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Elmer-Dixon MM, Fawcett LP, Sorensen EN, Maurer-Jones MA. Bovine Serum Albumin Bends Over Backward to Interact with Aged Plastics: A Model for Understanding Protein Attachment to Plastic Debris. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:10207-10215. [PMID: 38809092 PMCID: PMC11171446 DOI: 10.1021/acs.est.3c10028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/30/2024]
Abstract
Plastic pollution, a major environmental crisis, has a variety of consequences for various organisms within aquatic systems. Beyond the direct toxicity, plastic pollution has the potential to absorb biological toxins and invasive microbial species. To better understand the capability of environmental plastic debris to adsorb these species, we investigated the binding of the model protein bovine serum albumin (BSA) to polyethylene (PE) films at various stages of photodegradation. Circular dichroism and fluorescence studies revealed that BSA undergoes structural rearrangement to accommodate changes to the polymer's surface characteristics (i.e., crystallinity and oxidation state) that occur as the result of photodegradation. To understand how protein structure may inform docking of whole organisms, we studied biofilm formation of bacteriaShewanella oneidensison the photodegraded PE. Interestingly, biofilms preferentially formed on the photodegraded PE that correlated with the state of weathering that induced the most significant structural rearrangement of BSA. Taken together, our work suggests that there are optimal physical and chemical properties of photodegraded polymers that predict which plastic debris will carry biochemical or microbial hitchhikers.
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Affiliation(s)
- Margaret M. Elmer-Dixon
- Department
of Physics & Astronomy, University of
Minnesota, Duluth, Duluth, Minnesota 55812, United States
- Department
of Mechanical and Industrial Engineering, University of Minnesota, Duluth, Duluth, Minnesota 55812, United States
| | - Liam P. Fawcett
- Department
of Chemistry and Biochemistry, University
of Minnesota, Duluth, Duluth, Minnesota 55812, United States
| | - Emma N. Sorensen
- Department
of Chemistry and Biochemistry, University
of Minnesota, Duluth, Duluth, Minnesota 55812, United States
| | - Melissa A. Maurer-Jones
- Department
of Chemistry and Biochemistry, University
of Minnesota, Duluth, Duluth, Minnesota 55812, United States
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2
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Yonamine DK, Narciso Dos Reis VE, Feu AE, de Souza Borges W, Cardoso CL, Dinamarco TM. Ligand fishing approach to explore Amaryllidaceae alkaloids as potential antiviral candidates targeting SARS-CoV-2 Nsp4. J Pharm Biomed Anal 2024; 240:115935. [PMID: 38181554 DOI: 10.1016/j.jpba.2023.115935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/11/2023] [Accepted: 12/21/2023] [Indexed: 01/07/2024]
Abstract
Ligand fishing, also described as affinity-based assay, represents a convenient and efficient approach to separate potential ligands from complex matrixes or chemical libraries. This approach contributes to the identification of lead compounds that can bind to a specific target. In the context of COVID-19, the search for novel therapeutic agents is crucial. Small molecule-based antiviral drugs, such as Amaryllidaceae alkaloids, have been described as potential candidates because they can inhibit RNA viruses. Among various SARS-CoV-2 proteins, Nsp3, Nsp4, and Nsp6 play a crucial role in the pathogenicity of the virus and are attractive targets for developing COVID-19 treatments. These proteins are responsible for the replication/transcription complex (RTC) within double-membrane vesicles (DMVs), and their inhibition disrupts the virus's infectious cycle. Herein, we have successfully expressed and immobilized the SARS-CoV-2 Nsp4 protein on magnetic beads (Nsp4-MBs) and employed a ligand fishing assay to screen a collection of ten Amaryllidaceae-based alkaloids and applied to Hippeastrum aulicum extract. Remarkably, four out of ten alkaloids, namely 2-α-7-dimethoxyhomolycorine (6), haemanthamine (5), albomaculine (8), and tazettine (9), exhibited selective affinities for Nsp4. Albomaculine (8) and haemanthamine (5) were also identified from extract by the affinity assay. These findings highlight the potential of these alkaloids as model compounds for future drug discovery studies aimed at developing therapeutic interventions against SARS-CoV-2 infections.
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Affiliation(s)
- Deborah Kimie Yonamine
- Department of Chemistry, Laboratory of Protein Biotechnology (LaBioPro), Faculty of Philosophy, Science and Letters at Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP 14040-901, Brazil
| | - Vitor Eduardo Narciso Dos Reis
- Department of Chemistry, Group of Bioaffinity Chromatography and Natural Products (GCBPN), Faculty of Philosophy, Science and Letters at Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP 14040-901, Brazil
| | - Amanda Eiriz Feu
- Graduate Program in Chemistry, Federal University of Espírito Santo, Vitória, ES 29075-910, Brazil
| | - Warley de Souza Borges
- Graduate Program in Chemistry, Federal University of Espírito Santo, Vitória, ES 29075-910, Brazil
| | - Carmen Lúcia Cardoso
- Department of Chemistry, Group of Bioaffinity Chromatography and Natural Products (GCBPN), Faculty of Philosophy, Science and Letters at Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP 14040-901, Brazil
| | - Taisa Magnani Dinamarco
- Department of Chemistry, Laboratory of Protein Biotechnology (LaBioPro), Faculty of Philosophy, Science and Letters at Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP 14040-901, Brazil.
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3
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Conlon JM, Guilhaudis L, Attoub S, Coquet L, Leprince J, Jouenne T, Mechkarska M. Purification, conformational analysis and cytotoxic activities of host-defense peptides from the Tungara frog Engystomops pustulosus (Leptodactylidae; Leiuperinae). Amino Acids 2023; 55:1349-1359. [PMID: 37548712 PMCID: PMC10689532 DOI: 10.1007/s00726-023-03312-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 08/01/2023] [Indexed: 08/08/2023]
Abstract
The amphibian family Leptodactylidae is divided into three sub-families: Leiuperinae, Leptodactylinae, and Paratelmatobiinae. Host-defense peptides (HDPs) present in the skins of frogs belonging to the Leptodactylinae have been studied extensively, but information is limited regarding peptides from Leiuperinae species. Peptidomic analysis of norepinephrine-stimulated skin secretions from the Tungara frog Engystomops pustulosus (Leiuperinae) collected in Trinidad led to the isolation and structural characterization of previously undescribed pustulosin-1 (FWKADVKEIG KKLAAKLAEELAKKLGEQ), [Q28E] pustulosin-1 (pustulosin-2), and pustulosin-3 (DWKETAKELLKKIGAKVAQVISDKLNPAPQ). The primary structures of these peptides do not resemble those of previously described frog skin HDPs. In addition, the secretions contained tigerinin-1EP (GCKTYLIEPPVCT) with structural similarity to the tigerinins previously identified in skin secretions from frogs from the family Dicroglossidae. Pustulosin-1 and -3 adopted extended α-helical conformations in 25% trifluoroethanol-water and in the presence of cell membrane models (sodium dodecylsulfate and dodecylphosphocholine micelles). Pustulosin-1 and -3 displayed cytotoxic activity against a range of human tumor-derived cell lines (A549, MDA-MB-231, and HT29), but their therapeutic potential for development into anti-cancer agents is limited by their comparable cytotoxic activity against non-neoplastic human umbilical vein endothelial cells. The peptides also displayed weak antimicrobial activity against Escherichia coli (MIC = 125 µM) but were inactive against Staphylococcus aureus. Tigerinin-1EP was inactive against both the tumor-derived cells and bacteria.
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Affiliation(s)
- J Michael Conlon
- Diabetes Research Centre, School of Biomedical Sciences, Ulster University, Coleraine, BT52 1SA, Northern Ireland, UK.
| | - Laure Guilhaudis
- Laboratoire COBRA (UMR 6014 & FR 3038), INSA de Rouen, CNRS, Université Rouen Normandie, 76000, Rouen, France
| | - Samir Attoub
- Department of Pharmacology and Therapeutics, College of Medicine and Health Sciences, United Arab Emirates University, 17666, Al Ain, United Arab Emirates
| | - Laurent Coquet
- CNRS UAR2026, HeRacLeS-PISSARO PBS UMR 6270, Université Rouen Normandie, 76000, Rouen, France
| | - Jérôme Leprince
- CNRS UAR2026, HeRacLeS-PISSARO PBS UMR 6270, Université Rouen Normandie, 76000, Rouen, France
- INSERM, Normandie Université, NorDiC UMR 1239, HeRacLeS, US 51, PRIMACEN, Université Rouen Normandie, 76000, Rouen, France
| | - Thierry Jouenne
- CNRS UAR2026, HeRacLeS-PISSARO PBS UMR 6270, Université Rouen Normandie, 76000, Rouen, France
| | - Milena Mechkarska
- Department of Life Sciences, Faculty of Science and Technology, The University of The West Indies, St. Augustine Campus, St. Augustine, Trinidad and Tobago
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4
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Farhana R, Lei R, Pham K, Derrien V, Cedeño J, Rodriquez V, Bernad S, Lima FF, Miksovska J. Globin X: A highly stable intrinsically hexacoordinate globin. J Inorg Biochem 2022; 236:111976. [PMID: 36058051 DOI: 10.1016/j.jinorgbio.2022.111976] [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: 06/29/2022] [Revised: 08/10/2022] [Accepted: 08/18/2022] [Indexed: 12/15/2022]
Abstract
Several novel members of the vertebrate globin family were recently discovered with unique structural features that are not found in traditional penta-coordinate globins. Here we combine structural tools to better understand and recognize molecular determinants that contribute to the stability of hexacoordinate globin X (GbX) from Danio rerio (zebrafish). pH-induced unfolding data indicates increased stability of GbX with pHmid of 1.9 ± 0.1 for met GbXWT, 2.4 ± 0.1 for met GbXC65A, and 3.4 ± 0.1 for GbXH90V. These results are in good agreement with GbX unfolding experiments using GuHCl, where a ΔGunf 13.8 ± 2.5 kcal mol-1 and 16.3 ± 2.6 kcal mol-1 are observed for metGbXWT, and metGbXC65A constructs, respectively, and diminished stability is measured for GbXH90V, ΔGunf = 9.5 ± 3.6 kcal mol-1. The metGbXWT and metGbXC65A also exhibit high thermal stability (melting points of 118 °C and 107 °C, respectively). Native ion mobility - mass spectrometry (IM-MS) experiments showed a narrow charge state distribution (9-12+) characteristics of a native, structured protein; a single mobility band was observed for the native states. Collision induced unfolding IM-MS experiments showed a two-state transition, in good agreement with the solution studies. GbXWT retains the heme over a wide range of charge states, suggesting strong interactions between the prosthetic group and the apoprotein. The above results indicate that in addition to the disulfide bond and the heme iron hexa-coordination, other structural determinants enhance stability of this protein.
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Affiliation(s)
- Rifat Farhana
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States of America
| | - Ruipeng Lei
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States of America
| | - Khoa Pham
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States of America
| | - Valerie Derrien
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
| | - Jonathan Cedeño
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States of America
| | - Veronica Rodriquez
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States of America
| | - Sophie Bernad
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
| | - Francisco Fernandez Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States of America; Biomedical Science Institute, Florida International University, Miami, FL, United States of America
| | - Jaroslava Miksovska
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States of America; Biomedical Science Institute, Florida International University, Miami, FL, United States of America.
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5
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Monitoring the effect of SDS on the solvation dynamics and structural conformation of β-casein. J CHEM SCI 2022. [DOI: 10.1007/s12039-022-02092-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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6
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García-Gutiérrez P, Camarillo-Cadena M, Vera-Robles LI, Zubillaga RA, Hernández-Arana A. Circular dichroism spectroscopic assessment of structural changes upon protein thermal unfolding at contrasting pH: Comparison with molecular dynamics simulations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 274:121039. [PMID: 35245803 DOI: 10.1016/j.saa.2022.121039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 02/07/2022] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
In most instances, the usual fastness of protein unfolding events hinders determining changes in secondary structures associated with this process because these determinations rely on the recording of high-resolution circular dichroism (CD) spectra. In this work, far-UV CD spectra, recorded at ten-minute intervals, were used to evaluate the time course followed by four classes of secondary structures in the slow temperature-induced unfolding of yeast triosephosphate isomerase (yTIM) under distinct pH conditions. CONTIN-LL and SELCON3 algorithms were used for the deconvolution of spectra. Both algorithms furnished helix and unordered structure contents that changed according to first-order kinetics, agreeing with the behavior shown by CD data at specific wavelengths. Analyses of unfolded yTIM spectra, using a dataset that includes spectra of unfolded proteins and either one of the two algorithms, clearly showed a more unordered protein structure at high pH; this finding was corroborated with analysis of the difference spectra. Molecular dynamics (MD) simulations performed with AMBER and OPLS force fields resulted in more extensive loss of helices and gain in coils at high pH, in agreement with spectroscopic results. However, structural differences between low- and high-pH unfolded yTIM were relatively small. Comparison of results from CD and MD thus point to the need of fine-tuning of MD procedures.
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Affiliation(s)
- Ponciano García-Gutiérrez
- Departamento de Química. Universidad Autónoma Metropolitana-Iztapalapa. San Rafael Atlixco 186, Iztapalapa CDMX 09340, México
| | - Menandro Camarillo-Cadena
- Departamento de Química. Universidad Autónoma Metropolitana-Iztapalapa. San Rafael Atlixco 186, Iztapalapa CDMX 09340, México
| | - Liliana I Vera-Robles
- Departamento de Química. Universidad Autónoma Metropolitana-Iztapalapa. San Rafael Atlixco 186, Iztapalapa CDMX 09340, México
| | - Rafael A Zubillaga
- Departamento de Química. Universidad Autónoma Metropolitana-Iztapalapa. San Rafael Atlixco 186, Iztapalapa CDMX 09340, México.
| | - Andrés Hernández-Arana
- Departamento de Química. Universidad Autónoma Metropolitana-Iztapalapa. San Rafael Atlixco 186, Iztapalapa CDMX 09340, México.
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7
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Structure and Activity of a Selective Antibiofilm Peptide SK-24 Derived from the NMR Structure of Human Cathelicidin LL-37. Pharmaceuticals (Basel) 2021; 14:ph14121245. [PMID: 34959645 PMCID: PMC8703873 DOI: 10.3390/ph14121245] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/17/2021] [Accepted: 11/24/2021] [Indexed: 12/16/2022] Open
Abstract
The deployment of the innate immune system in humans is essential to protect us from infection. Human cathelicidin LL-37 is a linear host defense peptide with both antimicrobial and immune modulatory properties. Despite years of studies of numerous peptides, SK-24, corresponding to the long hydrophobic domain (residues 9–32) in the anionic lipid-bound NMR structure of LL-37, has not been investigated. This study reports the structure and activity of SK-24. Interestingly, SK-24 is entirely helical (~100%) in phosphate buffer (PBS), more than LL-37 (84%), GI-20 (75%), and GF-17 (33%), while RI-10 and 17BIPHE2 are essentially randomly coiled (helix%: 7–10%). These results imply an important role for the additional N-terminal amino acids (likely E16) of SK-24 in stabilizing the helical conformation in PBS. It is proposed herein that SK-24 contains the minimal sequence for effective oligomerization of LL-37. Superior to LL-37 and RI-10, SK-24 shows an antimicrobial activity spectrum comparable to the major antimicrobial peptides GF-17 and GI-20 by targeting bacterial membranes and forming a helical conformation. Like the engineered peptide 17BIPHE2, SK-24 has a stronger antibiofilm activity than LL-37, GI-20, and GF-17. Nevertheless, SK-24 is least hemolytic at 200 µM compared with LL-37 and its other peptides investigated herein. Combined, these results enabled us to appreciate the elegance of the long amphipathic helix SK-24 nature deploys within LL-37 for human antimicrobial defense. SK-24 may be a useful template of therapeutic potential.
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8
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Wang Q, Xu Q, Wang H, Han B, Xia D, Wang D, Zhang W. Molecular mechanisms of interaction between enzymes and Maillard reaction products formed from thermal hydrolysis pretreatment of waste activated sludge. WATER RESEARCH 2021; 206:117777. [PMID: 34688093 DOI: 10.1016/j.watres.2021.117777] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/10/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
Thermal hydrolysis pretreatment (THP) is often used to improve the anaerobic digestion performance of waste activated sludge (WAS) in wastewater treatment plants (WWTPs). During the THP process, the proteins and polysaccharides in the biomass will undergo hydrolysis and Maillard reaction, producing biorefractory organic substances, such as recalcitrant dissolved organic nitrogen (rDON) and melanoidins. In this study, a series of spectroscopy methods were used to quantitatively analyze the Maillard reaction of glucose and lysine, and the interaction mechanisms of the Maillard reaction products (MRPs) and lysozyme were investigated. Results showed that the typical aromatic heterocyclic structures in MRPs, such as pyrazine and furan, were found to quench molecular fluorescence of lysozyme, resulting in an unfolding of standard protein structure and increase in lysozyme hydrophobicity. Significant loss of enzyme activity was detected during this process. Thermodynamic parameters obtained from isothermal titration calorimetry (ITC) confirmed that the interaction between MRPs and lysozyme occurred both exothermically and spontaneously. Density functional theory (DFT) calculations suggested that the molecular interactions of MRPs and protein included parallel dislocation aromatic stacking, T-shaped vertical aromatic stacking, H-bond and H-bond coupled to aromatic stacking.
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Affiliation(s)
- Qiandi Wang
- School of Environmental Studies, China University of Geosciences, Wuhan, 430074, Hubei, China; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Qiongying Xu
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, Hubei, China
| | - Huidi Wang
- School of Environmental Studies, China University of Geosciences, Wuhan, 430074, Hubei, China
| | - Bo Han
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, Hubei, China
| | - Dasha Xia
- Hangzhou Yanqu Information Technology Co., Ltd., Hangzhou, 310012, China
| | - Dongsheng Wang
- School of Environmental Studies, China University of Geosciences, Wuhan, 430074, Hubei, China; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Weijun Zhang
- School of Environmental Studies, China University of Geosciences, Wuhan, 430074, Hubei, China.
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9
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Banerjee R, Sheet T, Banerjee S, Biondi B, Formaggio F, Toniolo C, Peggion C. C α-Methyl-l-valine: A Preferential Choice over α-Aminoisobutyric Acid for Designing Right-Handed α-Helical Scaffolds. Biochemistry 2021; 60:2704-2714. [PMID: 34463474 DOI: 10.1021/acs.biochem.1c00340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In synthetic peptides containing Gly and coded α-amino acids, one of the most common practices to enhance their helical extent is to incorporate a large number of l-Ala residues along with noncoded, strongly foldameric α-aminoisobutyric acid (Aib) units. Earlier studies have established that Aib-based peptides, with propensity for both the 310- and α-helices, have a tendency to form ordered three-dimensional structure that is much stronger than that exhibited by their l-Ala rich counterparts. However, the achiral nature of Aib induces an inherent, equal preference for the right- and left-handed helical conformations as found in Aib homopeptide stretches. This property poses challenges in the analysis of a model peptide helical conformation based on chirospectroscopic techniques like electronic circular dichroism (ECD), a very important tool for assigning secondary structures. To overcome such ambiguity, we have synthesized and investigated a thermally stable 14-mer peptide in which each of the Aib residues of our previously designed and reported analogue ABGY (where B stands for Aib) is replaced by Cα-methyl-l-valine (L-AMV). Analysis of the results described here from complementary ECD and 1H nuclear magnetic resonance spectroscopic techniques in a variety of environments firmly establishes that the L-AMV-containing peptide exhibits a significantly stronger preference compared to that of its Aib parent in terms of conferring α-helical character. Furthermore, being a chiral α-amino acid, L-AMV shows an intrinsic, extremely strong bias for a quite specific (right-handed) screw sense. These findings emphasize the relevance of L-AMV as a more appropriate unit for the design of right-handed α-helical peptide models that may be utilized as conformationally constrained scaffolds.
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Affiliation(s)
| | | | | | - Barbara Biondi
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Fernando Formaggio
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Claudio Toniolo
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Cristina Peggion
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
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10
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Halat M, Klimek-Chodacka M, Orleanska J, Baranska M, Baranski R. Electronic Circular Dichroism of the Cas9 Protein and gRNA:Cas9 Ribonucleoprotein Complex. Int J Mol Sci 2021; 22:2937. [PMID: 33805827 PMCID: PMC8002190 DOI: 10.3390/ijms22062937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 12/26/2022] Open
Abstract
The Streptococcus pyogenes Cas9 protein (SpCas9), a component of CRISPR-based immune system in microbes, has become commonly utilized for genome editing. This nuclease forms a ribonucleoprotein (RNP) complex with guide RNA (gRNA) which induces Cas9 structural changes and triggers its cleavage activity. Here, electronic circular dichroism (ECD) spectroscopy was used to confirm the RNP formation and to determine its individual components. The ECD spectra had characteristic features differentiating Cas9 and gRNA, the former showed a negative/positive profile with maxima located at 221, 209 and 196 nm, while the latter revealed positive/negative/positive/negative pattern with bands observed at 266, 242, 222 and 209 nm, respectively. For the first time, the experimental ECD spectrum of the gRNA:Cas9 RNP complex is presented. It exhibits a bisignate positive/negative ECD couplet with maxima at 273 and 235 nm, and it differs significantly from individual spectrum of each RNP components. Additionally, the Cas9 protein and RNP complex retained biological activity after ECD measurements and they were able to bind and cleave DNA in vitro. Hence, we conclude that ECD spectroscopy can be considered as a quick and non-destructive method of monitoring conformational changes of the Cas9 protein as a result of Cas9 and gRNA interaction, and identification of the gRNA:Cas9 RNP complex.
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Affiliation(s)
- Monika Halat
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; (M.H.); (J.O.)
| | - Magdalena Klimek-Chodacka
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. 29 Listopada 54, 31-425 Krakow, Poland;
| | - Jagoda Orleanska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; (M.H.); (J.O.)
| | - Malgorzata Baranska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; (M.H.); (J.O.)
- Jagiellonian Centre for Experimental Therapeutics (JCET), Bobrzyńskiego 14, 30-348 Krakow, Poland
| | - Rafal Baranski
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. 29 Listopada 54, 31-425 Krakow, Poland;
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11
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Sheet T, Banerjee R. Design of a Peptide-Based Model Leads for Scavenging Anions. ACS OMEGA 2020; 5:9759-9767. [PMID: 32391463 PMCID: PMC7203709 DOI: 10.1021/acsomega.9b04180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 04/03/2020] [Indexed: 06/11/2023]
Abstract
Among several peptide-based anion recognition motifs, the "CαNN" motif containing C-1 α, N0, and N+1 of three consecutive residues is unique in its mode of interaction. Having a spatial geometry of βαα or βαβ, this motif occurs in the N terminus of a helix and often found at the functional interface of a protein, mediating crucial biological significance upon interaction with anion(s). The interaction of anion(s) with chimeric peptide sequences containing the naturally occurring "CαNN" motif (CPS224Ac, CPS226, and CPS228) reported in our previous attempts strongly confirms that the information regarding the interaction is embedded within the local sequences of the motif segment. At these prevailing circumstances, an effort has been pursued to design novel scaffolds based on the "CαNN" motif for achieving better recognition of anion(s). Exploring the existing data set of the "CαNN" motif available in the FSSP database, four novel peptide-based scaffolds have been designed (DS1, DS2, DS3, and DS4), and preliminary screenings have been performed using computational approaches. Our initial work suggests that two (DS1 and DS3) out of the four scaffolds are potential candidates for better anion recognition. By employing biophysical characterization using both qualitative and quantitative measures, in this present study, we report the interaction of sulfate and phosphate ions with these two designed scaffolds, in which there is much better recognition of anions by these scaffolds than the natural sequences, justifying their logical engineering. Our observation strongly suggests that these designed scaffolds are better potential candidates than those of the naturally occurring "CαNN" motif in terms of anion recognition and could be utilized for the scavenging of anion(s) for different purposes.
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Affiliation(s)
- Tridip Sheet
- Department
of Bioinformatics, Maulana Abul Kalam Azad
University of Technology, West Bengal (Formerly Known as West Bengal
University of Technology), BF-142, Sector-1, Salt Lake, Kolkata 700064, India
| | - Raja Banerjee
- Department
of Bioinformatics, Maulana Abul Kalam Azad
University of Technology, West Bengal (Formerly Known as West Bengal
University of Technology), BF-142, Sector-1, Salt Lake, Kolkata 700064, India
- Department
of Biotechnology, Maulana Abul Kalam Azad
University of Technology, West Bengal (Formerly Known as West Bengal
University of Technology), BF-142, Sector-1, Salt Lake, Kolkata 700064, India
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12
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Ponomarenko NS, Kokhan O, Pokkuluri PR, Mulfort KL, Tiede DM. Examination of abiotic cofactor assembly in photosynthetic biomimetics: site-specific stereoselectivity in the conjugation of a ruthenium(II) tris(bipyridine) photosensitizer to a multi-heme protein. PHOTOSYNTHESIS RESEARCH 2020; 143:99-113. [PMID: 31925630 PMCID: PMC6989566 DOI: 10.1007/s11120-019-00697-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/02/2019] [Indexed: 05/18/2023]
Abstract
To understand design principles for assembling photosynthetic biohybrids that incorporate precisely-controlled sites for electron injection into redox enzyme cofactor arrays, we investigated the influence of chirality in assembly of the photosensitizer ruthenium(II)bis(2,2'-bipyridine)(4-bromomethyl-4'-methyl-2,2'-bipyridine), Ru(bpy)2(Br-bpy), when covalently conjugated to cysteine residues introduced by site-directed mutagenesis in the triheme periplasmic cytochrome A (PpcA) as a model biohybrid system. For two investigated conjugates that show ultrafast electron transfer, A23C-Ru and K29C-Ru, analysis by circular dichroism spectroscopy, CD, demonstrated site-specific chiral discrimination as a factor emerging from the close association between [Ru(bpy)3]2+ and heme cofactors. CD analysis showed the A23C-Ru and K29C-Ru conjugates to have distinct, but opposite, stereoselectivity for the Λ and Δ-Ru(bpy)2(Br-bpy) enantiomers, with enantiomeric excesses of 33.1% and 65.6%, respectively. In contrast, Ru(bpy)2(Br-bpy) conjugation to a protein site with high flexibility, represented by the E39C-Ru construct, exhibited a nearly negligible chiral selectivity, measured by an enantiomeric excess of 4.2% for the Λ enantiomer. Molecular dynamics simulations showed that site-specific stereoselectivity reflects steric constraints at the conjugating sites and that a high degree of chiral selectivity correlates to reduced structural disorder for [Ru(bpy)3]2+ in the linked assembly. This work identifies chiral discrimination as means to achieve site-specific, precise geometric positioning of introduced photosensitizers relative to the heme cofactors in manner that mimics the tuning of cofactors in photosynthesis.
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Affiliation(s)
- Nina S Ponomarenko
- Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA.
| | - Oleksandr Kokhan
- Department of Chemistry and Biochemistry, James Madison University, 901 Carrier Drive, Harrisonburg, VA, 22807, USA
| | - Phani R Pokkuluri
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA
| | - Karen L Mulfort
- Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA
| | - David M Tiede
- Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA.
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13
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Hoarau M, Koebke KJ, Chen Z, Marsh ENG. Probing Metal Ion Discrimination in a Protein Designed to Bind Uranyl Cation With Femtomolar Affinity. Front Mol Biosci 2019; 6:73. [PMID: 31552264 PMCID: PMC6736553 DOI: 10.3389/fmolb.2019.00073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 08/07/2019] [Indexed: 12/14/2022] Open
Abstract
The design of metal-binding sites in proteins that combine high affinity with high selectivity for the desired metal ion remains a challenging goal. Recently, a protein designed to display femtomolar affinity for UO22+, dubbed “Super Uranyl-binding Protein” (SUP), was described, with potential applications for removing UO22+ in water. Although it discriminated most metal ions present in seawater, the protein showed a surprisingly high affinity for Cu2+ ions. Here, we have investigated Cu2+ binding to SUP using a combination of electron paramagnetic resonance, fluorescence and circular dichroism spectroscopies. Our results provide evidence for two Cu2+ binding sites on SUP that are distinct from the UO22+ binding site, but one of which interferes with UO22+ binding. They further suggest that in solution the protein's secondary structure changes significantly in response to binding UO22+; in contrast, the crystal structures of the apo- and holo-protein are almost superimposable. These results provide insights for further improving the selectivity of SUP for UO22+, paving the way toward protein-based biomaterials for decontamination and/or recovery of uranium.
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Affiliation(s)
- Marie Hoarau
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States
| | - Karl J Koebke
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States
| | - Zhan Chen
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States
| | - E Neil G Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, United States
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14
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Gu Y, Natoli SN, Liu Z, Clark DS, Hartwig JF. Site-Selective Functionalization of (sp 3 )C-H Bonds Catalyzed by Artificial Metalloenzymes Containing an Iridium-Porphyrin Cofactor. Angew Chem Int Ed Engl 2019; 58:13954-13960. [PMID: 31356719 DOI: 10.1002/anie.201907460] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 07/12/2019] [Indexed: 12/25/2022]
Abstract
The selective functionalization of one C-H bond over others in nearly identical steric and electronic environments can facilitate the construction of complex molecules. We report site-selective functionalizations of C-H bonds, differentiated solely by remote substituents, catalyzed by artificial metalloenzymes (ArMs) that are generated from the combination of an evolvable P450 scaffold and an iridium-porphyrin cofactor. The generated systems catalyze the insertion of carbenes into the C-H bonds of a range of phthalan derivatives containing substituents that render the two methylene positions in each phthalan inequivalent. These reactions occur with site-selectivity ratios of up to 17.8:1 and, in most cases, with pairs of enzyme mutants that preferentially form each of the two constitutional isomers. This study demonstrates the potential of abiotic reactions catalyzed by metalloenzymes to functionalize C-H bonds with site selectivity that is difficult to achieve with small-molecule catalysts.
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Affiliation(s)
- Yang Gu
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Sean N Natoli
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Zhennan Liu
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - John F Hartwig
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
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15
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Gu Y, Natoli SN, Liu Z, Clark DS, Hartwig JF. Site‐Selective Functionalization of (sp
3
)C−H Bonds Catalyzed by Artificial Metalloenzymes Containing an Iridium‐Porphyrin Cofactor. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907460] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yang Gu
- Department of Chemistry University of California Berkeley CA 94720 USA
- Chemical Sciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley CA 94720 USA
| | - Sean N. Natoli
- Department of Chemistry University of California Berkeley CA 94720 USA
- Chemical Sciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley CA 94720 USA
| | - Zhennan Liu
- Department of Chemistry University of California Berkeley CA 94720 USA
- Chemical Sciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley CA 94720 USA
| | - Douglas S. Clark
- Department of Chemical and Biomolecular Engineering University of California Berkeley CA 94720 USA
- Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley CA 94720 USA
| | - John F. Hartwig
- Department of Chemistry University of California Berkeley CA 94720 USA
- Chemical Sciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley CA 94720 USA
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16
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Machado CA, Bentz KC, Tran R, Jenkins TA, Barnes BE, Diodati LE, Savin DA. Hierarchical Fractal Assemblies from Poly(ethylene oxide- b-lysine- b-leucine). Biomacromolecules 2019; 20:2557-2566. [PMID: 31244016 DOI: 10.1021/acs.biomac.9b00337] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Poly(ethylene oxide43- b-lysine62- b-leucine72) (wherein subscripts denote the degree of polymerization) was synthesized via ring-opening polymerization of N-carboxyanhydrides using an amine-terminated poly(ethylene oxide) macroinitiator, with polypeptide blocks produced by sequential monomer addition. Infrared and circular dichroism spectroscopy indicated that the peptide blocks in this polymer formed α-helices in the solid and solution states, respectively. In the aqueous solution, this polymer self-assembled into spherical micelles with a hydrodynamic radius of approximately 90 nm at concentrations between 0.05 and 0.20% w/w and pH values between 2 and 6.5. Upon preparation of transmission electron microscopy (TEM) grids, the micelles at pH 2 underwent hierarchical assembly to produce fractal assemblies, whereas small clusters were observed for micellar solutions at pH 6.5. Cryogenic-TEM of solutions showed spherical micelles, and dynamic light scattering showed no large (∼1 μm) aggregates in the solution, which suggests that fractal formation was a result of the drying process, and that fractals were not present in the solution. This system provides a facile route to nanostructured surfaces, which can be used for applications such as modulating cell adhesion or promoting the growth of neurons.
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Affiliation(s)
- Craig A Machado
- George & Josephine Butler Polymer Research Laboratory, Center for Macromolecular Science & Engineering, Department of Chemistry , University of Florida , Gainesville , Florida 32611 , United States
| | - Kyle C Bentz
- George & Josephine Butler Polymer Research Laboratory, Center for Macromolecular Science & Engineering, Department of Chemistry , University of Florida , Gainesville , Florida 32611 , United States
| | - Roger Tran
- George & Josephine Butler Polymer Research Laboratory, Center for Macromolecular Science & Engineering, Department of Chemistry , University of Florida , Gainesville , Florida 32611 , United States
| | - Taylor A Jenkins
- George & Josephine Butler Polymer Research Laboratory, Center for Macromolecular Science & Engineering, Department of Chemistry , University of Florida , Gainesville , Florida 32611 , United States
| | - Brooke E Barnes
- George & Josephine Butler Polymer Research Laboratory, Center for Macromolecular Science & Engineering, Department of Chemistry , University of Florida , Gainesville , Florida 32611 , United States
| | - Lily E Diodati
- George & Josephine Butler Polymer Research Laboratory, Center for Macromolecular Science & Engineering, Department of Chemistry , University of Florida , Gainesville , Florida 32611 , United States
| | - Daniel A Savin
- George & Josephine Butler Polymer Research Laboratory, Center for Macromolecular Science & Engineering, Department of Chemistry , University of Florida , Gainesville , Florida 32611 , United States
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Sahu S, Sheet T, Banerjee R. Interaction landscape of a 'C αNN' motif with arsenate and arsenite: a potential peptide-based scavenger of arsenic. RSC Adv 2019; 9:1062-1074. [PMID: 35517606 PMCID: PMC9059529 DOI: 10.1039/c8ra08225a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 12/08/2018] [Indexed: 12/01/2022] Open
Abstract
Arsenic (As) is a toxic metalloid that has drawn immense attention from the scientific community recently due to its fatal effects through its unwanted occurrence in ground water around the globe. The presence of an excess amount of water soluble arsenate and/or arsenite salt (permissible limit 10 μg L-1 as recommended by the WHO) in water has been correlated with several human diseases. Although arsenate (HAsO4 2-) is a molecular analogue of phosphate (HPO4 2-), phosphate is indispensable for life, while arsenic and its salts are toxic. Therefore, it is worthwhile to focus on the removal of arsenic from water. Towards this end, the design of peptide-based scaffolds for the recognition of arsenate and arsenite would add a new dimension. Utilizing the stereochemical similarity between arsenate (HAsO4 2-) and phosphate (HPO4 2-), we successfully investigated the recognition of arsenate and arsenite with a naturally occurring novel phosphate binding 'CαNN' motif and its related designed analogues. Using computational as well as biophysical approaches, for the first time, we report here that a designed peptide-based scaffold based on the 'CαNN' motif can recognize anions of arsenic in a thermodynamically favorable manner in a context-free system. This peptide-based arsenic binding agent has the potential for future development as a scavenger of arsenic anions to obtain arsenic free water.
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Affiliation(s)
- Subhankar Sahu
- Department of Biotechnology and Head Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly Known as West Bengal University of Technology) BF-142, Salt Lake Kolkata 700064 West Bengal India
| | - Tridip Sheet
- Department of Biotechnology and Head Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly Known as West Bengal University of Technology) BF-142, Salt Lake Kolkata 700064 West Bengal India
| | - Raja Banerjee
- Department of Biotechnology and Head Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly Known as West Bengal University of Technology) BF-142, Salt Lake Kolkata 700064 West Bengal India
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Auger M, Lefèvre T, Otis F, Voyer N, Auger M. Lipid membrane interactions of a fluorinated peptide with potential ion channel-forming ability. Pept Sci (Hoboken) 2019. [DOI: 10.1002/pep2.24051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Maud Auger
- Regroupement québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines (PROTEO), Centre de Recherche sur les Matériaux Avancés (CERMA), Centre Québécois sur les Matériaux Fonctionnels (CQMF), Département de Chimie, Université Laval, 1045 avenue de la Médecine; Québec QC Canada G1V 0A6
| | - Thierry Lefèvre
- Regroupement québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines (PROTEO), Centre de Recherche sur les Matériaux Avancés (CERMA), Centre Québécois sur les Matériaux Fonctionnels (CQMF), Département de Chimie, Université Laval, 1045 avenue de la Médecine; Québec QC Canada G1V 0A6
| | - François Otis
- PROTEO, Département de chimie; Université Laval, 1045 avenue de la Médecine; Québec QC Canada G1V 0A6
| | - Normand Voyer
- PROTEO, Département de chimie; Université Laval, 1045 avenue de la Médecine; Québec QC Canada G1V 0A6
| | - Michèle Auger
- Regroupement québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines (PROTEO), Centre de Recherche sur les Matériaux Avancés (CERMA), Centre Québécois sur les Matériaux Fonctionnels (CQMF), Département de Chimie, Université Laval, 1045 avenue de la Médecine; Québec QC Canada G1V 0A6
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