1
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Janes RW, Wallace BA. DichroPipeline: A suite of online and downloadable tools and resources for protein circular dichroism spectroscopic data analyses, interpretations, and their interoperability with other bioinformatics tools and resources. Protein Sci 2023; 32:e4817. [PMID: 37881887 PMCID: PMC10680340 DOI: 10.1002/pro.4817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 09/30/2023] [Indexed: 10/27/2023]
Abstract
Circular Dichroism (CD) spectroscopy is a widely-used method for characterizing individual protein structures in solutions, membranes, films and macromolecular complexes, as well as for probing macromolecular interactions, conformational changes associated with binding substrates, and in different functionally-related environments. This paper describes a series of related computational and display tools that have been developed over many years to aid in those characterizations and functional interpretations. The new DichroPipeline described herein links a series of format-compatible data processing, analysis, and display tools to enable users to facilely produce the spectra, which can then be made available in the Protein Circular Dichroism Data Bank (https://pcddb.cryst.bbk.ac.uk/) resource, in which the CD spectral and associated metadata for each entry are linked to other structural and functional data bases including the Protein Data Bank (PDB), and the UniProt sequence data base, amongst others. These tools and resources thus provide the basis for a wide range of traceable structural characterizations of soluble, membrane and intrinsically-disordered proteins.
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Affiliation(s)
- Robert W. Janes
- School of Biological and Behavioural SciencesQueen Mary University of LondonLondonUK
| | - B. A. Wallace
- School of Biological SciencesBirkbeck University of LondonLondonUK
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2
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Mathieu‐Gaedke M, Böker A, Glebe U. How to Characterize the Protein Structure and Polymer Conformation in Protein‐Polymer Conjugates – a Perspective. MACROMOL CHEM PHYS 2023. [DOI: 10.1002/macp.202200353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Maria Mathieu‐Gaedke
- Chair of Polymer Materials and Polymer Technologies Institute of Chemistry University of Potsdam Karl‐Liebknecht‐Str. 24–25 14476 Potsdam‐Golm Germany
- Fraunhofer Institute for Applied Polymer Research IAP Geiselbergstr. 69 14476 Potsdam‐Golm Germany
| | - Alexander Böker
- Chair of Polymer Materials and Polymer Technologies Institute of Chemistry University of Potsdam Karl‐Liebknecht‐Str. 24–25 14476 Potsdam‐Golm Germany
- Fraunhofer Institute for Applied Polymer Research IAP Geiselbergstr. 69 14476 Potsdam‐Golm Germany
| | - Ulrich Glebe
- Chair of Polymer Materials and Polymer Technologies Institute of Chemistry University of Potsdam Karl‐Liebknecht‐Str. 24–25 14476 Potsdam‐Golm Germany
- Fraunhofer Institute for Applied Polymer Research IAP Geiselbergstr. 69 14476 Potsdam‐Golm Germany
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3
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Hou J, Lei X, Liu B, Wang Z, Fang G, Liu J, Wang S. A study on the catalytic activity of polypeptides toward the hydrolysis of glucoside compounds gastrodin, polydatin and esculin. J Mater Chem B 2022; 10:9878-9886. [PMID: 36437799 DOI: 10.1039/d2tb01758j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The self-assembly of a series of catalytically active polypeptides toward hydrolysis of glucoside compounds, namely, gastrodin, polydatin and esculin was investigated. These active peptides are composed of two functional fragments: one is the hydrophobic sequence LHLHLRL, which forms assembling segments in the presence of Zn ions (Zn2+); another functional sequence of active peptides are catalytic sites such as Glu (E), Asp (D) and His (H), where carboxylic acids (-COOH) or imidazole groups act like scissors to cleave glucoside bonds of the compounds (according to the acid-base coupling mechanism). The effects of the amino acid sequence of the peptide, Zn2+ concentration, pH and the size or steric hindrance of glucoside compounds on the hydrolytic activity were studied. It was found that the crystalline structure of assembled peptides was crucial to provide the peptide with catalytic hydrolytic activity. Noncovalent interaction index was used to analyse the noncovalent interaction of PEs with glucoside compounds, including hydrogen bonds, van der Waals, and steric effect in the complexes. The binding energy of complexes, the direction and site of nucleophilic attack during deglycosylation processes were also investigated by molecular docking and the electron density Laplace function. This revealed that the differences in the hydrolytic activity of peptides toward glucoside compounds with different sizes originated from different hydrogen bond interactions between the peptides and substrates. These active peptides may find application in the preparation of drugs by de-glycosylation of natural compounds.
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Affiliation(s)
- Juan Hou
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Quality and Healthy of Tianjin, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China.
| | - Xiangmin Lei
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Quality and Healthy of Tianjin, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China.
| | - Borui Liu
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Zejiang Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Quality and Healthy of Tianjin, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China.
| | - Guozhen Fang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Quality and Healthy of Tianjin, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China.
| | - Jifeng Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Quality and Healthy of Tianjin, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China.
| | - Shuo Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Quality and Healthy of Tianjin, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China. .,Research Center of Food Science and Human Health, School of Medicine, Nankai University, Tianjin, 300071, P. R. China
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4
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Ni X, Zhang M, Zhang J, Zhang Z, Dong S, Zhao L. Molecular mechanism of two functional protein structure changes under 2,3-butanedione-induced oxidative stress and apoptosis effects in the hepatocytes. Int J Biol Macromol 2022; 218:969-980. [PMID: 35907461 DOI: 10.1016/j.ijbiomac.2022.07.171] [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: 04/27/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 11/24/2022]
Abstract
Food security has become closely watched with the occurrence of a series of food safety incidents in recent years. The widespread adoption of 2,3-butanedione (BUT), as a food additive, is an unpreventable significant risk factor to food security. Based on this, mouse hepatocyte AML-12 cells and two functional proteins (bovine serum albumin and lysozyme) were utilized as targeted receptors to study the adverse effects of BUT at the cellular and molecular levels. Results suggested that BUT could disrupt the redox balance of AML-12 cells, reducing glutathione (GSH) activity fell to 87.18 %, which cannot offset the production of reactive oxygen species (ROS). Meanwhile, the increasement of lipid peroxidation and malondialdehyde (MDA) levels were observed. The mitochondrial membrane function was also abnormal due to the excessive accumulation of ROS and eventually leads to cell apoptosis and death. At the molecular level, the exposure of BUT could alter the skeleton and secondary structure of bovine serum albumin (BSA) and lysozyme (LYZ), and it could statically quench the intrinsic fluorescence of proteins. The combined experiments confirmed proved the potentially toxic effects of BUT accumulation on the detoxification organ, providing theoretical support for the liver diseases caused by BUT exposure, and a reference for the risk assessment of occupational exposure of BUT.
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Affiliation(s)
- Xinyu Ni
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, PR China
| | - Miao Zhang
- College of Chemistry & Environmental Science, Hebei University, Baoding, Hebei 071002, PR China
| | - Jing Zhang
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, PR China
| | - Zhen Zhang
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, PR China
| | - Sijun Dong
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, PR China.
| | - Lining Zhao
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, PR China.
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5
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Chen J, Tieleman DP, Liang Q. Effects of Lid Domain Structural Changes on the Interactions between Peripheral Myelin Protein 2 and a Lipid Bilayer. J Phys Chem Lett 2022; 13:991-996. [PMID: 35060724 DOI: 10.1021/acs.jpclett.1c03961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Peripheral myelin protein 2 (P2) plays an important role in the stacking of the myelin membrane and lipid transport. Here we investigate the interactions between P2 and a model myelin membrane using molecular dynamics simulations, focusing on the effect of the L27D mutation and conformational changes in the α2-helix in the lid domain of P2. The L27D mutation weakens the binding of the lid domain of P2 on the membrane. The α2-helix is either folded or unfolded on the membrane. Compared with the α2-helix structure in water, the membrane stabilizes the structure of the α2-helix, whereas the unfolding of the α2-helix reduces the binding affinity of P2 on the membrane. These findings reveal the energetics of the mutant and the structural changes of P2 on the interactions between the protein and the lipid bilayer and help us to understand the microscopic mechanism of the formation of the myelin sheath structure and some neurological disorders.
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Affiliation(s)
- Jinyu Chen
- Center for Statistical and Theoretical Condensed Matter Physics and Department of Physics, Zhejiang Normal University, Jinhua 321004, P. R. China
| | - D Peter Tieleman
- Centre for Molecular Simulations and Department of Biological Science, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Qing Liang
- Center for Statistical and Theoretical Condensed Matter Physics and Department of Physics, Zhejiang Normal University, Jinhua 321004, P. R. China
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6
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Haslem L, Brown M, Zhang XA, Hays JM, Hays FA. Purification of Membrane Proteins Overexpressed in Saccharomyces cerevisiae. Methods Mol Biol 2022; 2507:143-173. [PMID: 35773581 PMCID: PMC9400948 DOI: 10.1007/978-1-0716-2368-8_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Membrane protein (MP) functional and structural characterization requires large quantities of high-purity protein for downstream studies. Barriers to MP characterization include ample overexpression, solubilization, and purification of target proteins while maintaining native activity and structure. These barriers can be overcome by utilizing an efficient purification protocol in a high-yield eukaryotic expression system such as Saccharomyces cerevisiae. S. cerevisiae offers improved protein folding and posttranslational modifications compared to prokaryotic expression systems. This chapter contains practices used to overcome barriers of solubilization and purification using S. cerevisiae that are broadly applicable to diverse membrane associated, and membrane integrated, protein targets.
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Affiliation(s)
- Landon Haslem
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Marina Brown
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Xin A Zhang
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Jennifer M Hays
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Franklin A Hays
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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7
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Biophysical characterisation of SMALPs. Biochem Soc Trans 2021; 49:2037-2050. [PMID: 34643233 DOI: 10.1042/bst20201088] [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: 08/02/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 11/17/2022]
Abstract
Membrane proteins such as receptors, ion channels and transport proteins are important drug targets. The structure-based study of membrane proteins is challenging, especially when the target protein contains both soluble and insoluble domains. Most membrane proteins are insoluble in aqueous solvent and embedded in the plasma membrane lipid bilayer, which significantly complicates biophysical studies. Poly(styrene-co-maleic acid) (SMA) and other polymer derivatives are increasingly common solubilisation agents, used to isolate membrane proteins stabilised in their native lipid environment in the total absence of detergent. Since the initial report of SMA-mediated solubilisation, and the formation of SMA lipid particles (SMALPs), this technique can directly isolate therapeutic targets from biological membranes, including G-protein coupled receptors (GPCRs). SMA now allows biophysical and structural analyses of membrane proteins in solution that was not previously possible. Here, we critically review several existing biophysical techniques compatible with SMALPs, with a focus on hydrodynamic analysis, microcalorimetric analysis and optical spectroscopic techniques.
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8
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Effect of setting data collection parameters on the reliability of a circular dichroism spectrum. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:687-697. [PMID: 33538870 DOI: 10.1007/s00249-021-01499-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/12/2020] [Accepted: 01/13/2021] [Indexed: 10/22/2022]
Abstract
Circular dichroism (CD) spectroscopy is a well-established biophysical technique used to investigate the structure of molecules. The analysis of a protein CD spectrum depends on the quality of the original CD data, which can be affected by the sample purity, background absorption of the additives/solvent/buffer, the choice of the parameters used for data collection, etc. In this paper, the CD spectrum of myoglobin was used as a model to exploit how variations on each data collection parameter could affect the final protein CD spectrum and, the subsequent effect of them on the quantitative analysis of protein secondary structure. Bioinformatics analysis carried out with SESCA package and PDBMD2CD server predicted a theoretical myoglobin CD spectrum, and a Monte Carlo-like model was implemented to estimate the uncertainty in secondary structure predictions performed with CDSSTR, Selcon 3 and ContinLL algorithms. An inappropriate choice of data collection parameters can lead to a misinterpretation of the CD data in terms of the protein structural content.
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9
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Azarakhsh F, Divsalar A, Saboury AA, Eidi A. Simultaneous delivery of oxali-palladium and iron nanoparticles by β-casein. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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10
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Shaheen A, Ismat F, Iqbal M, Haque A, Ul-Haq Z, Mirza O, De Zorzi R, Walz T, Rahman M. Characterization of the multidrug efflux transporter styMdtM from Salmonella enterica serovar Typhi. Proteins 2021; 89:1193-1204. [PMID: 33983672 DOI: 10.1002/prot.26141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/14/2021] [Accepted: 05/07/2021] [Indexed: 11/09/2022]
Abstract
Salmonellae are foodborne pathogens and the major cause of gastroenteritis in humans. Salmonellae express multidrug efflux transporters that play a key role in their drug resistance, which is becoming an increasing problem for therapeutic intervention. Despite their biomedical importance, the mechanisms underlying substrate transport by multidrug efflux transporters remain poorly understood. Here, we describe the first characterization of a multidrug transporter belonging to the major facilitator superfamily from the genus Salmonella. We show that several clinical Salmonella Typhi (S. Typhi) isolates constitutively express the styMdtM (STY4874) gene, which encodes a known multidrug-resistance (MDR) transporter. Guided by the structure of the Escherichia coli (E. coli) homolog, we studied two residues critical for substrate transport, Asp25 and Arg111. Mutation of Asp25 to glutamate did not affect the transport function of styMdtM, whereas mutation to alanine reduced its transport activity, suggesting that a negative charge at this position is critical for substrate translocation across the membrane. Substrate-affinity measurements by intrinsic fluorescence spectroscopy showed that the Asp25Ala mutant retained its capacity to bind substrate, albeit at a lower level. Mutation of Arg111 to alanine resulted in a decrease in secondary structure content of the transporter, and mutation to lysine completely destabilized the structure of the transporter. A homology model of styMdtM suggests that Arg111 is important for stabilizing the transmembrane domain by mediating necessary interactions between neighboring helices. Together, our studies provide new structural and mechanistic insights into the Salmonella MDR transporter styMdtM.
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Affiliation(s)
- Aqsa Shaheen
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, Pakistan.,Department of Biochemistry and Biotechnology, University of Gujrat, Gujrat, Punjab, Pakistan.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Fouzia Ismat
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, Pakistan
| | - Mazhar Iqbal
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, Pakistan
| | - Abdul Haque
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, Pakistan.,Akhuwat First University, Faisalabad, Punjab, Pakistan
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Sindh, Pakistan
| | - Osman Mirza
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rita De Zorzi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Thomas Walz
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA.,Laboratory of Molecular Electron Microscopy, Rockefeller University, New York, New York, USA
| | - Moazur Rahman
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, Pakistan.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA.,School of Biological Sciences, University of the Punjab, Lahore, Punjab, Pakistan
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11
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Wojciechowska M, Miszkiewicz J, Trylska J. Conformational Changes of Anoplin, W-MreB 1-9, and (KFF) 3K Peptides near the Membranes. Int J Mol Sci 2020; 21:ijms21249672. [PMID: 33352981 PMCID: PMC7766051 DOI: 10.3390/ijms21249672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 12/07/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022] Open
Abstract
Many peptides interact with biological membranes, but elucidating these interactions is challenging because cellular membranes are complex and peptides are structurally flexible. To contribute to understanding how the membrane-active peptides behave near the membranes, we investigated peptide structural changes in different lipid surroundings. We focused on two antimicrobial peptides, anoplin and W-MreB1–9, and one cell-penetrating peptide, (KFF)3K. Firstly, by using circular dichroism spectroscopy, we determined the secondary structures of these peptides when interacting with micelles, liposomes, E. coli lipopolysaccharides, and live E. coli bacteria. The peptides were disordered in the buffer, but anoplin and W-MreB1–9 displayed lipid-induced helicity. Yet, structural changes of the peptide depended on the composition and concentration of the membranes. Secondly, we quantified the destructive activity of peptides against liposomes by monitoring the release of a fluorescent dye (calcein) from the liposomes treated with peptides. We observed that only for anoplin and W-MreB1–9 calcein leakage from liposomes depended on the peptide concentration. Thirdly, bacterial growth inhibition assays showed that peptide conformational changes, evoked by the lipid environments, do not directly correlate with the antimicrobial activity of the peptides. However, understanding the relation between peptide structural properties, mechanisms of membrane disruption, and their biological activities can guide the design of membrane-active peptides.
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Affiliation(s)
- Monika Wojciechowska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland;
- Correspondence: (M.W.); (J.T.)
| | - Joanna Miszkiewicz
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland;
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland;
- Correspondence: (M.W.); (J.T.)
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12
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Höger GA, Wiegand M, Worbs B, Diederichsen U. Membrane-Associated Nucleobase-Functionalized β-Peptides (β-PNAs) Affecting Membrane Support and Lipid Composition. Chembiochem 2020; 21:2599-2603. [PMID: 32346953 PMCID: PMC7540700 DOI: 10.1002/cbic.202000172] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/26/2020] [Indexed: 11/18/2022]
Abstract
Protein-membrane interactions are essential to maintain membrane integrity and control membrane morphology and composition. Cytoskeletal proteins in particular are known to interact to a high degree with lipid bilayers and to line the cytoplasmic side of the plasma membrane with an extensive network structure. In order to gain a better mechanistical understanding of the protein-membrane interplay and possible membrane signaling, we started to develop a model system based on β-peptide nucleic acids (β-PNAs). These β-peptides are known to form stable hydrogen-bonded aggregates due to their helical secondary structure, which serve to pre-organize the attached nucleobases. After optimization of the β-PNA solid-phase peptide synthesis and validation of helix formation, the ability of the novel β-PNAs to dimerize and interact with lipid bilayers was investigated by both fluorescence and circular dichroism spectroscopy. It was shown that duplex formation occurs rapidly and with high specificity and could also be detected on the surfaces of the lipid bilayers. Hereby, the potential of a β-PNA-based peptide system to mimic membrane-associated protein networks could be demonstrated.
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Affiliation(s)
- Geralin A. Höger
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität GöttingenTammannstraße 237077GöttingenGermany
| | - Markus Wiegand
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität GöttingenTammannstraße 237077GöttingenGermany
| | - Brigitte Worbs
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität GöttingenTammannstraße 237077GöttingenGermany
| | - Ulf Diederichsen
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität GöttingenTammannstraße 237077GöttingenGermany
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13
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The structure and properties of MFG-E8 and the In vitro assessment of its toxic effects on myoblast cells. Protein Expr Purif 2020; 178:105720. [PMID: 32771447 DOI: 10.1016/j.pep.2020.105720] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 07/09/2020] [Accepted: 07/28/2020] [Indexed: 01/25/2023]
Abstract
Four high-molecular-weight protein fractions of milk fat globule membrane (MFGM) were isolated from bovine milk. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), MALDI-TOF/TOF™ and Liquid chromatography electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) were used to measure the molecular sizes of the MFGM. Fourier transform infrared spectroscopy (FT-IR) and circular dichroism (CD) were performed to determine the conformations of the MFGM. The results showed that the main protein (98.33%) in MFGM protein fraction 2 was Milk fat globule epidermal growth factor-VIII (MFG-E8), with a molecular weight of 47.82 kDa. The secondary structural component measurements showed that the MFG-E8 consisted of 5% helix, 70% sheet and 25% random coil, and the results matched well with the prediction by SSPro 5.1 bioinformatic analysis. The thermograms analysis revealed that Td and△H of MFG-E8 were 60.50°Cand 132.29 kJ/mol. The in vitro digestibility of MFG-E8 showed that it can be enzymatically hydrolyzed in the stomach and relatively stable in the intestinal fluid. The in vitro C2C12 and Caco2 cell activity tests indicated that MFG-E8 promoted the proliferation of C2C12 myoblast cells without cytotoxicity. The biological functional properties of MFG-E8 may be related to the fact that MFG-E8 possesses a high level of β-sheet structure. Our results suggested that MFG-E8 possesses broad prospects not only for use in functional food products but also as a source of natural anti-sarcopenia drugs.
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14
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Membrane interactions in drug delivery: Model cell membranes and orthogonal techniques. Adv Colloid Interface Sci 2020; 281:102177. [PMID: 32417568 DOI: 10.1016/j.cis.2020.102177] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 03/05/2020] [Accepted: 05/07/2020] [Indexed: 01/22/2023]
Abstract
To generate the desired effect in the human body, the active pharmaceutical ingredient usually needs to interact with a receptor located on the cell membrane or inside the cell. Thus, understanding membrane interactions is of great importance when it comes to the development and testing of new drug molecules or new drug delivery systems. Nowadays, there is a tremendous selection of both model cell membranes and of techniques that can be used to characterize interactions between selected model cell membranes and a drug molecule, an excipient, or a drug delivery system. Having such a wide selection of model cell membranes and techniques available makes it sometimes challenging to select the optimal combination for a specific study. Furthermore, it is difficult to compare results obtained using different model cell membranes and techniques, and not all in vitro studies translate as well to an estimation of the in vivo biological activity or understanding of mode of action. This review provides an overview of the available lipid bilayer-based model cell membranes and of the most widely employed techniques for studying membrane interactions. Finally, the need for employing complimentary characterization techniques in order to acquire more reliable and in-depth information is highlighted.
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15
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Matsuo K, Gekko K. Circular-Dichroism and Synchrotron-Radiation Circular-Dichroism Spectroscopy as Tools to Monitor Protein Structure in a Lipid Environment. Methods Mol Biol 2020; 2003:253-279. [PMID: 31218622 DOI: 10.1007/978-1-4939-9512-7_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Circular-dichroism (CD) spectroscopy is a powerful tool for the secondary-structure analysis of proteins. The structural information obtained by CD does not have atomic-level resolution (unlike X-ray crystallography and NMR spectroscopy), but it has the great advantage of being applicable to both nonnative and native proteins in a wide range of solution conditions containing lipids and detergents. The development of synchrotron-radiation CD (SRCD) instruments has greatly expanded the utility of this method by extending the spectra to the vacuum-ultraviolet region below 190 nm and producing information that is unobtainable by conventional CD instruments. Combining SRCD data with bioinformatics provides new insight into the conformational changes of proteins in a membrane environment.
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Affiliation(s)
- Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima, Japan
| | - Kunihiko Gekko
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima, Japan.
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16
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Matsuo K, Kumashiro M, Gekko K. Characterization of the mechanism of interaction between α1‐acid glycoprotein and lipid membranes by vacuum‐ultraviolet circular‐dichroism spectroscopy. Chirality 2020; 32:594-604. [DOI: 10.1002/chir.23208] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/27/2020] [Accepted: 02/17/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Koichi Matsuo
- Hiroshima Synchrotron Radiation CenterHiroshima University Higashi‐Hiroshima Japan
| | - Munehiro Kumashiro
- Department of Physical Science, Graduate School of ScienceHiroshima University Higashi‐Hiroshima Japan
| | - Kunihiko Gekko
- Hiroshima Synchrotron Radiation CenterHiroshima University Higashi‐Hiroshima Japan
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17
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Lopes-Rodrigues M, Matagne A, Zanuy D, Alemán C, Perpète EA, Michaux C. Structural and functional characterization of Solanum tuberosum VDAC36. Proteins 2019; 88:729-739. [PMID: 31833115 DOI: 10.1002/prot.25861] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/26/2019] [Accepted: 12/06/2019] [Indexed: 11/05/2022]
Abstract
As it forms water-filled channel in the mitochondria outer membrane and diffuses essential metabolites such as NADH and ATP, the voltage-dependent anion channel (VDAC) protein family plays a central role in all eukaryotic cells. In comparison with their mammalian homologues, little is known about the structural and functional properties of plant VDACs. In the present contribution, one of the two VDACs isoforms of Solanum tuberosum, stVDAC36, has been successfully overexpressed and refolded by an in-house method, as demonstrated by the information on its secondary and tertiary structure gathered from circular dichroism and intrinsic fluorescence. Cross-linking and molecular modeling studies have evidenced the presence of dimers and tetramers, and they suggest the formation of an intermolecular disulfide bond between two stVDAC36 monomers. The pore-forming activity was also assessed by liposome swelling assays, indicating a typical pore diameter between 2.0 and 2.7 nm. Finally, insights about the ATP binding inside the pore are given by docking studies and electrostatic calculations.
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Affiliation(s)
- Maximilien Lopes-Rodrigues
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Namur, Belgium.,Namur Institute of Structured Matter, University of Namur, Namur, Belgium.,Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, Barcelona, Spain.,Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Eduard Maristany, Barcelona, Spain
| | - André Matagne
- Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines (CIP), Université de Liège, Liège, Belgium
| | - David Zanuy
- Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, Barcelona, Spain
| | - Carlos Alemán
- Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, Barcelona, Spain.,Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Eduard Maristany, Barcelona, Spain
| | - Eric A Perpète
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Namur, Belgium.,Namur Institute of Structured Matter, University of Namur, Namur, Belgium.,Namur Research Institute for Life Sciences, University of Namur, Namur, Belgium
| | - Catherine Michaux
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Namur, Belgium.,Namur Institute of Structured Matter, University of Namur, Namur, Belgium.,Institute of Life-Earth-Environment, University of Namur, Namur, Belgium
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18
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Thaz CJ, Jayaraman G. Calcium ion induced thermodynamic stability, bisubstrate specificity, and differential organic solvent tolerance of a predominantly β-sheet serine protease from Bacillus aquimaris VITP4. Biotechnol Appl Biochem 2019; 66:955-961. [PMID: 31486109 DOI: 10.1002/bab.1811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/01/2019] [Indexed: 01/22/2023]
Abstract
The present study was aimed to get insights on the role of calcium ions on the thermodynamic stability, substrate specificity, and organic solvent compatibility of the extracellular protease produced by Bacillus aquimaris VITP4. Presence of Ca2+ enhanced the activity of the enzyme in the temperature range of 30-60 °C and increased the half-life from 164 to 234 Min. Circular dichroism experiments indicated that the temperature of half-denaturation (Tm ) of the protease increased from 76 to 86 °C. As judged by fluorescence emission profiles, the overall fold of the enzyme around the tryptophan residues could be similar. Further, thermal inactivation experiments revealed that the enzyme followed first order kinetics, with increase in energy for inactivation (Eai ) by 24.2 ± 1.2 kJ mol -1 in the presence of Ca2+ . Studies with synthetic peptides as well as with bovine serum albumin signified preferential hydrolysis of the peptide bonds at the C-terminus of alanine residues (with a kcat /KM of 141,400 M-1 Sec-1 ) and at the C-terminus of arginine residues with a lower specificity (72,400 M-1 Sec-1 ), indicating bisubstrate specificity of the enzyme. The enzyme was found to be compatible with organic solvents (50%, v/v) such as acetonitrile and butanol, indicating possible application under demanding nonaqueous conditions.
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Affiliation(s)
- Chittoor Jabeena Thaz
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Gurunathan Jayaraman
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
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19
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Wang F, Chen W, Abousalham A, Yang B, Wang Y. Exploring the influence of phospholipid monolayer conformation and environmental conditions on the interfacial binding of Gibberella Zeae lipase. Int J Biol Macromol 2019; 132:1051-1056. [PMID: 30922913 DOI: 10.1016/j.ijbiomac.2019.03.169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 10/27/2022]
Abstract
The involvement of different parameters on Gibberella zeae lipase (GZEL) membrane binding were characterized by using monomolecular film technology and circular dichroism spectroscopy. Among four kinds of phospholipid monolayers, 1,2‑dimyristoyl‑sn‑glycero‑3‑phosphoethanolamine have the highest maximum insertion pressure (MIP) value. Comparing the GZEL adsorption to phosphatidylcholine monolayers with different acyl chains in sn-1 and sn-2 positions, the higher MIP values were found for 1,2‑dilauroyl‑sn‑glycero‑3‑phosphocholine. Significantly improvement between 1,2‑dioleoyl‑sn‑glycero‑3‑phosphocholine and 1,2‑distearoyl‑sn‑glycero‑3‑phosphocholine suggested that the presence of fatty acid unsaturation may affect protein adsorption by changing the chemical structure in each phospholipid. The MIP value was shown higher (48.6 mN m-1) at pH 5 and pH 6 (47.5 ± 1.9 mN m-1) but decreased significantly (34.2 mN m-1) at pH 9. This may indicate that the proportion of helices in the protein decreases with the alteration of the catalytic center, thus affecting the binding of the protein to its substrate. The MIP values obviously decreased with increasing salt ion concentration, suggesting that excessive salt ion concentration may destabilize the secondary and tertiary structures of the protein, thereby affecting the characteristics of its adsorption at the interfaces. Present studies improve our understanding on the protein-membrane interaction of this enzyme.
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Affiliation(s)
- Fanghua Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Wuchong Chen
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Abdelkarim Abousalham
- Univ Lyon, Université Lyon 1, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires (ICBMS), UMR 5246 CNRS, Métabolisme, Enzymes et Mécanismes Moléculaires (MEM(2)), Bât Raulin, 43 Bd du 11 Novembre 1918, F-69622 Villeurbanne CEDEX, France
| | - Bo Yang
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
| | - Yonghua Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China.
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20
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Hasan M, Patel D, Ellis N, Brown SP, Lewandowski JR, Dixon AM. Modulation of Transmembrane Domain Interactions in Neu Receptor Tyrosine Kinase by Membrane Fluidity and Cholesterol. J Membr Biol 2019; 252:357-369. [DOI: 10.1007/s00232-019-00075-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/09/2019] [Indexed: 01/06/2023]
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21
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Zheng T, Chen Y, Shi Y, Feng H. High efficiency liposome fusion induced by reducing undesired membrane peptides interaction. OPEN CHEM 2019. [DOI: 10.1515/chem-2019-0004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractA full membrane fusion model which attains both complete lipid mixing and content mixing liposomal membranes mediated by coiled-coil forming lipopeptides LPK [L-PEG12-(KIAALKE)3] and LPE [L-PEG12-(EIAALEK)3] is presented. The electrostatic effects of lipid anchored peptides on fusion efficiency was investigated. For this, the original amino acid sequence of the membrane bound LPK was varied at its ‘f’-position of the helical structure, i.e. via mutating the anionic glutamate residues by either neutral serines or cationic lysines. Both CD and fluorescence measurements showed that replacing the negatively charged glutamate did not significantly alter the peptide ability to form a coiled coil, but lipid mixing and content mixing assays showed more efficient liposome-liposome fusion resulting in almost quantitative content mixing for the lysine mutated analogue (LPKK) in conjunction with LPE. A mechanism is proposed for a fusion model triggered by membrane destabilizing effects mediated by the membrane destabilizing activety of LPK in cooperation with the electrostatic activity of LPE. This new insight may enlightens the further development of a promising nano carrier tool for biomedical applications.
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Affiliation(s)
- Tingting Zheng
- Shenzhen Key Laboratory for Drug Addiction and Medication Safety, Department of Ultrasound, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, 518036 Shenzhen, Shenzhen, China
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, P. O. Box 9502, 2300RA, Leiden, The Netherlands
| | - Yun Chen
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, P. O. Box 9502, 2300RA, Leiden, The Netherlands
| | - Yu Shi
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, P. O. Box 9502, 2300RA, Leiden, The Netherlands
| | - Huanhuan Feng
- School of Materials Science and Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, China
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22
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Gekko K. Synchrotron-radiation vacuum-ultraviolet circular dichroism spectroscopy in structural biology: an overview. Biophys Physicobiol 2019; 16:41-58. [PMID: 30923662 PMCID: PMC6435020 DOI: 10.2142/biophysico.16.0_41] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 01/13/2019] [Indexed: 12/01/2022] Open
Abstract
Circular dichroism spectroscopy is widely used for analyzing the structures of chiral molecules, including biomolecules. Vacuum-ultraviolet circular dichroism (VUVCD) spectroscopy using synchrotron radiation can extend the short-wavelength limit into the vacuum-ultraviolet region (down to ~160 nm) to provide detailed and new information about the structures of biomolecules in combination with theoretical analysis and bioinformatics. The VUVCD spectra of saccharides can detect the high-energy transitions of chromophores such as hydroxy and acetal groups, disclosing the contributions of inter- or intramolecular hydrogen bonds to the equilibrium configuration of monosaccharides in aqueous solution. The roles of hydration in the fluctuation of the dihedral angles of carboxyl and amino groups of amino acids can be clarified by comparing the observed VUVCD spectra with those calculated theoretically. The VUVCD spectra of proteins markedly improves the accuracy of predicting the contents and number of segments of the secondary structures, and their amino acid sequences when combined with bioinformatics, for not only native but also nonnative and membrane-bound proteins. The VUVCD spectra of nucleic acids confirm the contributions of the base composition and sequence to the conformation in comparative analyses of synthetic poly-nucleotides composed of selected bases. This review surveys these recent applications of synchrotron-radiation VUVCD spectroscopy in structural biology, covering saccharides, amino acids, proteins, and nucleic acids.
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Affiliation(s)
- Kunihiko Gekko
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan
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23
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Das S, Bora N, Rohman MA, Sharma R, Jha AN, Singha Roy A. Molecular recognition of bio-active flavonoids quercetin and rutin by bovine hemoglobin: an overview of the binding mechanism, thermodynamics and structural aspects through multi-spectroscopic and molecular dynamics simulation studies. Phys Chem Chem Phys 2018; 20:21668-21684. [PMID: 30101248 DOI: 10.1039/c8cp02760a] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The binding of two bio-active flavonoids, quercetin and rutin, with bovine hemoglobin (BHb) was investigated by multi-spectroscopic and computational (molecular docking and molecular dynamics simulation) studies. The two flavonoids were found to quench the intrinsic fluorescence of BHb through a static quenching mechanism. The binding constants at 288 K were observed to be (14.023 ± 0.73) × 104 M-1 and (7.848 ± 0.20) × 104 M-1, respectively for quercetin and rutin binding with BHb. Both rutin and quercetin were observed to increase the polarity around the Trp residues of BHb as indicated by synchronous and 3D spectral studies. No significant alterations in the secondary structural components of the protein were caused during the binding of the flavonoids as studied by CD and FTIR studies. The negative molar Gibbs free energies indicated the spontaneity of the interaction processes while the binding processes were characterized by a negative enthalpy change (ΔH) and a positive entropy change (ΔS). The possibility of energy transfer from the donor (BHb) to the acceptor molecules (flavonoids) was indicated by the FRET studies. According to the fluorescence studies, the flavonoids interact near to the β2-Trp37 residue of BHb. Excellent correlations with the experimental studies were observed from the molecular docking and molecular dynamics (MD) simulation studies. Further investigations established that these flavonoids are efficient in the inhibition of glucose mediated glycation of BHb.
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Affiliation(s)
- Sourav Das
- Department of Chemistry, National Institute of Technology, Meghalaya, Shillong 793003, India.
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24
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Multiple Spectroscopic, Docking and Cytotoxic Study of a Synthesized 2,2' Bipyridin Phenyl Isopentylglycin Pt(II) Nitrate Complex: Human Serum Albumin and Breast Cancer Cell Line of MDA-MB231 as Targets. J Fluoresc 2018; 28:551-559. [PMID: 29476398 DOI: 10.1007/s10895-018-2216-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Accepted: 01/22/2018] [Indexed: 10/18/2022]
Abstract
In the present study, the biological activities of a new synthesized Pt(II)-complex, 2,2' bipyridinphenyl isopentylglycin Pt(II) nitrate was investigated via its interaction with the most important blood carrier protein of human serum albumin (HSA), using fluorescence and Far-UV circular dichroism (CD) spectroscopic techniques and also molecular docking. Moreover, cytotoxicity activity of the complex was studied against breast cancer cell line of MDA MB231 using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The Pt(II)-complex has a strong ability to quench the intrinsic fluorescence of HSA through a static quenching mechanism. According fluorescence quenching data, the binding parameters of the interaction were calculated and showed that hydrophobic interaction has an important role. The molecular docking results in coherent with fluorescence measurements illustrated that Pt(II) complex can bind to HSA at one position that located in the hydrophobic cavity of groove between drug site I and II. Also, experimental data on driving force in binding site was confirmed whereas theoretical results demonstrated Pt(II) complexinteract to HSA by hydrophobic interaction. Far-UV-CD results showed that Pt(II)-complex induced an increasing in the content of α-helical structure of the protein and stabilized it. Also, MTT assay represented growth inhibitory effect of the complex toward the breast cancer cell line.
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25
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Iyer A, Roeters SJ, Kogan V, Woutersen S, Claessens MMAE, Subramaniam V. C-Terminal Truncated α-Synuclein Fibrils Contain Strongly Twisted β-Sheets. J Am Chem Soc 2017; 139:15392-15400. [PMID: 28968082 PMCID: PMC5668890 DOI: 10.1021/jacs.7b07403] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
C-terminal truncations
of monomeric wild-type alpha-synuclein (henceforth
WT-αS) have been shown to enhance the formation of amyloid aggregates
both in vivo and in vitro and have
been associated with accelerated progression of Parkinson’s
disease (PD). The correlation with PD may not solely be a result of
faster aggregation, but also of which fibril polymorphs are preferentially
formed when the C-terminal residues are deleted. Considering that
different polymorphs are known to result in distinct pathologies,
it is important to understand how these truncations affect the organization
of αS into fibrils. Here we present high-resolution microscopy
and advanced vibrational spectroscopy studies that indicate that the
C-terminal truncation variant of αS, lacking residues 109–140
(henceforth referred to as 1–108-αS), forms amyloid fibrils
with a distinct structure and morphology. The 1–108-αS
fibrils have a unique negative circular dichroism band at ∼230
nm, a feature that differs from the canonical ∼218 nm band
usually observed for amyloid fibrils. We show evidence that 1–108-αS
fibrils consist of strongly twisted β-sheets with an increased
inter-β-sheet distance and a higher solvent exposure than WT-αS
fibrils, which is also indicated by the pronounced differences in
the 1D-IR (FTIR), 2D-IR, and vibrational circular dichroism spectra.
As a result of their distinct β-sheet structure, 1–108-αS
fibrils resist incorporation of WT-αS monomers.
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Affiliation(s)
- Aditya Iyer
- Nanoscale Biophysics Group, AMOLF , Science Park 104, Amsterdam 1098 XG, The Netherlands.,Nanobiophysics Group, MESA+ Institute for Nanotechnology, University of Twente , Drienerlolaan 5, Enschede 7522 NB, The Netherlands
| | - Steven J Roeters
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, Amsterdam 1098 XH, The Netherlands
| | - Vladimir Kogan
- Dannalab BV , Wethouder Beversstraat 185, Enschede 7543 BK, The Netherlands
| | - Sander Woutersen
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, Amsterdam 1098 XH, The Netherlands
| | - Mireille M A E Claessens
- Nanobiophysics Group, MESA+ Institute for Nanotechnology, University of Twente , Drienerlolaan 5, Enschede 7522 NB, The Netherlands
| | - Vinod Subramaniam
- Nanoscale Biophysics Group, AMOLF , Science Park 104, Amsterdam 1098 XG, The Netherlands.,Nanobiophysics Group, MESA+ Institute for Nanotechnology, University of Twente , Drienerlolaan 5, Enschede 7522 NB, The Netherlands.,Vrije Universiteit Amsterdam , De Boelelaan 1105, Amsterdam 1081 HV, The Netherlands
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26
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The folding, stability and function of lactose permease differ in their dependence on bilayer lipid composition. Sci Rep 2017; 7:13056. [PMID: 29026149 PMCID: PMC5638818 DOI: 10.1038/s41598-017-13290-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 09/19/2017] [Indexed: 11/22/2022] Open
Abstract
Lipids play key roles in Biology. Mechanical properties of the lipid bilayer influence their neighbouring membrane proteins, however it is unknown whether different membrane protein properties have the same dependence on membrane mechanics, or whether mechanics are tuned to specific protein processes of the protein. We study the influence of lipid lateral pressure and electrostatic effects on the in vitro reconstitution, folding, stability and function of a representative of the ubiquitous major facilitator transporter superfamily, lactose permease. Increasing the outward chain lateral pressure in the bilayer, through addition of lamellar phosphatidylethanolamine lipids, lowers lactose permease folding and reconstitution yields but stabilises the folded state. The presence of phosphatidylethanolamine is however required for correct folding and function. An increase in headgroup negative charge through the addition of phosphatidylglycerol lipids favours protein reconstitution but is detrimental to topology and function. Overall the in vitro folding, reconstitution, topology, stability and function of lactose permease are found to have different dependences on bilayer composition. A regime of lipid composition is found where all properties are favoured, even if suboptimal. This lays ground rules for rational control of membrane proteins in nanotechnology and synthetic biology by manipulating global bilayer properties to tune membrane protein behaviour.
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27
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Wu Q, Wan J, He Z, Liu R. Spectroscopic investigations on the conformational changes of lysozyme effected by different sizes of N-acetyl-l-cysteine-capped CdTe quantum dots. J Biochem Mol Toxicol 2017; 31. [PMID: 28902442 DOI: 10.1002/jbt.21982] [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: 07/08/2017] [Revised: 08/16/2017] [Accepted: 08/19/2017] [Indexed: 11/11/2022]
Abstract
The effect of N-acetyl-l-cysteine-capped CdTe quantum dots (NAC-CdTe QDs) with different sizes on lysozyme was investigated by isothermal titration calorimetry (ITC), enzyme activity assays, and multi-spectroscopic methods. ITC results proved that NAC-CdTe QDs can spontaneously bind with lysozyme and hydrophobic force plays a major role in stabilizing QDs-lysozyme complex. Multi-spectroscopic measurements revealed that NAC-CdTe QDs caused strong quenching of the lysozyme's fluorescence in a size-dependent quenching manner. Moreover, the changes of secondary structure and microenvironment in lysozyme caused by the NAC-CdTe QDs were higher with a bigger size. The results of enzyme activity assays showed that the interaction between lysozyme and NAC-CdTe QDs inhibited the activity of lysozyme and the inhibiting effect was in a size-dependent manner. Based on these results, we conclude that NAC-CdTe QDs with larger particle size had a larger impact on the structure and function of lysozyme.
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Affiliation(s)
- Qianqian Wu
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, Jinan, 250100, People's Republic of China
| | - Jingqiang Wan
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, Jinan, 250100, People's Republic of China
| | - Zhuo He
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, Jinan, 250100, People's Republic of China
| | - Rutao Liu
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, Jinan, 250100, People's Republic of China
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28
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Melo MMA, Daniele-Silva A, Teixeira DG, Estrela AB, Melo KRT, Oliveira VS, Rocha HAO, Ferreira LDS, Pontes DL, Lima JPMS, Silva-Júnior AA, Barbosa EG, Carvalho E, Fernandes-Pedrosa MF. Structure and in vitro activities of a Copper II-chelating anionic peptide from the venom of the scorpion Tityus stigmurus. Peptides 2017; 94:91-98. [PMID: 28552408 DOI: 10.1016/j.peptides.2017.05.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 05/21/2017] [Accepted: 05/22/2017] [Indexed: 01/09/2023]
Abstract
Anionic Peptides are molecules rich in aspartic acid (Asp) and/or glutamic acid (Glu) residues in the primary structure. This work presents, for the first time, structural characterization and biological activity assays of an anionic peptide from the venom of the scorpion Tityus stigmurus, named TanP. The three-dimensional structure of TanP was obtained by computational modeling and refined by molecular dynamic (MD) simulations. Furthermore, we have performed circular dichroism (CD) analysis to predict TanP secondary structure, and UV-vis spectroscopy to evaluate its chelating activity. CD indicated predominance of random coil conformation in aqueous medium, as well as changes in structure depending on pH and temperature. TanP has chelating activity on copper ions, which modified the peptide's secondary structure. These results were corroborated by MD data. The molar ratio of binding (TanP:copper) depends on the concentration of peptide: at lower TanP concentration, the molar ratio was 1:5 (TanP:Cu2+), whereas in concentrated TanP solution, the molar ratio was 1:3 (TanP:Cu2+). TanP was not cytotoxic to non-neoplastic or cancer cell lines, and showed an ability to inhibit the in vitro release of nitric oxide by LPS-stimulated macrophages. Altogether, the results suggest TanP is a promising peptide for therapeutic application as a chelating agent.
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Affiliation(s)
- Menilla M A Melo
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN, Brazil; Programa de Pós-Graduação em Ciências Farmacêuticas, UFRN, Natal, RN, Brazil
| | - Alessandra Daniele-Silva
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN, Brazil
| | - Diego G Teixeira
- Laboratório de Sistemas Metabólicos, Centro de Biociências, UFRN, Natal, RN, Brazil
| | - Andréia B Estrela
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN, Brazil
| | - Karolline R T Melo
- Laboratório de Biotecnologia de Polímeros Naturais, UFRN, Natal, RN, Brazil
| | | | - Hugo A O Rocha
- Laboratório de Biotecnologia de Polímeros Naturais, UFRN, Natal, RN, Brazil
| | | | - Daniel L Pontes
- Laboratório de Química de Coordenação e Polímeros, UFRN, Natal, RN, Brazil
| | - João P M S Lima
- Laboratório de Sistemas Metabólicos, Centro de Biociências, UFRN, Natal, RN, Brazil
| | - Arnóbio A Silva-Júnior
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN, Brazil; Programa de Pós-Graduação em Ciências Farmacêuticas, UFRN, Natal, RN, Brazil
| | - Euzebio G Barbosa
- Programa de Pós-Graduação em Ciências Farmacêuticas, UFRN, Natal, RN, Brazil; Laboratório de Química Farmacêutica, UFRN, Natal, RN, Brazil
| | - Eneas Carvalho
- Centro de Biotecnologia, Instituto Butantan, São Paulo, SP, Brazil
| | - Matheus F Fernandes-Pedrosa
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN, Brazil; Programa de Pós-Graduação em Ciências Farmacêuticas, UFRN, Natal, RN, Brazil.
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29
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Hill RLL, Vlach J, Parker LK, Christie GE, Saad JS, Dokland T. Derepression of SaPIbov1 Is Independent of φNM1 Type 2 dUTPase Activity and Is Inhibited by dUTP and dUMP. J Mol Biol 2017; 429:1570-1580. [PMID: 28400210 DOI: 10.1016/j.jmb.2017.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 04/05/2017] [Accepted: 04/05/2017] [Indexed: 11/16/2022]
Abstract
Staphylococcus aureus is an opportunistic human pathogen able to transfer virulence genes to other cells through the mobilization of S. aureus pathogenicity islands (SaPIs). SaPIs are derepressed and packaged into phage-like transducing particles by helper phages like 80α or φNM1. Phages 80α and φNM1 encode structurally distinct dUTPases, Dut80α (type 1) and DutNM1 (type 2). Both dUTPases can interact with the SaPIbov1 Stl master repressor, leading to derepression and mobilization. That two structurally distinct dUTPases bind the same repressor led us to speculate that dUTPase activity may be important to the derepression process. In type 1 dUTPases, Stl binding is inhibited by dUTP. The purpose of this study was to assess the involvement of dUTP binding and dUTPase activity in derepression by DutNM1. DutNM1 activity mutants were created and tested for dUTPase activity using a novel NMR-based assay. We found that all DutNM1 null activity mutants interacted with the SaPIbov1 Stl C-terminal domain, formed DutNM1-Stl heterodimers, and caused the release of the Pstr promoter. However, promoter release was inhibited in the presence of dUTP or dUMP. We tested two φNM1 mutant phages that had null enzyme activity and found that they could still mobilize SaPIbov1. These results show that only the apo form of DutNM1 is active in Stl derepression and that dUTPase activity is not necessary for the mobilization of SaPIbov1 by DutNM1.
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Affiliation(s)
- Rosanne L L Hill
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jiri Vlach
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Laura K Parker
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Gail E Christie
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Jamil S Saad
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Terje Dokland
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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Baral A, Satish L, Das DP, Sahoo H, Ghosh MK. Construing the interactions between MnO2 nanoparticle and bovine serum albumin: insight into the structure and stability of a protein–nanoparticle complex. NEW J CHEM 2017. [DOI: 10.1039/c7nj01227f] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Systematic experimental investigation of MnO2–BSA complexes in terms of the structure and stability of the protein as well as the aggregation of the nanoparticle.
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Affiliation(s)
- Ayonbala Baral
- Academy of Scientific and Innovative Research (AcSIR)
- CSIR-IMMT campus
- Bhubaneswar - 751013
- India
- Hydro & Electrometallurgy Department
| | - Lakkoji Satish
- Department of Chemistry
- National Institute of Technology Rourkela
- Rourkela – 769008
- India
| | - Dipti P. Das
- Academy of Scientific and Innovative Research (AcSIR)
- CSIR-IMMT campus
- Bhubaneswar - 751013
- India
- Colloids & Material Chemistry Dept
| | - Harekrushna Sahoo
- Department of Chemistry
- National Institute of Technology Rourkela
- Rourkela – 769008
- India
| | - Malay K. Ghosh
- Academy of Scientific and Innovative Research (AcSIR)
- CSIR-IMMT campus
- Bhubaneswar - 751013
- India
- Hydro & Electrometallurgy Department
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31
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Panigrahi R, Arutyunova E, Panwar P, Gimpl K, Keller S, Lemieux MJ. Reversible Unfolding of Rhomboid Intramembrane Proteases. Biophys J 2016; 110:1379-90. [PMID: 27028647 DOI: 10.1016/j.bpj.2016.01.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 01/18/2016] [Accepted: 01/22/2016] [Indexed: 12/20/2022] Open
Abstract
Denaturant-induced unfolding of helical membrane proteins provides insights into their mechanism of folding and domain organization, which take place in the chemically heterogeneous, anisotropic environment of a lipid membrane. Rhomboid proteases are intramembrane proteases that play key roles in various diseases. Crystal structures have revealed a compact helical bundle with a buried active site, which requires conformational changes for the cleavage of transmembrane substrates. A dimeric form of the rhomboid protease has been shown to be important for activity. In this study, we examine the mechanism of refolding for two distinct rhomboids to gain insight into their secondary structure-activity relationships. Although helicity is largely abolished in the unfolded states of both proteins, unfolding is completely reversible for HiGlpG but only partially reversible for PsAarA. Refolding of both proteins results in reassociation of the dimer, with a 90% regain of catalytic activity for HiGlpG but only a 70% regain for PsAarA. For both proteins, a broad, gradual transition from the native, folded state to the denatured, partly unfolded state was revealed with the aid of circular dichroism spectroscopy as a function of denaturant concentration, thus arguing against a classical two-state model as found for many globular soluble proteins. Thermal denaturation has irreversible destabilizing effects on both proteins, yet reveals important functional details regarding substrate accessibility to the buried active site. This concerted biophysical and functional analysis demonstrates that HiGlpG, with a simple six-transmembrane-segment organization, is more robust than PsAarA, which has seven predicted transmembrane segments, thus rendering HiGlpG amenable to in vitro studies of membrane-protein folding.
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Affiliation(s)
- Rashmi Panigrahi
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Elena Arutyunova
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Pankaj Panwar
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Katharina Gimpl
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany
| | - M Joanne Lemieux
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada.
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Anjomshoa M, Torkzadeh-Mahani M, Janczak J, Rizzoli C, Sahihi M, Ataei F, Dehkhodaei M. Synthesis, crystal structure and Hirshfeld surface analysis of copper(II) complexes: DNA- and BSA-binding, molecular modeling, cell imaging and cytotoxicity. Polyhedron 2016. [DOI: 10.1016/j.poly.2016.08.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Pahlke DM, Diederichsen U. Synthesis and characterization of β-peptide helices as transmembrane domains in lipid model membranes. J Pept Sci 2016; 22:636-641. [PMID: 27578420 DOI: 10.1002/psc.2912] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 08/04/2016] [Accepted: 08/04/2016] [Indexed: 11/07/2022]
Abstract
Aggregation, orientation and dynamics of transmembrane helices are of relevance for protein function and transmembrane signaling. To explore the interactions of transmembrane helices and the interdependence of peptide structure and lipid composition of the membranes, β-peptides were explored as model transmembrane domains. Various hydrophobic β-peptide sequences were synthesized by solid phase peptide synthesis. Conformational analyses of β-peptide helices were performed in organic solvents (methanol and 2,2,2-trifluoroethanol) and in large unilamellar liposomes (dimyristoylphosphatidylcholine, dipalmitoylphosphatidylcholine and dioleoylphosphatidylcholine) indicating 12- and 14-helix conformations, depending on β3 -amino acid sequences. The intrinsic tryptophan fluorescence of β3 -homotryptophan units inserted in the center or near the end of the sequence was used to verify the membrane insertion of the β-peptides. A characteristic blue shift with peripheral β3 -homotryptophan compared with β-peptides with central tryptophan served as indication for a transmembrane orientation of the β-peptides within the lipid bilayer. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Denis M Pahlke
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstraße 2, 37077, Göttingen, Germany
| | - Ulf Diederichsen
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstraße 2, 37077, Göttingen, Germany.
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Machado RJA, Estrela AB, Nascimento AKL, Melo MMA, Torres-Rêgo M, Lima EO, Rocha HAO, Carvalho E, Silva-Junior AA, Fernandes-Pedrosa MF. Characterization of TistH, a multifunctional peptide from the scorpion Tityus stigmurus: Structure, cytotoxicity and antimicrobial activity. Toxicon 2016; 119:362-70. [PMID: 27267248 DOI: 10.1016/j.toxicon.2016.06.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 05/31/2016] [Accepted: 06/02/2016] [Indexed: 12/31/2022]
Abstract
The presence of bioactive peptides in animal venoms has been targeted in scientific research for assessing biological activities, as well as mechanisms of action. A recent study by our group observed hypotensive action of TistH (Tityus stigmurus Hypotensin), a peptide deduced from the transcriptome of T. stigmurus venom gland. The present study aims to analyze TistH structure properties and to evaluate its toxicity on normal and tumor cells, its in vitro antimicrobial activity, as well as its inflammatory effect. Circular dichroism analyses of TistH showed a general predominance of α-helix conformation in TFE (20-70%) and structural stability to pH variations. TistH was not cytotoxic to normal cell lines (3T3, RAW and HEK), and also not to cancer cell lines (HeLa, B16, 786-0, SiHa and HepG2). The peptide did not present inflammatory activity up to 6 h after administered subcutaneously to Swiss mice. It was observed that concentrations of 4-1024 μg/mL of TistH produced no inhibition against the bacteria Staphylococcus aureus, Staphylococcus epidermidis e Pseudomonas aeruginosa. The results of antifungal assays showed a moderate activity of TistH against Candida albicans strain LM-108 and the filamentous fungus Trichophyton rubrum LM-640, with growth inhibition at a concentration of 1024 μg/mL. In contrast, the peptide presented a greater activity (MIC 128 μg/mL) against C. albicans LM-106, Candida tropicalis ATCC 13308 and Aspergillus flavus strains LM-247 and LM-26, fungi that cause oral and vaginal infections, candidiasis and respiratory allergies, respectively. The present data contribute to a better understanding of TistH and its possible use as a bioactive compound. This multifunctional peptide is capable of acting as anti-hypertensive, as well as to inhibit the growth of fungal strains, having low toxicity, which suggests its safety for using as a pharmacological agent.
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Affiliation(s)
- Richele J A Machado
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil; Programa de Pós-Graduação em Bioquímica, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Andréia B Estrela
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Ana K L Nascimento
- Programa de Pós-Graduação em Bioquímica, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Menilla M A Melo
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Manoela Torres-Rêgo
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Edeltrurdes O Lima
- Laboratório de Micologia, Departamento de Ciências Farmacêuticas, Universidade Federal da Paraíba, João Pessoa, PB, Brazil
| | - Hugo A O Rocha
- Programa de Pós-Graduação em Bioquímica, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Eneas Carvalho
- Centro de Biotecnologia, Instituto Butantan, São Paulo, SP, Brazil
| | - Arnóbio A Silva-Junior
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Matheus F Fernandes-Pedrosa
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil; Programa de Pós-Graduação em Bioquímica, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil.
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35
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Rost U, Steinem C, Diederichsen U. β-Glutamine-mediated self-association of transmembrane β-peptides within lipid bilayers. Chem Sci 2016; 7:5900-5907. [PMID: 30034732 PMCID: PMC6022121 DOI: 10.1039/c6sc01147k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 05/18/2016] [Indexed: 11/21/2022] Open
Abstract
The rational design and synthesis of novel transmembrane β-peptides forming stable secondary structures in a membrane environment are described. Their state of aggregation within the membrane is controlled by hydrogen bonds.
Transmembrane β-peptide helices and their association in lipid membranes are still widely unexplored. We designed and synthesized transmembrane β-peptides harboring different numbers of d-β3-glutamine residues (hGln) by solid phase peptide synthesis. By means of circular dichroism spectroscopic measurements, the secondary structure of the β-peptides reconstituted into unilamellar vesicles was determined to be similar to a right-handed 314-helix. Fluorescence spectroscopy using d-β3-tryptophan residues strongly suggested a transmembrane orientation. Two or three hGln served as recognition units between the helices to allow helix–helix assembly driven by hydrogen bond formation. The association state of the transmembrane β-peptides as a function of the number of hGln residues was investigated by fluorescence resonance energy transfer (FRET). Therefore, two fluorescence probes (NBD, TAMRA) were covalently attached to the side chains of the transmembrane β-peptide helices. The results clearly demonstrate that only β-peptides with hGln as recognition units assemble into oligomers, presumably trimers. Temperature dependent FRET experiments further show that the strength of the helix–helix association is a function of the number of hGln residues in the helix.
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Affiliation(s)
- U Rost
- Institute of Organic and Biomolecular Chemistry , Georg-August-University Goettingen , Tammannstr. 2 , 37077 Goettingen , Germany . ;
| | - C Steinem
- Institute of Organic and Biomolecular Chemistry , Georg-August-University Goettingen , Tammannstr. 2 , 37077 Goettingen , Germany . ;
| | - U Diederichsen
- Institute of Organic and Biomolecular Chemistry , Georg-August-University Goettingen , Tammannstr. 2 , 37077 Goettingen , Germany . ;
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36
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Singh N, Conte MP, Ulijn RV, Miravet JF, Escuder B. Insight into the esterase like activity demonstrated by an imidazole appended self-assembling hydrogelator. Chem Commun (Camb) 2016; 51:13213-6. [PMID: 26194473 DOI: 10.1039/c5cc04281j] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A low molecular weight hydrogelator with a covalently appended imidazole moiety is reported. Capable of percolating water in the pH range of 6 to 8, it proves to be an efficient catalyst upon self-assembly, showing Michaelis-Menten type kinetics. Activities at different pH values correlated with dramatic structural changes were observed. It can hydrolyse p-nitrophenyl acetate (pNPA) as well as inactivated esters, and L and D-phenylalanine methyl esters. The enhanced activity can be related to the conglomeration of catalytic groups upon aggregation resulting in their close proximity and the formation of hydrophobic pockets.
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Affiliation(s)
- Nishant Singh
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12071 Castelló, Spain.
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Matsuo K, Maki Y, Namatame H, Taniguchi M, Gekko K. Conformation of membrane-bound proteins revealed by vacuum-ultraviolet circular-dichroism and linear-dichroism spectroscopy. Proteins 2016; 84:349-59. [PMID: 26756612 DOI: 10.1002/prot.24981] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 12/09/2015] [Accepted: 12/19/2015] [Indexed: 12/16/2022]
Abstract
Knowledge of the conformations of a water-soluble protein bound to a membrane is important for understanding the membrane-interaction mechanisms and the membrane-mediated functions of the protein. In this study we applied vacuum-ultraviolet circular-dichroism (VUVCD) and linear-dichroism (LD) spectroscopy to analyze the conformations of α-lactalbumin (LA), thioredoxin (Trx), and β-lactoglobulin (LG) bound to phosphatidylglycerol liposomes. The VUVCD analysis coupled with a neural-network analysis showed that these three proteins have characteristic helix-rich conformations involving several helical segments, of which two amphiphilic or hydrophobic segments take part in interactions with the liposome. The LD analysis predicted the average orientations of these helix segments on the liposome: two amphiphilic helices parallel to the liposome surface for LA, two hydrophobic helices perpendicular to the liposome surface for Trx, and a hydrophobic helix perpendicular to and an amphiphilic helix parallel to the liposome surface for LG. This sequence-level information about the secondary structures and orientations was used to formulate interaction models of the three proteins at the membrane surface. This study demonstrates the validity of a combination of VUVCD and LD spectroscopy in conformational analyses of membrane-binding proteins, which are difficult targets for X-ray crystallography and nuclear magnetic resonance spectroscopy.
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Affiliation(s)
- Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima, 739-0046, Japan
| | - Yasuyuki Maki
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, Kiryu, 376-8515, Japan
| | - Hirofumi Namatame
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima, 739-0046, Japan
| | - Masaki Taniguchi
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima, 739-0046, Japan.,Department of Physical Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - Kunihiko Gekko
- Institute for Sustainable Sciences and Development, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
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Abstract
Circular dichroism spectra of helical bundle (red), beta barrel (blue), and mixed helical/sheet/unordered (green) membrane proteins.
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Affiliation(s)
- A. J. Miles
- Institute of Structural and Molecular Biology
- Birkbeck College
- University of London
- London
- UK
| | - B. A. Wallace
- Institute of Structural and Molecular Biology
- Birkbeck College
- University of London
- London
- UK
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Kroeger JK, Hassan K, Vörös A, Simm R, Saidijam M, Bettaney KE, Bechthold A, Paulsen IT, Henderson PJF, Kolstø AB. Bacillus cereus efflux protein BC3310 - a multidrug transporter of the unknown major facilitator family, UMF-2. Front Microbiol 2015; 6:1063. [PMID: 26528249 PMCID: PMC4601019 DOI: 10.3389/fmicb.2015.01063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 09/15/2015] [Indexed: 02/06/2023] Open
Abstract
Phylogenetic classification divides the major facilitator superfamily (MFS) into 82 families, including 25 families that are comprised of transporters with no characterized functions. This study describes functional data for BC3310 from Bacillus cereus ATCC 14579, a member of the “unknown major facilitator family-2” (UMF-2). BC3310 was shown to be a multidrug efflux pump conferring resistance to ethidium bromide, SDS and silver nitrate when heterologously expressed in Escherichia coli DH5α ΔacrAB. A conserved aspartate residue (D105) in putative transmembrane helix 4 was identified, which was essential for the energy dependent ethidium bromide efflux by BC3310. Transport proteins of the MFS comprise specific sequence motifs. Sequence analysis of UMF-2 proteins revealed that they carry a variant of the MFS motif A, which may be used as a marker to distinguish easily between this family and other MFS proteins. Genes orthologous to bc3310 are highly conserved within the B. cereus group of organisms and thus belong to the core genome, suggesting an important conserved functional role in the normal physiology of these bacteria.
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Affiliation(s)
- Jasmin K Kroeger
- Laboratory for Microbial Dynamics, Department of Pharmaceutical Biosciences, School of Pharmacy, University of Oslo Oslo, Norway ; Institut für Pharmazeutische Biologie und Biotechnologie, Albert-Ludwigs Universität Freiburg, Germany
| | - Karl Hassan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW, Australia
| | - Aniko Vörös
- Laboratory for Microbial Dynamics, Department of Pharmaceutical Biosciences, School of Pharmacy, University of Oslo Oslo, Norway
| | - Roger Simm
- Laboratory for Microbial Dynamics, Department of Pharmaceutical Biosciences, School of Pharmacy, University of Oslo Oslo, Norway
| | - Massoud Saidijam
- School of BioMedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds Leeds, UK
| | - Kim E Bettaney
- School of BioMedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds Leeds, UK
| | - Andreas Bechthold
- Institut für Pharmazeutische Biologie und Biotechnologie, Albert-Ludwigs Universität Freiburg, Germany
| | - Ian T Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW, Australia
| | - Peter J F Henderson
- School of BioMedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds Leeds, UK
| | - Anne-Brit Kolstø
- Laboratory for Microbial Dynamics, Department of Pharmaceutical Biosciences, School of Pharmacy, University of Oslo Oslo, Norway
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Uporov IV, Forlemu NY, Nori R, Aleksandrov T, Sango BA, Mbote YEB, Pothuganti S, Thomasson KA. Introducing DInaMo: A Package for Calculating Protein Circular Dichroism Using Classical Electromagnetic Theory. Int J Mol Sci 2015; 16:21237-76. [PMID: 26370961 PMCID: PMC4613251 DOI: 10.3390/ijms160921237] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Revised: 06/09/2015] [Accepted: 06/30/2015] [Indexed: 01/23/2023] Open
Abstract
The dipole interaction model is a classical electromagnetic theory for calculating circular dichroism (CD) resulting from the π-π* transitions of amides. The theoretical model, pioneered by J. Applequist, is assembled into a package, DInaMo, written in Fortran allowing for treatment of proteins. DInaMo reads Protein Data Bank formatted files of structures generated by molecular mechanics or reconstructed secondary structures. Crystal structures cannot be used directly with DInaMo; they either need to be rebuilt with idealized bond angles and lengths, or they need to be energy minimized to adjust bond lengths and bond angles because it is common for crystal structure geometries to have slightly short bond lengths, and DInaMo is sensitive to this. DInaMo reduces all the amide chromophores to points with anisotropic polarizability and all nonchromophoric aliphatic atoms including hydrogens to points with isotropic polarizability; all other atoms are ignored. By determining the interactions among the chromophoric and nonchromophoric parts of the molecule using empirically derived polarizabilities, the rotational and dipole strengths are determined leading to the calculation of CD. Furthermore, ignoring hydrogens bound to methyl groups is initially explored and proves to be a good approximation. Theoretical calculations on 24 proteins agree with experiment showing bands with similar morphology and maxima.
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Affiliation(s)
- Igor V Uporov
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
- Faculty of Chemistry, M. V. Lomonosov Moscow State University, GSP-1, 1-3 Leninskiye Gory, 119991 Moscow, Russia.
| | - Neville Y Forlemu
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
- Georgia Gwinnett College, 1000 University Center Lane, Lawrenceville, GA 30043, USA.
| | - Rahul Nori
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
| | - Tsvetan Aleksandrov
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
| | - Boris A Sango
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
| | - Yvonne E Bongfen Mbote
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
- James E. Hurley College of Science & Mathematics, Oklahoma Baptist University, OBU Box 61772, 500 W. University, Shawnee, OK 74804, USA.
| | - Sandeep Pothuganti
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
| | - Kathryn A Thomasson
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
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López-Peña I, Leigh BS, Schlamadinger DE, Kim JE. Insights into Protein Structure and Dynamics by Ultraviolet and Visible Resonance Raman Spectroscopy. Biochemistry 2015. [PMID: 26219819 DOI: 10.1021/acs.biochem.5b00514] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Raman spectroscopy is a form of vibrational spectroscopy based on inelastic scattering of light. In resonance Raman spectroscopy, the wavelength of the incident light falls within an absorption band of a chromophore, and this overlap of excitation and absorption energy greatly enhances the Raman scattering efficiency of the absorbing species. The ability to probe vibrational spectra of select chromophores within a complex mixture of molecules makes resonance Raman spectroscopy an excellent tool for studies of biomolecules. In this Current Topic, we discuss the type of molecular insights obtained from steady-state and time-resolved resonance Raman studies of a prototypical photoactive protein, rhodopsin. We also review recent efforts in ultraviolet resonance Raman investigations of soluble and membrane-associated biomolecules, including integral membrane proteins and antimicrobial peptides. These examples illustrate that resonance Raman is a sensitive, selective, and practical method for studying the structures of biological molecules, and the molecular bonding, geometry, and environments of protein cofactors, the backbone, and side chains.
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Affiliation(s)
- Ignacio López-Peña
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Brian S Leigh
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Diana E Schlamadinger
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Judy E Kim
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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Wu Q, Zhang H, Sun T, Zhang B, Liu R. Probing the toxic mechanism of Ag⁺ with lysozyme. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 151:124-130. [PMID: 26125992 DOI: 10.1016/j.saa.2015.06.080] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 06/19/2015] [Accepted: 06/22/2015] [Indexed: 06/04/2023]
Abstract
Silver (Ag) is widely used in human activities, which provides possibilities to distribute in organisms and tissues, resulting in harmful effects on human health. In this work, lysozyme was chosen as the target molecule to study the mechanism of toxic interactions between Ag(+) and protein using fluorescence emission spectra, synchronous fluorescence spectra, UV-vis absorption spectra, circular dichroism (CD) spectra, isothermal titration calorimetry (ITC), and enzyme activity assay. The results of fluorescence emission and synchronous fluorescence showed that there were interactions between Ag(+) and lysozyme by eliminating the inner filter effect (IFE). Data from UV-vis spectra indicated that the frame structure of lysozyme became looser with Ag(+) existent, while the micro-environment of aromatic amino acid residues did not show any significant alteration. CD results suggested that the secondary structure of lysozyme presented a decrease in α-helix contents with the increasing amount of Ag(+). ITC results showed Ag(+) can spontaneously bind with lysozyme through hydrogen bonding and van der Waals forces with one binding site (Ka=1.93×10(6)). The lysozyme activity was inhibited by Ag(+) according to the enzyme activity assay, revealing that Ag(+) bound to lysozyme at the active site which resulted in inhibition of lysozyme activity. This work showed that Ag(+) can cause damages to the structure and function of lysozyme.
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Affiliation(s)
- Qianqian Wu
- School of Environmental Science and Engineering, China-America CRC for Environment & Health, Shandong Province, Shandong University, 27# Shanda South Road, Jinan 250100, PR China
| | - Hao Zhang
- School of Environmental Science and Engineering, China-America CRC for Environment & Health, Shandong Province, Shandong University, 27# Shanda South Road, Jinan 250100, PR China
| | - Tao Sun
- School of Environmental Science and Engineering, China-America CRC for Environment & Health, Shandong Province, Shandong University, 27# Shanda South Road, Jinan 250100, PR China
| | - Bin Zhang
- School of Environmental Science and Engineering, China-America CRC for Environment & Health, Shandong Province, Shandong University, 27# Shanda South Road, Jinan 250100, PR China
| | - Rutao Liu
- School of Environmental Science and Engineering, China-America CRC for Environment & Health, Shandong Province, Shandong University, 27# Shanda South Road, Jinan 250100, PR China.
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43
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de Melo ET, Estrela AB, Santos ECG, Machado PRL, Farias KJS, Torres TM, Carvalho E, Lima JPMS, Silva-Júnior AA, Barbosa EG, Fernandes-Pedrosa MDF. Structural characterization of a novel peptide with antimicrobial activity from the venom gland of the scorpion Tityus stigmurus: Stigmurin. Peptides 2015; 68:3-10. [PMID: 25805002 DOI: 10.1016/j.peptides.2015.03.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 03/02/2015] [Accepted: 03/05/2015] [Indexed: 01/05/2023]
Abstract
A new antimicrobial peptide, herein named Stigmurin, was selected based on a transcriptomic analysis of the Brazilian yellow scorpion Tityus stigmurus venom gland, an underexplored source for toxic peptides with possible biotechnological applications. Stigmurin was investigated in silico, by circular dichroism (CD) spectroscopy, and in vitro. The CD spectra suggested that this peptide interacts with membranes, changing its conformation in the presence of an amphipathic environment, with predominance of random coil and beta-sheet structures. Stigmurin exhibited antibacterial and antifungal activity, with minimal inhibitory concentrations ranging from 8.7 to 69.5μM. It was also showed that Stigmurin is toxic against SiHa and Vero E6 cell lines. The results suggest that Stigmurin can be considered a potential anti-infective drug.
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Affiliation(s)
- Edinara Targino de Melo
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Andréia Bergamo Estrela
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | | | | | | | - Taffarel Melo Torres
- Departamento de Ciências Animais, Universidade Federal Rural do Semi-Árido, Mossoró, RN, Brazil
| | - Enéas Carvalho
- Centro de Biotecnologia, Instituto Butantan, São Paulo, SP, Brazil
| | | | - Arnóbio Antonio Silva-Júnior
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | | | - Matheus de Freitas Fernandes-Pedrosa
- Laboratório de Tecnologia e Biotecnologia Farmacêutica, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil; Programa de Pós-Graduação em Bioquímica, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil.
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44
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Experimental characterization of adsorbed protein orientation, conformation, and bioactivity. Biointerphases 2015; 10:019002. [PMID: 25708632 DOI: 10.1116/1.4906485] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Protein adsorption on material surfaces is a common phenomenon that is of critical importance in many biotechnological applications. The structure and function of adsorbed proteins are tightly interrelated and play a key role in the communication and interaction of the adsorbed proteins with the surrounding environment. Because the bioactive state of a protein on a surface is a function of the orientation, conformation, and accessibility of its bioactive site(s), the isolated determination of just one or two of these factors will typically not be sufficient to understand the structure-function relationships of the adsorbed layer. Rather a combination of methods is needed to address each of these factors in a synergistic manner to provide a complementary dataset to characterize and understand the bioactive state of adsorbed protein. Over the past several years, the authors have focused on the development of such a set of complementary methods to address this need. These methods include adsorbed-state circular dichroism spectropolarimetry to determine adsorption-induced changes in protein secondary structure, amino-acid labeling/mass spectrometry to assess adsorbed protein orientation and tertiary structure by monitoring adsorption-induced changes in residue solvent accessibility, and bioactivity assays to assess adsorption-induced changes in protein bioactivity. In this paper, the authors describe the methods that they have developed and/or adapted for each of these assays. The authors then provide an example of their application to characterize how adsorption-induced changes in protein structure influence the enzymatic activity of hen egg-white lysozyme on fused silica glass, high density polyethylene, and poly(methyl-methacrylate) as a set of model systems.
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45
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May B, Elliott C, Iwata M, Young L, Shearman J, Albury MS, Moore AL. Expression and crystallization of the plant alternative oxidase. Methods Mol Biol 2015; 1305:281-299. [PMID: 25910742 DOI: 10.1007/978-1-4939-2639-8_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The alternative oxidase (AOX) is an integral monotopic membrane protein located on the inner surface of the inner mitochondrial membrane. Branching from the traditional respiratory chain at the quinone pool, AOX is responsible for cyanide-resistant respiration in plants and fungi, heat generation in thermogenic plants, and survival of parasites, such as Trypanosoma brucei, in the human host. A recently solved AOX structure provides insight into its active site, thereby facilitating rational phytopathogenic and antiparasitic drug design. Here, we describe expression of recombinant AOX using two different expression systems. Purification protocols for the production of highly pure and stable AOX protein in sufficient quantities to facilitate further kinetic, biophysical, and structural analyses are also described.
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Affiliation(s)
- Benjamin May
- Department of Biochemistry and Molecular Biology, School of Life Sciences, University of Sussex, John Maynard Smith Building, Falmer, Brighton, BN1 9QG, UK
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46
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Liu XY, Zeng HY, Liao MC, Claude Alain Gohi BF, Feng B. Determination of the kinetics and influence of the mercury ion on papain catalytic activity. RSC Adv 2015. [DOI: 10.1039/c5ra12068c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The effect of the mercury ion on papain activity of the substrate casein and its mechanism were investigated.
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Affiliation(s)
- Xue-Ying Liu
- Biotechnology Institute
- College of Chemical Engineering
- Xiangtan University
- Xiangtan 411105
- China
| | - Hong-Yan Zeng
- Biotechnology Institute
- College of Chemical Engineering
- Xiangtan University
- Xiangtan 411105
- China
| | - Meng-Chen Liao
- Biotechnology Institute
- College of Chemical Engineering
- Xiangtan University
- Xiangtan 411105
- China
| | | | - Bo Feng
- Biotechnology Institute
- College of Chemical Engineering
- Xiangtan University
- Xiangtan 411105
- China
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47
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Reddy PM, Umapathi R, Venkatesu P. A green approach to offset the perturbation action of 1-butyl-3-methylimidazolium iodide on α-chymotrypsin. Phys Chem Chem Phys 2015; 17:184-90. [DOI: 10.1039/c4cp04180a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The presence of [Bmim][Br] counteracts the strong denaturation action of [Bmim][I].
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Affiliation(s)
| | - R. Umapathi
- Department of Chemistry
- University of Delhi
- Delhi-110 007
- India
| | - P. Venkatesu
- Department of Chemistry
- University of Delhi
- Delhi-110 007
- India
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Sauer DF, Bocola M, Broglia C, Arlt M, Zhu LL, Brocker M, Schwaneberg U, Okuda J. Hybrid Ruthenium ROMP Catalysts Based on an Engineered Variant of β-Barrel Protein FhuA ΔCVFtev: Effect of Spacer Length. Chem Asian J 2014; 10:177-82. [DOI: 10.1002/asia.201403005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 11/10/2014] [Indexed: 01/12/2023]
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49
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Biological Evaluation of a New Synthesized Pt(II) Complex by Cytotoxic and Spectroscopic Studies. Cell Biochem Biophys 2014; 71:1415-24. [DOI: 10.1007/s12013-014-0364-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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50
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Foo ACY, Harvey BGR, Metz JJ, Goto NK. Influence of hydrophobic mismatch on the catalytic activity of Escherichia coli GlpG rhomboid protease. Protein Sci 2014; 24:464-73. [PMID: 25307614 DOI: 10.1002/pro.2585] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 10/09/2014] [Indexed: 12/21/2022]
Abstract
Rhomboids comprise a broad family of intramembrane serine proteases that are found in a wide range of organisms and participate in a diverse array of biological processes. High-resolution structures of the catalytic transmembrane domain of the Escherichia coli GlpG rhomboid have provided numerous insights that help explain how hydrolytic cleavage can be achieved below the membrane surface. Key to this are observations that GlpG hydrophobic domain dimensions may not be sufficient to completely span the native lipid bilayer. This formed the basis for a model where hydrophobic mismatch Induces thinning of the local membrane environment to promote access to transmembrane substrates. However, hydrophobic mismatch also has the potential to alter the functional properties of the rhomboid, a possibility we explore in the current work. For this purpose, we purified the catalytic transmembrane domain of GlpG into phosphocholine or maltoside detergent micelles of varying alkyl chain lengths, and assessed proteolytic function with a model water-soluble substrate. Catalytic turnover numbers were found to depend on detergent alkyl chain length, with saturated chains containing 10-12 carbon atoms supporting maximal activity. Similar results were obtained in phospholipid bicelles, with no proteolytic activity being detected in longer-chain lipids. Although differences in thermal stability and GlpG oligomerization could not explain these activity differences, circular dichroism spectra suggest that mismatch gives rise to a small change in structure. Overall, these results demonstrate that hydrophobic mismatch can exert an inhibitory effect on rhomboid activity, with the potential for changes in local membrane environment to regulate activity in vivo.
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Affiliation(s)
- Alexander C Y Foo
- Department of Chemistry, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
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