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Wan X, Shahrear S, Chew SW, Vilaplana F, Mäkelä MR. Discovery of alkaline laccases from basidiomycete fungi through machine learning-based approach. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:120. [PMID: 39261970 PMCID: PMC11391777 DOI: 10.1186/s13068-024-02566-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 09/02/2024] [Indexed: 09/13/2024]
Abstract
BACKGROUND Laccases can oxidize a broad spectrum of substrates, offering promising applications in various sectors, such as bioremediation, biomass fractionation in future biorefineries, and synthesis of biochemicals and biopolymers. However, laccase discovery and optimization with a desirable pH optimum remains a challenge due to the labor-intensive and time-consuming nature of the traditional laboratory methods. RESULTS This study presents a machine learning (ML)-integrated approach for predicting pH optima of basidiomycete fungal laccases, utilizing a small, curated dataset against a vast metagenomic data. Comparative computational analyses unveiled the structural and pH-dependent solubility differences between acidic and neutral-alkaline laccases, helping us understand the molecular bases of enzyme pH optimum. The pH profiling of the two ML-predicted alkaline laccase candidates from the basidiomycete fungus Lepista nuda further validated our computational approach, showing the accuracy of this comprehensive method. CONCLUSIONS This study uncovers the efficacy of ML in the prediction of enzyme pH optimum from minimal datasets, marking a significant step towards harnessing computational tools for systematic screening of enzymes for biotechnology applications.
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Affiliation(s)
- Xing Wan
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Biocenter 1, Viikinkaari 9, 00790, Helsinki, Finland.
| | - Sazzad Shahrear
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Biocenter 1, Viikinkaari 9, 00790, Helsinki, Finland
| | - Shea Wen Chew
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Biocenter 1, Viikinkaari 9, 00790, Helsinki, Finland
| | - Francisco Vilaplana
- Division of Glycoscience, Department of Chemistry, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, Roslagstullbacken 21, 11421, Stockholm, Sweden
| | - Miia R Mäkelä
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Biocenter 1, Viikinkaari 9, 00790, Helsinki, Finland.
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150, Espoo, Finland.
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2
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Morrell AH, Warren NJ, Thornton PD. The Production of Polysarcosine-Containing Nanoparticles by Ring-Opening Polymerization-Induced Self-Assembly. Macromol Rapid Commun 2024; 45:e2400103. [PMID: 38597209 DOI: 10.1002/marc.202400103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/02/2024] [Indexed: 04/11/2024]
Abstract
N-carboxyanhydride ring-opening polymerization-induced self-assembly (NCA ROPISA) offers a convenient route for generating poly(amino acid)-based nanoparticles in a single step, crucially avoiding the need for post-polymerization self-assembly. Most examples of NCA ROPISA make use of a poly(ethylene glycol) (PEG) hydrophilic stabilizing block, however this non-biodegradable, oil-derived polymer may cause an immunological response in some individuals. Alternative water-soluble polymers are therefore highly sought. This work reports the synthesis of wholly poly(amino acid)-based nanoparticles, through the chain-extension of a polysarcosine macroinitiator with L-Phenylalanine-NCA (L-Phe-NCA) and Alanine-NCA (Ala-NCA), via aqueous NCA ROPISA. The resulting polymeric structures comprise of predominantly anisotropic, rod-like nanoparticles, with morphologies primarily influenced by the secondary structure of the hydrophobic poly(amino acid) that enables their formation.
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Affiliation(s)
- Anna H Morrell
- School of Chemical and Process Engineering, University of Leeds, Leeds, LS2 9JT, UK
| | - Nicholas J Warren
- School of Chemical and Process Engineering, University of Leeds, Leeds, LS2 9JT, UK
| | - Paul D Thornton
- Leeds Institute of Textiles and Colour (LITAC), School of Design, University of Leeds, Leeds, LS2 9JT, UK
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3
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Li L, Zhou L, Jiang C, Liu Z, Meng D, Luo F, He Q, Yin H. AI-driven pan-proteome analyses reveal insights into the biohydrometallurgical properties of Acidithiobacillia. Front Microbiol 2023; 14:1243987. [PMID: 37744906 PMCID: PMC10512742 DOI: 10.3389/fmicb.2023.1243987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023] Open
Abstract
Microorganism-mediated biohydrometallurgy, a sustainable approach for metal recovery from ores, relies on the metabolic activity of acidophilic bacteria. Acidithiobacillia with sulfur/iron-oxidizing capacities are extensively studied and applied in biohydrometallurgy-related processes. However, only 14 distinct proteins from Acidithiobacillia have experimentally determined structures currently available. This significantly hampers in-depth investigations of Acidithiobacillia's structure-based biological mechanisms pertaining to its relevant biohydrometallurgical processes. To address this issue, we employed a state-of-the-art artificial intelligence (AI)-driven approach, with a median model confidence of 0.80, to perform high-quality full-chain structure predictions on the pan-proteome (10,458 proteins) of the type strain Acidithiobacillia. Additionally, we conducted various case studies on de novo protein structural prediction, including sulfate transporter and iron oxidase, to demonstrate how accurate structure predictions and gene co-occurrence networks can contribute to the development of mechanistic insights and hypotheses regarding sulfur and iron utilization proteins. Furthermore, for the unannotated proteins that constitute 35.8% of the Acidithiobacillia proteome, we employed the deep-learning algorithm DeepFRI to make structure-based functional predictions. As a result, we successfully obtained gene ontology (GO) terms for 93.6% of these previously unknown proteins. This study has a significant impact on improving protein structure and function predictions, as well as developing state-of-the-art techniques for high-throughput analysis of large proteomic data.
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Affiliation(s)
- Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Lei Zhou
- Beijing Research Institute of Chemical Engineering and Metallurgy, Beijing, China
| | - Chengying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Feng Luo
- School of Computing, Clemson University, Clemson, SC, United States
| | - Qiang He
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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4
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Van Raad D, Huber T, Otting G. Improved spectral resolution of [ 13C, 1H]-HSQC spectra of aromatic amino acid residues in proteins produced by cell-free synthesis from inexpensive 13C-labelled precursors. JOURNAL OF BIOMOLECULAR NMR 2023; 77:183-190. [PMID: 37338652 PMCID: PMC10406723 DOI: 10.1007/s10858-023-00420-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/23/2023] [Indexed: 06/21/2023]
Abstract
Cell-free protein synthesis using eCells allows production of amino acids from inexpensive 13C-labelled precursors. We show that the metabolic pathway converting pyruvate, glucose and erythrose into aromatic amino acids is maintained in eCells. Judicious choice of 13C-labelled starting material leads to proteins, where the sidechains of aromatic amino acids display [13C,1H]-HSQC cross-peaks free of one-bond 13C-13C couplings. Selective 13C-labelling of tyrosine and phenylalanine residues is achieved simply by using different compositions of the reaction buffers.
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Affiliation(s)
- Damian Van Raad
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia.
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia.
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia.
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Anderson AJ, Dodge GJ, Allen KN, Imperiali B. Co-conserved sequence motifs are predictive of substrate specificity in a family of monotopic phosphoglycosyl transferases. Protein Sci 2023; 32:e4646. [PMID: 37096962 PMCID: PMC10186338 DOI: 10.1002/pro.4646] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 04/26/2023]
Abstract
Monotopic phosphoglycosyl transferases (monoPGTs) are an expansive superfamily of enzymes that catalyze the first membrane-committed step in the biosynthesis of bacterial glycoconjugates. MonoPGTs show a strong preference for their cognate nucleotide diphospho-sugar (NDP-sugar) substrates. However, despite extensive characterization of the monoPGT superfamily through previous development of a sequence similarity network comprising >38,000 nonredundant sequences, the connection between monoPGT sequence and NDP-sugar substrate specificity has remained elusive. In this work, we structurally characterize the C-terminus of a prototypic monoPGT for the first time and show that 19 C-terminal residues play a significant structural role in a subset of monoPGTs. This new structural information facilitated the identification of co-conserved sequence "fingerprints" that predict NDP-sugar substrate specificity for this subset of monoPGTs. A Hidden Markov model was generated that correctly assigned the substrate of previously unannotated monoPGTs. Together, these structural, sequence, and biochemical analyses have delivered new insight into the determinants guiding substrate specificity of monoPGTs and have provided a strategy for assigning the NDP-sugar substrate of a subset of enzymes in the superfamily that use UDP-di-N-acetyl bacillosamine. Moving forward, this approach may be applied to identify additional sequence motifs that serve as fingerprints for monoPGTs of differing UDP-sugar substrate specificity.
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Affiliation(s)
- Alyssa J. Anderson
- Department of Biology and Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Greg J. Dodge
- Department of Biology and Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Karen N. Allen
- Department of ChemistryBoston UniversityBostonMassachusettsUSA
| | - Barbara Imperiali
- Department of Biology and Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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6
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Fenanir F, Semmeq A, Benguerba Y, Badawi M, Dziurla MA, Amira S, Laouer H. In silico investigations of some Cyperus rotundus compounds as potential anti-inflammatory inhibitors of 5-LO and LTA4H enzymes. J Biomol Struct Dyn 2022; 40:11571-11586. [PMID: 34355673 DOI: 10.1080/07391102.2021.1960197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The present study aimed to experimentally identify the essential oil of Algerian Cyperus rotundus L. and to model the interaction of some known anti-inflammatory molecules with two key enzymes involved in inflammation, 5-Lypoxygenase (5-LO) and leukotriene A4 hydrolase (LTA4H). Gas chromatography/gas chromatography-mass spectrometry (GC/GC-MS) revealed that 92.7% of the essential oil contains 35 compounds, including oxygenated sesquiterpenes (44.2%), oxygenated monoterpenes (30.2%), monoterpene hydrocarbons (11.8%) and sesquiterpene hydrocarbons (6.5%). The major identified oxygenated terpenes are humulene oxide II, caryophyllene oxide, khusinol, agarospirol, spathulinol and trans-pinocarveol Myrtenol and α-terpineol are known to exhibit anti-inflammatory activities. Several complexes obtained after docking the natural terpenes with 5-LO and LTA4H have shown strong hydrogen bonding interactions. The best docking energies were found with α-terpineol, Myrtenol and khusinol. The interaction between the natural products and amino-acid residues HIS367, ILE673 and GLN363 appears to be critical for 5-LO inhibition, while the interaction with residues GLU271, HIS295, TYR383, TYR378, GLU318, GLU296 and ASP375 is critical for LTA4H inhibition. Molecular dynamics (MD) trajectories of the selected docked complexes showed stable backbone root mean square deviation (RMSD), supporting the stability of the natural product-enzyme interaction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fares Fenanir
- Laboratory of Valorization of Natural and biological Resources, University Ferhat Abbas, Sétif, Algeria
| | - Abderrahmane Semmeq
- Laboratoire de Physique et Chimie Théoriques (UMR 7019), CNRS-Université de Lorraine, Saint-Avold, France
| | - Yacine Benguerba
- Laboratoire des Matériaux Polymères Multiphasiques, LMPMP, Université Ferhat ABBAS, Sétif, Algeria
| | - Michael Badawi
- Laboratoire de Physique et Chimie Théoriques (UMR 7019), CNRS-Université de Lorraine, Saint-Avold, France.,IUT de Moselle-Est, Université de Lorraine, Saint-Avold, France
| | | | - Smain Amira
- Laboratory of Phytotherapy Applied to Chroniques Diseases, University Ferhat Abbas, Sétif, Algeria
| | - Hocine Laouer
- Laboratory of Valorization of Natural and biological Resources, University Ferhat Abbas, Sétif, Algeria
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7
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Liu H. AlphaFold and Structural Mass Spectrometry Enable Interrogations on the Intrinsically Disordered Regions in Cyanobacterial Light-harvesting Complex Phycobilisome. J Mol Biol 2022; 434:167831. [PMID: 36116541 DOI: 10.1016/j.jmb.2022.167831] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 11/29/2022]
Abstract
Intrinsically disordered proteins/regions (IDPRs) are a very large and functionally important class of proteins that participate in weak multivalent interactions in protein complexes. They are recalcitrant for interrogations using X-ray crystallography and cryo-EM. The IDPRs observed at the interface of the photosynthetic pigment protein complexes (PPCs) remain much less clear, e.g., the major cyanobacterial light-harvesting complex (PBS) contains an unstructured PB-loop insertion in the phycocyanobilin domain (PB domain) of ApcE (the largest polypeptide in PBS). Here, a joint platform is built to probe such structural domains. This platform is characterized by two-round progressive justifications of in silico models by using the structural mass spectrometry data. First, the AlphaFold-generated 3D structure of the PB domain (containing PB-loop) was justified in the context of PBS. Second, docking the AlphaFold-generated ApcG (a ligand) into the first-step justified structure (a receptor). The final ligand-receptor complex was then subjected to a second-round justification, again, by using unequivocal isotopically-encoded cross-links identified in LC-MS/MS. This work reveals a full-length PB-loop structure modelled in the PBS basal cylinder, free from any spatial conflicts against the other subunits in PBS. The structure of PB domain highlights the close associations of the intrinsically disordered PB-loop with its binding partners in PBS, including ApcG, another IDPR. The PB-loop region involved in the binding of photosystem II (PSII) is also discussed in the context of excitation energy transfer regulation. This work calls attention to the highly disordered, yet interrogatable interface between the light-harvesting antenna complexes and the reaction centers.
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Affiliation(s)
- Haijun Liu
- Department of Biology Washington University in St. Louis, St. Louis, MO 63130, USA.
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8
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Triple ionization and fragmentation of benzene trimers following ultrafast intermolecular Coulombic decay. Nat Commun 2022; 13:5335. [PMID: 36088449 PMCID: PMC9464219 DOI: 10.1038/s41467-022-33032-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/25/2022] [Indexed: 11/25/2022] Open
Abstract
Intermolecular interactions involving aromatic rings are ubiquitous in biochemistry and they govern the properties of many organic materials. Nevertheless, our understanding of the structures and dynamics of aromatic clusters remains incomplete, in particular for systems beyond the dimers, despite their high presence in many macromolecular systems such as DNA and proteins. Here, we study the fragmentation dynamics of benzene trimer that represents a prototype of higher-order aromatic clusters. The trimers are initially ionized by electron-collision with the creation of a deep-lying carbon 2s−1 state or one outer-valence and one inner-valence vacancies at two separate molecules. The system can thus relax via ultrafast intermolecular decay mechanisms, leading to the formation of C\documentclass[12pt]{minimal}
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\begin{document}$${}_{6}{{{{{{{{{\rm{H}}}}}}}}}_{6}}^{+}$$\end{document}6H6+ trications and followed by a concerted three-body Coulomb explosion. Triple-coincidence ion momentum spectroscopy, accompanied by ab-initio calculations and further supported by strong-field laser experiments, allows us to elucidate the details on the fragmentation dynamics of benzene trimers. Higher-order aromatic clusters are prevalent in biochemical systems, but a full understanding of their structural and dynamical properties is lacking. Here, the authors demonstrate that inner-valence ionization can induce ultrafast relaxation and further fragmentation mechanisms in benzene trimers.
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Mayol GF, Defelipe LA, Arcon JP, Turjanski AG, Marti MA. Solvent Sites Improve Docking Performance of Protein–Protein Complexes and Protein–Protein Interface-Targeted Drugs. J Chem Inf Model 2022; 62:3577-3588. [DOI: 10.1021/acs.jcim.2c00264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gonzalo F. Mayol
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Lucas A. Defelipe
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
- European Molecular Biology Laboratory - Hamburg Unit, Notkestrasse 85, Hamburg 22607, Germany
| | - Juan Pablo Arcon
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
- Institute for Research in Biomedicine (IRB), 08028 Barcelona, Spain
- The Barcelona Institute of Science and Technology, 08036 Barcelona, Spain
| | - Adrian G. Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Marcelo A. Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
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Song W, Li Q, Wang T, Li Y, Fan T, Zhang J, Wang Q, Pan J, Dong Q, Sun ZS, Wang Y. Putative complement control protein CSMD3 dysfunction impairs synaptogenesis and induces neurodevelopmental disorders. Brain Behav Immun 2022; 102:237-250. [PMID: 35245678 DOI: 10.1016/j.bbi.2022.02.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/10/2022] [Accepted: 02/26/2022] [Indexed: 12/23/2022] Open
Abstract
Recent studies have reported that complement-related proteins modulate brain development through regulating synapse processes in the cortex. CSMD3 belongs to a group of putative complement control proteins. However, its role in the central nervous system and synaptogenesis remains largely unknown. Here we report that CSMD3 deleterious mutations occur frequently in patients with neurodevelopmental disorders (NDDs). Csmd3 is predominantly expressed in cortical neurons of the developing cortex. In mice, Csmd3 disruption induced retarded development and NDD-related behaviors. Csmd3 deficiency impaired synaptogenesis and neurogenesis, allowing fewer neurons reaching the cortical plate. Csmd3 deficiency also induced perturbed functional networks in the developing cortex, involving a number of downregulated synapse-associated genes that influence early synaptic organization and upregulated genes related to immune activity. Our study provides mechanistic insights into the endogenous regulation of complement-related proteins in synaptic development and supports the pathological role of CSMD3 in NDDs.
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Affiliation(s)
- Wei Song
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Quan Li
- School of Life Sciences, Hebei University, Baoding 071002, China
| | - Tao Wang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuanyuan Li
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianda Fan
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Jianghong Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingqing Wang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinrong Pan
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiwen Dong
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhong Sheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; School of Life Sciences, Hebei University, Baoding 071002, China; Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China; State Key Laboratory of Integrated Management of Pest Insects and Rodents, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yan Wang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China.
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11
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Abatedaga I, Perez Mora B, Tuttobene M, Müller G, Biancotti D, Borsarelli CD, Valle L, Mussi MA. Characterization of BLUF-photoreceptors present in Acinetobacter nosocomialis. PLoS One 2022; 17:e0254291. [PMID: 35442978 PMCID: PMC9020721 DOI: 10.1371/journal.pone.0254291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 03/01/2022] [Indexed: 11/18/2022] Open
Abstract
Acinetobacter nosocomialis is a Gram-negative opportunistic pathogen, whose ability to cause disease in humans is well recognized. Blue light has been shown to modulate important physiological traits related to persistence and virulence in this microorganism. In this work, we characterized the three Blue Light sensing Using FAD (BLUF) domain-containing proteins encoded in the A. nosocomialis genome, which account for the only canonical light sensors present in this microorganism. By focusing on a light-modulated bacterial process such as motility, the temperature dependence of light regulation was studied, as well as the expression pattern and spectroscopic characteristics of the different A. nosocomialis BLUFs. Our results show that the BLUF-containing proteins AnBLUF65 and AnBLUF46 encode active photoreceptors in the light-regulatory temperature range when expressed recombinantly. In fact, AnBLUF65 is an active photoreceptor in the temperature range from 15°C to 37°C, while AnBLUF46 between 15°C to 32°C, in vitro. In vivo, only the Acinetobacter baumannii BlsA’s ortholog AnBLUF65 was expressed in A. nosocomialis cells recovered from motility plates. Moreover, complementation assays showed that AnBLUF65 is able to mediate light regulation of motility in A. baumannii ΔblsA strain at 30°C, confirming its role as photoreceptor and in modulation of motility by light. Intra-protein interactions analyzed using 3D models built based on A. baumannii´s BlsA photoreceptor, show that hydrophobic/aromatic intra-protein interactions may contribute to the stability of dark/light- adapted states of the studied proteins, reinforcing the previous notion on the importance of these interactions in BLUF photoreceptors. Overall, the results presented here reveal the presence of BLUF photoreceptors in A. nosocomialis with idiosyncratic characteristics respect to the previously characterized A. baumannii’s BlsA, both regarding the photoactivity temperature-dependency as well as expression patterns, contributing thus to broaden our knowledge on the BLUF family.
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Affiliation(s)
- Inés Abatedaga
- Instituto de Bionanotecnología del NOA (INBIONATEC-CONICET), Universidad Nacional de Santiago del Estero (UNSE), Santiago del Estero, Argentina
| | - Bárbara Perez Mora
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario (UNR), Rosario, Argentina
| | - Marisel Tuttobene
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario (UNR), Rosario, Argentina
| | - Gabriela Müller
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario (UNR), Rosario, Argentina
| | - Daiana Biancotti
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario (UNR), Rosario, Argentina
| | - Claudio D. Borsarelli
- Instituto de Bionanotecnología del NOA (INBIONATEC-CONICET), Universidad Nacional de Santiago del Estero (UNSE), Santiago del Estero, Argentina
- Instituto de Ciencias Químicas (ICQ), Facultad de Agronomía y Agroindustrias (FAyA), UNSE, Santiago del Estero, Argentina
| | - Lorena Valle
- Instituto de Bionanotecnología del NOA (INBIONATEC-CONICET), Universidad Nacional de Santiago del Estero (UNSE), Santiago del Estero, Argentina
- Instituto de Ciencias Químicas (ICQ), Facultad de Agronomía y Agroindustrias (FAyA), UNSE, Santiago del Estero, Argentina
- * E-mail: (MAM); (LV)
| | - Maria A. Mussi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario (UNR), Rosario, Argentina
- * E-mail: (MAM); (LV)
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12
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Structure of the Yeast Cell Wall Integrity Sensor Wsc1 Reveals an Essential Role of Surface-Exposed Aromatic Clusters. J Fungi (Basel) 2022; 8:jof8040379. [PMID: 35448610 PMCID: PMC9024836 DOI: 10.3390/jof8040379] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 12/28/2022] Open
Abstract
In the yeast Saccharomyces cerevisiae and other ascomycetes, the maintenance of cell wall integrity is governed by a family of plasma-membrane spanning sensors that include the Wsc-type proteins. These cell wall proteins apparently sense stress-induced mechanical forces at the cell surface and target the cell wall integrity (CWI) signaling pathway, but the structural base for their sensor function is yet unknown. Here, we solved a high-resolution crystal structure of the extracellular cysteine-rich domain (CRD) of yeast Wsc1, which shows the characteristic PAN/Apple domain fold with two of the four Wsc1 disulfide bridges being conserved in other PAN domain cores. Given the general function of PAN domains in mediating protein–protein and protein–carbohydrate interactions, this finding underpins the importance of Wsc domains in conferring sensing and localization functions. Our Wsc1 CRD structure reveals an unusually high number of surface-exposed aromatic residues that are conserved in other fungal CRDs, and can be arranged into three solvent-exposed clusters. Mutational analysis demonstrates that two of the aromatic clusters are required for conferring S. cerevisiae Wsc1-dependent resistance to the glucan synthase inhibitor caspofungin, and the chitin-binding agents Congo red and Calcofluor white. These findings suggest an essential role of surface-exposed aromatic clusters in fungal Wsc-type sensors that might include an involvement in stress-induced sensor-clustering required to elicit appropriate cellular responses via the downstream CWI pathway.
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13
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Bedart C, Renault N, Chavatte P, Porcherie A, Lachgar A, Capron M, Farce A. SINAPs: A Software Tool for Analysis and Visualization of Interaction Networks of Molecular Dynamics Simulations. J Chem Inf Model 2022; 62:1425-1436. [PMID: 35239339 PMCID: PMC8966674 DOI: 10.1021/acs.jcim.1c00854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As long as the structural study of molecular mechanisms requires multiple molecular dynamics reflecting contrasted bioactive states, the subsequent analysis of molecular interaction networks remains a bottleneck to be fairly treated and requires a user-friendly 3D view of key interactions. Structural Interaction Network Analysis Protocols (SINAPs) is a proprietary python tool developed to (i) quickly solve key interactions able to distinguish two protein states, either from two sets of molecular dynamics simulations or from two crystallographic structures, and (ii) render a user-friendly 3D view of these key interactions through a plugin of UCSF Chimera, one of the most popular open-source viewing software for biomolecular systems. Through two case studies, glucose transporter-1 (GLUT-1) and A2A adenosine receptor (A2AR), SINAPs easily pinpointed key interactions observed experimentally and relevant for their bioactivities. This very effective tool was thus applied to identify the amino acids involved in the molecular enzymatic mechanisms ruling the activation of an immunomodulator drug candidate, P28 glutathione-S-transferase (P28GST). SINAPs is freely available at https://github.com/ParImmune/SINAPs.
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Affiliation(s)
- Corentin Bedart
- Univ.
Lille, Inserm, CHU Lille, U1286 - Infinite - Institute for Translational
Research in Inflammation, F-59000 Lille, France,Par’Immune,
Bio-incubateur Eurasanté, 70 rue du Dr. Yersin, 59120 Loos-Lez-Lille, France,
| | - Nicolas Renault
- Univ.
Lille, Inserm, CHU Lille, U1286 - Infinite - Institute for Translational
Research in Inflammation, F-59000 Lille, France
| | - Philippe Chavatte
- Univ.
Lille, Inserm, CHU Lille, U1286 - Infinite - Institute for Translational
Research in Inflammation, F-59000 Lille, France
| | - Adeline Porcherie
- Par’Immune,
Bio-incubateur Eurasanté, 70 rue du Dr. Yersin, 59120 Loos-Lez-Lille, France
| | - Abderrahim Lachgar
- Par’Immune,
Bio-incubateur Eurasanté, 70 rue du Dr. Yersin, 59120 Loos-Lez-Lille, France
| | - Monique Capron
- Univ.
Lille, Inserm, CHU Lille, U1286 - Infinite - Institute for Translational
Research in Inflammation, F-59000 Lille, France,Par’Immune,
Bio-incubateur Eurasanté, 70 rue du Dr. Yersin, 59120 Loos-Lez-Lille, France
| | - Amaury Farce
- Univ.
Lille, Inserm, CHU Lille, U1286 - Infinite - Institute for Translational
Research in Inflammation, F-59000 Lille, France,
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14
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A Filamentous Bacteriophage Protein Inhibits Type IV Pili To Prevent Superinfection of Pseudomonas aeruginosa. mBio 2022; 13:e0244121. [PMID: 35038902 PMCID: PMC8764522 DOI: 10.1128/mbio.02441-21] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that causes infections in a variety of settings. Many P. aeruginosa isolates are infected by filamentous Pf bacteriophage integrated into the bacterial chromosome as a prophage. Pf virions can be produced without lysing P. aeruginosa. However, cell lysis can occur during superinfection, which occurs when Pf virions successfully infect a host lysogenized by a Pf prophage. Temperate phages typically encode superinfection exclusion mechanisms to prevent host lysis by virions of the same or similar species. In this study, we sought to elucidate the superinfection exclusion mechanism of Pf phage. Initially, we observed that P. aeruginosa that survive Pf superinfection are transiently resistant to Pf-induced plaquing and are deficient in twitching motility, which is mediated by type IV pili (T4P). Pf utilize T4P as a cell surface receptor, suggesting that T4P are suppressed in bacteria that survive superinfection. We tested the hypothesis that a Pf-encoded protein suppresses T4P to mediate superinfection exclusion by expressing Pf proteins in P. aeruginosa and measuring plaquing and twitching motility. We found that the Pf protein PA0721, which we termed Pf superinfection exclusion (PfsE), promoted resistance to Pf infection and suppressed twitching motility by binding the T4P protein PilC. Because T4P play key roles in biofilm formation and virulence, the ability of Pf phage to modulate T4P via PfsE has implications in the ability of P. aeruginosa to persist at sites of infection. IMPORTANCE Pf bacteriophage (phage) are filamentous viruses that infect Pseudomonas aeruginosa and enhance its virulence potential. Pf virions can lyse and kill P. aeruginosa through superinfection, which occurs when an already infected cell is infected by the same or similar phage. Here, we show that a small, highly conserved Pf phage protein (PA0721, PfsE) provides resistance to superinfection by phages that use the type IV pilus as a cell surface receptor. PfsE does this by inhibiting assembly of the type IV pilus via an interaction with PilC. As the type IV pilus plays important roles in virulence, the ability of Pf phage to modulate its assembly has implications for P. aeruginosa pathogenesis.
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15
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Puglisi R. Protein Mutations and Stability, a Link with Disease: The Case Study of Frataxin. Biomedicines 2022; 10:biomedicines10020425. [PMID: 35203634 PMCID: PMC8962269 DOI: 10.3390/biomedicines10020425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 11/16/2022] Open
Abstract
Protein mutations may lead to pathologies by causing protein misfunction or propensity to degradation. For this reason, several studies have been performed over the years to determine the capability of proteins to retain their native conformation under stress condition as well as factors to explain protein stabilization and the mechanisms behind unfolding. In this review, we explore the paradigmatic example of frataxin, an iron binding protein involved in Fe–S cluster biogenesis, and whose impairment causes a neurodegenerative disease called Friedreich’s Ataxia (FRDA). We summarize what is known about most common point mutations identified so far in heterozygous FRDA patients, their effects on frataxin structure and function and the consequences of its binding with partners.
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Affiliation(s)
- Rita Puglisi
- UK Dementia Research Institute at the Wohl Institute of King's College London, London SE59RT, UK
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16
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Aromatic Side Chain at Position 412 of SERINC5 Exerts Restriction Activity toward HIV-1 and Other Retroviruses. J Virol 2021; 95:e0063421. [PMID: 34190600 DOI: 10.1128/jvi.00634-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The host transmembrane protein SERINC5 is incorporated into viral particles and restricts infection by certain retroviruses. However, what motif of SERINC5 mediates this process remains elusive. By conducting mutagenesis analyses, we found that the substitution of phenylalanine with alanine at position 412 (F412A) resulted in a >75-fold reduction in SERINC5's restriction function. The F412A substitution also resulted in the loss of SERINC5's function to sensitize HIV-1 neutralization by antibodies recognizing the envelope's membrane proximal region. A series of biochemical analyses revealed that F412A showed steady-state protein expression, localization at the cellular membrane, and incorporation into secreted virus particles to a greater extent than in the wild type. Furthermore, introduction of several amino acid mutations at this position revealed that the aromatic side chains, including phenylalanine, tyrosine, and tryptophan, were required to maintain SERINC5 functions to impair the virus-cell fusion process and virion infectivity. Moreover, the wild-type SERINC5 restricted infection of lentiviruses pseudotyped with envelopes of murine leukemia viruses, simian immunodeficiency virus, and HIV-2, and F412A abrogated this function. Taken together, our results highlight the importance of the aromatic side chain at SERINC5 position 412 to maintain its restriction function against diverse retrovirus envelopes. IMPORTANCE The host protein SERINC5 is incorporated into progeny virions of certain retroviruses and restricts the infectivity of these viruses or sensitizes the envelope glycoprotein to a class of neutralizing antibodies. However, how and which part of SERINC5 engages with the diverse array of retroviral envelopes and exerts its antiretroviral functions remain elusive. During mutagenesis analyses, we eventually found that the single substitution of phenylalanine with alanine, but not with tyrosine or tryptophan, at position 412 (F412A) resulted in the loss of SERINC5's functions toward diverse retroviruses, whereas F412A showed steady-state protein expression, localization at the cellular membrane, and incorporation into progeny virions to a greater extent than the wild type. Results suggest that the aromatic side chain at position 412 of SERINC5 plays a critical role in mediating antiviral functions toward various retroviruses, thus providing additional important information regarding host and retrovirus interaction.
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17
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Al Mughram MH, Catalano C, Bowry JP, Safo MK, Scarsdale JN, Kellogg GE. 3D Interaction Homology: Hydropathic Analyses of the "π-Cation" and "π-π" Interaction Motifs in Phenylalanine, Tyrosine, and Tryptophan Residues. J Chem Inf Model 2021; 61:2937-2956. [PMID: 34101460 DOI: 10.1021/acs.jcim.1c00235] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Three-dimensional (3D) maps of the hydropathic environments of protein amino acid residues are information-rich descriptors of preferred conformations, interaction types and energetics, and solvent accessibility. The interactions made by each residue are the primary factor for rotamer selection and the secondary, tertiary, and even quaternary protein structure. Our evolving basis set of environmental data for each residue type can be used to understand the protein structure. This work focuses on the aromatic residues phenylalanine, tyrosine, and tryptophan and their structural roles. We calculated and analyzed side chain-to-environment 3D maps for over 70,000 residues of these three types that reveal, with respect to hydrophobic and polar interactions, the environment around each. After binning with backbone ϕ/ψ and side chain χ1, we clustered each bin by 3D similarities between map-map pairs. For each of the three residue types, four bins were examined in detail: one in the β-pleat, two in the right-hand α-helix, and one in the left-hand α-helix regions of the Ramachandran plot. For high degrees of side chain burial, encapsulation of the side chain by hydrophobic interactions is ubiquitous. The more solvent-exposed side chains are more likely to be involved in polar interactions with their environments. Evidence for π-π interactions was observed in about half of the residues surveyed [phenylalanine (PHE): 53.3%, tyrosine (TYR): 34.1%, and tryptophan (TRP): 55.7%], but on an energy basis, this contributed to only ∼4% of the total. Evidence for π-cation interactions was observed in 14.1% of PHE, 8.3% of TYR, and 26.8% of TRP residues, but on an energy basis, this contributed to only ∼1%. This recognition of even these subtle interactions in the 3D hydropathic environment maps is key support for our interaction homology paradigm of protein structure elucidation and possibly prediction.
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Affiliation(s)
- Mohammed H Al Mughram
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States
| | - Claudio Catalano
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States
| | - John P Bowry
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, United States
| | - Martin K Safo
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States.,Institute of Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0133, United States
| | - J Neel Scarsdale
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, United States.,Institute of Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0133, United States
| | - Glen E Kellogg
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States.,Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, United States.,Institute of Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0133, United States
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18
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Hu H, Wang Q, Du J, Liu Z, Ding Y, Xue H, Zhou C, Feng L, Zhang N. Aha1 Exhibits Distinctive Dynamics Behavior and Chaperone-Like Activity. Molecules 2021; 26:molecules26071943. [PMID: 33808352 PMCID: PMC8037086 DOI: 10.3390/molecules26071943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 03/25/2021] [Accepted: 03/25/2021] [Indexed: 12/21/2022] Open
Abstract
Aha1 is the only co-chaperone known to strongly stimulate the ATPase activity of Hsp90. Meanwhile, besides the well-studied co-chaperone function, human Aha1 has also been demonstrated to exhibit chaperoning activity against stress-denatured proteins. To provide structural insights for a better understanding of Aha1's co-chaperone and chaperone-like activities, nuclear magnetic resonance (NMR) techniques were used to reveal the unique structure and internal dynamics features of full-length human Aha1. We then found that, in solution, both the two domains of Aha1 presented distinctive thermal stabilities and dynamics behaviors defined by their primary sequences and three-dimensional structures. The low thermal stability (melting temperature of Aha128-162: 54.45 °C) and the internal dynamics featured with slow motions on the µs-ms time scale were detected for Aha1's N-terminal domain (Aha1N). The aforementioned experimental results suggest that Aha1N is in an energy-unfavorable state, which would therefore thermostatically favor the interaction of Aha1N with its partner proteins such as Hsp90's middle domain. Differently from Aha1N, Aha1C (Aha1's C-terminal domain) exhibited enhanced thermal stability (melting temperature of Aha1204-335: 72.41 °C) and the internal dynamics featured with intermediate motions on the ps-ns time scale. Aha1C's thermal and structural stabilities make it competent for the stabilization of the exposed hydrophobic groove of dimerized Hsp90's N-terminal domain. Of note, according to the NMR data and the thermal shift results, although the very N-terminal region (M1-W27) and the C-terminal relaxin-like factor (RLF) motif showed no tight contacts with the remaining parts of human Aha1, they were identified to play important roles in the recognition of intrinsically disordered pathological α-synuclein.
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Affiliation(s)
- Huifang Hu
- Analytical Research Center for Organic and Biological Molecules, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; (H.H.); (J.D.); (Y.D.)
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China;
| | - Qing Wang
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China;
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jingwen Du
- Analytical Research Center for Organic and Biological Molecules, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; (H.H.); (J.D.); (Y.D.)
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China;
| | - Zhijun Liu
- National Facility for Protein Science in Shanghai, ZhangJiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China; (Z.L.); (H.X.)
| | - Yiluan Ding
- Analytical Research Center for Organic and Biological Molecules, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; (H.H.); (J.D.); (Y.D.)
| | - Hongjuan Xue
- National Facility for Protein Science in Shanghai, ZhangJiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China; (Z.L.); (H.X.)
| | - Chen Zhou
- Analytical Research Center for Organic and Biological Molecules, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; (H.H.); (J.D.); (Y.D.)
- Correspondence: (C.Z.); (L.F.); (N.Z.)
| | - Linyin Feng
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China;
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Correspondence: (C.Z.); (L.F.); (N.Z.)
| | - Naixia Zhang
- Analytical Research Center for Organic and Biological Molecules, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; (H.H.); (J.D.); (Y.D.)
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China;
- Correspondence: (C.Z.); (L.F.); (N.Z.)
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19
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Mitra D, Das Mohapatra PK. Discovery of Novel Cyclic Salt Bridge in Thermophilic Bacterial Protease and Study of its Sequence and Structure. Appl Biochem Biotechnol 2021; 193:1688-1700. [PMID: 33683551 DOI: 10.1007/s12010-021-03547-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/26/2021] [Indexed: 11/30/2022]
Abstract
The plausible explanation behind the stability of thermophilic protein is still yet to be defined more clearly. Here, an in silico study has been undertaken by investigating the sequence and structure of protease from thermophilic (tPro) bacteria and mesophilic (mPro) bacteria. Results showed that charged and uncharged polar residues have higher abundance in tPro. In extreme environment, the tPro is stabilized by high number of isolated and network salt bridges. A novel cyclic salt bridge is also found in a structure of tPro. High number of metal ion-binding site also helps in protein stabilization of thermophilic protease. Aromatic-aromatic interactions also play a crucial role in tPro stabilization. Formation of long network aromatic-aromatic interactions also first time reported here. Finally, the present study provides a major insight with a newly identified cyclic salt bridge in the stability of the enzyme, which may be helpful for protein engineering. It is also used in industrial applications for human welfare.
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Affiliation(s)
- Debanjan Mitra
- Department of Microbiology, Raiganj University, Raiganj, WB, India
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20
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Dixit K, Karanth NM, Nair S, Kumari K, Chakrabarti KS, Savithri HS, Sarma SP. Aromatic Interactions Drive the Coupled Folding and Binding of the Intrinsically Disordered Sesbania mosaic Virus VPg Protein. Biochemistry 2020; 59:4663-4680. [PMID: 33269926 DOI: 10.1021/acs.biochem.0c00721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The plant Sesbania mosaic virus [a (+)-ssRNA sobemovirus] VPg protein is intrinsically disordered in solution. For the virus life cycle, the VPg protein is essential for replication and for polyprotein processing that is carried out by a virus-encoded protease. The nuclear magnetic resonance (NMR)-derived tertiary structure of the protease-bound VPg shows it to have a novel tertiary structure with an α-β-β-β topology. The quaternary structure of the high-affinity protease-VPg complex (≈27 kDa) has been determined using HADDOCK protocols with NMR (residual dipolar coupling, dihedral angle, and nuclear Overhauser enhancement) restraints and mutagenesis data as inputs. The geometry of the complex is in excellent agreement with long-range orientational restraints such as residual dipolar couplings and ring-current shifts. A "vein" of aromatic residues on the protease surface is pivotal for the folding of VPg via intermolecular edge-to-face π···π stacking between Trp271 and Trp368 of the protease and VPg, respectively, and for the CH···π interactions between Leu361 of VPg and Trp271 of the protease. The structure of the protease-VPg complex provides a molecular framework for predicting sites of important posttranslational modifications such as RNA linkage and phosphorylation and a better understanding of the coupled folding upon binding of intrinsically disordered proteins. The structural data presented here augment the limited structural data available on viral proteins, given their propensity for structural disorder.
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Affiliation(s)
- Karuna Dixit
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - N Megha Karanth
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Smita Nair
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Khushboo Kumari
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | | | - Handanahal S Savithri
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Siddhartha P Sarma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
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21
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Mohapatra SB, Manoj N. A conserved π-helix plays a key role in thermoadaptation of catalysis in the glycoside hydrolase family 4. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140523. [PMID: 32853774 DOI: 10.1016/j.bbapap.2020.140523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/22/2020] [Accepted: 07/29/2020] [Indexed: 01/21/2023]
Abstract
Here, we characterize the role of a π-helix in the molecular mechanisms underlying thermoadaptation in the glycoside hydrolase family 4 (GH4). The interspersed π-helix present in a subgroup is evolutionarily related to a conserved α-helix in other orthologs by a single residue insertion/deletion event. The insertional residue, Phe407, in a hyperthermophilic α-glucuronidase, makes specific interactions across the inter-subunit interface. In order to establish the sequence-structure-stability implications of the π-helix, the wild-type and the deletion variant (Δ407) were characterized. The variant showed a significant lowering of melting temperature and optimum temperature for the highest activity. Crystal structures of the proteins show a transformation of the π-helix to a continuous α-helix in the variant, identical to that in orthologs lacking this insertion. Thermodynamic parameters were determined from stability curves representing the temperature dependence of unfolding free energy. Though the proteins display maximum stabilities at similar temperatures, a higher melting temperature in the wild-type is achieved by a combination of higher enthalpy and lower heat capacity of unfolding. Comparisons of the structural changes, and the activity and thermodynamic profiles allow us to infer that specific non-covalent interactions, and the existence of residual structure in the unfolded state, are crucial determinants of its thermostability. These features permit the enzyme to balance the preservation of structure at a higher temperature with the thermodynamic stability required for optimum catalysis.
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Affiliation(s)
- Samar Bhallabha Mohapatra
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Narayanan Manoj
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India.
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22
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Andersson CD, Mishra BK, Forsgren N, Ekström F, Linusson A. Physical Mechanisms Governing Substituent Effects on Arene-Arene Interactions in a Protein Milieu. J Phys Chem B 2020; 124:6529-6539. [PMID: 32610016 PMCID: PMC7467712 DOI: 10.1021/acs.jpcb.0c03778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/26/2020] [Indexed: 11/28/2022]
Abstract
Arene-arene interactions play important roles in protein-ligand complex formation. Here, we investigate the characteristics of arene-arene interactions between small organic molecules and aromatic amino acids in protein interiors. The study is based on X-ray crystallographic data and quantum mechanical calculations using the enzyme acetylcholinesterase and selected inhibitory ligands as a model system. It is shown that the arene substituents of the inhibitors dictate the strength of the interaction and the geometry of the resulting complexes. Importantly, the calculated interaction energies correlate well with the measured inhibitor potency. Non-hydrogen substituents strengthened all interaction types in the protein milieu, in keeping with results for benzene dimer model systems. The interaction energies were dispersion-dominated, but substituents that induced local dipole moments increased the electrostatic contribution and thus yielded more strongly bound complexes. These findings provide fundamental insights into the physical mechanisms governing arene-arene interactions in the protein milieu and thus into molecular recognition between proteins and small molecules.
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Affiliation(s)
| | - Brijesh Kumar Mishra
- International
Institute of Information Technology, Bangalore, Karnataka 560003, India
| | - Nina Forsgren
- CBRN
Defense and Security, Swedish Defense Research
Agency, SE-90621 Umeå, Sweden
| | - Fredrik Ekström
- CBRN
Defense and Security, Swedish Defense Research
Agency, SE-90621 Umeå, Sweden
| | - Anna Linusson
- Department
of Chemistry, Umeå University, SE-90187 Umeå, Sweden
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23
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Miotto M, Olimpieri PP, Di Rienzo L, Ambrosetti F, Corsi P, Lepore R, Tartaglia GG, Milanetti E. Insights on protein thermal stability: a graph representation of molecular interactions. Bioinformatics 2020; 35:2569-2577. [PMID: 30535291 PMCID: PMC6662296 DOI: 10.1093/bioinformatics/bty1011] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/29/2018] [Accepted: 12/07/2018] [Indexed: 11/14/2022] Open
Abstract
Motivation Understanding the molecular mechanisms of thermal stability is a challenge in protein biology. Indeed, knowing the temperature at which proteins are stable has important theoretical implications, which are intimately linked with properties of the native fold, and a wide range of potential applications from drug design to the optimization of enzyme activity. Results Here, we present a novel graph-theoretical framework to assess thermal stability based on the structure without any a priori information. In this approach we describe proteins as energy-weighted graphs and compare them using ensembles of interaction networks. Investigating the position of specific interactions within the 3D native structure, we developed a parameter-free network descriptor that permits to distinguish thermostable and mesostable proteins with an accuracy of 76% and area under the receiver operating characteristic curve of 78%. Availability and implementation Code is available upon request to edoardo.milanetti@uniroma1.it Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Mattia Miotto
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, Rome, Italy.,Center for Life Nano Science@Sapienza, Instituto Italiano di Tecnologia, Viale Regina Elena, 291 Roma (RM), Italy.,Soft and Living Matter Laboratory, Institute of Nanotechnology, Consiglio Nazionale delle Ricerche, Rome, Italy
| | | | - Lorenzo Di Rienzo
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, Rome, Italy
| | - Francesco Ambrosetti
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, Rome, Italy.,Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, the Netherlands
| | - Pietro Corsi
- Department of Science, Università degli Studi "Roma Tre", via della Vasca Navale 84, Rome, Italy
| | - Rosalba Lepore
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader St. 88, Barcelona, Spain.,Institucio' Catalana de Recerca i Estudis Avancats (ICREA), 23 Passeig Lluìs Companys, Barcelona, Spain.,Department of Biology and Biotechnology, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome, Italy
| | - Edoardo Milanetti
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, Rome, Italy.,Center for Life Nano Science@Sapienza, Instituto Italiano di Tecnologia, Viale Regina Elena, 291 Roma (RM), Italy
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24
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Padilla-Sanchez V. In silico analysis of SARS-CoV-2 spike glycoprotein and insights into antibody binding. RESEARCH IDEAS AND OUTCOMES 2020. [DOI: 10.3897/rio.6.e55281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China in December 2019. Since then, COVID-19, the disease caused by SARS-CoV-2, has become a rapidly spreading pandemic that has reached most countries in the world. So far, there are no vaccines or therapeutics to fight this virus. Here, I present an in silico analysis of the virus spike glycoprotein (recently determined at atomic resolution) and provide insights into how antibodies against the 2002 virus SARS-CoV might be modified to neutralize SARS-CoV-2. I ran docking experiments with Rosetta Dock to determine which substitutions in the 80R and m396 antibodies might improve the binding of these to SARS-CoV-2 and used molecular visualization and analysis software, including UCSF Chimera and Rosetta Dock, as well as other bioinformatics tools, including SWISS-MODEL. Supercomputers, including Bridges Large, Stampede and Frontera, were used for macromolecular assemblies and large scale analysis and visualization.
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25
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Lanzarotti E, Defelipe LA, Marti MA, Turjanski AG. Aromatic clusters in protein-protein and protein-drug complexes. J Cheminform 2020; 12:30. [PMID: 33431014 PMCID: PMC7206889 DOI: 10.1186/s13321-020-00437-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 04/30/2020] [Indexed: 11/10/2022] Open
Abstract
Aromatic rings are important residues for biological interactions and appear to a large extent as part of protein-drug and protein-protein interactions. They are relevant for both protein stability and molecular recognition processes due to their natural occurrence in aromatic aminoacids (Trp, Phe, Tyr and His) as well as in designed drugs since they are believed to contribute to optimizing both affinity and specificity of drug-like molecules. Despite the mentioned relevance, the impact of aromatic clusters on protein-protein and protein-drug complexes is still poorly characterized, especially in those that go beyond a dimer. In this work, we studied protein-drug and protein-protein complexes and systematically analyzed the presence and structure of their aromatic clusters. Our results show that aromatic clusters are highly prevalent in both protein-protein and protein-drug complexes, and suggest that protein-protein aromatic clusters have idealized interactions, probably because they were optimized by evolution, as compared to protein-drug clusters that were manually designed. Interestingly, the configuration, solvent accessibility and secondary structure of aromatic residues in protein-drug complexes shed light on the relation between these properties and compound affinity, allowing researchers to better design new molecules.
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Affiliation(s)
- Esteban Lanzarotti
- Departamento de Computación, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Lucas A Defelipe
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,IQUIBICEN/UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,European Molecular Biology Laboratory Hamburg, Notkestraße 85, 22607, Hamburg, Germany
| | - Marcelo A Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,IQUIBICEN/UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Adrián G Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina. .,IQUIBICEN/UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
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26
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Maiolo D, Pizzi A, Gori A, Gazzera L, Demitri N, Genoni A, Baggi F, Moda F, Terraneo G, Baldelli Bombelli F, Metrangolo P, Resnati G. Halogenation of the N-Terminus Tyrosine 10 Promotes Supramolecular Stabilization of the Amyloid-β Sequence 7-12. ChemistryOpen 2020; 9:253-260. [PMID: 32110506 PMCID: PMC7041548 DOI: 10.1002/open.201900350] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/07/2020] [Indexed: 12/16/2022] Open
Abstract
Here, we demonstrate that introduction of halogen atoms at the tyrosine 10 phenol ring of the DSGYEV sequence derived from the flexible amyloid-β N-terminus, promotes its self-assembly in the solid state. In particular, we report the crystal structures of two halogen-modified sequences, which we found to be stabilized in the solid state by halogen-mediated interactions. The structural study is corroborated by Non-Covalent Interaction (NCI) analysis. Our results prove that selective halogenation of an amino acid enhances the supramolecular organization of otherwise unstructured biologically-relevant sequences. This method may develop as a general strategy for stabilizing highly polymorphic peptide regions.
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Affiliation(s)
- Daniele Maiolo
- Dept. Chem., Mater., and Chem. Eng. “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
| | - Andrea Pizzi
- Dept. Chem., Mater., and Chem. Eng. “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
| | - Alessandro Gori
- Istituto di Scienze e Tecnologie ChimicheNational Research Council of ItalyVia M. Bianco 920131MilanoItaly
| | - Lara Gazzera
- Dept. Chem., Mater., and Chem. Eng. “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
| | - Nicola Demitri
- Elettra – Sincrotrone TriesteS.S. 14 Km 163.5 in Area Science Park34149Basovizza – TriesteItaly
| | - Alessandro Genoni
- Laboratoire de Physique et Chimie ThéoriquesUniversité de Lorraine and CNRS UMR CNRS 70191 Boulevard Arago57078MetzFrance
| | - Fulvio Baggi
- Fondazione IRCCS Istituto Neurologico “Carlo Besta”Via G. Celoria 1120133MilanItaly
| | - Fabio Moda
- Fondazione IRCCS Istituto Neurologico “Carlo Besta”Via G. Celoria 1120133MilanItaly
| | - Giancarlo Terraneo
- Dept. Chem., Mater., and Chem. Eng. “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
- Istituto di Scienze e Tecnologie ChimicheNational Research Council of ItalyVia M. Bianco 920131MilanoItaly
| | | | - Pierangelo Metrangolo
- Dept. Chem., Mater., and Chem. Eng. “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
| | - Giuseppe Resnati
- Dept. Chem., Mater., and Chem. Eng. “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
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27
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Ilyas H, Kim J, Lee D, Malmsten M, Bhunia A. Structural insights into the combinatorial effects of antimicrobial peptides reveal a role of aromatic-aromatic interactions in antibacterial synergism. J Biol Chem 2019; 294:14615-14633. [PMID: 31383740 DOI: 10.1074/jbc.ra119.009955] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/02/2019] [Indexed: 01/10/2023] Open
Abstract
The recent development of plants that overexpress antimicrobial peptides (AMPs) provides opportunities for controlling plant diseases. Because plants employ a broad-spectrum antimicrobial defense, including those based on AMPs, transgenic modification for AMP overexpression represents a potential way to utilize a defense system already present in plants. Herein, using an array of techniques and approaches, we report on VG16KRKP and KYE28, two antimicrobial peptides, which in combination exhibit synergistic antimicrobial effects against plant pathogens and are resistant against plant proteases. Investigating the structural origin of these synergistic antimicrobial effects with NMR spectroscopy of the complex formed between these two peptides and their mutated analogs, we demonstrate the formation of an unusual peptide complex, characterized by the formation of a bulky hydrophobic hub, stabilized by aromatic zippers. Using three-dimensional structure analyses of the complex in bacterial outer and inner membrane components and when bound to lipopolysaccharide (LPS) or bacterial membrane mimics, we found that this structure is key for elevating antimicrobial potency of the peptide combination. We conclude that the synergistic antimicrobial effects of VG16KRKP and KYE28 arise from the formation of a well-defined amphiphilic dimer in the presence of LPS and also in the cytoplasmic bacterial membrane environment. Together, these findings highlight a new application of solution NMR spectroscopy to solve complex structures to study peptide-peptide interactions, and they underscore the importance of structural insights for elucidating the antimicrobial effects of AMP mixtures.
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Affiliation(s)
- Humaira Ilyas
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - JaeWoong Kim
- Department of Fine Chemistry, Seoul National University of Science and Technology, Seoul 139743, Korea
| | - DongKuk Lee
- Department of Fine Chemistry, Seoul National University of Science and Technology, Seoul 139743, Korea
| | - Martin Malmsten
- Department of Pharmacy, Uppsala University, SE-75123 Uppsala, Sweden .,Department of Pharmacy, University of Copenhagen, DK 2100, Copenhagen, Denmark
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
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28
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Actin stabilizing compounds show specific biological effects due to their binding mode. Sci Rep 2019; 9:9731. [PMID: 31278311 PMCID: PMC6611809 DOI: 10.1038/s41598-019-46282-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/26/2019] [Indexed: 11/08/2022] Open
Abstract
Actin binding compounds are widely used tools in cell biology. We compare the biological and biochemical effects of miuraenamide A and jasplakinolide, a structurally related prototypic actin stabilizer. Though both compounds have similar effects on cytoskeletal morphology and proliferation, they affect migration and transcription in a distinctive manner, as shown by a transcriptome approach in endothelial cells. In vitro, miuraenamide A acts as an actin nucleating, F-actin polymerizing and stabilizing compound, just like described for jasplakinolide. However, in contrast to jasplakinolide, miuraenamide A competes with cofilin, but not gelsolin or Arp2/3 for binding to F-actin. We propose a binding mode of miuraenamide A, explaining both its similarities and its differences to jasplakinolide. Molecular dynamics simulations suggest that the bromophenol group of miurenamide A interacts with residues Tyr133, Tyr143, and Phe352 of actin. This shifts the D-loop of the neighboring actin, creating tighter packing of the monomers, and occluding the binding site of cofilin. Since relatively small changes in the molecular structure give rise to this selectivity, actin binding compounds surprisingly are promising scaffolds for creating actin binders with specific functionality instead of just "stabilizers".
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29
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Trinh HN, Jang SH, Lee C. Functional characterization of a SNP (F51S) found in human alpha 1-antitrypsin. Mol Genet Genomic Med 2019; 7:e819. [PMID: 31251477 PMCID: PMC6687665 DOI: 10.1002/mgg3.819] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 03/16/2019] [Accepted: 05/29/2019] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Alpha 1-antitrypsin (A1AT) deficiency is related to lung and liver diseases, including pulmonary emphysema and liver cirrhosis in humans. Genetic variations including single nucleotide polymorphisms (SNPs) of SERPINA1 are responsible for A1AT deficiency, but the characteristics of the SNPs are not well-understood. Here, we investigated the features of a rare SNP (F51S) of A1AT, which introduces an additional N-glycosylation site in the N-terminal region of A1AT. METHODS We evaluated the F51S variant compared with the wild-type (WT) A1AT with regard to expression in CHO-K1 cells, trypsin inhibitory activity, polymerization, and thermal stability. RESULTS The recombinant F51S protein expressed in CHO-K1 cells was mostly retained inside cells. The F51S variant had trypsin inhibitory activity, but reduced thermal stability compared with the WT A1AT. The native acrylamide gel data showed that F51S tended to prevent polymerization of A1AT. CONCLUSION The results of this study indicate that Phe51 and the surrounding hydrophobic residue cluster plays an important role in the conformation and secretion of A1AT and suggest the harmful effects of a rare F51S SNP in human health.
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Affiliation(s)
- Hong-Nhung Trinh
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - Sei-Heon Jang
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - ChangWoo Lee
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
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30
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Yusof NA, Kamaruddin S, Abu Bakar FD, Mahadi NM, Abdul Murad AM. Structural and functional insights into TRiC chaperonin from a psychrophilic yeast, Glaciozyma antarctica. Cell Stress Chaperones 2019; 24:351-368. [PMID: 30649671 PMCID: PMC6439030 DOI: 10.1007/s12192-019-00969-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 01/04/2019] [Accepted: 01/08/2019] [Indexed: 12/29/2022] Open
Abstract
Studies on TCP1-1 ring complex (TRiC) chaperonin have shown its indispensable role in folding cytosolic proteins in eukaryotes. In a psychrophilic organism, extreme cold temperature creates a low-energy environment that potentially causes protein denaturation with loss of activity. We hypothesized that TRiC may undergo evolution in terms of its structural molecular adaptation in order to facilitate protein folding in low-energy environment. To test this hypothesis, we isolated G. antarctica TRiC (GaTRiC) and found that the expression of GaTRiC mRNA in G. antarctica was consistently expressed at all temperatures indicating their importance in cell regulation. Moreover, we showed GaTRiC has the ability of a chaperonin whereby denatured luciferase can be folded to the functional stage in its presence. Structurally, three categories of residue substitutions were found in α, β, and δ subunits: (i) bulky/polar side chains to alanine or valine, (ii) charged residues to alanine, and (iii) isoleucine to valine that would be expected to increase intramolecular flexibility within the GaTRiC. The residue substitutions observed in the built structures possibly affect the hydrophobic, hydrogen bonds, and ionic and aromatic interactions which lead to an increase in structural flexibility. Our structural and functional analysis explains some possible structural features which may contribute to cold adaptation of the psychrophilic TRiC folding chamber.
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Affiliation(s)
- Nur Athirah Yusof
- Biotechnology Research Institute, Universiti Malaysia Sabah, 88400, Kota Kinabalu, Sabah, Malaysia.
| | - Shazilah Kamaruddin
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Farah Diba Abu Bakar
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Nor Muhammad Mahadi
- Malaysia Genome Institute, Jalan Bangi, 43000, Kajang, Selangor Darul Ehsan, Malaysia
| | - Abdul Munir Abdul Murad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
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31
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Kumar CK, Deval Sathiyashivan S, Masram DT, Jose KVJ, Sathiyendiran M. Experimental and theoretical investigation of intramolecular cooperativity in cyclic benzene trimer motif. RSC Adv 2019; 9:753-760. [PMID: 35517582 PMCID: PMC9059549 DOI: 10.1039/c8ra06647g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 12/18/2018] [Indexed: 12/04/2022] Open
Abstract
A series of new symmetrical tripodal molecules 1a–4b with a central benzene scaffold substituted with methyl/ethyl groups and three benzimidazolyl units having a bithiophene/biphenyl/5-alkylthiophene motif at the 2-position via a –CH2– unit were synthesized and characterized by elemental analysis, HR-MS, and NMR spectroscopy. NMR spectral data reveal that all molecules adopt a cyclic benzene trimer (CBT) using three benzimidazolyl units. Intramolecular cooperative edge-to-face C–H⋯π interactions stabilize the CBT motif in solution and are strong in ethyl substituted molecules (1b–4b) compared to methyl substituted (1a–4a) ones. However, the strength of the CBT unit in the tripodal molecule is independent of the length of the substituent at the 2-position of the benzimidazolyl unit. The relative 1H NMR chemical shift calculated at the MPW1PW91/6-311+G(d,p) level of theory corroborates the experimental values, and the calculations predict the distribution of the structures into syn isomers. The relative change in the NMR chemical shift is justified by the relative change in the magnitude of the (3,+3) critical point (CP) in the molecular electrostatic potential (MESP) topography. Also, a linear correlation of the intramolecular C–H⋯π interactions evaluated at M062X/6-311+G(d,p) with the relative NMR chemical shift suggest the latter as a measure of intramolecular cooperativity. A family of biaryl/alkylthiophene (R–R) benzimidazolyl-based tripodal molecules with cyclic benzene trimer (CBT) motif was synthesized and studied by NMR spectroscopy and MPW1PW91/6-311+G(d,p) theory.![]()
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32
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Filling the Void: Introducing Aromatic Interactions into Solvent Tunnels To Enhance Lipase Stability in Methanol. Appl Environ Microbiol 2018; 84:AEM.02143-18. [PMID: 30217852 DOI: 10.1128/aem.02143-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 09/12/2018] [Indexed: 12/17/2022] Open
Abstract
An enhanced stability of enzymes in organic solvents is desirable under industrial conditions. The potential of lipases as biocatalysts is mainly limited by their denaturation in polar alcohols. In this study, we focused on selected solvent tunnels in lipase from Geobacillus stearothermophilus T6 to improve its stability in methanol during biodiesel synthesis. Using rational mutagenesis, bulky aromatic residues were incorporated to occupy solvent channels and induce aromatic interactions leading to a better inner core packing. The chemical and structural characteristics of each solvent tunnel were systematically analyzed. Selected residues were replaced with Phe, Tyr, or Trp. Overall, 16 mutants were generated and screened in 60% methanol, from which 3 variants showed an enhanced stability up to 81-fold compared with that of the wild type. All stabilizing mutations were found in the longest tunnel detected in the "closed-lid" X-ray structure. The combination of Phe substitutions in an A187F/L360F double mutant resulted in an increase in unfolding temperature (Tm ) of 7°C in methanol and a 3-fold increase in biodiesel synthesis yield from waste chicken oil. A kinetic analysis with p-nitrophenyl laurate revealed that all mutants displayed lower hydrolysis rates (k cat), though their stability properties mostly determined the transesterification capability. Seven crystal structures of different variants were solved, disclosing new π-π or CH/π intramolecular interactions and emphasizing the significance of aromatic interactions for improved solvent stability. This rational approach could be implemented for the stabilization of other enzymes in organic solvents.IMPORTANCE Enzymatic synthesis in organic solvents holds increasing industrial opportunities in many fields; however, one major obstacle is the limited stability of biocatalysts in such a denaturing environment. Aromatic interactions play a major role in protein folding and stability, and we were inspired by this to redesign enzyme voids. The rational protein engineering of solvent tunnels of lipase from Geobacillus stearothermophilus is presented here, offering a promising approach to introduce new aromatic interactions within the enzyme core. We discovered that longer tunnels leading from the surface to the enzyme active site were more beneficial targets for mutagenesis for improving lipase stability in methanol during biodiesel biosynthesis. A structural analysis of the variants confirmed the generation of new interactions involving aromatic residues. This work provides insights into stability-driven enzyme design by targeting the solvent channel void.
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33
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Dimitriou PS, Denesyuk AI, Nakayama T, Johnson MS, Denessiouk K. Distinctive structural motifs co-ordinate the catalytic nucleophile and the residues of the oxyanion hole in the alpha/beta-hydrolase fold enzymes. Protein Sci 2018; 28:344-364. [PMID: 30311984 DOI: 10.1002/pro.3527] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/04/2018] [Accepted: 10/08/2018] [Indexed: 12/17/2022]
Abstract
The alpha/beta-hydrolases (ABH) are among the largest structural families of proteins that are found in nature. Although they vary in their sequence and function, the ABH enzymes use a similar acid-base-nucleophile catalytic mechanism to catalyze reactions on different substrates. Because ABH enzymes are biocatalysts with a wide range of potential applications, protein engineering has taken advantage of their catalytic versatility to develop enzymes with industrial applications. This study is a comprehensive analysis of 40 ABH enzyme families focusing on two identified substructures: the nucleophile zone and the oxyanion zone, which co-ordinate the catalytic nucleophile and the residues of the oxyanion hole, and independently reported as critical for the enzymatic activity. We also frequently observed an aromatic cluster near the nucleophile and oxyanion zones, and opposite the ligand-binding site. The nucleophile zone, the oxyanion zone and the residue cluster enriched in aromatic side chains comprise a three-dimensional structural organization that shapes the active site of ABH enzymes and plays an important role in the enzymatic function by structurally stabilizing the catalytic nucleophile and the residues of the oxyanion hole. The structural data support the notion that the aromatic cluster can participate in co-ordination of the catalytic histidine loop, and properly place the catalytic histidine next to the catalytic nucleophile.
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Affiliation(s)
- Polytimi S Dimitriou
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland
| | - Alexander I Denesyuk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland.,Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Toru Nakayama
- Tohoku University, Biomolecular Engineering, Sendai, Miyagi, 980-8579, Japan
| | - Mark S Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland.,Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, Turku, 20520, Finland
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34
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Mathew S, Al Thani AA, Yassine HM. Computational screening of known broad-spectrum antiviral small organic molecules for potential influenza HA stem inhibitors. PLoS One 2018; 13:e0203148. [PMID: 30180218 PMCID: PMC6122827 DOI: 10.1371/journal.pone.0203148] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 08/15/2018] [Indexed: 12/26/2022] Open
Abstract
Background With the emergence of new influenza virus strains that are resistant to current inhibitors such as oseltamivir (anti-neuraminidase (NA)) and amantadine (anti-M2 proton channel), influenza A viruses continue to be a serious threat to the public health worldwide. With this in view, there is a persistent need for the development of broader and more effective vaccines and therapeutics. Identification of broadly neutralizing antibodies (bNAbs) that recognize relatively invariant structures on influenza haemagglutinin (HA) stem has invigorated efforts to develop universal influenza vaccines. Aim The current computational study is designed to identify potential flavonoid inhibitors that bind to the contact epitopes of HA stem that are targeted by broadly neutralizing antibodies (bNAb). Method In this study, we utilized the three-dimensional crystallographic structure of different HA subtypes (H1, H2, H5, H3, and H7) in complex with bNAb to screen for potential broadly reactive influenza inhibitors. We performed Quantitative Structure-Activity and Relationship (QSAR) for 100 natural compounds known for their antiviral activity and performed molecular docking using AutoDock 4.2 suite. Furthermore, we conducted virtual screening of 1413 bioassay hit compounds by using virtual lab bench CLC Drug Discovery. Results The results showed 18 lead flavonoids with strong binding abilities to bNAb epitopes of various HA subtypes. These 18 broadly reactive compounds exhibited significant interactions with an average of seven Hbonds, docking energy of -22.43 kcal·mol−1, and minimum interaction energy of -4.65 kcal·mol−1, with functional contact residues. Procyanidin depicted strong interactions with group 1 HAs, whereas both sorbitol and procyanidin exhibited significant interactions with group 2 HAs. Conclusion Using in silico docking analysis, we identified 18 bioactive flavonoids with potential strong binding cababilities to influenza HA-stems of various subtypes, which are the target for bNAb. The virtual screened bioassay hit compounds depicted a high number of Hbonds but low interaction and docking values compared to antiviral flavonoids. Using structure-based design and nanotechnology-based approaches, identified molecules could be modified to generate next generation anti-influenza drugs.
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Affiliation(s)
- Shilu Mathew
- Biomedical Research Center, Qatar University, Doha, Qatar
| | - Asmaa A. Al Thani
- Biomedical Research Center, Qatar University, Doha, Qatar
- College of Health Sciences, Qatar University, Doha, Qatar
| | - Hadi M. Yassine
- Biomedical Research Center, Qatar University, Doha, Qatar
- College of Health Sciences, Qatar University, Doha, Qatar
- * E-mail:
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35
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León I, Usabiaga I, Arnaiz PF, Lesarri A, Fernández JA. Stepwise Nucleation of Aniline: Emergence of Spectroscopic Fingerprints of the Liquid Phase. Chemistry 2018; 24:10291-10295. [DOI: 10.1002/chem.201802015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/30/2018] [Indexed: 11/12/2022]
Affiliation(s)
- Iker León
- Department Of Physical Chemistryt; University of the Basque Country (UPV/EHU); Barrio Sarriena, S/N 48940 Leioa Spain
- Present address: Grupo de Espectrocopía Molecular; Edificio Quifima; Laboratorios de Espectroscopia y Bioespectroscopia Unidad Asociada CSIC; Parque Científico UVa; Universidad de Valladolid; 47011 Valladolid Spain
| | - Imanol Usabiaga
- Department Of Physical Chemistryt; University of the Basque Country (UPV/EHU); Barrio Sarriena, S/N 48940 Leioa Spain
- Present address: Dipartimento di Chimica “Giacomo Ciamician”; Università degli Studi di Bologna; via Selmi 2 I-40126 Bologna Italy
| | - Pedro F. Arnaiz
- Department Of Physical Chemistryt; University of the Basque Country (UPV/EHU); Barrio Sarriena, S/N 48940 Leioa Spain
| | - Alberto Lesarri
- Department of Physical Chemistry and Inorganic Chemistry; University of Valladolid; 47005 Valladolid Spain
| | - José A. Fernández
- Department Of Physical Chemistryt; University of the Basque Country (UPV/EHU); Barrio Sarriena, S/N 48940 Leioa Spain
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36
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Bendre AD, Ramasamy S, Suresh CG. Analysis of Kunitz inhibitors from plants for comprehensive structural and functional insights. Int J Biol Macromol 2018; 113:933-943. [PMID: 29499268 DOI: 10.1016/j.ijbiomac.2018.02.148] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 02/21/2018] [Accepted: 02/23/2018] [Indexed: 01/11/2023]
Abstract
Legume Kunitz type trypsin inhibitor (KTI) family is one of the most versatile families of proteins. A typical KTI features a single peptide folded in β-trefoil manner, with the molecular weight about 20-22kDa and two disulphide bonds. The members are known to inhibit a wide range of serpins proteases at the same time many of them possess unique features. Copaifera langsdorffii Trypsin inhibitor (CTI) has a β-trefoil fold made up of two non-covalently bound polypeptide chains with only a single disulfide bridge. Delonix regia Trypsin inhibitor (DrTI) has one amino acid insertion between P1 and P2 of the reactive site distorting its conformation. Bauhinia bauhinioides Cruzipain inhibitor (BbCI) has a conservative β-trefoil fold but lacks disulfide bonds. Such subtle differences in structures make Kunitz inhibitors different from other inhibitor families. Most of the studies on these inhibitors are focused towards their proposed role in defense from insect pests and wounding but their exact physiological role in nature is still uncharted. Thus, it would be very interesting to closely analyze the structural details of these inhibitors in order to ascertain their biological role and other fascinating applications.
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Affiliation(s)
- Ameya D Bendre
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-NCL campus, Pune 411008, India
| | - Sureshkumar Ramasamy
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune 411008, India.
| | - C G Suresh
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune 411008, India
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Cornell TA, Ardejani MS, Fu J, Newland SH, Zhang Y, Orner BP. A Structure-Based Assembly Screen of Protein Cage Libraries in Living Cells: Experimentally Repacking a Protein–Protein Interface To Recover Cage Formation in an Assembly-Frustrated Mutant. Biochemistry 2018; 57:604-613. [DOI: 10.1021/acs.biochem.7b01000] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thomas A. Cornell
- Department
of Chemistry, King’s College London, London, U.K
- Division
of Chemistry and Biological Chemistry, Nanyang Technological University, Singapore
| | - Maziar S. Ardejani
- Department
of Chemistry, King’s College London, London, U.K
- Division
of Chemistry and Biological Chemistry, Nanyang Technological University, Singapore
| | - Jing Fu
- Division
of Chemistry and Biological Chemistry, Nanyang Technological University, Singapore
| | | | - Yu Zhang
- Division
of Chemistry and Biological Chemistry, Nanyang Technological University, Singapore
| | - Brendan P. Orner
- Department
of Chemistry, King’s College London, London, U.K
- Division
of Chemistry and Biological Chemistry, Nanyang Technological University, Singapore
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38
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Allodi MA, Otto JP, Sohail SH, Saer RG, Wood RE, Rolczynski BS, Massey SC, Ting PC, Blankenship RE, Engel GS. Redox Conditions Affect Ultrafast Exciton Transport in Photosynthetic Pigment-Protein Complexes. J Phys Chem Lett 2018; 9:89-95. [PMID: 29236502 DOI: 10.1021/acs.jpclett.7b02883] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Pigment-protein complexes in photosynthetic antennae can suffer oxidative damage from reactive oxygen species generated during solar light harvesting. How the redox environment of a pigment-protein complex affects energy transport on the ultrafast light-harvesting time scale remains poorly understood. Using two-dimensional electronic spectroscopy, we observe differences in femtosecond energy-transfer processes in the Fenna-Matthews-Olson (FMO) antenna complex under different redox conditions. We attribute these differences in the ultrafast dynamics to changes to the system-bath coupling around specific chromophores, and we identify a highly conserved tyrosine/tryptophan chain near the chromophores showing the largest changes. We discuss how the mechanism of tyrosine/tryptophan chain oxidation may contribute to these differences in ultrafast dynamics that can moderate energy transfer to downstream complexes where reactive oxygen species are formed. These results highlight the importance of redox conditions on the ultrafast transport of energy in photosynthesis. Tailoring the redox environment may enable energy transport engineering in synthetic light-harvesting systems.
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Affiliation(s)
- Marco A Allodi
- Department of Chemistry, The Institute for Biophysical Dynamics, The James Franck Institute, The University of Chicago , Chicago, Illinois 60637, United States
| | - John P Otto
- Department of Chemistry, The Institute for Biophysical Dynamics, The James Franck Institute, The University of Chicago , Chicago, Illinois 60637, United States
| | - Sara H Sohail
- Department of Chemistry, The Institute for Biophysical Dynamics, The James Franck Institute, The University of Chicago , Chicago, Illinois 60637, United States
| | | | - Ryan E Wood
- Department of Chemistry, The Institute for Biophysical Dynamics, The James Franck Institute, The University of Chicago , Chicago, Illinois 60637, United States
| | - Brian S Rolczynski
- Department of Chemistry, The Institute for Biophysical Dynamics, The James Franck Institute, The University of Chicago , Chicago, Illinois 60637, United States
| | - Sara C Massey
- Department of Chemistry, The Institute for Biophysical Dynamics, The James Franck Institute, The University of Chicago , Chicago, Illinois 60637, United States
| | - Po-Chieh Ting
- Department of Chemistry, The Institute for Biophysical Dynamics, The James Franck Institute, The University of Chicago , Chicago, Illinois 60637, United States
| | | | - Gregory S Engel
- Department of Chemistry, The Institute for Biophysical Dynamics, The James Franck Institute, The University of Chicago , Chicago, Illinois 60637, United States
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Aray Y, Aguilera-García R, Izquierdo DR. Exploring the nature of the H-bonds between the human class II MHC protein, HLA-DR1 (DRB*0101) and the influenza virus hemagglutinin peptide, HA306-318, using the quantum theory of atoms in molecules. J Biomol Struct Dyn 2017; 37:48-64. [PMID: 29246090 DOI: 10.1080/07391102.2017.1418432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The nature of the H-bonds between the human protein HLA-DR1 (DRB*0101) and the hemagglutinin peptide HA306-318 has been studied using the Quantum Theory of Atoms in Molecules for the first time. We have found four H-bond groups: one conventional CO··HN bond group and three nonconventional CO··HC, π··HC involving aromatic rings and HN··HCaliphatic groups. The calculated electron density at the determined H-bond critical points suggests the follow protein pocket binding trend: P1 (2,311) >> P9 (1.109) > P4 (0.950) > P6 (0.553) > P7 (0.213) which agrees and reveal the nature of experimental findings, showing that P1 produces by a long way the strongest binding of the HLA-DR1 human protein molecule with the peptide backbone as consequence of the vast number of H-bonds in the P1 area and at the same time the largest specific binding of the peptide Tyr308 residue with aromatic residues located at the binding groove floor. The present results suggest the topological analysis of the electronic density as a valuable tool that allows a non-arbitrary partition of the pockets binding energy via the calculated electron density at the determined critical points.
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Affiliation(s)
- Yosslen Aray
- a Facultad de Ciencias , Universidad de Ciencias Aplicadas y Ambientales, UDCA , Bogotá , Colombia
| | - Ricardo Aguilera-García
- a Facultad de Ciencias , Universidad de Ciencias Aplicadas y Ambientales, UDCA , Bogotá , Colombia
| | - Daniel R Izquierdo
- a Facultad de Ciencias , Universidad de Ciencias Aplicadas y Ambientales, UDCA , Bogotá , Colombia
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40
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Krittayavathananon A, Sawangphruk M. Impedimetric Sensor of ss-HSDNA/Reduced Graphene Oxide Aerogel Electrode toward Aflatoxin B1 Detection: Effects of Redox Mediator Charges and Hydrodynamic Diffusion. Anal Chem 2017; 89:13283-13289. [PMID: 29171757 DOI: 10.1021/acs.analchem.7b03329] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Here, an impedimetric biosensor for determination and quantification of an aflatoxin B1 (AFB1) level using a reduced graphene oxide aerogel labeled with a single strand DNA (ss-HSDNA/rGOae) modified on a rotating disk electrode (RDE) is presented. Owing to the large biomolecule biding on the electrode, an electron transfer is interrupted and not easily accessible to a target molecule. To address this issue, we aim to study two effects; one considers electro-redox mediators and the other considers the hydrodynamic effect. By observing a cyclic voltammetric response from the ss-HSDNA/rGOae electrode in three different charges of the redox mediators (i.e., neutral FcCH2OH, cationic Ru(NH3)63+, and anionic Fe(CN)64-) in a phosphate buffer solution (PBS) containing AFB1, the magnitude of anodic current at 50 mV s-1 is 825, 615, and 550 mA cm-1, respectively, which is significant dominated by the charge of the redox probe. The effect of hydrodynamic diffusion of the ss-HSDNA/rGOae rotating disk electrode (RDE) toward AFB1 detection using FcCH2OH as the redox mediator was recorded by applying a range of rotating speed from 500 to 4000 rpm. Increasing rotating speed reduces the charge transfer resistance resulting in the lower detectable level for AFB1 quantification. In the case of 4000 rpm, the AFB1 can be detected with a limit of detection of 0.04 ng/mL and a linear range of 1 × 10-10 to 7 × 10-8g/mL.
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Affiliation(s)
- Atiweena Krittayavathananon
- Department of Chemical and Biomolecular Engineering, School of Energy Science and Technology, Vidyasirimedhi Institute of Science and Technology , Rayong 21210, Thailand
| | - Montree Sawangphruk
- Department of Chemical and Biomolecular Engineering, School of Energy Science and Technology, Vidyasirimedhi Institute of Science and Technology , Rayong 21210, Thailand
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41
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Janis B, Uversky VN, Menze MA. Potential functions of LEA proteins from the brine shrimp Artemia franciscana - anhydrobiosis meets bioinformatics. J Biomol Struct Dyn 2017; 36:3291-3309. [PMID: 28971739 DOI: 10.1080/07391102.2017.1387177] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Late embryogenesis abundant (LEA) proteins are a large group of anhydrobiosis-associated intrinsically disordered proteins, which are commonly found in plants and some animals. The brine shrimp Artemia franciscana is the only known animal that expresses LEA proteins from three, and not only one, different groups in its anhydrobiotic life stage. The reason for the higher complexity in the A. franciscana LEA proteome (LEAome), compared with other anhydrobiotic animals, remains mostly unknown. To address this issue, we have employed a suite of bioinformatics tools to evaluate the disorder status of the Artemia LEAome and to analyze the roles of intrinsic disorder in functioning of brine shrimp LEA proteins. We show here that A. franciscana LEA proteins from different groups are more similar to each other than one originally expected, while functional differences among members of group three are possibly larger than commonly anticipated. Our data show that although these proteins are characterized by a large variety of forms and possible functions, as a general strategy, A. franciscana utilizes glassy matrix forming LEAs concurrently with proteins that more readily interact with binding partners. It is likely that the function(s) of both types, the matrix-forming and partner-binding LEA proteins, are regulated by changing water availability during desiccation.
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Affiliation(s)
- Brett Janis
- a Department of Biology , University of Louisville , Louisville 40292 , KY , USA
| | - Vladimir N Uversky
- b Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine , University of South Florida , Tampa 33612 , FL , USA.,c Institute for Biological Instrumentation , Russian Academy of Sciences , Moscow Region, Pushchino 142290 , Russia
| | - Michael A Menze
- a Department of Biology , University of Louisville , Louisville 40292 , KY , USA
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Maung MS, Shon YS. Effects of Noncovalent Interactions on the Catalytic Activity of Unsupported Colloidal Palladium Nanoparticles Stabilized with Thiolate Ligands. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2017; 121:20882-20891. [PMID: 29326755 PMCID: PMC5758047 DOI: 10.1021/acs.jpcc.7b07109] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
This article presents the systematic evaluation of colloidal palladium nanoparticles functionalized with well-defined small organic ligands that provide spatial control of the geometric and electronic surface properties of nanoparticle catalysts. Palladium nanoparticles stabilized with thiolate ligands of different structures and functionalities (linear alkyl vs cyclohexyl vs phenyl) are synthesized using the thiosulfate protocol in a two-phase system. The structure and composition of palladium nanoparticles are characterized using transmission electron microscopy, thermogravimetric analysis, NMR, and UV-vis spectroscopies. The catalysis studies show that the chemical and structural compositions of monolayers surrounding the nanoparticle core greatly influence the overall activity and selectivity of colloidal palladium nanoparticle catalysts for the hydrogenation, isomerization, and hydrogenolysis of allylic alcohols. Especially, noncovalent interactions between surface phenyl ligands and incoming aromatic substrates are found to have a profound influence on the selectivity of colloidal palladium nanoparticles.
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Affiliation(s)
| | - Young-Seok Shon
- Corresponding Author: . Telephone: 562-985-4466. Fax: 562-985-8547
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43
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Defelipe LA, Osman F, Marti MA, Turjanski AG. Structural and mechanistic comparison of the Cyclopropane Mycolic Acid Synthases (CMAS) protein family of Mycobacterium tuberculosis. Biochem Biophys Res Commun 2017; 498:288-295. [PMID: 28859976 DOI: 10.1016/j.bbrc.2017.08.119] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/31/2017] [Accepted: 08/27/2017] [Indexed: 11/19/2022]
Abstract
Tuberculosis (TB) is a chronic disease caused by the bacillus Mycobacterium tuberculosis(Mtb) and remains a leading cause of mortality worldwide. The bacteria has an external wall which protects it from being killed, and the enzymes involved in the biosynthesis of the cell wall components have been proposed as promising targets for future drug development efforts. Cyclopropane Mycolic Acid Synthases (CMAS) constitute a group of ten homologous enzymes which belong to the mycolic acid biosynthesis pathway. These enzymes have S-adenosyl-l-methionine (SAM) dependent methyltransferase activity with a peculiarity, each one of them has strong substrate selectivity and reaction specificity, being able to produce among other things cyclopropanes or methyl-alcohol groups from the lipid olefin group. How each CMAS processes its substrate and how the specificity and selectivity are encoded in the protein sequence and structure, is still unclear. In this work, by using a combination of modeling tools, including comparative modeling, docking, all-atom MD and QM/MM methodologies we studied in detail the reaction mechanism of cmaA2, mmaA4, and mmaA1 CMAS and described the molecular determinants that lead to different products. We have modeled the protein-substrate complex structure and determined the free energy pathway for the reaction. The combination of modeling tools at different levels of complexity allows having a complete picture of the CMAS structure-activity relationship.
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Affiliation(s)
- Lucas A Defelipe
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2620, Ciudad Autónoma de Buenos Aires, Argentina; IQUIBICEN-UBA/CONICET, Intendente Güiraldes 2620, Ciudad Autónoma de Buenos Aires, Argentina
| | - Federico Osman
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2620, Ciudad Autónoma de Buenos Aires, Argentina
| | - Marcelo A Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2620, Ciudad Autónoma de Buenos Aires, Argentina; IQUIBICEN-UBA/CONICET, Intendente Güiraldes 2620, Ciudad Autónoma de Buenos Aires, Argentina.
| | - Adrián G Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2620, Ciudad Autónoma de Buenos Aires, Argentina; IQUIBICEN-UBA/CONICET, Intendente Güiraldes 2620, Ciudad Autónoma de Buenos Aires, Argentina.
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44
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Balakrishnan S, Sarma SP. Engineering Aromatic–Aromatic Interactions To Nucleate Folding in Intrinsically Disordered Regions of Proteins. Biochemistry 2017; 56:4346-4359. [DOI: 10.1021/acs.biochem.7b00437] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Swati Balakrishnan
- Molecular
Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Siddhartha P. Sarma
- Molecular
Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
- NMR
Research Center, Indian Institute of Science, Bangalore, Karnataka 560012, India
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45
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Ugur I, Cinar SA, Dedeoglu B, Aviyente V, Hawthorne MF, Liu P, Liu F, Houk KN, Jiménez-Osés G. 1,3-Dipolar Cycloaddition Reactions of Low-Valent Rhodium and Iridium Complexes with Arylnitrile N-Oxides. J Org Chem 2017; 82:5096-5101. [PMID: 28414468 PMCID: PMC5679111 DOI: 10.1021/acs.joc.7b00282] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reactions between low-valent Rh(I) and Ir(I) metal-carbonyl complexes and arylnitrile oxides possess the electronic and structural features of 1,3-dipolar cycloadditions. Density functional theory (DFT) calculations on these reactions, involving both cyclopentadienyl and carboranyl ligands on the metal carbonyl, explain the ease of the chemical processes and the stabilities of the resulting metallaisoxazolin-5-ones. The metal-carbonyl bond has partial double bond character according to the Wiberg index calculated through NBO analysis, and so the reaction can be considered a normal 1,3-dipolar cycloaddition involving M═C bonds. The rates of formation of the metallacycloadducts are controlled by distortion energy, analogous to their organic counterparts. The superior ability of anionic Ir complexes to share their electron density and accommodate higher oxidation states explains their calculated higher reactivity toward cycloaddition, as compared to Rh analogues.
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Affiliation(s)
- Ilke Ugur
- Department of Chemistry, Bogazici University, Bebek, Istanbul 34342, Turkey
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, United States
| | | | - Burcu Dedeoglu
- Foundations Development Directorate, Sabancı University, Tuzla-Orhanlı, Istanbul 34956, Turkey
| | - Viktorya Aviyente
- Department of Chemistry, Bogazici University, Bebek, Istanbul 34342, Turkey
| | - M. Frederick Hawthorne
- International Institute of Nano and Molecular Medicine, University of Missouri, Columbia, Missouri 65211-3450, United States
| | - Peng Liu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, United States
| | - Fang Liu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, United States
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, United States
| | - Gonzalo Jiménez-Osés
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
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46
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Corradini MG, Demol M, Boeve J, Ludescher RD, Joye IJ. Fluorescence Spectroscopy as a Tool to Unravel the Dynamics of Protein Nanoparticle Formation by Liquid Antisolvent Precipitation. FOOD BIOPHYS 2017. [DOI: 10.1007/s11483-017-9477-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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47
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Werner JP, Mitchell JM, Taracila MA, Bonomo RA, Powers RA. Exploring the potential of boronic acids as inhibitors of OXA-24/40 β-lactamase. Protein Sci 2017; 26:515-526. [PMID: 27997706 DOI: 10.1002/pro.3100] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/08/2016] [Accepted: 12/08/2016] [Indexed: 01/01/2023]
Abstract
β-lactam antibiotics are crucial to the management of bacterial infections in the medical community. Due to overuse and misuse, clinically significant bacteria are now resistant to many commercially available antibiotics. The most widespread resistance mechanism to β-lactams is the expression of β-lactamase enzymes. To overcome β-lactamase mediated resistance, inhibitors were designed to inactivate these enzymes. However, current inhibitors (clavulanic acid, tazobactam, and sulbactam) for β-lactamases also contain the characteristic β-lactam ring, making them susceptible to resistance mechanisms employed by bacteria. This presents a critical need for novel, non-β-lactam inhibitors that can circumvent these resistance mechanisms. The carbapenem-hydrolyzing class D β-lactamases (CHDLs) are of particular concern, given that they efficiently hydrolyze potent carbapenem antibiotics. Unfortunately, these enzymes are not inhibited by clinically available β-lactamase inhibitors, nor are they effectively inhibited by the newest, non-β-lactam inhibitor, avibactam. Boronic acids are known transition state analog inhibitors of class A and C β-lactamases, and are not extensively characterized as inhibitors of class D β-lactamases. Importantly, boronic acids provide a novel way to potentially inhibit class D β-lactamases. Sixteen boronic acids were selected and tested for inhibition of the CHDL OXA-24/40. Several compounds were identified as effective inhibitors of OXA-24/40, with Ki values as low as 5 μM. The X-ray crystal structures of OXA-24/40 in complex with BA3, BA4, BA8, and BA16 were determined and revealed the importance of interactions with hydrophobic residues Tyr112 and Trp115. These boronic acids serve as progenitors in optimization efforts of a novel series of inhibitors for class D β-lactamases.
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Affiliation(s)
- Josephine P Werner
- Department of Chemistry, Grand Valley State University, Allendale, Michigan, 49401
| | - Joshua M Mitchell
- Department of Chemistry, Grand Valley State University, Allendale, Michigan, 49401
| | - Magdalena A Taracila
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, 44106.,Departments of Medicine, Pharmacology, Biochemistry and Molecular Biology, and Microbiology, Case Western Reserve University, Cleveland, Ohio, 44106
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, 44106.,Departments of Medicine, Pharmacology, Biochemistry and Molecular Biology, and Microbiology, Case Western Reserve University, Cleveland, Ohio, 44106
| | - Rachel A Powers
- Department of Chemistry, Grand Valley State University, Allendale, Michigan, 49401
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48
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Sachleben JR, Adhikari AN, Gawlak G, Hoey RJ, Liu G, Joachimiak A, Montelione GT, Sosnick TR, Koide S. Aromatic claw: A new fold with high aromatic content that evades structural prediction. Protein Sci 2017; 26:208-217. [PMID: 27750371 PMCID: PMC5275723 DOI: 10.1002/pro.3069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 10/13/2016] [Accepted: 10/14/2016] [Indexed: 11/12/2022]
Abstract
We determined the NMR structure of a highly aromatic (13%) protein of unknown function, Aq1974 from Aquifex aeolicus (PDB ID: 5SYQ). The unusual sequence of this protein has a tryptophan content five times the normal (six tryptophan residues of 114 or 5.2% while the average tryptophan content is 1.0%) with the tryptophans occurring in a WXW motif. It has no detectable sequence homology with known protein structures. Although its NMR spectrum suggested that the protein was rich in β-sheet, upon resonance assignment and solution structure determination, the protein was found to be primarily α-helical with a small two-stranded β-sheet with a novel fold that we have termed an Aromatic Claw. As this fold was previously unknown and the sequence unique, we submitted the sequence to CASP10 as a target for blind structural prediction. At the end of the competition, the sequence was classified a hard template based model; the structural relationship between the template and the experimental structure was small and the predictions all failed to predict the structure. CSRosetta was found to predict the secondary structure and its packing; however, it was found that there was little correlation between CSRosetta score and the RMSD between the CSRosetta structure and the NMR determined one. This work demonstrates that even in relatively small proteins, we do not yet have the capacity to accurately predict the fold for all primary sequences. The experimental discovery of new folds helps guide the improvement of structural prediction methods.
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Affiliation(s)
| | | | - Grzegorz Gawlak
- Department of Biochemistry and Molecular BiologyUniversity of ChicagoChicagoIllinois
| | - Robert J. Hoey
- Department of Biochemistry and Molecular BiologyUniversity of ChicagoChicagoIllinois
| | - Gaohua Liu
- Northeast Structural Genomics Consortium (NESG), Department of Molecular Biology and Biochemistry, School of Arts and Sciences, and Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, and Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New JerseyPiscatawayNew Jersey
| | - Andrzej Joachimiak
- Department of Biochemistry and Molecular BiologyUniversity of ChicagoChicagoIllinois
- Biological Sciences Division, Argonne National LaboratoryArgonneIllinois
| | - Gaetano T. Montelione
- Northeast Structural Genomics Consortium (NESG), Department of Molecular Biology and Biochemistry, School of Arts and Sciences, and Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, and Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New JerseyPiscatawayNew Jersey
| | - Tobin R. Sosnick
- Department of Biochemistry and Molecular BiologyUniversity of ChicagoChicagoIllinois
| | - Shohei Koide
- Department of Biochemistry and Molecular BiologyUniversity of ChicagoChicagoIllinois
- Department of Biochemistry and Molecular Pharmacology and the Perlmutter Cancer CenterNew York University School of MedicineNew YorkNew York
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49
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Kumar R, Gaurav A, Pal S, Tewari AK. A Case of Folding Pattern in Flexible Tripodal of N-Substituted Bisethylenamine Bridged Pyridazinone Dimers. ChemistrySelect 2017. [DOI: 10.1002/slct.201601897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ranjeet Kumar
- Department of Chemistry (Centre of Advanced Studies); Institute of Science; Banaras Hindu University; Varanasi 221005 India
| | - Archana Gaurav
- Department of Chemistry (Centre of Advanced Studies); Institute of Science; Banaras Hindu University; Varanasi 221005 India
| | - Shiv Pal
- Indian Institute of Science Education and Research, Pune; Dr. Homi Bhabha Road, Pashan Pune 411008 India
| | - Ashish Kumar Tewari
- Department of Chemistry (Centre of Advanced Studies); Institute of Science; Banaras Hindu University; Varanasi 221005 India
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50
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Sathiyashivan SD, Kumar CK, Shankar B, Sathiyendiran M, Masram DT. Perfect symmetrical cyclic aromatic trimer motif in tripodal molecule. RSC Adv 2017. [DOI: 10.1039/c7ra01682d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
A family of substituted benzimidazolyl-based tripodal molecules with alkyl substituted spacers was synthesized, showing perfect symmetric cyclic aromatic trimer motifs which remained intact in the solid as well as solution state.
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