451
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Liu X, Yang Q, Yang M, Du Z, Wei C, Zhang T, Liu B, Liu J. Ultrasound-assisted Maillard reaction of ovalbumin/xylose: The enhancement of functional properties and its mechanism. ULTRASONICS SONOCHEMISTRY 2021; 73:105477. [PMID: 33652292 PMCID: PMC7921010 DOI: 10.1016/j.ultsonch.2021.105477] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/04/2021] [Accepted: 01/26/2021] [Indexed: 05/23/2023]
Abstract
This study aims to optimize the ultrasound treatment conditions for enhancing the degree of glycation (DG) of ovalbumin (OVA)-xylose conjugates through Maillard reaction and investigate the correlation between DG and functional properties affected by structural changes. The structural and functional properties of classical heating OVA, glycated OVA, ultrasonic treated OVA, and ultrasound-assisted glycated OVA were investigated to explore the interaction mechanism of ultrasound treatment on foaming and emulsifying properties improvement. Results indicated that the ultrasound assistance increased free sulfhydryl content, surface hydrophobicity and particle size of OVA-xylose conjugates, and thus enhancing the surface properties, which were strongly linear correlated with DG under different glycation parameters (pH, xylose/OVA ratio, heating time). Additionally, circular dichroism spectroscopy analysis revealed that ultrasound promoted the conversion of α-helices to β-sheets and unfolded structures, which was consistent with the formation of short amyloid-like aggregates that observed by atomic force microscopy phenomenon. Overall, our study provides new insights into the effects of ultrasound treatment on Maillard-induced protein functional properties enhancement, which may be a new strategy to tune the DG and functionality of protein-saccharide grafts during ultrasound processing.
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Affiliation(s)
- Xuanting Liu
- Jilin Provincial Key Laboratory of Nutrition and Functional Food, Jilin University, Changchun 130062, China; College of Food Science and Engineering, Jilin University, Changchun 130062, China.
| | - Qi Yang
- Jilin Provincial Key Laboratory of Nutrition and Functional Food, Jilin University, Changchun 130062, China; College of Food Science and Engineering, Jilin University, Changchun 130062, China.
| | - Meng Yang
- Jilin Provincial Key Laboratory of Nutrition and Functional Food, Jilin University, Changchun 130062, China; College of Food Science and Engineering, Jilin University, Changchun 130062, China.
| | - Zhiyang Du
- Jilin Provincial Key Laboratory of Nutrition and Functional Food, Jilin University, Changchun 130062, China; College of Food Science and Engineering, Jilin University, Changchun 130062, China.
| | - Chen Wei
- Jilin Provincial Key Laboratory of Nutrition and Functional Food, Jilin University, Changchun 130062, China; College of Food Science and Engineering, Jilin University, Changchun 130062, China.
| | - Ting Zhang
- Jilin Provincial Key Laboratory of Nutrition and Functional Food, Jilin University, Changchun 130062, China; College of Food Science and Engineering, Jilin University, Changchun 130062, China.
| | - Boqun Liu
- Jilin Provincial Key Laboratory of Nutrition and Functional Food, Jilin University, Changchun 130062, China; College of Food Science and Engineering, Jilin University, Changchun 130062, China.
| | - Jingbo Liu
- Jilin Provincial Key Laboratory of Nutrition and Functional Food, Jilin University, Changchun 130062, China; College of Food Science and Engineering, Jilin University, Changchun 130062, China.
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452
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Balogh RK, Németh E, Jones NC, Hoffmann SV, Jancsó A, Gyurcsik B. A study on the secondary structure of the metalloregulatory protein CueR: effect of pH, metal ions and DNA. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:491-500. [PMID: 33907862 DOI: 10.1007/s00249-021-01539-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/13/2021] [Accepted: 04/14/2021] [Indexed: 11/30/2022]
Abstract
The response of CueR towards environmental changes in solution was investigated. CueR is a bacterial metal ion selective transcriptional metalloregulator protein, which controls the concentration of copper ions in the cell. Although several articles have been devoted to the discussion of the structural and functional features of this protein, CueR has not previously been extensively characterized in solution. Here, we studied the effect of change in pH, temperature, and the presence of specific or non-specific binding partners on the secondary structure of CueR with circular dichroism (CD) spectroscopy. A rather peculiar reversible pH-dependent secondary structure transformation was observed, elucidated and supplemented with pKa estimation by PROPKA and CpHMD simulations suggesting an important role of His(76) and His(94) in this process. CD experiments revealed that the presence of DNA prevents this structural switch, suggesting that DNA locks CueR in the α-helical-rich form. In contrast to the non-cognate metal ions HgII, CdII and ZnII, the presence of the cognate AgI ion affects the secondary structure of CueR, most probably by stabilizing the metal ion and DNA-binding domains of the protein.
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Affiliation(s)
- Ria K Balogh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720, Hungary
| | - Eszter Németh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720, Hungary.,Institute of Enzymology, Genome Stability Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2, Budapest, 1117, Hungary
| | - Nykola C Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000, Aarhus C, Denmark
| | - Søren Vrønning Hoffmann
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000, Aarhus C, Denmark
| | - Attila Jancsó
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720, Hungary
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720, Hungary.
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453
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Xu X, Du C, Ren Z, Zhang M, Ma L. Conformational Change and Activity Enhancement of Rabbit Muscle Lactate Dehydrogenase Induced by Polyethyleneimine. ACS OMEGA 2021; 6:10859-10865. [PMID: 34056239 PMCID: PMC8153759 DOI: 10.1021/acsomega.1c00562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/01/2021] [Indexed: 06/12/2023]
Abstract
For a better understanding on the interaction between polyethyleneimine (PEI) and proteins, spectroscopic studies including UV-vis absorption, resonance Rayleigh scattering, fluorescence, and circular dichroism were conducted to reveal the conformational change of rabbit muscle lactate dehydrogenase (rmLDH) and related to the bioactivity of the enzyme. Regardless of the electrostatic repulsion, PEI could bind on the surface of rmLDH, a basic protein, via hydrogen binding of the dense amine groups and hydrophobic interaction of methyl groups. The competitive binding by PEI led to a reduction of the binding efficiency of rmLDH toward β-nicotinamide adenine dinucleotide, the coenzyme, and sodium pyruvate, the substrate. However, the complex formation with PEI induced a less ordered conformation and an enhanced surface hydrophobicity of rmLDH, facilitating the turnover of the enzyme and generally resulting in an increased activity. PEI of higher molecular weight was more efficient to induce alteration in the conformation and catalytic activity of the enzyme.
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Affiliation(s)
| | | | | | | | - Lin Ma
- .
Phone: +86-771-3233718. Fax: +86-0771-3233718
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454
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Cattani G, Bocedi A, Gambardella G, Iavarone F, Boroumand M, Castagnola M, Ricci G. Trypsinogen and chymotrypsinogen: the mysterious hyper-reactivity of selected cysteines is still present after their divergent evolution. FEBS J 2021; 288:6003-6018. [PMID: 33876866 DOI: 10.1111/febs.15886] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/11/2021] [Accepted: 04/16/2021] [Indexed: 12/24/2022]
Abstract
An enigmatic and never described hyper-reactivity of most of the cysteines resident in the reduced, molten globule-like intermediate of a few proteins has been recently discovered. In particular, all ten cysteines of chymotrypsinogen showed hundred times increased reactivity against hydrophobic reagents. A single cysteine (Cys1) was also found thousand times more reactive toward GSSG, making speculate that a single glutathionylation could represent the primordial event of its oxidative folding. In the present study, we compare these kinetic properties with those present in trypsinogen taken in its reduced, molten globule-like intermediate and identify the origin of these unusual properties. Despite the divergent evolution of these two proteins, the different amount of disulfides and the very different 3D localization of three disulfides, their hyper-reactivity toward hydrophobic thiol reagents and disulfides is very similar. Mass spectrometry identifies two cysteines in trypsinogen, Cys148 and Cys197, 800 times more reactive toward GSSG than an unperturbed protein cysteine. These results point toward a stringent and accurate preservation of these peculiar kinetic properties during a divergent evolution suggesting some important role, which at the present can only be hypothesized. Similar extraordinary hyper-reactivity has been found also in albumin, ribonuclease, and lysozyme confirming that it cannot be considered a kinetic singularity of a single protein. Interestingly, the very flexible and fluctuating structures like those typical of the molten globule status prove capable of enabling sophisticated actions typical of enzymes such as binding to GSSG with relevant specificity and high affinity (KD = 0.4 mm) and accelerating the reaction of its cysteines by thousands of times.
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Affiliation(s)
- Giada Cattani
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Italy
| | - Alessio Bocedi
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Italy
| | - Giorgia Gambardella
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Italy
| | - Federica Iavarone
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica Sacro Cuore, Rome, Italy.,Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Mozhgan Boroumand
- Laboratorio di Proteomica, Centro Europeo di Ricerca sul Cervello, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Massimo Castagnola
- Laboratorio di Proteomica, Centro Europeo di Ricerca sul Cervello, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Giorgio Ricci
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Italy
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455
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Fukui N, Yamamoto H, Miyabe M, Aoyama Y, Hongo K, Mizobata T, Kawahata I, Yabuki Y, Shinoda Y, Fukunaga K, Kawata Y. An α-synuclein decoy peptide prevents cytotoxic α-synuclein aggregation caused by fatty acid binding protein 3. J Biol Chem 2021; 296:100663. [PMID: 33862084 PMCID: PMC8131325 DOI: 10.1016/j.jbc.2021.100663] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 04/07/2021] [Accepted: 04/12/2021] [Indexed: 12/23/2022] Open
Abstract
α-synuclein (αSyn) is a protein known to form intracellular aggregates during the manifestation of Parkinson’s disease. Previously, it was shown that αSyn aggregation was strongly suppressed in the midbrain region of mice that did not possess the gene encoding the lipid transport protein fatty acid binding protein 3 (FABP3). An interaction between these two proteins was detected in vitro, suggesting that FABP3 may play a role in the aggregation and deposition of αSyn in neurons. To characterize the molecular mechanisms that underlie the interactions between FABP3 and αSyn that modulate the cellular accumulation of the latter, in this report, we used in vitro fluorescence assays combined with fluorescence microscopy, transmission electron microscopy, and quartz crystal microbalance assays to characterize in detail the process and consequences of FABP3–αSyn interaction. We demonstrated that binding of FABP3 to αSyn results in changes in the aggregation mechanism of the latter; specifically, a suppression of fibrillar forms of αSyn and also the production of aggregates with an enhanced cytotoxicity toward mice neuro2A cells. Because this interaction involved the C-terminal sequence region of αSyn, we tested a peptide derived from this region of αSyn (αSynP130-140) as a decoy to prevent the FABP3–αSyn interaction. We observed that the peptide competitively inhibited binding of αSyn to FABP3 in vitro and in cultured cells. We propose that administration of αSynP130-140 might be used to prevent the accumulation of toxic FABP3-αSyn oligomers in cells, thereby preventing the progression of Parkinson’s disease.
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Affiliation(s)
- Naoya Fukui
- Department of Chemistry and Biotechnology, Faculty of Engineering/Graduate School of Engineering, Tottori University, Tottori, Japan
| | - Hanae Yamamoto
- Department of Chemistry and Biotechnology, Faculty of Engineering/Graduate School of Engineering, Tottori University, Tottori, Japan
| | - Moe Miyabe
- Department of Chemistry and Biotechnology, Faculty of Engineering/Graduate School of Engineering, Tottori University, Tottori, Japan
| | - Yuki Aoyama
- Department of Chemistry and Biotechnology, Faculty of Engineering/Graduate School of Engineering, Tottori University, Tottori, Japan
| | - Kunihiro Hongo
- Department of Chemistry and Biotechnology, Faculty of Engineering/Graduate School of Engineering, Tottori University, Tottori, Japan; Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Tottori, Japan; Center for Research on Green Sustainable Chemistry, Tottori University, Tottori, Japan
| | - Tomohiro Mizobata
- Department of Chemistry and Biotechnology, Faculty of Engineering/Graduate School of Engineering, Tottori University, Tottori, Japan; Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Tottori, Japan; Center for Research on Green Sustainable Chemistry, Tottori University, Tottori, Japan
| | - Ichiro Kawahata
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Yasushi Yabuki
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Yasuharu Shinoda
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Kohji Fukunaga
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Yasushi Kawata
- Department of Chemistry and Biotechnology, Faculty of Engineering/Graduate School of Engineering, Tottori University, Tottori, Japan; Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Tottori, Japan; Center for Research on Green Sustainable Chemistry, Tottori University, Tottori, Japan.
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456
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Naphthalimide-Containing BP100 Leads to Higher Model Membranes Interactions and Antimicrobial Activity. Biomolecules 2021; 11:biom11040542. [PMID: 33917850 PMCID: PMC8068292 DOI: 10.3390/biom11040542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/26/2021] [Accepted: 04/06/2021] [Indexed: 11/17/2022] Open
Abstract
In a large variety of organisms, antimicrobial peptides (AMPs) are primary defenses against pathogens. BP100 (KKLFKKILKYL-NH2), a short, synthetic, cationic AMP, is active against bacteria and displays low toxicity towards eukaryotic cells. BP100 acquires a α-helical conformation upon interaction with membranes and increases membrane permeability. Despite the volume of information available, the action mechanism of BP100, the selectivity of its biological effects, and possible applications are far from consensual. Our group synthesized a fluorescent BP100 analogue containing naphthalimide linked to its N-terminal end, NAPHT-BP100 (Naphthalimide-AAKKLFKKILKYL-NH2). The fluorescence properties of naphthalimides, especially their spectral sensitivity to microenvironment changes, are well established, and their biological activities against transformed cells and bacteria are known. Naphthalimide derived compounds are known to interact with DNA disturbing related processes as replication and transcription, and used as anticancer agents due to this property. A wide variety of techniques were used to demonstrate that NAPHT-BP100 bound to and permeabilized zwitterionic POPC and negatively charged POPC:POPG liposomes and, upon interaction, acquired a α-helical structure. Membrane surface high peptide/lipid ratios triggered complete permeabilization of the liposomes in a detergent-like manner. Membrane disruption was driven by charge neutralization, lipid aggregation, and bilayer destabilization. NAPHT-BP100 also interacted with double-stranded DNA, indicating that this peptide could also affect other cellular processes besides causing membrane destabilization. NAPHT-BP100 showed increased antibacterial and hemolytic activities, compared to BP100, and may constitute an efficient antimicrobial agent for dermatological use. By conjugating BP100 and naphthalimide DNA binding properties, NAPHT-BP100 bound to a large extent to the bacterial membrane and could more efficiently destabilize it. We also speculate that peptide could enter the bacteria cell and interact with its DNA in the cytoplasm.
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457
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Patel JG, Narra HP, Sepuru KM, Sahni A, Golla SR, Sahni A, Singh A, Schroeder CLC, Chowdhury IH, Popov VL, Sahni SK. Evolution, purification, and characterization of RC0497: a peptidoglycan amidase from the prototypical spotted fever species Rickettsia conorii. Biol Chem 2021; 401:249-262. [PMID: 31299006 DOI: 10.1515/hsz-2018-0389] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 06/29/2019] [Indexed: 12/12/2022]
Abstract
Rickettsial species have independently lost several genes owing to reductive evolution while retaining those predominantly implicated in virulence, survival, and biosynthetic pathways. In this study, we have identified a previously uncharacterized Rickettsia conorii gene RC0497 as an N-acetylmuramoyl-L-alanine amidase constitutively expressed during infection of cultured human microvascular endothelial cells at the levels of both mRNA transcript and encoded protein. A homology-based search of rickettsial genomes reveals that RC0497 homologs, containing amidase_2 family and peptidoglycan binding domains, are highly conserved among the spotted fever group (SFG) rickettsiae. The recombinant RC0497 protein exhibits α-helix secondary structure, undergoes a conformational change in the presence of zinc, and exists as a dimer at higher concentrations. We have further ascertained the enzymatic activity of RC0497 via demonstration of its ability to hydrolyze Escherichia coli peptidoglycan. Confocal microscopy on E. coli expressing RC0497 and transmission immunoelectron microscopy of R. conorii revealed its localization predominantly to the cell wall, septal regions of replicating bacteria, and the membrane of vesicles pinching off the cell wall. In summary, we have identified and functionally characterized RC0497 as a peptidoglycan hydrolase unique to spotted fever rickettsiae, which may potentially serve as a novel moonlighting protein capable of performing multiple functions during host-pathogen interactions.
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Affiliation(s)
- Jignesh G Patel
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Hema P Narra
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Krishna Mohan Sepuru
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Abha Sahni
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Sandhya R Golla
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Aishwarya Sahni
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Amber Singh
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Casey L C Schroeder
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Imran H Chowdhury
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Vsevolod L Popov
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Sanjeev K Sahni
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
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458
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Augustine G, Aarthy M, Thiagarajan H, Selvaraj S, Kamini NR, Shanmugam G, Ayyadurai N. Self-Assembly and Mechanical Properties of Engineered Protein Based Multifunctional Nanofiber for Accelerated Wound Healing. Adv Healthc Mater 2021; 10:e2001832. [PMID: 33480482 DOI: 10.1002/adhm.202001832] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/05/2020] [Indexed: 12/15/2022]
Abstract
The present work reports a new route for preparing tunable multifunctional biomaterials through the combination of synthetic biology and material chemistry. Genetically encoded catechol moiety is evolved in a nanofiber mat with defined surface and secondary reactive functional chemistry, which promotes self-assembly and wet adhesion property of the protein. The catechol moiety is further exploited for the controlled release of boric acid that provides a congenial cellular microenvironment for accelerated wound healing. The presence of 3,4-dihydroxyphenylalanine in the nanofiber mat act as a stimulus to trigger cell proliferation, migration, and vascularization to accelerate wound healing. Electron paramagnetic resonance, NMR, FTIR, and circular dichroism spectroscopy confirm the structural integrity, antioxidant property, and controlled release of boric acid. Fluorescent and scanning electron microscopy reveals the 3D architecture of nanofiber mat, which favors fibroblast growth, endothelial cell attachment, and tube formation, which are the desirable properties of a wound-healing material. Animal studies in the murine wound healing model assert that the multifunctional biomaterial significantly improve re-epithelialization and accelerate wound closure.
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Affiliation(s)
- George Augustine
- Department of Biochemistry and Biotechnology Council of Scientific and Industrial Research (CSIR)—Central Leather Research Institute (CLRI) Chennai 600020 India
| | - Mayilvahanan Aarthy
- Department of Biochemistry and Biotechnology Council of Scientific and Industrial Research (CSIR)—Central Leather Research Institute (CLRI) Chennai 600020 India
| | - Hemalatha Thiagarajan
- Department of Biochemistry and Biotechnology Council of Scientific and Industrial Research (CSIR)—Central Leather Research Institute (CLRI) Chennai 600020 India
| | - Sowmya Selvaraj
- Inorganic and Physical Chemistry Laboratory Council of Scientific and Industrial Research—Central Leather Research Institute Adyar Chennai 600020 India
| | - Numbi Ramdu Kamini
- Department of Biochemistry and Biotechnology Council of Scientific and Industrial Research (CSIR)—Central Leather Research Institute (CLRI) Chennai 600020 India
| | - Ganesh Shanmugam
- Department of Organic and Bioorganic chemistry Council of Scientific and Industrial Research (CSIR)—Central Leather Research Institute (CLRI) Chennai 600020 India
| | - Niraikulam Ayyadurai
- Department of Biochemistry and Biotechnology Council of Scientific and Industrial Research (CSIR)—Central Leather Research Institute (CLRI) Chennai 600020 India
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459
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Liu Z, Tang X, Feng F, Xu J, Wu C, Dai G, Yue W, Zhong W, Xu K. Molecular design of peptide amphiphiles for controlled self-assembly and drug release. J Mater Chem B 2021; 9:3326-3334. [PMID: 33881438 DOI: 10.1039/d1tb00173f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide amphiphile-based supramolecular hydrogels hold great promise in drug delivery applications. To cater for a specific drug dose in a demanding biomedical scenario, sophisticated design of peptide amphiphile (PA) molecules is required to tune their self-assembling behaviours as well as drug releasing profiles. Herein, we designed a series of PAs with various capping groups and C-terminal amino acids to systematically optimize their self-assembling capabilities for controlled drug release. First, we evaluated the influence of N-terminal capping groups to find that the 2-naphthylacetyl moiety (Nap) greatly assisted hydrogelation of PAs. Next, self-assembling behaviours of Nap-capped PAs were compared among three candidates that bore varying hydrophilic moieties at the C-terminus (Nap-C12-VVAAG, Nap-C12-VVAAD and Nap-C12-VVAADD, denoted as 1-G, 1-D, and 1-DD). It was found that 1-G and 1-D co-assembled with doxorubicin (DOX) and calcium ions (Ca2+) at a higher efficiency than 1-DD, for 1-G/Ca2+/DOX and 1-D/Ca2+/DOX hydrogels displayed a dense nanofibrillar network, with lower minimal gelation concentrations and greater storage modulus values. Interestingly, these PA/Ca2+/DOX hydrogels exhibited tunable release rates of DOX in vitro, with fast release of DOX found in 1-DD/Ca2+/DOX and slow release in 1-G/Ca2+/DOX and 1-D/Ca2+/DOX. Further cell experiments demonstrated that 1-G/Ca2+/DOX and 1-D/Ca2+/DOX exhibited higher inhibitory efficacy against HeLa cells, as compared to DOX solution and 1-DD/Ca2+/DOX. Finally, PA/Ca2+/DOX hydrogels displayed a longer retention time of DOX than aqueous DOX solution in animal experiments, and sustained release of DOX from hydrogels was also evidenced by slow and persisting accumulation of DOX in the major organs of hydrogel-treated mice.
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Affiliation(s)
- Ziqi Liu
- Department of Chemistry, China Pharmaceutical University, Nanjing 210009, China.
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460
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Shao H, Huang W, Avilan L, Receveur-Bréchot V, Puppo C, Puppo R, Lebrun R, Gontero B, Launay H. A new type of flexible CP12 protein in the marine diatom Thalassiosira pseudonana. Cell Commun Signal 2021; 19:38. [PMID: 33761918 PMCID: PMC7992989 DOI: 10.1186/s12964-021-00718-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/09/2021] [Indexed: 12/11/2022] Open
Abstract
Background CP12 is a small chloroplast protein that is widespread in various photosynthetic organisms and is an actor of the redox signaling pathway involved in the regulation of the Calvin Benson Bassham (CBB) cycle. The gene encoding this protein is conserved in many diatoms, but the protein has been overlooked in these organisms, despite their ecological importance and their complex and still enigmatic evolutionary background. Methods A combination of biochemical, bioinformatics and biophysical methods including electrospray ionization-mass spectrometry, circular dichroism, nuclear magnetic resonance spectroscopy and small X ray scattering, was used to characterize a diatom CP12. Results Here, we demonstrate that CP12 is expressed in the marine diatom Thalassiosira pseudonana constitutively in dark-treated and in continuous light-treated cells as well as in all growth phases. This CP12 similarly to its homologues in other species has some features of intrinsically disorder protein family: it behaves abnormally under gel electrophoresis and size exclusion chromatography, has a high net charge and a bias amino acid composition. By contrast, unlike other known CP12 proteins that are monomers, this protein is a dimer as suggested by native electrospray ionization-mass spectrometry and small angle X-ray scattering. In addition, small angle X-ray scattering revealed that this CP12 is an elongated cylinder with kinks. Circular dichroism spectra indicated that CP12 has a high content of α-helices, and nuclear magnetic resonance spectroscopy suggested that these helices are unstable and dynamic within a millisecond timescale. Together with in silico predictions, these results suggest that T. pseudonana CP12 has both coiled coil and disordered regions. Conclusions These findings bring new insights into the large family of dynamic proteins containing disordered regions, thus increasing the diversity of known CP12 proteins. As it is a protein that is more abundant in many stresses, it is not devoted to one metabolism and in particular, it is not specific to carbon metabolism. This raises questions about the role of this protein in addition to the well-established regulation of the CBB cycle. Choregraphy of metabolism by CP12 proteins in Viridiplantae and Heterokonta. While the monomeric CP12 in Viridiplantae is involved in carbon assimilation, regulating phosphoribulokinase (PRK) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) through the formation of a ternary complex, in Heterokonta studied so far, the dimeric CP12 is associated with Ferredoxin-NADP reductase (FNR) and GAPDH. The Viridiplantae CP12 can bind metal ions and can be a chaperone, the Heterokonta CP12 is more abundant in all stresses (C, N, Si, P limited conditions) and is not specific to a metabolism. ![]()
Video Abstract
Supplementary Information The online version contains supplementary material available at 10.1186/s12964-021-00718-x.
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Affiliation(s)
- Hui Shao
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France
| | - Wenmin Huang
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France.,Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Luisana Avilan
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France.,Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | | | - Carine Puppo
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France
| | - Rémy Puppo
- CNRS FR 3479, Plate-Forme Protéomique de L'Institut de Microbiologie de La Méditerranée (IMM), Aix Marseille Univ, 13009, Marseille, France
| | - Régine Lebrun
- CNRS FR 3479, Plate-Forme Protéomique de L'Institut de Microbiologie de La Méditerranée (IMM), Aix Marseille Univ, 13009, Marseille, France
| | - Brigitte Gontero
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France.
| | - Hélène Launay
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France.
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461
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Wang Y, Wang Q, Wang Q, Wang Y, Li Z, Lan X, Dong J, Gao W, Han Q, Zhang Z. Dynamically adjustable-induced THz circular dichroism and biosensing application of symmetric silicon-graphene-metal composite nanostructures. OPTICS EXPRESS 2021; 29:8087-8097. [PMID: 33820261 DOI: 10.1364/oe.419614] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/10/2021] [Indexed: 06/12/2023]
Abstract
Induced circular dichroism (ICD) has been used to detect biomolecular conformations through the coupling between chiral molecules and achiral metal nanostructures with the localized surface plasmon (LSP). However, this ICD is always weak and cannot be dynamically adjusted. Here, we put dielectric and graphene nanostructures on a metal-substrate for restricting more light energies and obtaining dynamic adjustable performance. A composite nanostructure array composed of achiral silicon-nanorods on a metal-substrate and graphene-ribbons (ASMG) is theoretically investigated. Two strong ICD signals appear in the THz region. Near-field magnetic distributions of ASMG reveal that the two strong ICD signals are mainly due to the surface plasmon resonances (SPPs) on the metal-substrate and LSP in the graphene nanostructures, respectively. The ICD signals strongly depend on the geometric parameters of ASMG and are dynamically adjusted by just changing the Fermi levels of graphene-ribbons. In addition, left-handed ASMG and right-handed ASMG can be used to identify the chiral molecular solutions with different chiralities. The maximum enhancement factor of the chiral molecular solutions could reach up to 3500 times in the THz region. These results can help to design dynamically adjustable THz chiral sensors and promote their application in biological monitoring and asymmetric catalysis.
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462
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A Tryptophan 'Gate' in the CRISPR-Cas3 Nuclease Controls ssDNA Entry into the Nuclease Site, That When Removed Results in Nuclease Hyperactivity. Int J Mol Sci 2021; 22:ijms22062848. [PMID: 33799639 PMCID: PMC8001533 DOI: 10.3390/ijms22062848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 12/18/2022] Open
Abstract
Cas3 is a ssDNA-targeting nuclease-helicase essential for class 1 prokaryotic CRISPR immunity systems, which has been utilized for genome editing in human cells. Cas3-DNA crystal structures show that ssDNA follows a pathway from helicase domains into a HD-nuclease active site, requiring protein conformational flexibility during DNA translocation. In genetic studies, we had noted that the efficacy of Cas3 in CRISPR immunity was drastically reduced when temperature was increased from 30 °C to 37 °C, caused by an unknown mechanism. Here, using E. coli Cas3 proteins, we show that reduced nuclease activity at higher temperature corresponds with measurable changes in protein structure. This effect of temperature on Cas3 was alleviated by changing a single highly conserved tryptophan residue (Trp-406) into an alanine. This Cas3W406A protein is a hyperactive nuclease that functions independently from temperature and from the interference effector module Cascade. Trp-406 is situated at the interface of Cas3 HD and RecA1 domains that is important for maneuvering DNA into the nuclease active site. Molecular dynamics simulations based on the experimental data showed temperature-induced changes in positioning of Trp-406 that either blocked or cleared the ssDNA pathway. We propose that Trp-406 forms a 'gate' for controlling Cas3 nuclease activity via access of ssDNA to the nuclease active site. The effect of temperature in these experiments may indicate allosteric control of Cas3 nuclease activity caused by changes in protein conformations. The hyperactive Cas3W406A protein may offer improved Cas3-based genetic editing in human cells.
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463
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Portelinha J, Heilemann K, Jin J, Angeles-Boza AM. Unraveling the implications of multiple histidine residues in the potent antimicrobial peptide Gaduscidin-1. J Inorg Biochem 2021; 219:111391. [PMID: 33770667 DOI: 10.1016/j.jinorgbio.2021.111391] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/07/2021] [Accepted: 02/07/2021] [Indexed: 12/26/2022]
Abstract
The development of antimicrobial peptides (AMPs) as potential therapeutics requires resolving the foundational principles behind their structure-activity relationships. The role of histidine residues within AMPs remains a mystery despite the fact that several potent peptides containing this amino acid are being considered for further clinical development. Gaduscidin-1 (Gad-1) is a potent AMP from Atlantic cod fish that has a total of five His residues. Herein, the role of His residues and metal-potentiated activity of Gad-1 was studied. The five His residues contribute to the broad-spectrum activity of Gad-1. We demonstrated that Gad-1 can coordinate two Cu2+ ions, one at the N-terminus and one at the C-terminus, where the C-terminal binding site is a novel Cu2+ binding motif. High affinity Cu2+ binding at both sites was observed using mass spectrometry and isothermal titration calorimetry. Electron paramagnetic resonance was used to determine the coordination environment of the Cu2+ ions. Cu2+ binding was shown to be responsible for an increase in antimicrobial activity and a new mode of action. Along with the traditional AMP mode of action of pore formation, Gad-1 in the presence of Cu2+ (per)oxidizes lipids. Importantly, His3, His11, His17, and His21 were found to be important to lipid (per)oxidation. This insight will help further understand the inclusion and role of His residues in AMPs, the role of the novel C-terminal binding site, and can contribute to the field of designing potent AMPs that bind metal ions to potentiate activity.
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Affiliation(s)
- Jasmin Portelinha
- Department of Chemistry, University of Connecticut, 55 N. Eagleville Road, Storrs, CT 06269, United States of America
| | - Kara Heilemann
- Department of Chemistry, University of Connecticut, 55 N. Eagleville Road, Storrs, CT 06269, United States of America
| | - Jing Jin
- Magnetic Resonance Center, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, United States of America
| | - Alfredo M Angeles-Boza
- Department of Chemistry, University of Connecticut, 55 N. Eagleville Road, Storrs, CT 06269, United States of America; Institute of Material Science, University of Connecticut, 97 N. Eagleville Road, Storrs, CT 06269, United States of America.
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464
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Turbant F, Partouche D, El Hamoui O, Trépout S, Legoubey T, Wien F, Arluison V. Apomorphine Targets the Pleiotropic Bacterial Regulator Hfq. Antibiotics (Basel) 2021; 10:antibiotics10030257. [PMID: 33806663 PMCID: PMC8000489 DOI: 10.3390/antibiotics10030257] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/24/2021] [Accepted: 02/27/2021] [Indexed: 12/15/2022] Open
Abstract
Hfq is a bacterial regulator with key roles in gene expression. The protein notably regulates translation efficiency and RNA decay in Gram-negative bacteria, thanks to its binding to small regulatory noncoding RNAs. This property is of primary importance for bacterial adaptation and survival in hosts. Small RNAs and Hfq are, for instance, involved in the response to antibiotics. Previous work has shown that the E. coli Hfq C-terminal region (Hfq-CTR) self-assembles into an amyloid structure. It was also demonstrated that the green tea compound EpiGallo Catechin Gallate (EGCG) binds to Hfq-CTR amyloid fibrils and remodels them into nonamyloid structures. Thus, compounds that target the amyloid region of Hfq may be used as antibacterial agents. Here, we show that another compound that inhibits amyloid formation, apomorphine, may also serve as a new antibacterial. Our results provide an alternative in order to repurpose apomorphine, commonly used in the treatment of Parkinson’s disease, as an antibiotic to block bacterial adaptation to treat infections.
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Affiliation(s)
- Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France; (F.T.); (D.P.); (T.L.)
| | - David Partouche
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France; (F.T.); (D.P.); (T.L.)
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France;
| | - Omar El Hamoui
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France;
| | - Sylvain Trépout
- Institut Curie, Inserm US43, and CNRS UMS2016, 91405 Orsay CEDEX, France;
| | - Théa Legoubey
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France; (F.T.); (D.P.); (T.L.)
| | - Frank Wien
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France;
- Correspondence: (F.W.); or (V.A.); Tel.: +33-(0)169359665 (F.W.); +33-(0)169083282 (V.A.)
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France; (F.T.); (D.P.); (T.L.)
- UFR Sciences du Vivant, Université de Paris, 75006 Paris CEDEX, France
- Correspondence: (F.W.); or (V.A.); Tel.: +33-(0)169359665 (F.W.); +33-(0)169083282 (V.A.)
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465
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Fibrilar Polymorphism of the Bacterial Extracellular Matrix Protein TasA. Microorganisms 2021; 9:microorganisms9030529. [PMID: 33806534 PMCID: PMC8000256 DOI: 10.3390/microorganisms9030529] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/23/2021] [Accepted: 03/01/2021] [Indexed: 12/25/2022] Open
Abstract
Functional amyloid proteins often appear as fibers in extracellular matrices of microbial soft colonies. In contrast to disease-related amyloid structures, they serve a functional goal that benefits the organism that secretes them, which is the reason for the title “functional”. Biofilms are a specific example of a microbial community in which functional amyloid fibers play a role. Functional amyloid proteins contribute to the mechanical stability of biofilms and mediate the adhesion of the cells to themselves as well as to surfaces. Recently, it has been shown that functional amyloid proteins also play a regulatory role in biofilm development. TasA is the major proteinaceous fibrilar component of the extracellular matrix of biofilms made of the soil bacterium and Gram-positive Bacillus subtilis. We have previously shown, as later corroborated by others, that in acidic solutions, TasA forms compact aggregates that are composed of tangled fibers. Here, we show that in a neutral pH and above a certain TasA concentration, the fibers of TasA are elongated and straight and that they bundle up in highly concentrated salt solutions. TasA fibers resemble the canonic amyloid morphology; however, these fibers also bear an interesting nm-scale periodicity along the fiber axis. At the molecular level, TasA fibers contain a twisted β-sheet structure, as indicated by circular dichroism measurements. Our study shows that the morphology of TasA fibers depends on the environmental conditions. Different fibrilar morphologies may be related with different functional roles in biofilms, ranging from granting biofilms with a mechanical support to acting as antibiotic agents.
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466
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Varma N, Singh A, Ravi VK, Thakur M, Kumar S. Deltamethrin modulates the native structure of Hen Egg White Lysozyme and induces its aggregation at physiological pH. Colloids Surf B Biointerfaces 2021; 201:111646. [PMID: 33652208 DOI: 10.1016/j.colsurfb.2021.111646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/26/2021] [Accepted: 02/16/2021] [Indexed: 10/22/2022]
Abstract
Deltamethrin, a type II pyrethroid pesticide was initially considered as safe for human use. Recent studies have reported several pathophysiological effects of deltamethrin on human and non-human species. However, its effect on structure and function of protein leading to progressive neurodegeneration is poorly understood. In present study, we investigated the interaction of deltamethrin with Hen Egg White Lysozyme (HEWL) at physiological pH and tried to understand the effect of pesticide on structure and function of protein. Employing different biophysical techniques, we shown that deltamethrin induces in vitro aggregation of HEWL in concentration dependent manner. Interaction of pesticide with different amino acids, followed by exposure of hydrophobic regions was driving force of aggregation process. Apart from modulating the hydrophobic domain, deltamethrin is observed to reduce α-helical and promote β-sheet content of lysozyme, eventually converting the globular protein into ThT sensitive amyloid fibrils and amorphous aggregates. Our study also indicate that deltamethrin induced aggregation reduces the catalytic activity of lysozyme.
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Affiliation(s)
- Neelakant Varma
- Laboratory of Forensic Biology and Biotechnology, School of Forensic Science, National Forensic Sciences University, Gandhinagar, Gujarat, 382 007, India(1)
| | - Abhishek Singh
- Laboratory of Forensic Biology and Biotechnology, School of Forensic Science, National Forensic Sciences University, Gandhinagar, Gujarat, 382 007, India(1); Zoological Survey of India, New Alipore, Kolkata, West Bengal, 700 053, India
| | - Vijay K Ravi
- Centre for Nanoscience and Nanotechnology, Aryabhatta Knowledge University, Mithapur, Patna, Bihar, 800 001, India
| | - Mukesh Thakur
- Zoological Survey of India, New Alipore, Kolkata, West Bengal, 700 053, India
| | - Satish Kumar
- Laboratory of Forensic Biology and Biotechnology, School of Forensic Science, National Forensic Sciences University, Gandhinagar, Gujarat, 382 007, India(1).
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467
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Haridhasapavalan KK, Ranjan SH, Bhattacharyya S, Thummer RP. Soluble expression, purification, and secondary structure determination of human MESP1 transcription factor. Appl Microbiol Biotechnol 2021; 105:2363-2376. [PMID: 33651130 DOI: 10.1007/s00253-021-11194-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 02/04/2021] [Accepted: 02/19/2021] [Indexed: 02/06/2023]
Abstract
Transcription factor MESP1 is a crucial factor regulating cardiac, hematopoietic, and skeletal myogenic development. Besides, it also contributes to the generation of functional cardiomyocytes. Here, we report the soluble expression and purification of the full-length human MESP1 protein from the heterologous system, which can be delivered into the target mammalian cells. To generate this biological macromolecule, we cloned its codon-optimized gene sequence fused to a nuclear localization sequence, a cell-penetrating peptide, and a His-tag into the protein expression vector and expressed in the bacterial system (E. coli strain BL21(DE3)). Subsequently, we have screened and identified the optimal expression parameters to obtain this recombinant fusion protein in soluble form from E. coli and examined its expression concerning the placement of fusion tags at either terminal. Further, we have purified this recombinant fusion protein to homogeneity under native conditions. Notably, this purified fusion protein has maintained its secondary structure after purification, primarily comprising α-helices and random coils. This molecular tool can potentially replace its genetic and viral forms in the cardiac reprogramming of fibroblasts to induce a cardiac transcriptional profile in an integration-free manner and elucidating its role in various biological processes and diseases. KEY POINTS: • Screening of the suitable gene construct was performed and identified. • Screening of optimal expression conditions was performed and identified. • Native purification of recombinant human MESP1 protein from E. coli was performed. • Recombinant MESP1 protein has retained its secondary structure after purification.
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Affiliation(s)
- Krishna Kumar Haridhasapavalan
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Sujal Harsh Ranjan
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Srirupa Bhattacharyya
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Rajkumar P Thummer
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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468
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Staton GJ, Clegg SR, Ainsworth S, Armstrong S, Carter SD, Radford AD, Darby A, Wastling J, Hall N, Evans NJ. Dissecting the molecular diversity and commonality of bovine and human treponemes identifies key survival and adhesion mechanisms. PLoS Pathog 2021; 17:e1009464. [PMID: 33780514 PMCID: PMC8049484 DOI: 10.1371/journal.ppat.1009464] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 04/15/2021] [Accepted: 03/10/2021] [Indexed: 12/13/2022] Open
Abstract
Here, we report the first complete genomes of three cultivable treponeme species from bovine digital dermatitis (DD) skin lesions, two comparative human treponemes, considered indistinguishable from bovine DD species, and a bovine gastrointestinal (GI) treponeme isolate. Key genomic differences between bovine and human treponemes implicate microbial mechanisms that enhance knowledge of how DD, a severe disease of ruminants, has emerged into a prolific, worldwide disease. Bovine DD treponemes have additional oxidative stress genes compared to nearest human-isolated relatives, suggesting better oxidative stress tolerance, and potentially explaining how bovine strains can colonize skin surfaces. Comparison of both bovine DD and GI treponemes as well as bovine pathogenic and human non-pathogenic saprophyte Treponema phagedenis strains indicates genes encoding a five-enzyme biosynthetic pathway for production of 2,3-diacetamido-2,3-dideoxy-d-mannuronic acid, a rare di-N-acetylated mannuronic acid sugar, as important for pathogenesis. Bovine T. phagedenis strains further differed from human strains by having unique genetic clusters including components of a type IV secretion system and a phosphate utilisation system including phoU, a gene associated with osmotic stress survival. Proteomic analyses confirmed bovine derived T. phagedenis exhibits expression of PhoU but not the putative secretion system, whilst the novel mannuronic acid pathway was expressed in near entirety across the DD treponemes. Analysis of osmotic stress response in water identified a difference between bovine and human T. phagedenis with bovine strains exhibiting enhanced survival. This novel mechanism could enable a selective advantage, allowing environmental persistence and transmission of bovine T. phagedenis. Finally, we investigated putative outer membrane protein (OMP) ortholog families across the DD treponemes and identified several families as multi-specific adhesins capable of binding extra cellular matrix (ECM) components. One bovine pathogen specific adhesin ortholog family showed considerable serodiagnostic potential with the Treponema medium representative demonstrating considerable disease specificity (91.6%). This work has shed light on treponeme host adaptation and has identified candidate molecules for future diagnostics, vaccination and therapeutic intervention.
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Affiliation(s)
- Gareth J. Staton
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | - Simon R. Clegg
- School of Life Sciences, College of Science, University of Lincoln, Brayford Pool Campus, Lincoln, United Kingdom
| | - Stuart Ainsworth
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | - Stuart Armstrong
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | - Stuart D. Carter
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | - Alan D. Radford
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | - Alistair Darby
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | - Jonathan Wastling
- Faculty of Natural Sciences, Keele University, Keele, Staffordshire, United Kingdom
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
- Department of Biological Sciences, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Nicholas J. Evans
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, United Kingdom
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469
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Mallart S, Ingenito R, Bianchi E, Bresciani A, Esposito S, Gallo M, Magotti P, Monteagudo E, Orsatti L, Roversi D, Santoprete A, Tucci F, Veneziano M, Bartsch R, Boehm C, Brasseur D, Bruneau P, Corbier A, Froissant J, Gauzy-Lazo L, Gervat V, Marguet F, Menguy I, Minoletti C, Nicolas MF, Pasquier O, Poirier B, Raux A, Riva L, Janiak P, Strobel H, Duclos O, Illiano S. Identification of Potent and Long-Acting Single-Chain Peptide Mimetics of Human Relaxin-2 for Cardiovascular Diseases. J Med Chem 2021; 64:2139-2150. [PMID: 33555858 DOI: 10.1021/acs.jmedchem.0c01533] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The insulin-like peptide human relaxin-2 was identified as a hormone that, among other biological functions, mediates the hemodynamic changes occurring during pregnancy. Recombinant relaxin-2 (serelaxin) has shown beneficial effects in acute heart failure, but its full therapeutic potential has been hampered by its short half-life and the need for intravenous administration limiting its use to intensive care units. In this study, we report the development of long-acting potent single-chain relaxin peptide mimetics. Modifications in the B-chain of relaxin, such as the introduction of specific mutations and the trimming of the sequence to an optimal size, resulted in potent, structurally simplified peptide agonists of the relaxin receptor Relaxin Family Peptide Receptor 1 (RXFP1) (e.g., 54). Introduction of suitable spacers and fatty acids led to the identification of single-chain lipidated peptide agonists of RXFP1, with sub-nanomolar activity, high subcutaneous bioavailability, extended half-lives, and in vivo efficacy (e.g., 64).
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Affiliation(s)
- Sergio Mallart
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Raffaele Ingenito
- Peptides and Small Molecules R&D Department, IRBM Spa, Via Pontina Km 30 600, Pomezia, Rome 00 071, Italy
| | - Elisabetta Bianchi
- Peptides and Small Molecules R&D Department, IRBM Spa, Via Pontina Km 30 600, Pomezia, Rome 00 071, Italy
| | - Alberto Bresciani
- Department of Translational Biology, IRBM Spa, Via Pontina Km 30 600, Pomezia, Rome 00 071, Italy
| | - Simone Esposito
- DMPK, IRBM Spa, Via Pontina Km 30 600, Pomezia, Rome 00 071, Italy
| | - Mariana Gallo
- Structural Biology, IRBM Spa, Via Pontina Km 30 600, Pomezia, Rome 00 071, Italy
| | - Paola Magotti
- Peptides and Small Molecules R&D Department, IRBM Spa, Via Pontina Km 30 600, Pomezia, Rome 00 071, Italy
| | - Edith Monteagudo
- DMPK, IRBM Spa, Via Pontina Km 30 600, Pomezia, Rome 00 071, Italy
| | - Laura Orsatti
- DMPK, IRBM Spa, Via Pontina Km 30 600, Pomezia, Rome 00 071, Italy
| | - Daniela Roversi
- Peptides and Small Molecules R&D Department, IRBM Spa, Via Pontina Km 30 600, Pomezia, Rome 00 071, Italy
| | - Alessia Santoprete
- Peptides and Small Molecules R&D Department, IRBM Spa, Via Pontina Km 30 600, Pomezia, Rome 00 071, Italy
| | - Federica Tucci
- Peptides and Small Molecules R&D Department, IRBM Spa, Via Pontina Km 30 600, Pomezia, Rome 00 071, Italy
| | - Maria Veneziano
- DMPK, IRBM Spa, Via Pontina Km 30 600, Pomezia, Rome 00 071, Italy
| | - Régine Bartsch
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Claudius Boehm
- Industrial Affairs, iCMC, Sanofi-Aventis R&D, Industriepark Höchst, Frankfurt 65926, Germany
| | - Denis Brasseur
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Patricia Bruneau
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Alain Corbier
- Cardio-Vascular and metabolism, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Jacques Froissant
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Laurence Gauzy-Lazo
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Vincent Gervat
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Frank Marguet
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Isabelle Menguy
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Claire Minoletti
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Marie-Françoise Nicolas
- Preclinical Development Sciences, Sanofi R&D, 13 quai Jules Guesde, Vitry sur Seine 94400, France
| | - Olivier Pasquier
- DMPK France, Sanofi R&D, 3 digue d'Alfortville, Alfortville 94140, France
| | - Bruno Poirier
- Cardio-Vascular and metabolism, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Alexandre Raux
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Laurence Riva
- Cardio-Vascular and metabolism, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Philip Janiak
- Cardio-Vascular and metabolism, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Hartmut Strobel
- Peptides and Small Molecules R&D Department, IRBM Spa, Via Pontina Km 30 600, Pomezia, Rome 00 071, Italy
| | - Olivier Duclos
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Stephane Illiano
- Cardio-Vascular and metabolism, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
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470
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Hirano A, Wada M, Sato TK, Kameda T. The solubility of N-acetyl amino acid amides in organic acid and alcohol solutions: Mechanistic insight into structural protein solubilization. Int J Biol Macromol 2021; 178:607-615. [PMID: 33631265 DOI: 10.1016/j.ijbiomac.2021.02.141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/03/2021] [Accepted: 02/18/2021] [Indexed: 10/22/2022]
Abstract
Structural proteins such as spider silk and silkworm silk are generally poorly soluble in aqueous and organic solutions, making them difficult to manipulate in manufacturing processes. Although some organic acids and alcohols, such as formic acid and hexafluoroisopropanol (HFIP), effectively solubilize poorly soluble proteins, little is known about their protein solubilization mechanism. In this study, the solubility of N-acetyl amino acid amide compounds in organic solvents-formic acid, acetic acid, HFIP and isopropanol-was measured to clarify the protein solubilization mechanism at the amino acid residue level. On the basis of thermodynamic analyses of the solubility in terms of the transfer free energy (from water to organic solvents), every organic solvent was found to be effective in thermodynamically stabilizing hydrophobic amino acid side chains in the liquid phase. Formic acid and HFIP were comparably effective in the stabilization of the polypeptide backbone, whereas acetic acid and isopropanol were ineffective. Therefore, the significant solubilizing effect of formic acid and HFIP on the structural proteins was attributed to their favorable interactions with hydrophobic amino acid side chains and with the polypeptide backbone of the proteins. The present findings are useful for the optimization of protein manipulation and amino acid sequence design.
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Affiliation(s)
- Atsushi Hirano
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan.
| | - Momoyo Wada
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan
| | - Takehiro K Sato
- Spiber Inc., 234-1 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Koto, Tokyo 135-0064, Japan
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471
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Heat-induced self-assembling of BSA at the isoelectric point. Int J Biol Macromol 2021; 177:40-47. [PMID: 33607130 DOI: 10.1016/j.ijbiomac.2021.02.112] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/05/2021] [Accepted: 02/15/2021] [Indexed: 11/21/2022]
Abstract
Materials based on ordered protein aggregates have recently received a lot of attention for their application as drug carriers, due to their biocompatibility and their ability to sequester many biological fluids. Bovine serum albumin (BSA) is a good candidate for this use due to its high availability and tendency to aggregate and gel under acidic conditions. In the present work, we employ spectroscopic techniques to investigate the heat-induced BSA aggregation at the molecular scale, in the 12-84 °C temperature range, at pH = 5 where two different isoforms of the protein are stable. Samples at low and high protein concentration are examined. With the advantage of the combined use of FTIR and CD, we recognize the aggregation-prone species and the different distribution of secondary structures, conformational rearrangements and types of aggregates, of millimolar compared to micromolar BSA solutions. Further, as a new tool, we use the Maximum Entropy Method to fit the kinetic curves to investigate the distribution of kinetic constants of the complex hierarchical aggregation process. Finally, we characterize the activation energy of the initial self-assembling step to observe that the formation of both small and large aggregates is driven by the same interactions.
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472
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Kefala A, Amprazi M, Mylonas E, Kotsifaki D, Providaki M, Pozidis C, Fotiadou M, Kokkinidis M. Probing Protein Folding with Sequence-Reversed α-Helical Bundles. Int J Mol Sci 2021; 22:ijms22041955. [PMID: 33669383 PMCID: PMC7920257 DOI: 10.3390/ijms22041955] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/11/2021] [Accepted: 02/11/2021] [Indexed: 12/22/2022] Open
Abstract
Recurrent protein folding motifs include various types of helical bundles formed by α-helices that supercoil around each other. While specific patterns of amino acid residues (heptad repeats) characterize the highly versatile folding motif of four-α-helical bundles, the significance of the polypeptide chain directionality is not sufficiently understood, although it determines sequence patterns, helical dipoles, and other parameters for the folding and oligomerization processes of bundles. To investigate directionality aspects in sequence-structure relationships, we reversed the amino acid sequences of two well-characterized, highly regular four-α-helical bundle proteins and studied the folding, oligomerization, and structural properties of the retro-proteins, using Circular Dichroism Spectroscopy (CD), Size Exclusion Chromatography combined with Multi-Angle Laser Light Scattering (SEC-MALS), and Small Angle X-ray Scattering (SAXS). The comparison of the parent proteins with their retro-counterparts reveals that while the α-helical character of the parents is affected to varying degrees by sequence reversal, the folding states, oligomerization propensities, structural stabilities, and shapes of the new molecules strongly depend on the characteristics of the heptad repeat patterns. The highest similarities between parent and retro-proteins are associated with the presence of uninterrupted heptad patterns in helical bundles sequences.
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Affiliation(s)
- Aikaterini Kefala
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas (IMBB-FORTH), 70013 Heraklion, Greece; (A.K.); (M.A.); (E.M.); (D.K.); (M.P.); (C.P.)
- Department of Biology, University of Crete, 70013 Heraklion, Greece;
| | - Maria Amprazi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas (IMBB-FORTH), 70013 Heraklion, Greece; (A.K.); (M.A.); (E.M.); (D.K.); (M.P.); (C.P.)
- Department of Biology, University of Crete, 70013 Heraklion, Greece;
| | - Efstratios Mylonas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas (IMBB-FORTH), 70013 Heraklion, Greece; (A.K.); (M.A.); (E.M.); (D.K.); (M.P.); (C.P.)
| | - Dina Kotsifaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas (IMBB-FORTH), 70013 Heraklion, Greece; (A.K.); (M.A.); (E.M.); (D.K.); (M.P.); (C.P.)
| | - Mary Providaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas (IMBB-FORTH), 70013 Heraklion, Greece; (A.K.); (M.A.); (E.M.); (D.K.); (M.P.); (C.P.)
| | - Charalambos Pozidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas (IMBB-FORTH), 70013 Heraklion, Greece; (A.K.); (M.A.); (E.M.); (D.K.); (M.P.); (C.P.)
| | - Melina Fotiadou
- Department of Biology, University of Crete, 70013 Heraklion, Greece;
| | - Michael Kokkinidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas (IMBB-FORTH), 70013 Heraklion, Greece; (A.K.); (M.A.); (E.M.); (D.K.); (M.P.); (C.P.)
- Department of Biology, University of Crete, 70013 Heraklion, Greece;
- Correspondence: ; Tel.: +30-2810-394350
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473
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Zheng RH, Wei WM, Liu YY. Theoretical study on spectral differences of polypeptides constituted by L- and D-amino acids. Mol Phys 2021. [DOI: 10.1080/00268976.2020.1812747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Ren-Hui Zheng
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Wen-Mei Wei
- School of Basic Medical Science, Anhui Medical University, Hefei, People’s Republic of China
| | - Yan-Ying Liu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, People’s Republic of China
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474
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Thool M, Dey C, Bhattacharyya S, Sudhagar S, Thummer RP. Generation of a Recombinant Stem Cell-Specific Human SOX2 Protein from Escherichia coli Under Native Conditions. Mol Biotechnol 2021; 63:327-338. [PMID: 33570706 DOI: 10.1007/s12033-021-00305-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2021] [Indexed: 02/06/2023]
Abstract
The stem cell-specific SOX2 transcription factor is critical for early embryonic development and the maintenance of embryonic and neural stem cell identity. It is also crucial for the generation of induced pluripotent and neural stem cells, thus providing immense prospect in patient-specific therapies. Here, we report soluble expression and purification of human SOX2 protein under native conditions from a bacterial system. To generate this macromolecule, we codon-optimized the protein-coding sequence and fused it to a nuclear localization signal, a protein transduction domain, and a His-tag. This was then cloned into a protein expression vector and was expressed in Escherichia coli. Subsequently, we have screened and identified the optimal expression conditions to obtain recombinant fusion protein in a soluble form and studied its expression concerning the position of fusion tags at either terminal. Furthermore, we purified two versions of recombinant SOX2 fusion proteins to homogeneity under native conditions and demonstrated that they maintained their secondary structure. This molecular tool can substitute genetic and viral forms of SOX2 to facilitate the derivation of integration-free induced pluripotent and neural stem cells. Furthermore, it can be used in elucidating its role in stem cells, various cellular processes and diseases, and for structural and biochemical studies.
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Affiliation(s)
- Madhuri Thool
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.,Department of Biotechnology, National Institute of Pharmaceutical Education and Research Guwahati, Changsari, Guwahati, Assam, 781101, India
| | - Chandrima Dey
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Srirupa Bhattacharyya
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - S Sudhagar
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research Guwahati, Changsari, Guwahati, Assam, 781101, India
| | - Rajkumar P Thummer
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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475
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Ryder BD, Matlahov I, Bali S, Vaquer-Alicea J, van der Wel PCA, Joachimiak LA. Regulatory inter-domain interactions influence Hsp70 recruitment to the DnaJB8 chaperone. Nat Commun 2021; 12:946. [PMID: 33574241 PMCID: PMC7878476 DOI: 10.1038/s41467-021-21147-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 01/15/2021] [Indexed: 01/18/2023] Open
Abstract
The Hsp40/Hsp70 chaperone families combine versatile folding capacity with high substrate specificity, which is mainly facilitated by Hsp40s. The structure and function of many Hsp40s remain poorly understood, particularly oligomeric Hsp40s that suppress protein aggregation. Here, we used a combination of biochemical and structural approaches to shed light on the domain interactions of the Hsp40 DnaJB8, and how they may influence recruitment of partner Hsp70s. We identify an interaction between the J-Domain (JD) and C-terminal domain (CTD) of DnaJB8 that sequesters the JD surface, preventing Hsp70 interaction. We propose a model for DnaJB8-Hsp70 recruitment, whereby the JD-CTD interaction of DnaJB8 acts as a reversible switch that can control the binding of Hsp70. These findings suggest that the evolutionarily conserved CTD of DnaJB8 is a regulatory element of chaperone activity in the proteostasis network.
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Affiliation(s)
- Bryan D Ryder
- Molecular Biophysics Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Irina Matlahov
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Sofia Bali
- Molecular Biophysics Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jaime Vaquer-Alicea
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Neuroscience Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands.
| | - Lukasz A Joachimiak
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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476
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Zhao H, Wu D, Nguyen A, Li Y, Adão RC, Valkov E, Patterson GH, Piszczek G, Schuck P. Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.08.430344. [PMID: 33594360 PMCID: PMC7885910 DOI: 10.1101/2021.02.08.430344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Nucleocapsid (N) protein of the SARS-CoV-2 virus packages the viral genome into well-defined ribonucleoprotein particles, but the molecular pathway is still unclear. N-protein is dimeric and consists of two folded domains with nucleic acid (NA) binding sites, surrounded by intrinsically disordered regions that promote liquid-liquid phase separation. Here we use biophysical tools to study N-protein interactions with oligonucleotides of different length, examining the size, composition, secondary structure, and energetics of the resulting states. We observe formation of supramolecular clusters or nuclei preceding growth into phase-separated droplets. Short hexanucleotide NA forms compact 2:2 N-protein/NA complexes with reduced disorder. Longer oligonucleotides expose additional N-protein interactions and multi-valent protein-NA interactions, which generate higher-order mixed oligomers and simultaneously promote growth of droplets. Phase separation is accompanied by a significant increase in protein secondary structure, different from that caused by initial NA binding, which may contribute to the assembly of ribonucleoprotein particles within molecular condensates.
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Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, 13 South Drive, Bethesda, MD 20892, USA
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, 50 South Drive, Bethesda, MD 20892, USA
| | - Ai Nguyen
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, 13 South Drive, Bethesda, MD 20892, USA
| | - Yan Li
- Protein/Peptide Sequencing Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Regina C. Adão
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, 13 South Drive, Bethesda, MD 20892, USA
| | - Eugene Valkov
- Messenger RNA Regulation and Decay Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Building 560, Room 21–105A, Frederick, MD 21702
| | - George H. Patterson
- Section on Biophotonics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, 50 South Drive, Bethesda, MD 20892, USA
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, 13 South Drive, Bethesda, MD 20892, USA
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477
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Mitra R, Gadkari VV, Meinen BA, van Mierlo CPM, Ruotolo BT, Bardwell JCA. Mechanism of the small ATP-independent chaperone Spy is substrate specific. Nat Commun 2021; 12:851. [PMID: 33558474 PMCID: PMC7870927 DOI: 10.1038/s41467-021-21120-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/08/2021] [Indexed: 11/17/2022] Open
Abstract
ATP-independent chaperones are usually considered to be holdases that rapidly bind to non-native states of substrate proteins and prevent their aggregation. These chaperones are thought to release their substrate proteins prior to their folding. Spy is an ATP-independent chaperone that acts as an aggregation inhibiting holdase but does so by allowing its substrate proteins to fold while they remain continuously chaperone bound, thus acting as a foldase as well. The attributes that allow such dual chaperoning behavior are unclear. Here, we used the topologically complex protein apoflavodoxin to show that the outcome of Spy's action is substrate specific and depends on its relative affinity for different folding states. Tighter binding of Spy to partially unfolded states of apoflavodoxin limits the possibility of folding while bound, converting Spy to a holdase chaperone. Our results highlight the central role of the substrate in determining the mechanism of chaperone action.
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Affiliation(s)
- Rishav Mitra
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Varun V Gadkari
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Ben A Meinen
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | | | | | - James C A Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
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478
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Generation of cell-permeant recombinant human transcription factor GATA4 from E. coli. Bioprocess Biosyst Eng 2021; 44:1131-1146. [PMID: 33559005 DOI: 10.1007/s00449-021-02516-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/17/2021] [Indexed: 12/11/2022]
Abstract
Transcription factor GATA4 is expressed during early embryogenesis and is vital for proper development. In addition, it is a crucial reprogramming factor for deriving functional cardiomyocytes and was recently identified as a tumor suppressor protein in various cancers. To generate a safe and effective molecular tool that can potentially be used in a cell reprogramming process and as an anti-cancer agent, we have identified optimal expression parameters to obtain soluble expression of human GATA4 in E. coli and purified the same to homogeneity under native conditions using immobilized metal ion affinity chromatography. The identity of GATA4 protein was confirmed using western blotting and mass spectrometry. Using circular dichroism spectroscopy, it was demonstrated that the purified recombinant protein has maintained its secondary structure, primarily comprising of random coils and α-helices. Subsequently, this purified recombinant protein was applied to human cells and was found that it was non-toxic and able to enter the cells as well as translocate to the nucleus. Prospectively, this cell- and nuclear-permeant molecular tool is suitable for cell reprogramming experiments and can be a safe and effective therapeutic agent for cancer therapy.
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479
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da Costa A, Pereira AM, Sampaio P, Rodríguez-Cabello JC, Gomes AC, Casal M, Machado R. Protein-Based Films Functionalized with a Truncated Antimicrobial Peptide Sequence Display Broad Antimicrobial Activity. ACS Biomater Sci Eng 2021; 7:451-461. [PMID: 33492122 DOI: 10.1021/acsbiomaterials.0c01262] [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: 11/29/2022]
Abstract
The increasing bacterial resistance to antibiotics is driving strong demand for new antimicrobial biomaterials. This work describes the fabrication of free-standing films exhibiting antimicrobial properties by combining, in the same polypeptide chain, an elastin-like recombinamer comprising 200 repetitions of the pentamer VPAVG (A200) and an 18-amino-acid truncated variant of the antimicrobial peptide BMAP-28, termed BMAP-18. The fusion protein BMAP-18A200 was overexpressed and conveniently purified by a simplified and scalable nonchromatographic process. Free-standing films of BMAP-18A200 demonstrated to be stable without requiring cross-linking agents and displayed high antimicrobial activity against skin pathogens including Gram-negative and Gram-positive bacteria as well as unicellular and filamentous fungi. The antimicrobial activity of the films was mediated by direct contact of cells with the film surface, resulting in compromised structural integrity of microbial cells. Furthermore, the BMAP-18A200 films showed no cytotoxicity on normal human cell lines (skin fibroblasts and keratinocytes). All of these results highlight the potential of these biotechnological multifunctional polymers as new drug-free materials to prevent and treat microbial infections.
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Affiliation(s)
- André da Costa
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Ana M Pereira
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Paula Sampaio
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - José Carlos Rodríguez-Cabello
- Bioforge (Group for Advanced Materials and Nanobiotechnology), Centro I+D, Universidad de Valladolid, 47011 Valladolid, Spain.,Networking Research Centre on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-47011 Valladolid, Spain
| | - Andreia C Gomes
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Margarida Casal
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Raul Machado
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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480
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Dekan Z, Kremsmayr T, Keov P, Godin M, Teakle N, Dürrauer L, Xiang H, Gharib D, Bergmayr C, Hellinger R, Gay M, Vilaseca M, Kurzbach D, Albericio F, Alewood PF, Gruber CW, Muttenthaler M. Nature-inspired dimerization as a strategy to modulate neuropeptide pharmacology exemplified with vasopressin and oxytocin. Chem Sci 2021; 12:4057-4062. [PMID: 34163676 PMCID: PMC8179488 DOI: 10.1039/d0sc05501h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Vasopressin (VP) and oxytocin (OT) are cyclic neuropeptides that regulate fundamental physiological functions via four G protein-coupled receptors, V1aR, V1bR, V2R, and OTR. Ligand development remains challenging for these receptors due to complex structure–activity relationships. Here, we investigated dimerization as a strategy for developing ligands with novel pharmacology. We regioselectively synthesised and systematically studied parallel, antiparallel and N- to C-terminal cyclized homo- and heterodimer constructs of VP, OT and dVDAVP (1-deamino-4-valine-8-d-arginine-VP). All disulfide-linked dimers, except for the head-to-tail cyclized constructs, retained nanomolar potency despite the structural implications of dimerization. Our results support a single chain interaction for receptor activation. Dimer orientation had little impact on activity, except for the dVDAVP homodimers, where an antagonist to agonist switch was observed at the V1aR. This study provides novel insights into the structural requirements of VP/OT receptor activation and spotlights dimerization as a strategy to modulate pharmacology, a concept also frequently observed in nature. Structural and pharmacological study of parallel, antiparallel and N- to C-terminal cyclized homo- and heterodimers of vasopressin and oxytocin. This study spotlights dimerization as a strategy to modulate the pharmacology of neuropeptides.![]()
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Affiliation(s)
- Zoltan Dekan
- Institute for Molecular Bioscience, The University of Queensland Brisbane 4072 Australia
| | - Thomas Kremsmayr
- Institute of Biological Chemistry, University of Vienna Währingerstraße 38 1090 Vienna Austria
| | - Peter Keov
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland Brisbane 4072 Australia
| | - Mathilde Godin
- Institute for Molecular Bioscience, The University of Queensland Brisbane 4072 Australia
| | - Ngari Teakle
- Institute for Molecular Bioscience, The University of Queensland Brisbane 4072 Australia
| | - Leopold Dürrauer
- Institute of Biological Chemistry, University of Vienna Währingerstraße 38 1090 Vienna Austria
| | - Huang Xiang
- Center for Physiology and Pharmacology, Medical University of Vienna Schwarzspanierstraße 17 1090 Vienna Austria
| | - Dalia Gharib
- Center for Physiology and Pharmacology, Medical University of Vienna Schwarzspanierstraße 17 1090 Vienna Austria
| | - Christian Bergmayr
- Center for Physiology and Pharmacology, Medical University of Vienna Schwarzspanierstraße 17 1090 Vienna Austria
| | - Roland Hellinger
- Center for Physiology and Pharmacology, Medical University of Vienna Schwarzspanierstraße 17 1090 Vienna Austria
| | - Marina Gay
- Institute for Research in Biomedicine Barcelona C/ Baldiri Reixac 10 08028 Barcelona Spain
| | - Marta Vilaseca
- Institute for Research in Biomedicine Barcelona C/ Baldiri Reixac 10 08028 Barcelona Spain
| | - Dennis Kurzbach
- Institute of Biological Chemistry, University of Vienna Währingerstraße 38 1090 Vienna Austria
| | - Fernando Albericio
- Department of Organic Chemistry, University of Barcelona Barcelona Science Park, Baldiri Reixac 10 08028 Barcelona Spain
| | - Paul F Alewood
- Institute for Molecular Bioscience, The University of Queensland Brisbane 4072 Australia
| | - Christian W Gruber
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland Brisbane 4072 Australia.,Center for Physiology and Pharmacology, Medical University of Vienna Schwarzspanierstraße 17 1090 Vienna Austria
| | - Markus Muttenthaler
- Institute for Molecular Bioscience, The University of Queensland Brisbane 4072 Australia .,Institute of Biological Chemistry, University of Vienna Währingerstraße 38 1090 Vienna Austria
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481
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Strandberg E, Wadhwani P, Ulrich AS. Antibiotic Potential and Biophysical Characterization of Amphipathic β-Stranded [XZ]n Peptides With Alternating Cationic and Hydrophobic Residues. FRONTIERS IN MEDICAL TECHNOLOGY 2021; 3:622096. [PMID: 35047904 PMCID: PMC8757834 DOI: 10.3389/fmedt.2021.622096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/12/2021] [Indexed: 11/13/2022] Open
Abstract
Cationic membrane-active peptides are considered to be promising candidates for antibiotic treatment. Many natural and artificial sequences show an antimicrobial activity when they are able to take on an amphipathic fold upon membrane binding, which in turn perturbs the integrity of the lipid bilayer. Most known structures are α-helices and β-hairpins, but also cyclic knots and other irregular conformations are known. Linear β-stranded antimicrobial peptides are not so common in nature, but numerous model sequences have been designed. Interestingly, many of them tend to be highly membranolytic, but also have a significant tendency to self-assemble into β-sheets by hydrogen-bonding. In this minireview we examine the literature on such amphipathic peptides consisting of simple repetitive sequences of alternating cationic and hydrophobic residues, and discuss their advantages and disadvantages. Their interactions with lipids have been characterized with a number of biophysical techniques—especially circular dichroism, fluorescence, and infrared—in order to determine their secondary structure, membrane binding, aggregation tendency, and ability to permeabilize vesicles. Their activities against bacteria, biofilms, erythrocytes, and human cells have also been studied using biological assays. In line with the main scope of this Special Issue, we attempt to correlate the biophysical results with the biological data, and in particular we discuss which properties (length, charge, aggregation tendency, etc.) of these simple model peptides are most relevant for their biological function. The overview presented here offers ideas for future experiments, and also suggests a few design rules for promising β-stranded peptides to develop efficient antimicrobial agents.
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Affiliation(s)
- Erik Strandberg
- Karlsruhe Institute of Technology, Institute of Biological Interfaces (IBG-2), Karlsruhe, Germany
| | - Parvesh Wadhwani
- Karlsruhe Institute of Technology, Institute of Biological Interfaces (IBG-2), Karlsruhe, Germany
| | - Anne S. Ulrich
- Karlsruhe Institute of Technology, Institute of Biological Interfaces (IBG-2), Karlsruhe, Germany
- Karlsruhe Institute of Technology, Institute of Organic Chemistry, Karlsruhe, Germany
- *Correspondence: Anne S. Ulrich
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482
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Motifs of the C-terminal domain of MCM9 direct localization to sites of mitomycin-C damage for RAD51 recruitment. J Biol Chem 2021; 296:100355. [PMID: 33539926 PMCID: PMC7949153 DOI: 10.1016/j.jbc.2021.100355] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 01/28/2021] [Indexed: 11/20/2022] Open
Abstract
The MCM8/9 complex is implicated in aiding fork progression and facilitating homologous recombination (HR) in response to several DNA damage agents. MCM9 itself is an outlier within the MCM family containing a long C-terminal extension (CTE) comprising 42% of the total length, but with no known functional components and high predicted disorder. In this report, we identify and characterize two unique motifs within the primarily unstructured CTE that are required for localization of MCM8/9 to sites of mitomycin C (MMC)-induced DNA damage. First, an unconventional “bipartite-like” nuclear localization (NLS) motif consisting of two positively charged amino acid stretches separated by a long intervening sequence is required for the nuclear import of both MCM8 and MCM9. Second, a variant of the BRC motif (BRCv) similar to that found in other HR helicases is necessary for localization to sites of MMC damage. The MCM9-BRCv directly interacts with and recruits RAD51 downstream to MMC-induced damage to aid in DNA repair. Patient lymphocytes devoid of functional MCM9 and discrete MCM9 knockout cells have a significantly impaired ability to form RAD51 foci after MMC treatment. Therefore, the disordered CTE in MCM9 is functionally important in promoting MCM8/9 activity and in recruiting downstream interactors; thus, requiring full-length MCM9 for proper DNA repair.
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483
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Yperman K, Wang J, Eeckhout D, Winkler J, Vu LD, Vandorpe M, Grones P, Mylle E, Kraus M, Merceron R, Nolf J, Mor E, De Bruyn P, Loris R, Potocký M, Savvides SN, De Rybel B, De Jaeger G, Van Damme D, Pleskot R. Molecular architecture of the endocytic TPLATE complex. SCIENCE ADVANCES 2021; 7:eabe7999. [PMID: 33637534 PMCID: PMC7909872 DOI: 10.1126/sciadv.abe7999] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/15/2021] [Indexed: 05/03/2023]
Abstract
Eukaryotic cells rely on endocytosis to regulate their plasma membrane proteome and lipidome. Most eukaryotic groups, except fungi and animals, have retained the evolutionary ancient TSET complex as an endocytic regulator. Unlike other coatomer complexes, structural insight into TSET is lacking. Here, we reveal the molecular architecture of plant TSET [TPLATE complex (TPC)] using an integrative structural approach. We identify crucial roles for specific TSET subunits in complex assembly and membrane interaction. Our data therefore generate fresh insight into the differences between the hexameric TSET in Dictyostelium and the octameric TPC in plants. Structural elucidation of this ancient adaptor complex represents the missing piece in the coatomer puzzle and vastly advances our functional as well as evolutionary insight into the process of endocytosis.
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Affiliation(s)
- Klaas Yperman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Jie Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Joanna Winkler
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Michael Vandorpe
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Peter Grones
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Evelien Mylle
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Michael Kraus
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Romain Merceron
- Department of Biochemistry and Microbiology, Ghent University, 9052 Ghent, Belgium
- VIB Center for Inflammation Research, 9052 Ghent, Belgium
| | - Jonah Nolf
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Eliana Mor
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Pieter De Bruyn
- Vrije Universiteit Brussel, Structural Biology Brussels, Department of Biotechnology, 1050 Brussels, Belgium
- VIB-VUB Center for Structural Biology, Structural Biology Research Center, Molecular Recognition Unit, 1050 Brussels, Belgium
| | - Remy Loris
- VIB-VUB Center for Structural Biology, Structural Biology Research Center, Molecular Recognition Unit, 1050 Brussels, Belgium
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, 16502 Prague 6, Czech Republic
| | - Martin Potocký
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, 16502 Prague 6, Czech Republic
| | - Savvas N Savvides
- Department of Biochemistry and Microbiology, Ghent University, 9052 Ghent, Belgium
- VIB Center for Inflammation Research, 9052 Ghent, Belgium
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium.
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Roman Pleskot
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium.
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, 16502 Prague 6, Czech Republic
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484
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Grishin SY, Dzhus UF, Selivanova OM, Balobanov VA, Surin AK, Galzitskaya OV. Comparative Analysis of Aggregation of Thermus thermophilus Ribosomal Protein bS1 and Its Stable Fragment. BIOCHEMISTRY (MOSCOW) 2021; 85:344-354. [PMID: 32564739 DOI: 10.1134/s0006297920030104] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Functionally important multidomain bacterial protein bS1 is the largest ribosomal protein of subunit 30S. It interacts with both mRNA and proteins and is prone to aggregation, although this process has not been studied in detail. Here, we obtained bacterial strains overproducing ribosomal bS1 protein from Thermus thermophilus and its stable fragment bS1(49) and purified these proteins. Using fluorescence spectroscopy, dynamic light scattering, and high-performance liquid chromatography combined with mass spectrometric analysis of products of protein limited proteolysis, we demonstrated that disordered regions at the N- and C-termini of bS1 can play a key role in the aggregation of this protein. The truncated fragment bS1(49) was less prone to aggregation compared to the full-size bS1. The revealed properties of the studied proteins can be used to obtain protein crystals for elucidating the structure of the bS1 stable fragment.
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Affiliation(s)
- S Yu Grishin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - U F Dzhus
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - O M Selivanova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - V A Balobanov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - A K Surin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia. .,State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, 142279, Russia.,Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - O V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia. .,Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
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485
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S. mansoni SmKI-1 Kunitz-domain: Leucine point mutation at P1 site generates enhanced neutrophil elastase inhibitory activity. PLoS Negl Trop Dis 2021; 15:e0009007. [PMID: 33465126 PMCID: PMC7846107 DOI: 10.1371/journal.pntd.0009007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 01/29/2021] [Accepted: 11/24/2020] [Indexed: 12/14/2022] Open
Abstract
The Schistosoma mansoni SmKI-1 protein is composed of two domains: a Kunitz-type serine protease inhibitor motif (KD) and a C-terminus domain with no similarity outside the genera. Our previous work has demonstrated that KD plays an essential role in neutrophil elastase (NE) binding blockage, in neutrophil influx and as a potential anti-inflammatory molecule. In order to enhance NE blocking capacity, we analyzed the KD sequence from a structure-function point of view and designed specific point mutations in order to enhance NE affinity. We substituted the P1 site residue at the reactive site for a leucine (termed RL-KD), given its central role for KD's inhibition to NE. We have also substituted a glutamic acid that strongly interacts with the P1 residue for an alanine, to help KD to be buried on NE S1 site (termed EA-KD). KD and the mutant proteins were evaluated in silico by molecular docking to human NE, expressed in Escherichia coli and tested towards its NE inhibitory activity. Both mutated proteins presented enhanced NE inhibitory activity in vitro and RL-KD presented the best performance. We further tested RL-KD in vivo in an experimental model of monosodium urate (MSU)-induced acute arthritis. RL-KD showed reduced numbers of total cells and neutrophils in the mouse knee cavity when compared to KD. Nevertheless, both RL-KD and KD reduced mice hypernociception in a similar fashion. In summary, our results demonstrated that both mutated proteins showed enhanced NE inhibitory activity in vitro. However, RL-KD had a prominent effect in diminishing inflammatory parameters in vivo.
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486
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Alvarado D, Cardoso-Arenas S, Corrales-García LL, Clement H, Arenas I, Montero-Dominguez PA, Olamendi-Portugal T, Zamudio F, Csoti A, Borrego J, Panyi G, Papp F, Corzo G. A Novel Insecticidal Spider Peptide that Affects the Mammalian Voltage-Gated Ion Channel hKv1.5. Front Pharmacol 2021; 11:563858. [PMID: 33597864 PMCID: PMC7883638 DOI: 10.3389/fphar.2020.563858] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 10/26/2020] [Indexed: 11/20/2022] Open
Abstract
Spider venoms include various peptide toxins that modify the ion currents, mainly of excitable insect cells. Consequently, scientific research on spider venoms has revealed a broad range of peptide toxins with different pharmacological properties, even for mammal species. In this work, thirty animal venoms were screened against hKv1.5, a potential target for atrial fibrillation therapy. The whole venom of the spider Oculicosa supermirabilis, which is also insecticidal to house crickets, caused voltage-gated potassium ion channel modulation in hKv1.5. Therefore, a peptide from the spider O. supermirabilis venom, named Osu1, was identified through HPLC reverse-phase fractionation. Osu1 displayed similar biological properties as the whole venom; so, the primary sequence of Osu1 was elucidated by both of N-terminal degradation and endoproteolytic cleavage. Based on its primary structure, a gene that codifies for Osu1 was constructed de novo from protein to DNA by reverse translation. A recombinant Osu1 was expressed using a pQE30 vector inside the E. coli SHuffle expression system. recombinant Osu1 had voltage-gated potassium ion channel modulation of human hKv1.5, and it was also as insecticidal as the native toxin. Due to its novel primary structure, and hypothesized disulfide pairing motif, Osu1 may represent a new family of spider toxins.
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Affiliation(s)
- Diana Alvarado
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Samuel Cardoso-Arenas
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Ligia-Luz Corrales-García
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
- Departamento de Alimentos, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia, Medellín, Colombia
| | - Herlinda Clement
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Iván Arenas
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Pavel Andrei Montero-Dominguez
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Timoteo Olamendi-Portugal
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Fernando Zamudio
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Agota Csoti
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Jesús Borrego
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Gyorgy Panyi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Ferenc Papp
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gerardo Corzo
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
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487
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Quartey MO, Nyarko JNK, Maley JM, Barnes JR, Bolanos MAC, Heistad RM, Knudsen KJ, Pennington PR, Buttigieg J, De Carvalho CE, Leary SC, Parsons MP, Mousseau DD. The Aβ(1-38) peptide is a negative regulator of the Aβ(1-42) peptide implicated in Alzheimer disease progression. Sci Rep 2021; 11:431. [PMID: 33432101 PMCID: PMC7801637 DOI: 10.1038/s41598-020-80164-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 12/17/2020] [Indexed: 12/14/2022] Open
Abstract
The pool of β-Amyloid (Aβ) length variants detected in preclinical and clinical Alzheimer disease (AD) samples suggests a diversity of roles for Aβ peptides. We examined how a naturally occurring variant, e.g. Aβ(1-38), interacts with the AD-related variant, Aβ(1-42), and the predominant physiological variant, Aβ(1-40). Atomic force microscopy, Thioflavin T fluorescence, circular dichroism, dynamic light scattering, and surface plasmon resonance reveal that Aβ(1-38) interacts differently with Aβ(1-40) and Aβ(1-42) and, in general, Aβ(1-38) interferes with the conversion of Aβ(1-42) to a β-sheet-rich aggregate. Functionally, Aβ(1-38) reverses the negative impact of Aβ(1-42) on long-term potentiation in acute hippocampal slices and on membrane conductance in primary neurons, and mitigates an Aβ(1-42) phenotype in Caenorhabditis elegans. Aβ(1-38) also reverses any loss of MTT conversion induced by Aβ(1-40) and Aβ(1-42) in HT-22 hippocampal neurons and APOE ε4-positive human fibroblasts, although the combination of Aβ(1-38) and Aβ(1-42) inhibits MTT conversion in APOE ε4-negative fibroblasts. A greater ratio of soluble Aβ(1-42)/Aβ(1-38) [and Aβ(1-42)/Aβ(1-40)] in autopsied brain extracts correlates with an earlier age-at-death in males (but not females) with a diagnosis of AD. These results suggest that Aβ(1-38) is capable of physically counteracting, potentially in a sex-dependent manner, the neuropathological effects of the AD-relevant Aβ(1-42).
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Affiliation(s)
- Maa O Quartey
- Cell Signalling Laboratory, Department of Psychiatry, University of Saskatchewan, GB41 HSB, 107 Wiggins Rd., Saskatoon, SK, S7N 5E5, Canada
| | - Jennifer N K Nyarko
- Cell Signalling Laboratory, Department of Psychiatry, University of Saskatchewan, GB41 HSB, 107 Wiggins Rd., Saskatoon, SK, S7N 5E5, Canada
| | - Jason M Maley
- Saskatchewan Structural Sciences Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jocelyn R Barnes
- Division of BioMedical Sciences (Neurosciences), Memorial University of Newfoundland, St. John's, NL, Canada
| | | | - Ryan M Heistad
- Cell Signalling Laboratory, Department of Psychiatry, University of Saskatchewan, GB41 HSB, 107 Wiggins Rd., Saskatoon, SK, S7N 5E5, Canada
| | - Kaeli J Knudsen
- Cell Signalling Laboratory, Department of Psychiatry, University of Saskatchewan, GB41 HSB, 107 Wiggins Rd., Saskatoon, SK, S7N 5E5, Canada
| | - Paul R Pennington
- Cell Signalling Laboratory, Department of Psychiatry, University of Saskatchewan, GB41 HSB, 107 Wiggins Rd., Saskatoon, SK, S7N 5E5, Canada
| | - Josef Buttigieg
- Department of Biology, University of Regina, Regina, SK, Canada
| | | | - Scot C Leary
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Matthew P Parsons
- Division of BioMedical Sciences (Neurosciences), Memorial University of Newfoundland, St. John's, NL, Canada
| | - Darrell D Mousseau
- Cell Signalling Laboratory, Department of Psychiatry, University of Saskatchewan, GB41 HSB, 107 Wiggins Rd., Saskatoon, SK, S7N 5E5, Canada.
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488
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Sinha D, Sinha D, Dutta A, Chakraborty T, Mondal R, Seal S, Poddar A, Chatterjee S, Sau S. Alternative Sigma Factor of Staphylococcus aureus Interacts with the Cognate Antisigma Factor Primarily Using Its Domain 3. Biochemistry 2021; 60:135-151. [PMID: 33406357 DOI: 10.1021/acs.biochem.0c00881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
σB, an alternative sigma factor, is usually employed to tackle the general stress response in Staphylococcus aureus and other Gram-positive bacteria. This protein, involved in S. aureus-mediated pathogenesis, is typically blocked by RsbW, an antisigma factor having serine kinase activity. σB, a σ70-like sigma factor, harbors three conserved domains designated σB2, σB3, and σB4. To better understand the interaction between RsbW and σB or its domains, we have studied their recombinant forms, rRsbW, rσB, rσB2, rσB3, and rσB4, using different probes. The results show that none of the rσB domains, unlike rσB, showed binding to a cognate DNA in the presence of a core RNA polymerase. However, both rσB2 and rσB3, like rσB, interacted with rRsbW, and the order of their rRsbW binding affinity looks like rσB > rσB3 > rσB2. Furthermore, the reaction between rRsbW and rσB or rσB3 was exothermic and occurred spontaneously. rRsbW and rσB3 also associate with each other at a stoichiometry of 2:1, and different types of noncovalent bonds might be responsible for their interaction. A structural model of the RsbW-σB3 complex that has supported our experimental results indicated the binding of rσB3 at the putative dimeric interface of RsbW. A genetic study shows that the tentative dimer-forming region of RsbW is crucial for preserving its rσB binding ability, serine kinase activity, and dimerization ability. Additionally, a urea-induced equilibrium unfolding study indicated a notable thermodynamic stabilization of σB3 in the presence of RsbW. Possible implications of the stabilization data in drug discovery were discussed at length.
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Affiliation(s)
- Debabrata Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal 700054, India
| | - Debasmita Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal 700054, India
| | - Anindya Dutta
- Department of Biophysics, Bose Institute, Kolkata, West Bengal 700054, India
| | - Tushar Chakraborty
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal 700054, India
| | - Rajkrishna Mondal
- Department of Biotechnology, Nagaland University, Dimapur, Nagaland 797112, India
| | - Soham Seal
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal 700054, India
| | - Asim Poddar
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal 700054, India
| | | | - Subrata Sau
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal 700054, India
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489
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Mukai M, Takahara M, Takada A, Takahara A. Preparation of an (inorganic/organic) hybrid hydrogel from a peptide oligomer and a tubular aluminosilicate nanofiber. RSC Adv 2021; 11:4901-4905. [PMID: 35424462 PMCID: PMC8694537 DOI: 10.1039/d0ra09514a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/19/2021] [Indexed: 11/26/2022] Open
Abstract
‘Imogolite’, a tubular inorganic nanotube surface, was modified with a peptide oligomer to prepare a hybrid hydrogel. The formation of the gels was confirmed by conducting a vial inversion test and rheological measurements. The surface modification of imogolite with the peptide oligomer was verified by performing thermogravimetric analysis and circular dichroism measurements. Furthermore, the formation of the network-like morphology of the prepared hydrogel was confirmed by scanning force microscopy. ‘Imogolite’, a tubular inorganic nanotube surface, was modified with a peptide oligomer to prepare a hybrid hydrogel.![]()
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Affiliation(s)
- Masaru Mukai
- Institute for Materials Chemistry and Engineering
- Kyushu University
- Fukuoka 819-0395
- Japan
| | - Mari Takahara
- Department of Materials Science & Chemical Engineering
- National Institute of Technology
- Kitakyushu College
- Kitakyushu
- Japan
| | - Akihiko Takada
- Institute for Materials Chemistry and Engineering
- Kyushu University
- Fukuoka 819-0395
- Japan
| | - Astushi Takahara
- Institute for Materials Chemistry and Engineering
- Kyushu University
- Fukuoka 819-0395
- Japan
- Next Generation Adhesion Technology Research Center
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490
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Caillet-Saguy C, Brûlé S, Wolff N, Raynal B. PDZ Sample Quality Assessment by Biochemical and Biophysical Characterizations. Methods Mol Biol 2021; 2256:89-124. [PMID: 34014518 DOI: 10.1007/978-1-0716-1166-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
PDZ domains are small globular domains involved in protein-protein interactions. They participate in a wide range of critical cellular processes. These domains, very abundant in the human proteome, are widely studied by high-throughput interactomics approaches and by biophysical and structural methods. However, the quality of the results is strongly related to the optimal folding and solubility of the domains. We provide here a detailed description of protocols for a strict quality assessment of the PDZ constructs. We describe appropriate experimental approaches that have been selected to overcome the small size of such domains to check the purity, identity, homogeneity, stability, and folding of samples.
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Affiliation(s)
| | - Sébastien Brûlé
- Institut Pasteur, Plate-forme de Biophysique Moléculaire, CNRS UMR 3528, Paris, France
| | - Nicolas Wolff
- Institut Pasteur, Unité Récepteurs-Canaux, CNRS UMR 3571, Paris, France.
| | - Bertrand Raynal
- Institut Pasteur, Plate-forme de Biophysique Moléculaire, CNRS UMR 3528, Paris, France
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491
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Kapoor S, Kodesia A, Kalidas N, Ashish, Thakur KG. Structural characterization of Myxococcus xanthus MglC, a component of the polarity control system, and its interactions with its paralog MglB. J Biol Chem 2021; 296:100308. [PMID: 33493516 PMCID: PMC7949163 DOI: 10.1016/j.jbc.2021.100308] [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: 12/23/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 11/28/2022] Open
Abstract
The δ-proteobacteria Myxococcus xanthus displays social (S) and adventurous (A) motilities, which require pole-to-pole reversal of the motility regulator proteins. Mutual gliding motility protein C (MglC), a paralog of GTPase-activating protein Mutual gliding motility protein B (MglB), is a member of the polarity module involved in regulating motility. However, little is known about the structure and function of MglC. Here, we determined ∼1.85 Å resolution crystal structure of MglC using Selenomethionine Single-wavelength anomalous diffraction. The crystal structure revealed that, despite sharing <9% sequence identity, both MglB and MglC adopt a Regulatory Light Chain 7 family fold. However, MglC has a distinct ∼30° to 40° shift in the orientation of the functionally important α2 helix compared with other structural homologs. Using isothermal titration calorimetry and size-exclusion chromatography, we show that MglC binds MglB in 2:4 stoichiometry with submicromolar range dissociation constant. Using small-angle X-ray scattering and molecular docking studies, we show that the MglBC complex consists of a MglC homodimer sandwiched between two homodimers of MglB. A combination of size-exclusion chromatography and site-directed mutagenesis studies confirmed the MglBC interacting interface obtained by molecular docking studies. Finally, we show that the C-terminal region of MglB, crucial for binding its established partner MglA, is not required for binding MglC. These studies suggest that the MglB uses distinct interfaces to bind MglA and MglC. Based on these data, we propose a model suggesting a new role for MglC in polarity reversal in M. xanthus.
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Affiliation(s)
- Srajan Kapoor
- Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, G. N. Ramachandran Protein Centre, Chandigarh, India
| | - Akriti Kodesia
- Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, G. N. Ramachandran Protein Centre, Chandigarh, India
| | - Nidhi Kalidas
- Council of Scientific and Industrial Research-Institute of Microbial Technology, G. N. Ramachandran Protein Centre, Chandigarh, India
| | - Ashish
- Council of Scientific and Industrial Research-Institute of Microbial Technology, G. N. Ramachandran Protein Centre, Chandigarh, India
| | - Krishan Gopal Thakur
- Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, G. N. Ramachandran Protein Centre, Chandigarh, India.
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492
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Ge F, Hu J, Zhu YH, Arif M, Yu DJ. TargetMM: Accurate Missense Mutation Prediction by Utilizing Local and Global Sequence Information with Classifier Ensemble. Comb Chem High Throughput Screen 2021; 25:38-52. [DOI: 10.2174/1386207323666201204140438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/22/2020] [Accepted: 10/26/2020] [Indexed: 11/22/2022]
Abstract
Aim and Objective:
Missense mutation (MM) may lead to various human diseases by
disabling proteins. Accurate prediction of MM is important and challenging for both protein
function annotation and drug design. Although several computational methods yielded acceptable
success rates, there is still room for further enhancing the prediction performance of MM.
Materials and Methods:
In the present study, we designed a new feature extracting method, which
considers the impact degree of residues in the microenvironment range to the mutation site.
Stringent cross-validation and independent test on benchmark datasets were performed to evaluate
the efficacy of the proposed feature extracting method. Furthermore, three heterogeneous
prediction models were trained and then ensembled for the final prediction. By combining the
feature representation method and classifier ensemble technique, we reported a novel MM
predictor called TargetMM for identifying the pathogenic mutations from the neutral ones.
Results:
Comparison outcomes based on statistical evaluation demonstrate that TargetMM
outperforms the prior advanced methods on the independent test data. The source codes and
benchmark datasets of TargetMM are freely available at https://github.com/sera616/TargetMM.git
for academic use.
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Affiliation(s)
- Fang Ge
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094,China
| | - Jun Hu
- College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023,China
| | - Yi-Heng Zhu
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094,China
| | - Muhammad Arif
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094,China
| | - Dong-Jun Yu
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094,China
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493
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Wang F, Wang Y, Jiang L, Wang W, Sang J, Wang X, Lu F, Liu F. The food additive fast green FCF inhibits α-synuclein aggregation, disassembles mature fibrils and protects against amyloid-induced neurotoxicity. Food Funct 2021; 12:5465-5477. [PMID: 33997868 DOI: 10.1039/d0fo03301d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
α-Synuclein (α-syn) aggregates into cytotoxic amyloid fibrils, which are recognized as the defining neuropathological feature of Parkinson's disease (PD). Therefore, inhibiting α-syn fibrillogenesis and disrupting the preformed fibrils are both considered attractive strategies to cure PD. We discovered that a safe food additive, fast green FCF, is capable of inhibiting α-synuclein fibrillogenesis and reducing the related cytotoxicity. Thioflavin T fluorescence assays demonstrated that fast green FCF could inhibit the fibrillogenesis α-synuclein. In the presence of 100 μM fast green FCF, amorphous aggregates were formed and observed by atomic force microscopy. Toxicity assays in cell cultures revealed that fast green FCF significantly reduced the cytotoxicity of α-syn. Molecular dynamics simulations revealed the potential mechanism of the interactions between fast green FCF and α-synuclein. Fast green FCF greatly disrupted the α-synuclein pentamer and reduced the β-sheet content by reducing both nonpolar and polar interactions. Furthermore, two binding sites were identified, named region I (Y39-K45) and region II (H50-Q62). Our data reveal that electrostatic interactions, hydrogen bonds, and π-π interactions synergistically contribute to the binding of fast green FCF to the α-synuclein pentamer. These results indicate that fast green FCF is a candidate prototype for the development of drugs against the aggregation of amyloid fibrils in PD.
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Affiliation(s)
- Fenghua Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, P. R. China.
| | - Ying Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, P. R. China.
| | - Luying Jiang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, P. R. China.
| | - Wenqian Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, P. R. China.
| | - Jingcheng Sang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, P. R. China.
| | - Xinyu Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, P. R. China.
| | - Fuping Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, P. R. China.
| | - Fufeng Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education; Tianjin Key Laboratory of Industrial Microbiology; College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, P. R. China.
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494
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Tohda R, Tanaka H, Mutoh R, Zhang X, Lee YH, Konuma T, Ikegami T, Migita CT, Kurisu G. Crystal structure of higher plant heme oxygenase-1 and its mechanism of interaction with ferredoxin. J Biol Chem 2021; 296:100217. [PMID: 33839679 PMCID: PMC7948506 DOI: 10.1074/jbc.ra120.016271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/08/2020] [Accepted: 12/21/2020] [Indexed: 11/06/2022] Open
Abstract
Heme oxygenase (HO) converts heme to carbon monoxide, biliverdin, and free iron, products that are essential in cellular redox signaling and iron recycling. In higher plants, HO is also involved in the biosynthesis of photoreceptor pigment precursors. Despite many common enzymatic reactions, the amino acid sequence identity between plant-type and other HOs is exceptionally low (∼19.5%), and amino acids that are catalytically important in mammalian HO are not conserved in plant-type HOs. Structural characterization of plant-type HO is limited to spectroscopic characterization by electron spin resonance, and it remains unclear how the structure of plant-type HO differs from that of other HOs. Here, we have solved the crystal structure of Glycine max (soybean) HO-1 (GmHO-1) at a resolution of 1.06 Å and carried out the isothermal titration calorimetry measurements and NMR spectroscopic studies of its interaction with ferredoxin, the plant-specific electron donor. The high-resolution X-ray structure of GmHO-1 reveals several novel structural components: an additional irregularly structured region, a new water tunnel from the active site to the surface, and a hydrogen-bonding network unique to plant-type HOs. Structurally important features in other HOs, such as His ligation to the bound heme, are conserved in GmHO-1. Based on combined data from X-ray crystallography, isothermal titration calorimetry, and NMR measurements, we propose the evolutionary fine-tuning of plant-type HOs for ferredoxin dependency in order to allow adaptation to dynamic pH changes on the stroma side of the thylakoid membrane in chloroplast without losing enzymatic activity under conditions of fluctuating light.
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Affiliation(s)
- Rei Tohda
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan; Department of Macromolecular Science, Osaka University, Toyonaka, Osaka, Japan
| | - Hideaki Tanaka
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan; Department of Macromolecular Science, Osaka University, Toyonaka, Osaka, Japan
| | - Risa Mutoh
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Xuhong Zhang
- Graduate School of Medical Science, Yamagata University, Yamagata, Yamagata, Japan
| | - Young-Ho Lee
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Chungbuk, South Korea; Graduate School of Analytical Science and Technology, Chungnam National University, Yuseong-gu, Daejeon, South Korea; Research Headquarters, Korea Brain Research Institute, Dong-gu, Daegu, South Korea; Bio-Analytical Science, University of Science and Technology, Yuseong-gu, Daejeon, South Korea
| | - Tsuyoshi Konuma
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama, Japan
| | - Takahisa Ikegami
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama, Japan
| | - Catharina T Migita
- Department of Biological Chemistry, Yamaguchi University, Yoshida, Yamaguchi, Japan
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan; Department of Macromolecular Science, Osaka University, Toyonaka, Osaka, Japan.
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495
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BeStSel: From Secondary Structure Analysis to Protein Fold Prediction by Circular Dichroism Spectroscopy. Methods Mol Biol 2021; 2199:175-189. [PMID: 33125651 DOI: 10.1007/978-1-0716-0892-0_11] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Far-UV circular dichroism (CD) spectroscopy is a classical method for the study of the secondary structure of polypeptides in solution. It has been the general view that the α-helix content can be estimated accurately from the CD spectra. However, the technique was less reliable to estimate the β-sheet contents as a consequence of the structural variety of the β-sheets, which is reflected in a large spectral diversity of the CD spectra of proteins containing this secondary structure component. By taking into account the parallel or antiparallel orientation and the twist of the β-sheets, the Beta Structure Selection (BeStSel) method provides an improved β-structure determination and its performance is more accurate for any of the secondary structure types compared to previous CD spectrum analysis algorithms. Moreover, BeStSel provides extra information on the orientation and twist of the β-sheets which is sufficient for the prediction of the protein fold.The advantage of CD spectroscopy is that it is a fast and inexpensive technique with easy data processing which can be used in a wide protein concentration range and under various buffer conditions. It is especially useful when the atomic resolution structure is not available, such as the case of protein aggregates, membrane proteins or natively disordered chains, for studying conformational transitions, testing the effect of the environmental conditions on the protein structure, for verifying the correct fold of recombinant proteins in every scientific fields working on proteins from basic protein science to biotechnology and pharmaceutical industry. Here, we provide a brief step-by-step guide to record the CD spectra of proteins and their analysis with the BeStSel method.
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496
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Wien F, Geinguenaud F, Grange W, Arluison V. SRCD and FTIR Spectroscopies to Monitor Protein-Induced Nucleic Acid Remodeling. Methods Mol Biol 2021; 2209:87-108. [PMID: 33201464 DOI: 10.1007/978-1-0716-0935-4_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Fourier transform infrared (FTIR) and circular dichroism (CD) spectroscopies are fast techniques providing important information about the conformation of nucleic acids and proteins. These vibrational and electronic absorption spectroscopies are extremely sensitive to any change in molecular structure. While numerous reviews describe how to analyze DNA structure alone or in the presence of proteins using FTIR and CD, analyses of RNA are scarce. Nevertheless, RNA remodeling proteins are important factors involved in a multitude of roles in the cell. In this chapter, we present applications of synchrotron radiation circular dichroism (SRCD) and FTIR to analyze how proteins may change RNA structure. These include the analysis of RNA melting, or stabilization, of change in helical parameters and base stacking. The effects on the structure of RNA remodeling proteins are also presented.
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Affiliation(s)
- Frank Wien
- Synchrotron SOLEIL, L'Orme des Merisiers Saint Aubin, Gif-sur-Yvette, France
| | - Frédéric Geinguenaud
- Plateforme CNanoMat, UFR SMBH, Université Paris 13, Bobigny, France.,Inserm, U1148, Laboratory for Vascular Translational Science, UFR SMBH, Université Paris 13, Bobigny, France
| | - Wilfried Grange
- Institut de Physique et Chimie des Matériaux de Strasbourg, CNRS UMR 7504, Strasbourg, France.,Université de Paris, F-75006, Paris, France
| | - Véronique Arluison
- Université de Paris, F-75006, Paris, France. .,Laboratoire Léon Brillouin LLB, CEA, CNRS UMR 12, Université Paris Saclay, CEA Saclay, Gif-sur-Yvette, France.
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497
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Bernardi AV, Gerolamo LE, de Gouvêa PF, Yonamine DK, Pereira LMS, de Oliveira AHC, Uyemura SA, Dinamarco TM. LPMO AfAA9_B and Cellobiohydrolase AfCel6A from A. fumigatus Boost Enzymatic Saccharification Activity of Cellulase Cocktail. Int J Mol Sci 2020; 22:E276. [PMID: 33383972 PMCID: PMC7795096 DOI: 10.3390/ijms22010276] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/21/2020] [Accepted: 12/24/2020] [Indexed: 01/02/2023] Open
Abstract
Cellulose is the most abundant polysaccharide in lignocellulosic biomass, where it is interlinked with lignin and hemicellulose. Bioethanol can be produced from biomass. Since breaking down biomass is difficult, cellulose-active enzymes secreted by filamentous fungi play an important role in degrading recalcitrant lignocellulosic biomass. We characterized a cellobiohydrolase (AfCel6A) and lytic polysaccharide monooxygenase LPMO (AfAA9_B) from Aspergillus fumigatus after they were expressed in Pichia pastoris and purified. The biochemical parameters suggested that the enzymes were stable; the optimal temperature was ~60 °C. Further characterization revealed high turnover numbers (kcat of 147.9 s-1 and 0.64 s-1, respectively). Surprisingly, when combined, AfCel6A and AfAA9_B did not act synergistically. AfCel6A and AfAA9_B association inhibited AfCel6A activity, an outcome that needs to be further investigated. However, AfCel6A or AfAA9_B addition boosted the enzymatic saccharification activity of a cellulase cocktail and the activity of cellulase Af-EGL7. Enzymatic cocktail supplementation with AfCel6A or AfAA9_B boosted the yield of fermentable sugars from complex substrates, especially sugarcane exploded bagasse, by up to 95%. The synergism between the cellulase cocktail and AfAA9_B was enzyme- and substrate-specific, which suggests a specific enzymatic cocktail for each biomass by up to 95%. The synergism between the cellulase cocktail and AfAA9_B was enzyme- and substrate-specific, which suggests a specific enzymatic cocktail for each biomass.
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Affiliation(s)
- Aline Vianna Bernardi
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
| | - Luis Eduardo Gerolamo
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
| | - Paula Fagundes de Gouvêa
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
| | - Deborah Kimie Yonamine
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
| | - Lucas Matheus Soares Pereira
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
| | - Arthur Henrique Cavalcante de Oliveira
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
| | - Sérgio Akira Uyemura
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-903, Brazil;
| | - Taisa Magnani Dinamarco
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
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498
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Sinha D, Sinha D, Banerjee N, Rai P, Seal S, Chakraborty T, Chatterjee S, Sau S. A conserved arginine residue in a staphylococcal anti-sigma factor is required to preserve its kinase activity, structure, and stability. J Biomol Struct Dyn 2020; 40:4972-4986. [PMID: 33356973 DOI: 10.1080/07391102.2020.1864475] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
RsbW, σB, and RsbV, encoded by Staphylococcus aureus and related bacteria, act as an anti-sigma factor, an sigma factor, and an anti-anti-sigma factor, respectively. The interaction between RsbW and σB blocks the transcription initiation activity of the latter protein. RsbW also functions as a serine kinase and phosphorylates RsbV in the presence of ATP. Our modeling study indicates that the RsbW-RsbV complex is stabilized by twenty-four intermolecular non-covalent bonds. Of the bond-forming RsbW residues, Arg 23, and Glu 49 are conserved residues. To understand the roles of Arg 23 in RsbW, rRsbW[R23A], a recombinant S. aureus RsbW (rRsbW) harboring Arg to Ala change at position 23, was investigated using various probes. The results reveal that rRsbW[R23A], like rRsbW, exists as the dimers in the aqueous solution. However, rRsbW[R23A], unlike rRsbW, neither interacted with a chimeric RsbV (rRsbV) nor formed the phosphorylated rRsbV in the presence of ATP. Furthermore, the tertiary structure and hydrophobic surface area of rRsbW[R23A] matched little with those of rRsbW. Conversely, both rRsbW[R23A] and rRsbW showed interaction with a recombinant σB (rσB). rRsbW and rRsbW[R23A] were also unfolded via the formation of at least one intermediate in the presence of urea. However, the thermodynamic stability of rRsbW significantly differed from that of rRsbW[R23A]. Our molecular dynamics (MD) simulation study also reveals the substantial change of structure, dimension, and stability of RsbW due to the above mutation. The ways side chain of critical Arg 23 contributes to maintaining the tertiary structure, and stability of RsbW was elaborately discussed.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Debasmita Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Debabrata Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Nilanjan Banerjee
- Department of Biophysics, Bose Institute, Kolkata, West Bengal, India
| | - Priya Rai
- Department of Biophysics, Bose Institute, Kolkata, West Bengal, India
| | - Soham Seal
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | | | | | - Subrata Sau
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
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499
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Bostan F, Surmeli NB. Cloning, expression, and characterization of a novel sericin-like protein. Biotechnol Appl Biochem 2020; 69:136-144. [PMID: 33368658 DOI: 10.1002/bab.2089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/13/2020] [Indexed: 11/08/2022]
Abstract
Silk consists of two proteins called fibroin and sericin. While fibroin is used in the textile industry and has various biomaterial applications, sericin has been considered as waste material until recently. Sericin is a multicomponent protein and it has important properties such as biocompatibility, biodegradability, cryoprotectivity, and antioxidant. Sericin from silkworm cocoons can be obtained by chemical, enzymatic, and heat treatment methods. However, sericin obtained with these treatment methods is not of consistent and high quality. Moreover, the exposure of sericin to harsh conditions during extraction leads to inconsistencies in the composition and structure of the sericin obtained. The inconsistencies in sericin structure and composition decrease application of sericin as a biomaterial. Here, we produce a sericin-like protein (Ser4mer) with native sequence of sericin encoding four repeats of the conserved 38 amino acid motif recombinantly in Escherichia coli and characterize its structural properties. Ser4mer protein shows similar structure to native sericin and higher solubility than previously obtained recombinant sericin-like proteins. Recombinant production of a soluble sericin-like protein will significantly expand its applications as a biomaterial. In addition, recombinant production of silk proteins will allow us to understand sequence-structure relationships in these proteins.
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Affiliation(s)
- Fatmanur Bostan
- Program in Biotechnology and Bioengineering, İzmir Institute of Technology, Gülbahce, Urla Izmir, Turkey
| | - Nur Basak Surmeli
- Department of Bioengineering, İzmir Institute of Technology, Gülbahce, Urla Izmir, Turkey
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500
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New RRC, Bui TTT, Bogus M. Binding Interactions of Peptide Aptamers. Molecules 2020; 25:molecules25246055. [PMID: 33371475 PMCID: PMC7767479 DOI: 10.3390/molecules25246055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/11/2020] [Accepted: 12/16/2020] [Indexed: 11/17/2022] Open
Abstract
Peptide aptamers are short amino acid chains that are capable of binding specifically to ligands in the same way as their much larger counterparts, antibodies. Ligands of therapeutic interest that can be targeted are other peptide chains or loops located on the surface of protein receptors (e.g., GCPR), which take part in cell-to-cell communications either directly or via the intermediary of hormones or signalling molecules. To confer on aptamers the same sort of conformational rigidity that characterises an antibody binding site, aptamers are often constructed in the form of cyclic peptides, on the assumption that this will encourage stronger binding interactions than would occur if the aptamers were simply linear chains. However, no formal studies have been conducted to confirm the hypothesis that linear peptides will engage in stronger binding interactions with cyclic peptides than with other linear peptides. In this study, the interaction of a model cyclic decamer with a series of linear peptide constructs was compared with that of a linear peptide with the same sequence, showing that the cyclic configuration does confer benefits by increasing the strength of binding.
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Affiliation(s)
- Roger R. C. New
- Vaxcine (UK) Limited, London Bioscience Innovation Centre, London NW1 0NH, UK;
- Faculty of Science & Technology, Middlesex University, Hendon, London NW4 4BT, UK
- Correspondence: or
| | - Tam T. T. Bui
- Centre for Biomolecular Spectroscopy and Institute of Pharmaceutical Science, King’s College, London SE1 1UL, UK;
| | - Michal Bogus
- Vaxcine (UK) Limited, London Bioscience Innovation Centre, London NW1 0NH, UK;
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