1
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Pantelopulos GA, Abraham CB, Straub JE. Cholesterol and Lipid Rafts in the Biogenesis of Amyloid-β Protein and Alzheimer's Disease. Annu Rev Biophys 2024; 53:455-486. [PMID: 38382114 DOI: 10.1146/annurev-biophys-062823-023436] [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: 02/23/2024]
Abstract
Cholesterol has been conjectured to be a modulator of the amyloid cascade, the mechanism that produces the amyloid-β (Aβ) peptides implicated in the onset of Alzheimer's disease. We propose that cholesterol impacts the genesis of Aβ not through direct interaction with proteins in the bilayer, but indirectly by inducing the liquid-ordered phase and accompanying liquid-liquid phase separations, which partition proteins in the amyloid cascade to different lipid domains and ultimately to different endocytotic pathways. We explore the full process of Aβ genesis in the context of liquid-ordered phases induced by cholesterol, including protein partitioning into lipid domains, mechanisms of endocytosis experienced by lipid domains and secretases, and pH-controlled activation of amyloid precursor protein secretases in specific endocytotic environments. Outstanding questions on the essential role of cholesterol in the amyloid cascade are identified for future studies.
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Affiliation(s)
| | - Conor B Abraham
- Department of Chemistry, Boston University, Boston, Massachusetts, USA;
| | - John E Straub
- Department of Chemistry, Boston University, Boston, Massachusetts, USA;
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2
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Newson W, Capezza AJ, Kuktaite R, Hedenqvist MS, Johansson E. Green Chemistry to Modify Functional Properties of Crambe Protein Isolate-Based Thermally Formed Films. ACS OMEGA 2023; 8:20342-20351. [PMID: 37323394 PMCID: PMC10268266 DOI: 10.1021/acsomega.3c00113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/19/2023] [Indexed: 06/17/2023]
Abstract
Proteins are promising precursors to be used in production of sustainable materials with properties resembling plastics, although protein modification or functionalization is often required to obtain suitable product characteristics. Here, effects of protein modification were evaluated by crosslinking behavior using high-performance liquid chromatography (HPLC), secondary structure using infrared spectroscopy (IR), liquid imbibition and uptake, and tensile properties of six crambe protein isolates modified in solution before thermal pressing. The results showed that a basic pH (10), especially when combined with the commonly used, although moderately toxic, crosslinking agent glutaraldehyde (GA), resulted in a decrease in crosslinking in unpressed samples, as compared to acidic pH (4) samples. After pressing, a more crosslinked protein matrix with an increase in β-sheets was obtained in basic samples compared to acidic samples, mainly due to the formation of disulfide bonds, which led to an increase in tensile strength, and liquid uptake with less material resolved. A treatment of pH 10 + GA, combined either with a heat or citric acid treatment, did not increase crosslinking or improve the properties in pressed samples, as compared to pH 4 samples. Fenton treatment at pH 7.5 resulted in a similar amount of crosslinking as the pH 10 + GA treatment, although with a higher degree of peptide/irreversible bonds. The strong bond formation resulted in lack of opportunities to disintegrate the protein network by all extraction solutions tested (even for 6 M urea + 1% sodium dodecyl sulfate + 1% dithiothreitol). Thus, the highest crosslinking and best properties of the material produced from crambe protein isolates were obtained by pH 10 + GA and pH 7.5 + Fenton, where Fenton is a greener and more sustainable solution than GA. Therefore, chemical modification of crambe protein isolates is effecting both sustainability and crosslinking behavior, which might have an effect on product suitability.
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Affiliation(s)
- William
R. Newson
- Department
of Plant Breeding, Swedish University of
Agricultural Sciences, P.O. Box 190, SE-234 22 Lomma, Sweden
| | - Antonio J. Capezza
- Department
of Plant Breeding, Swedish University of
Agricultural Sciences, P.O. Box 190, SE-234 22 Lomma, Sweden
- Department
of Fibre and Polymer Technology, Royal Institute
of Technology, SE-10044 Stockholm, Sweden
| | - Ramune Kuktaite
- Department
of Plant Breeding, Swedish University of
Agricultural Sciences, P.O. Box 190, SE-234 22 Lomma, Sweden
| | - Mikael S. Hedenqvist
- Department
of Fibre and Polymer Technology, Royal Institute
of Technology, SE-10044 Stockholm, Sweden
| | - Eva Johansson
- Department
of Plant Breeding, Swedish University of
Agricultural Sciences, P.O. Box 190, SE-234 22 Lomma, Sweden
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3
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Sanchez Ramirez DO, Tonetti C, Cruz-Maya I, Guarino V, Peila R, Carletto RA, Varesano A, Vineis C. Design of cysteine-S-sulfonated keratin via pH driven processes: Micro-Structural Properties, biocidal activity and in vitro validation. Eur Polym J 2022. [DOI: 10.1016/j.eurpolymj.2022.111169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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4
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Tariq N, Kume T, Luo L, Cai Z, Dong S, Macgregor RB. Dimethyl sulfoxide (DMSO) as a stabilizing co-solvent for G-quadruplex DNA. Biophys Chem 2022; 282:106741. [DOI: 10.1016/j.bpc.2021.106741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/05/2021] [Accepted: 12/09/2021] [Indexed: 11/16/2022]
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5
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Sanawar H, Kim L, Farhat N, van Loosdrecht M, Vrouwenvelder J. Periodic chemical cleaning with urea: disintegration of biofilms and reduction of key biofilm-forming bacteria from reverse osmosis membranes. WATER RESEARCH X 2021; 13:100117. [PMID: 34585132 PMCID: PMC8456046 DOI: 10.1016/j.wroa.2021.100117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 06/13/2023]
Abstract
Biofouling is one of the major factors causing decline in membrane performance in reverse osmosis (RO) plants, and perhaps the biggest hurdle of membrane technology. Chemical cleaning is periodically carried out at RO membrane installations aiming to restore membrane performance. Typical cleaning agents used in the water treatment industry include sodium hydroxide (NaOH) and hydrochloric acid (HCl) in sequence. Rapid biofilm regrowth and related membrane performance decline after conventional chemical cleaning is a routinely observed phenomenon due to the inefficient removal of biomass from membrane modules. Since extracellular polymeric substances (EPS) make up the strongest and predominant structural framework of biofilms, disintegration of the EPS matrix should be the main target for enhanced biomass removal. Previously, we demonstrated at lab-scale the use of concentrated urea as a chemical cleaning agent for RO membrane systems. The protein denaturation property of urea was exploited to solubilize the proteinaceous foulants, weakening the EPS layer, resulting in enhanced biomass solubilization and removal from RO membrane systems. In this work, we investigated the impact of repeated chemical cleaning cycles with urea/HCl as well as NaOH/HCl on biomass removal and the potential adaptation of the biofilm microbial community. Chemical cleaning with urea/HCl was consistently more effective than NaOH/HCl cleaning over 6 cleaning and regrowth cycles. At the end of the 6 cleaning cycles, the percent reduction was 35% and 41% in feed channel pressure drop, 50% and 70% in total organic carbon, 30% and 40% in EPS proteins, and 40% and 66% in the peak intensities of protein-like matter, after NaOH/HCl cleaning and Urea/HCl cleaning, respectively. 16S ribosomal RNA (rRNA) gene sequencing of the biofilm microbial community revealed that urea cleaning does not select for key biofouling families such as Sphingomonadaceae and Xanthomonadaceae that are known to survive conventional chemical cleaning and produce adhesive EPS. This study reaffirmed that urea possesses all the desirable properties of a chemical cleaning agent, i.e., it dissolves the existing fouling layer, delays fresh fouling accumulation by inhibiting the production of a more viscous EPS, does not cause damage to the membranes, is chemically stable, and environmentally friendly as it can be recycled for cleaning.
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Affiliation(s)
- H. Sanawar
- Water Desalination and Reuse Center (WDRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - L.H. Kim
- Water Desalination and Reuse Center (WDRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - N.M. Farhat
- Water Desalination and Reuse Center (WDRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - M.C.M. van Loosdrecht
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - J.S. Vrouwenvelder
- Water Desalination and Reuse Center (WDRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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Abstract
Sirtuins are a large enzyme family involved in installing and removing post-translational modifications involving lysine side chains. These enzymes have been of intense research interest and we now understand many details of their mechanism, although later steps of the deacetylase activity have remained a mystery. In this issue of Cell Chemical Biology, Wang et al. (2017) capture a late intermediate of SIRT2 catalysis and describe its structure.
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Affiliation(s)
- Schuyler Lee
- Department of Biomedical Research, National Jewish Health, 1400 Jackson St, Denver, CO 80206, USA
| | - Zhongzhou Chen
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Gongyi Zhang
- Department of Biomedical Research, National Jewish Health, 1400 Jackson St, Denver, CO 80206, USA.
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7
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Ghosh S, Salama F, Dines M, Lahav A, Adir N. Biophysical and structural characterization of the small heat shock protein HspA from Thermosynechococcus vulcanus in 2 M urea. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:442-452. [PMID: 30711645 DOI: 10.1016/j.bbapap.2018.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/29/2018] [Accepted: 12/11/2018] [Indexed: 10/27/2022]
Abstract
Small heat shock proteins (sHSPs) belong to the superfamily of molecular chaperones. They prevent aggregation of partially unfolded or misfolded client proteins, providing protection to organisms under stress conditions. Here, we report the biophysical and structural characterization of a small heat shock protein (HspA) from a thermophilic cyanobacterium Thermosynechococcus vulcanus in the presence of 2 M urea. HspA has been shown to be important for the protection of Photosystem II and the Phycobilisome antenna complex at elevated temperatures. Heterologously expressed HspA requires the presence of 1-2 M urea to maintain its solubility at concentrations required for most characterization methods. Spectroscopic studies reveal the presence of the β-sheet structure and intactness of the tertiary fold in HspA. In vitro assays show that the HspA maintains chaperone-like activity in protecting soluble proteins from thermal aggregation. Chromatography and electron microscopy show that the HspA exists as a mixture of oligomeric forms in the presence of 2 M urea. HspA was successfully crystallized only in the presence of 2 M urea. The crystal structure of HspA shows urea-induced loss of about 30% of the secondary structure without major alteration in the tertiary structure of the protein. The electron density maps reveal changes in the hydrogen bonding network which we attribute to the presence of urea. The crystal structure of HspA demonstrates a mixture of both direct interactions between urea and protein functionalities and interactions between urea and the surrounding solvent that indirectly affect the protein, which are in accordance with previously published studies.
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Affiliation(s)
- Sudeshna Ghosh
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Faris Salama
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Monica Dines
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Avital Lahav
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Noam Adir
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel.
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8
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Lee S, Wang C, Liu H, Xiong J, Jiji R, Hong X, Yan X, Chen Z, Hammel M, Wang Y, Dai S, Wang J, Jiang C, Zhang G. Hydrogen bonds are a primary driving force for de novo protein folding. Acta Crystallogr D Struct Biol 2017; 73:955-969. [PMID: 29199976 PMCID: PMC5713874 DOI: 10.1107/s2059798317015303] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 10/20/2017] [Indexed: 01/09/2023] Open
Abstract
The protein-folding mechanism remains a major puzzle in life science. Purified soluble activation-induced cytidine deaminase (AID) is one of the most difficult proteins to obtain. Starting from inclusion bodies containing a C-terminally truncated version of AID (residues 1-153; AID153), an optimized in vitro folding procedure was derived to obtain large amounts of AID153, which led to crystals with good quality and to final structural determination. Interestingly, it was found that the final refolding yield of the protein is proline residue-dependent. The difference in the distribution of cis and trans configurations of proline residues in the protein after complete denaturation is a major determining factor of the final yield. A point mutation of one of four proline residues to an asparagine led to a near-doubling of the yield of refolded protein after complete denaturation. It was concluded that the driving force behind protein folding could not overcome the cis-to-trans proline isomerization, or vice versa, during the protein-folding process. Furthermore, it was found that successful refolding of proteins optimally occurs at high pH values, which may mimic protein folding in vivo. It was found that high pH values could induce the polarization of peptide bonds, which may trigger the formation of protein secondary structures through hydrogen bonds. It is proposed that a hydrophobic environment coupled with negative charges is essential for protein folding. Combined with our earlier discoveries on protein-unfolding mechanisms, it is proposed that hydrogen bonds are a primary driving force for de novo protein folding.
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Affiliation(s)
- Schuyler Lee
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206, USA
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Denver, Aurora, CO 80206, USA
| | - Chao Wang
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206, USA
| | - Haolin Liu
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206, USA
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Denver, Aurora, CO 80206, USA
| | - Jian Xiong
- Department of Chemistry, University of Missouri, Columbus, Mississippi, USA
| | - Renee Jiji
- Department of Chemistry, University of Missouri, Columbus, Mississippi, USA
| | - Xia Hong
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206, USA
| | - Xiaoxue Yan
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206, USA
| | - Zhangguo Chen
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Denver, Aurora, CO 80206, USA
| | - Michal Hammel
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yang Wang
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206, USA
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Denver, Aurora, CO 80206, USA
| | - Shaodong Dai
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206, USA
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Denver, Aurora, CO 80206, USA
| | - Jing Wang
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Denver, Aurora, CO 80206, USA
| | - Chengyu Jiang
- Department of Biochemistry and Molecular Biology, Peking Union Medical College, Beijing 100005, People’s Republic of China
| | - Gongyi Zhang
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206, USA
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Denver, Aurora, CO 80206, USA
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9
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Chandramohan A, Tulsian NK, Anand GS. Dissecting Orthosteric Contacts for a Reverse-Fragment-Based Ligand Design. Anal Chem 2017. [PMID: 28628309 DOI: 10.1021/acs.analchem.7b00587] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Orthosteric sites on proteins are formed typically from noncontiguous interacting sites in three-dimensional space where the composite binding interaction of a biological ligand is mediated by multiple synergistic interactions of its constituent functional groups. Through these multiple interactions, ligands stabilize both the ligand binding site and the local secondary structure. However, relative energetic contributions of the individual contacts in these protein-ligand interactions are difficult to resolve. Deconvolution of the contributions of these various functional groups in natural inhibitors/ligand would greatly aid in iterative fragment-based drug discovery (FBDD). In this study, we describe an approach of progressive unfolding of a target protein using a gradient of denaturant urea to reveal the individual energetic contributions of various ligand-functional groups to the affinity of the entire ligand. Through calibrated unfolding of two protein-ligand systems: cAMP-bound regulatory subunit of Protein Kinase A (RIα) and IBMX-bound phosphodiesterase8 (PDE8), monitored by amide hydrogen-deuterium exchange mass spectrometry, we show progressive disruption of individual orthosteric contacts in the ligand binding sites, allowing us to rank the energetic contributions of these individual interactions. In the two cAMP-binding sites of RIα, exocyclic phosphate oxygens of cAMP were identified to mediate stronger interactions than ribose 2'-OH in both the RIα-cAMP binding interfaces. Further, we have also ranked the relative contributions of the different functional groups of IBMX based on their interactions with the orthosteric residues of PDE8. This strategy for deconstruction of individual binding sites and identification of the strongest functional group interaction in enzyme orthosteric sites offers a rational starting point for FBDD.
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Affiliation(s)
- Arun Chandramohan
- Department of Biological Sciences, National University of Singapore , 14 Science Drive 4, Singapore 117543
| | - Nikhil K Tulsian
- Department of Biological Sciences, National University of Singapore , 14 Science Drive 4, Singapore 117543
| | - Ganesh S Anand
- Department of Biological Sciences, National University of Singapore , 14 Science Drive 4, Singapore 117543
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10
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Dumard CH, Barroso SPC, Santos ACV, Alves NS, Couceiro JNSS, Gomes AMO, Santos PS, Silva JL, Oliveira AC. Stability of different influenza subtypes: How can high hydrostatic pressure be a useful tool for vaccine development? Biophys Chem 2017; 231:116-124. [PMID: 28410940 DOI: 10.1016/j.bpc.2017.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 04/05/2017] [Accepted: 04/05/2017] [Indexed: 01/15/2023]
Abstract
BACKGROUND Avian influenza A viruses can cross naturally into mammals and cause severe diseases, as observed for H5N1. The high lethality of human infections causes major concerns about the real risk of a possible pandemic of severe diseases to which human susceptibility may be high and universal. High hydrostatic pressure (HHP) is a valuable tool for studies regarding the folding of proteins and the assembly of macromolecular structures such as viruses; furthermore, HHP has already been demonstrated to promote viral inactivation. METHODS Here, we investigated the structural stability of avian and human influenza viruses using spectroscopic and light-scattering techniques. We found that both particles have similar structural stabilities and that HHP promotes structural changes. RESULTS HHP induced slight structural changes to both human and avian influenza viruses, and these changes were largely reversible when the pressure returned to its initial level. The spectroscopic data showed that H3N2 was more pressure-sensitive than H3N8. Structural changes did not predict changes in protein function, as H3N2 fusion activity was not affected, while H3N8 fusion activity drastically decreased. The fusion activity of H1N1 was also strongly affected by HHP. In all cases, HHP caused inactivation of the different influenza viruses. CONCLUSIONS HHP may be a useful tool for vaccine development, as it induces minor and reversible structural changes that may be associated with partial preservation of viral biological activities and may potentiate their immunogenic response while abolishing their infectivity. We also confirmed that, although pressure does not promote drastic changes in viral particle structure, it can distinctly affect viral fusion activity.
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Affiliation(s)
- Carlos Henrique Dumard
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Brazil
| | - Shana P C Barroso
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Brazil
| | - Ana Clara V Santos
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Brazil
| | - Nathalia S Alves
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Brazil
| | - José Nelson S S Couceiro
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
| | - Andre M O Gomes
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Brazil
| | - Patricia S Santos
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Brazil
| | - Jerson L Silva
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Brazil.
| | - Andréa C Oliveira
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Brazil.
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11
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Cha HJ, Jang DS, Jin KS, Choi KY. Structural analyses combined with small-angle X-ray scattering reveals that the retention of heme is critical for maintaining the structure of horseradish peroxidase under denaturing conditions. Amino Acids 2017; 49:715-723. [PMID: 28144743 DOI: 10.1007/s00726-016-2372-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/23/2016] [Indexed: 11/29/2022]
Abstract
We analyzed the structure of horseradish peroxidase (HRP) under denaturing conditions of 9 M urea or 6 M guanidine hydrochloride (GdnHCl). Far-UV circular dichroism (CD) spectra indicated the existence of native-like secondary structure of holo-HRP in 9 M urea. In addition, slight changes in near-UV and Soret region CD spectra of holo-HRP in 9 M urea suggest that the tertiary structure of holo-HRP and the binding of heme remain partially intact in this condition. A transition in the thermal unfolding transition curve of holo-HRP in 9 M urea indicated the existence of a considerable amount of secondary structure. However, no secondary structure, tertiary structure, or interaction between heme and HRP were observed in holo-HRP in 6 M GdnHCl. Small-angle X-ray scattering indicated that although distal and proximal domains of holo-HRP in 9 M urea might be partially unfolded, the central region that contains the heme might maintain its tertiary structure. Our results suggest that retention of the heme is essential for maintenance of the structure of HRP under highly denaturing conditions.
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Affiliation(s)
- Hyung Jin Cha
- Pohang Accelerator Laboratory, Pohang University of Science and Technology (POSTECH), Pohang, Korea
| | - Do Soo Jang
- Department of Life Sciences, POSTECH, Pohang, Korea.,Huons Co., Ltd., Seongnam, Korea
| | - Kyeong Sik Jin
- Pohang Accelerator Laboratory, Pohang University of Science and Technology (POSTECH), Pohang, Korea.
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12
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Time-dependent X-ray diffraction studies on urea/hen egg white lysozyme complexes reveal structural changes that indicate onset of denaturation. Sci Rep 2016; 6:32277. [PMID: 27573790 PMCID: PMC5004150 DOI: 10.1038/srep32277] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 08/05/2016] [Indexed: 01/10/2023] Open
Abstract
Temporal binding of urea to lysozyme was examined using X-ray diffraction of single crystals of urea/lysozyme complexes prepared by soaking native lysozyme crystals in solutions containing 9 M urea. Four different soak times of 2, 4, 7 and 10 hours were used. The five crystal structures (including the native lysozyme), refined to 1.6 Å resolution, reveal that as the soaking time increased, more and more first-shell water molecules are replaced by urea. The number of hydrogen bonds between urea and the protein is similar to that between protein and water molecules replaced by urea. However, the number of van der Waals contacts to protein from urea is almost double that between the protein and the replaced water. The hydrogen bonding and van der Waals interactions are initially greater with the backbone and later with side chains of charged residues. Urea altered the water-water hydrogen bond network both by replacing water solvating hydrophobic residues and by shortening the first-shell intra-water hydrogen bonds by 0.2 Å. These interaction data suggest that urea uses both 'direct' and 'indirect' mechanisms to unfold lysozyme. Specific structural changes constitute the first steps in lysozyme unfolding by urea.
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13
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Lo SY, Säbel CE, Mapletoft JP, Siemann S. Influence of chemical denaturants on the activity, fold and zinc status of anthrax lethal factor. Biochem Biophys Rep 2015; 1:68-77. [PMID: 29124135 PMCID: PMC5668564 DOI: 10.1016/j.bbrep.2015.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 03/11/2015] [Accepted: 03/12/2015] [Indexed: 11/17/2022] Open
Abstract
Anthrax lethal factor (LF) is a zinc-dependent endopeptidase which, through a process facilitated by protective antigen, translocates to the host cell cytosol in a partially unfolded state. In the current report, the influence of urea and guanidine hydrochloride (GdnHCl) on LF׳s catalytic function, fold and metal binding was assessed at neutral pH. Both urea and GdnHCl were found to inhibit LF prior to the onset of unfolding, with the inhibition by the latter denaturant being a consequence of its ionic strength. With the exception of demetallated LF (apoLF) in urea, unfolding, as monitored by tryptophan fluorescence spectroscopy, was found to follow a two-state (native to unfolded) mechanism. Analysis of the metal status of LF with 4-(2-pyridylazoresorcinol) (PAR) following urea or GdnHCl exposure suggests the enzyme to be capable of maintaining its metal ion passed the observed unfolding transition in a chelator-inaccessible form. Although an increase in the concentration of the denaturants eventually allowed the chelator access to the protein׳s zinc ion, such process is not correlated with the release of the metal ion. Indeed, significant dissociation of the zinc ion from LF was not observed even at 6 M urea, and only high concentrations of GdnHCl (>3 M) were capable of inducing the release of the metal ion from the protein. Hence, the current study demonstrates not only the propensity of LF to tightly bind its zinc ion beyond the spectroscopically determined unfolding transition, but also the utility of PAR as a structural probe. Lethal factor (LF) is strongly inhibited by guanidine hydrochloride. Except of apoLF in urea, unfolding follows a two-state mechanism. LF shields and retains its zinc ion in an unfolded state. Pyridylazoresorcinol is a useful probe to assess metal accessibility and release.
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Key Words
- 4-(2-pyridylazo)resorcinol
- CD, circular dichroism
- Chemical denaturants
- DPA, dipicolinic acid
- EDTA, ethylenediaminetetraacetic acid
- EF, edema factor
- LF, anthrax lethal factor
- Lethal factor
- MWCO, molecular weight cut-off
- PA, protective antigen
- PAR, 4-(2-pyridylazo)resorcinol
- Protein folding
- S-pNA, lethal factor substrate
- SASA, solvent-accessible surface area
- SOD, superoxide dismutase
- Tryptophan fluorescence
- Zinc
- ZnLF, zinc-containing lethal factor
- cps, counts per second
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Affiliation(s)
- Suet Y. Lo
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Crystal E. Säbel
- Bharti School of Engineering, Laurentian University, Sudbury, Ontario, Canada
| | | | - Stefan Siemann
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
- Correspondence to: Department of Chemistry and Biochemistry, Laurentian University, 935 Ramsey Lake Road, Sudbury, Ontario, Canada P3E 2C6. Tel.: +1 705 675 1151; fax: +1 705 675 4844.
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