mechanics calculations explain the bases for robust mono-MTase but weak di-MTase activities of SUVH5. Given that the majority of eukaryotic proteins, including those involved in epigenetic gene regulation, contain more than one domain, our study suggests that understanding the allosteric regulation among multiple domains of proteins is relevant for unravelling biological outcomes.
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Affiliation(s)
- Suman Abhishek
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Sangareddy, India
| | - Waghela Deeksha
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Sangareddy, India
| | - Eerappa Rajakumara
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Sangareddy, India
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41
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Javorsky A, Maddumage JC, Mackie ERR, Soares da Costa TP, Humbert PO, Kvansakul M. Structural insight into the Scribble PDZ domains interaction with the oncogenic Human T-cell lymphotrophic virus-1 (HTLV-1) Tax1 PBM. FEBS J 2023; 290:974-987. [PMID: 36029163 PMCID: PMC10952772 DOI: 10.1111/febs.16607] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 07/14/2022] [Accepted: 08/25/2022] [Indexed: 11/28/2022]
Abstract
Scribble (Scrib) is a highly conserved cell polarity regulator that harbours potent tumour suppressor activity and plays an important role in cell migration. Dysregulation of polarity is associated with poor prognosis during viral infections. Human T-cell lymphotrophic virus-1 (HTLV-1) encodes for the oncogenic Tax1 protein, a modulator of the transcription of viral and human proteins that can cause cell cycle dysregulation as well as a loss of genomic integrity. Previous studies established that Scribble interacts with Tax1 via its C-terminal PDZ-binding motif (PBM), leading to aggregation of polarity regulators and subsequent perturbation of host cell adhesion, proliferation, and signalling. Using isothermal titration calorimetry, we now show that all four PDZ domains of Scribble bind to Tax1 PBM. We then determined crystal structures of Scribble PDZ1, PDZ2 and PDZ3 domains bound to Tax1 PBM. Our findings establish a structural basis for Tax1-mediated subversion of Scribble-mediated cell polarity signalling and provide the platform for mechanistic studies to examine Tax1 induced mislocalization of Scribble and the associated changes in cellular architecture and subsequent tumorigenesis.
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Affiliation(s)
- Airah Javorsky
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVic.Australia
| | - Janesha C. Maddumage
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVic.Australia
| | - Emily R. R. Mackie
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVic.Australia
| | - Tatiana P. Soares da Costa
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVic.Australia
| | - Patrick O. Humbert
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVic.Australia
- Research Centre for Molecular Cancer PreventionLa Trobe UniversityMelbourneVic.Australia
- Department of Biochemistry & PharmacologyUniversity of MelbourneMelbourneVic.Australia
- Department of Clinical PathologyUniversity of MelbourneMelbourneVic.Australia
| | - Marc Kvansakul
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVic.Australia
- Research Centre for Molecular Cancer PreventionLa Trobe UniversityMelbourneVic.Australia
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42
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Perez Tobia J, Huang PJJ, Ding Y, Saran Narayan R, Narayan A, Liu J. Machine Learning Directed Aptamer Search from Conserved Primary Sequences and Secondary Structures. ACS Synth Biol 2023; 12:186-195. [PMID: 36594697 DOI: 10.1021/acssynbio.2c00462] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Computer-aided prediction of aptamer sequences has been focused on primary sequence alignment and motif comparison. We observed that many aptamers have a conserved hairpin, yet the sequence of the hairpin can be highly variable. Taking such secondary structure information into consideration, a new algorithm combining conserved primary sequences and secondary structures is developed, which combines three scores based on sequence abundance, stability, and structure, respectively. This algorithm was used in the prediction of aptamers from the caffeine and theophylline selections. In the late rounds of the selections, when the libraries were converged, the predicted sequences matched well with the most abundant sequences. When the libraries were far from convergence and the sequences were deemed challenging for traditional analysis methods, this algorithm still predicted aptamer sequences that were experimentally verified by isothermal titration calorimetry. This algorithm paves a new way to look for patterns in aptamer selection libraries and mimics the sequence evolution process. It will help shorten the aptamer selection time and promote the biosensor and chemical biology applications of aptamers.
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Affiliation(s)
- Javier Perez Tobia
- Department of Computer Science, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Yuzhe Ding
- Department of Chemistry, Waterloo Institute for Nanotechnology, Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran Narayan
- Department of Chemistry, Waterloo Institute for Nanotechnology, Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Apurva Narayan
- Department of Computer Science, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada.,Department of Computer Science, Western University, London, Ontario N6A 3K7, Canada.,Systems Design Engineering, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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43
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Nefedova VV, Kopylova GV, Shchepkin DV, Kochurova AM, Kechko OI, Borzova VA, Ryabkova NS, Katrukha IA, Mitkevich VA, Bershitsky SY, Levitsky DI, Matyushenko AM. Impact of Troponin in Cardiomyopathy Development Caused by Mutations in Tropomyosin. Int J Mol Sci 2022; 23:ijms232415723. [PMID: 36555368 PMCID: PMC9779223 DOI: 10.3390/ijms232415723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Tropomyosin (Tpm) mutations cause inherited cardiac diseases such as hypertrophic and dilated cardiomyopathies. We applied various approaches to investigate the role of cardiac troponin (Tn) and especially the troponin T (TnT) in the pathogenic effects of Tpm cardiomyopathy-associated mutations M8R, K15N, A277V, M281T, and I284V located in the overlap junction of neighboring Tpm dimers. Using co-sedimentation assay and viscosity measurements, we showed that TnT1 (fragment of TnT) stabilizes the overlap junction of Tpm WT and all Tpm mutants studied except Tpm M8R. However, isothermal titration calorimetry (ITC) indicated that TnT1 binds Tpm WT and all Tpm mutants similarly. By using ITC, we measured the direct KD of the Tpm overlap region, N-end, and C-end binding to TnT1. The ITC data revealed that the Tpm C-end binds to TnT1 independently from the N-end, while N-end does not bind. Therefore, we suppose that Tpm M8R binds to TnT1 without forming the overlap junction. We also demonstrated the possible role of Tn isoform composition in the cardiomyopathy development caused by M8R mutation. TnT1 dose-dependently reduced the velocity of F-actin-Tpm filaments containing Tpm WT, Tpm A277V, and Tpm M281T mutants in an in vitro motility assay. All mutations impaired the calcium regulation of the actin-myosin interaction. The M281T and I284V mutations increased the calcium sensitivity, while the K15N and A277V mutations reduced it. The Tpm M8R, M281T, and I284V mutations under-inhibited the velocity at low calcium concentrations. Our results demonstrate that Tpm mutations likely implement their pathogenic effects through Tpm interaction with Tn, cardiac myosin, or other protein partners.
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Affiliation(s)
- Victoria V. Nefedova
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
- Correspondence:
| | - Galina V. Kopylova
- Institute of Immunology and Physiology of the Russian Academy of Sciences, 620049 Yekaterinburg, Russia
| | - Daniil V. Shchepkin
- Institute of Immunology and Physiology of the Russian Academy of Sciences, 620049 Yekaterinburg, Russia
| | - Anastasia M. Kochurova
- Institute of Immunology and Physiology of the Russian Academy of Sciences, 620049 Yekaterinburg, Russia
| | - Olga I. Kechko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Science, 119991 Moscow, Russia
| | - Vera A. Borzova
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Natalia S. Ryabkova
- Department of Biochemistry, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- HyTest Ltd., 20520 Turku, Finland
| | - Ivan A. Katrukha
- Department of Biochemistry, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- HyTest Ltd., 20520 Turku, Finland
| | - Vladimir A. Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Science, 119991 Moscow, Russia
| | - Sergey Y. Bershitsky
- Institute of Immunology and Physiology of the Russian Academy of Sciences, 620049 Yekaterinburg, Russia
| | - Dmitrii I. Levitsky
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
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Kluska K, Chorążewska A, Peris-Díaz MD, Adamczyk J, Krężel A. Non-Conserved Amino Acid Residues Modulate the Thermodynamics of Zn(II) Binding to Classical ββα Zinc Finger Domains. Int J Mol Sci 2022; 23:ijms232314602. [PMID: 36498928 PMCID: PMC9735795 DOI: 10.3390/ijms232314602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022] Open
Abstract
Classical zinc fingers domains (ZFs) bind Zn(II) ion by a pair of cysteine and histidine residues to adopt a characteristic and stable ββα fold containing a small hydrophobic core. As a component of transcription factors, they recognize specific DNA sequences to transcript particular genes. The loss of Zn(II) disrupts the unique structure and function of the whole protein. It has been shown that the saturation of ZFs under cellular conditions is strictly related to their affinity for Zn(II). High affinity warrants their constant saturation, while medium affinity results in their transient structurization depending on cellular zinc availability. Therefore, there must be factors hidden in the sequence and structure of ZFs that impact Zn(II)-to-protein affinities to control their function. Using molecular dynamics simulations and experimental spectroscopic and calorimetric approaches, we showed that particular non-conserved residues derived from ZF sequences impact hydrogen bond formation. Our in silico and in vitro studies show that non-conserved residues can alter metal-coupled folding mechanisms and overall ZF stability. Furthermore, we show that Zn(II) binding to ZFs can also be entropically driven. This preference does not correlate either with Zn(II) binding site or with the extent of the secondary structure but is strictly related to a reservoir of interactions within the second coordination shell, which may loosen or tighten up the structure. Our findings shed new light on how the functionality of ZFs is modulated by non-coordinating residues diversity under cellular conditions. Moreover, they can be helpful for systematic backbone alteration of native ZF ββα scaffold to create artificial foldamers and proteins with improved stability.
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Mohanakumar S, Lee N, Wiegand S. Complementary Experimental Methods to Obtain Thermodynamic Parameters of Protein Ligand Systems. Int J Mol Sci 2022; 23:ijms232214198. [PMID: 36430678 PMCID: PMC9692857 DOI: 10.3390/ijms232214198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/10/2022] [Accepted: 11/12/2022] [Indexed: 11/18/2022] Open
Abstract
In recent years, thermophoresis has emerged as a promising tool for quantifying biomolecular interactions. The underlying microscopic physical effect is still not understood, but often attributed to changes in the hydration layer once the binding occurs. To gain deeper insight, we investigate whether non-equilibrium coefficients can be related to equilibrium properties. Therefore, we compare thermophoretic data measured by thermal diffusion forced Rayleigh scattering (TDFRS) (which is a non-equilibrium process) with thermodynamic data obtained by isothermal titration calorimetry (ITC) (which is an equilibrium process). As a reference system, we studied the chelation reaction between ethylenediaminetetraacetic acid (EDTA) and calcium chloride (CaCl2) to relate the thermophoretic behavior quantified by the Soret coefficient ST to the Gibb's free energy ΔG determined in the ITC experiment using an expression proposed by Eastman. Finally, we have studied the binding of the protein Bovine Carbonic Anhydrase I (BCA I) to two different benzenesulfonamide derivatives: 4-fluorobenzenesulfonamide (4FBS) and pentafluorobenzenesulfonamide (PFBS). For all three systems, we find that the Gibb's free energies calculated from ST agree with ΔG from the ITC experiment. In addition, we also investigate the influence of fluorescent labeling, which allows measurements in a thermophoretic microfluidic cell. Re-examination of the fluorescently labeled system using ITC showed a strong influence of the dye on the binding behavior.
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Affiliation(s)
- Shilpa Mohanakumar
- IBI-4—Biomacromolecular Systems and Processes, Forschungszentrum Jülich GmbH, D-52428 Jülich, Germany
| | - Namkyu Lee
- IBI-4—Biomacromolecular Systems and Processes, Forschungszentrum Jülich GmbH, D-52428 Jülich, Germany
| | - Simone Wiegand
- IBI-4—Biomacromolecular Systems and Processes, Forschungszentrum Jülich GmbH, D-52428 Jülich, Germany
- Chemistry Department-Physical Chemistry, University of Colgone, D-50939 Cologne, Germany
- Correspondence: ; Tel.: +49-2461-61-6654
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Zelencova-Gopejenko D, Grandane A, Loza E, Lola D, Sipola A, Liepinsh E, Arsenyan P, Jaudzems K. Binding versus Enzymatic Processing of ε-Trimethyllysine Dioxygenase Substrate Analogues. ACS Med Chem Lett 2022; 13:1723-1729. [PMID: 36385923 PMCID: PMC9661700 DOI: 10.1021/acsmedchemlett.2c00261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 10/17/2022] [Indexed: 11/29/2022] Open
Abstract
ε-Trimethyllysine dioxygenase (TMLD) is a non-heme Fe(II) and α-ketoglutarate dependent oxygenase that catalyzes the stereospecific hydroxylation of ε-trimethyl-l-lysine (TML) to β-hydroxy-TML during the first step of l-carnitine biosynthesis. Targeting TMLD with inhibitors is a viable strategy for the treatment of cardiovascular diseases. Herein, we report a methodology for isothermal titration calorimetry analysis of TMLD substrate analogue binding to the enzyme. Despite the high structural similarity of the tested compounds, two different binding mechanisms (enthalpy- and entropy-driven) were observed, giving insight into the ligand (substrate) selectivity of TMLD. We demonstrate that the method allows distinguishing a natural substrate-like binding mode, which correlates with the ability of the compounds to serve as substrates in the TMLD catalytic reaction.
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Affiliation(s)
| | - Aiga Grandane
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Einars Loza
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Daina Lola
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Anda Sipola
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Edgars Liepinsh
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Pavel Arsenyan
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Kristaps Jaudzems
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
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Marin A, Taraban MB, Patel V, Yu YB, Andrianov AK. Supramolecular Protein-Polyelectrolyte Assembly at Near Physiological Conditions-Water Proton NMR, ITC, and DLS Study. Molecules 2022; 27:7424. [PMID: 36364250 PMCID: PMC9656440 DOI: 10.3390/molecules27217424] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 11/15/2023] Open
Abstract
The in vivo potency of polyphosphazene immunoadjuvants is inherently linked to the ability of these ionic macromolecules to assemble with antigenic proteins in aqueous solutions and form physiologically stable supramolecular complexes. Therefore, in-depth knowledge of interactions in this biologically relevant system is a prerequisite for a better understanding of mechanism of immunoadjuvant activity. Present study explores a self-assembly of polyphosphazene immunoadjuvant-PCPP and a model antigen-lysozyme in a physiologically relevant environment-saline solution and neutral pH. Three analytical techniques were employed to characterize reaction thermodynamics, water-solute structural organization, and supramolecular dimensions: isothermal titration calorimetry (ITC), water proton nuclear magnetic resonance (wNMR), and dynamic light scattering (DLS). The formation of lysozyme-PCPP complexes at near physiological conditions was detected by all methods and the avidity was modulated by a physical state and dimensions of the assemblies. Thermodynamic analysis revealed the dissociation constant in micromolar range and the dominance of enthalpy factor in interactions, which is in line with previously suggested model of protein charge anisotropy and small persistence length of the polymer favoring the formation of high affinity complexes. The paper reports advantageous use of wNMR method for studying protein-polymer interactions, especially for low protein-load complexes.
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Affiliation(s)
- Alexander Marin
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | - Marc B. Taraban
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - Vanshika Patel
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - Y. Bruce Yu
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - Alexander K. Andrianov
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
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Yusof NAM, Razali SA, Mohd Padzil A, Lau BYC, Baharum SN, Nor Muhammad NA, Raston NHA, Chong CM, Ikhsan NFM, Situmorang ML, Fei LC. Computationally Designed Anti-LuxP DNA Aptamer Suppressed Flagellar Assembly- and Quorum Sensing-Related Gene Expression in Vibrio parahaemolyticus. Biology (Basel) 2022; 11:1600. [PMID: 36358301 PMCID: PMC9687752 DOI: 10.3390/biology11111600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 10/22/2022] [Accepted: 10/26/2022] [Indexed: 11/29/2023]
Abstract
(1) Background: Quorum sensing (QS) is the chemical communication between bacteria that sense chemical signals in the bacterial population to control phenotypic changes through the regulation of gene expression. The inhibition of QS has various potential applications, particularly in the prevention of bacterial infection. QS can be inhibited by targeting the LuxP, a periplasmic receptor protein that is involved in the sensing of the QS signaling molecule known as the autoinducer 2 (AI-2). The sensing of AI-2 by LuxP transduces the chemical information through the inner membrane sensor kinase LuxQ protein and activates the QS cascade. (2) Methods: An in silico approach was applied to design DNA aptamers against LuxP in this study. A method combining molecular docking and molecular dynamics simulations was used to select the oligonucleotides that bind to LuxP, which were then further characterized using isothermal titration calorimetry. Subsequently, the bioactivity of the selected aptamer was examined through comparative transcriptome analysis. (3) Results: Two aptamer candidates were identified from the ITC, which have the lowest dissociation constants (Kd) of 0.2 and 0.5 micromolar. The aptamer with the lowest Kd demonstrated QS suppression and down-regulated the flagellar-assembly-related gene expression. (4) Conclusions: This study developed an in silico approach to design an aptamer that possesses anti-QS properties.
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Affiliation(s)
- Nur Afiqah Md Yusof
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
| | - Siti Aisyah Razali
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Nerus 21030, Terengganu, Malaysia
| | - Azyyati Mohd Padzil
- Malaysia Genome and Vaccine Institute (MGVI), National Institute of Biotechnology Malaysia (NIBM), Jalan Bangi, Kajang 43000, Selangor, Malaysia
| | - Benjamin Yii Chung Lau
- Malaysian Palm Oil Board, Persiaran Institusi, Bandar Baru Bangi, Kajang 43000, Selangor, Malaysia
| | - Syarul Nataqain Baharum
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
| | - Nor Azlan Nor Muhammad
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
| | - Nurul Hanun Ahmad Raston
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
| | - Chou Min Chong
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Natrah Fatin Mohd Ikhsan
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | | | - Low Chen Fei
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
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Boyeldieu A, Poli J, Ali Chaouche A, Fierobe H, Giudici‐Orticoni M, Méjean V, Jourlin‐Castelli C. Multiple detection of both attractants and repellents by the dCache-chemoreceptor SO_1056 of Shewanella oneidensis. FEBS J 2022; 289:6752-6766. [PMID: 35668695 PMCID: PMC9796306 DOI: 10.1111/febs.16548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 05/17/2022] [Accepted: 06/06/2022] [Indexed: 01/01/2023]
Abstract
Chemoreceptors are usually transmembrane proteins dedicated to the detection of compound gradients or signals in the surroundings of a bacterium. After detection, they modulate the activation of CheA-CheY, the core of the chemotactic pathway, to allow cells to move upwards or downwards depending on whether the signal is an attractant or a repellent, respectively. Environmental bacteria such as Shewanella oneidensis harbour dozens of chemoreceptors or MCPs (methyl-accepting chemotaxis proteins). A recent study revealed that MCP SO_1056 of S. oneidensis binds chromate. Here, we show that this MCP also detects an additional attractant (l-malate) and two repellents (nickel and cobalt). The experiments were performed in vivo by the agarose-in-plug technique after overproducing MCP SO_1056 and in vitro, when possible, by submitting the purified ligand-binding domain (LBD) of SO_1056 to a thermal shift assay (TSA) coupled to isothermal titration calorimetry (ITC). ITC assays revealed a KD of 3.4 μm for l-malate and of 47.7 μm for nickel. We conclude that MCP SO_1056 binds attractants and repellents of unrelated composition. The LBD of SO_1056 belongs to the double Cache_1 family and is highly homologous to PctA, a chemoreceptor from Pseudomonas aeruginosa that detects several amino acids. Therefore, LBDs of the same family can bind diverse compounds, confirming that experimental approaches are required to define accurate LBD-binding molecules or signals.
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Affiliation(s)
- Anne Boyeldieu
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP, UMR7281), Centre National de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée (IMM), Institut Microbiologie, Bioénergies et Biotechnologie (IM2B)Aix Marseille UniversitéFrance,Present address:
Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS)Université de Toulouse, UPSFrance
| | - Jean‐Pierre Poli
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP, UMR7281), Centre National de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée (IMM), Institut Microbiologie, Bioénergies et Biotechnologie (IM2B)Aix Marseille UniversitéFrance,Université de Corse Pasquale PaoliCorteFrance
| | - Amine Ali Chaouche
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP, UMR7281), Centre National de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée (IMM), Institut Microbiologie, Bioénergies et Biotechnologie (IM2B)Aix Marseille UniversitéFrance
| | - Henri‐Pierre Fierobe
- Laboratoire de Chimie Bactérienne (LCB, UMR7283), Centre National de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée (IMM), Institut Microbiologie, Bioénergies et Biotechnologie (IM2B)Aix Marseille UniversitéFrance
| | - Marie‐Thérèse Giudici‐Orticoni
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP, UMR7281), Centre National de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée (IMM), Institut Microbiologie, Bioénergies et Biotechnologie (IM2B)Aix Marseille UniversitéFrance
| | - Vincent Méjean
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP, UMR7281), Centre National de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée (IMM), Institut Microbiologie, Bioénergies et Biotechnologie (IM2B)Aix Marseille UniversitéFrance
| | - Cécile Jourlin‐Castelli
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP, UMR7281), Centre National de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée (IMM), Institut Microbiologie, Bioénergies et Biotechnologie (IM2B)Aix Marseille UniversitéFrance
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50
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Popelka H, Klionsky DJ. When acidic residues do not mimic phosphorylation: high-affinity binding of the reticulophagy receptor TEX264 to LC3/GABARAP. Autophagy 2022; 18:2515-2518. [PMID: 36041015 PMCID: PMC9629098 DOI: 10.1080/15548627.2022.2119350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Substrates that are selected for degradation by autophagy interact in more complex eukaryotes with Atg8-family proteins via the LC3-interacting region (LIR) that is often preceded by either acidic residues or phosphorylated serine or threonine. These upstream amino acid residues increase the binding affinity of the LIR motif to its binding site on the surface of LC3/GABARAP. It is not fully understood whether or how phosphorylation functionally replaces acidic residues in the LIR-Atg8-family protein interactions. A recent study by Chino et al. discussed in this article analyzed the phosphorylation of two serine residues upstream of the LIR motif in TEX264, a reticulophagy receptor that exhibits a high binding affinity to LC3/GABARAP proteins. The authors found a structural basis for the high-affinity interaction yielded by phosphorylation but not by an acidic residue in place of phosphoserine. Furthermore, finding that phosphorylation of TEX264 generates its high binding affinity to Atg8-family proteins uncovers a mechanistic alternative to that utilized by other reticulophagy receptors when they interact with LC3/GABARAP.Abbreviations: CSNK2: casein kinase 2; ER: endoplasmic reticulum; IDPR: intrinsically disordered protein region; LIR: LC3-interacting region; p-S: phosphorylated serine.
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Affiliation(s)
- Hana Popelka
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Daniel J Klionsky
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
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