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Szadkowska M, Olewniczak M, Kloska A, Jankowska E, Kapusta M, Rybak B, Wyrzykowski D, Zmudzinska W, Gieldon A, Kocot A, Kaczorowska AK, Nierzwicki L, Makowska J, Kaczorowski T, Plotka M. A Novel Cryptic Clostridial Peptide That Kills Bacteria by a Cell Membrane Permeabilization Mechanism. Microbiol Spectr 2022; 10:e0165722. [PMID: 36094301 PMCID: PMC9602519 DOI: 10.1128/spectrum.01657-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/23/2022] [Indexed: 12/31/2022] Open
Abstract
This work reports detailed characteristics of the antimicrobial peptide Intestinalin (P30), which is derived from the LysC enzyme of Clostridium intestinale strain URNW. The peptide shows a broader antibacterial spectrum than the parental enzyme, showing potent antimicrobial activity against clinical strains of Gram-positive staphylococci and Gram-negative pathogens and causing between 3.04 ± 0.12 log kill for Pseudomonas aeruginosa PAO1 and 7.10 ± 0.05 log kill for multidrug-resistant Acinetobacter baumannii KPD 581 at a 5 μM concentration. Moreover, Intestinalin (P30) prevents biofilm formation and destroys 24-h and 72-h biofilms formed by Acinetobacter baumannii CRAB KPD 205 (reduction levels of 4.28 and 2.62 log CFU/mL, respectively). The activity of Intestinalin is combined with both no cytotoxicity and little hemolytic effect against mammalian cells. The nuclear magnetic resonance and molecular dynamics (MD) data show a high tendency of Intestinalin to interact with the bacterial phospholipid cell membrane. Although positively charged, Intestinalin resides in the membrane and aggregates into small oligomers. Negatively charged phospholipids stabilize peptide oligomers to form water- and ion-permeable pores, disrupting the integrity of bacterial cell membranes. Experimental data showed that Intestinalin interacts with negatively charged lipoteichoic acid (logK based on isothermal titration calorimetry, 7.45 ± 0.44), causes membrane depolarization, and affects membrane integrity by forming large pores, all of which result in loss of bacterial viability. IMPORTANCE Antibiotic resistance is rising rapidly among pathogenic bacteria, becoming a global public health problem that threatens the effectiveness of therapies for many infectious diseases. In this respect, antimicrobial peptides appear to be an interesting alternative to combat bacterial pathogens. Here, we report the characteristics of an antimicrobial peptide (of 30 amino acids) derived from the clostridial LysC enzyme. The peptide showed killing activity against clinical strains of Gram-positive and Gram-negative pathogens. Experimental data and computational modeling showed that this peptide forms transmembrane pores, directly engaging the negatively charged phospholipids of the bacterial cell membrane. Consequently, dissipation of the electrochemical gradient across cell membranes affects many vital processes, such as ATP synthesis, motility, and transport of nutrients. This kind of dysfunction leads to the loss of bacterial viability. Our firm conviction is that the presented study will be a helpful resource in searching for novel antimicrobial peptides that could have the potential to replace conventional antibiotics.
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Affiliation(s)
- Monika Szadkowska
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Michal Olewniczak
- Department of Physical Chemistry, Gdansk University of Technology, Gdansk, Poland
| | - Anna Kloska
- Department of Medical Biology and Genetics, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Elzbieta Jankowska
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | - Malgorzata Kapusta
- Department of Plant Cytology and Embryology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Bartosz Rybak
- Department of Environmental Toxicology, Faculty of Health Sciences with Institute of Maritime and Tropical Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Dariusz Wyrzykowski
- Department of General and Inorganic Chemistry, Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | - Wioletta Zmudzinska
- Laboratory of Biopolymer Structure, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Artur Gieldon
- Laboratory of Simulation of Polymers, Department of Theoretical Chemistry, Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | - Aleksandra Kocot
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Anna-Karina Kaczorowska
- Collection of Plasmids and Microorganisms, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Lukasz Nierzwicki
- Department of Physical Chemistry, Gdansk University of Technology, Gdansk, Poland
| | - Joanna Makowska
- Department of General and Inorganic Chemistry, Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | - Tadeusz Kaczorowski
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Magdalena Plotka
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Gdansk, Poland
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Selvam P, De S, Paira P, Kumar SKA, Kumar R S, Moorthy A, Ghosh A, Kuo YC, Banerjee S, Jenifer SK. In vitro studies on the selective cytotoxic effect of luminescent Ru( ii)- p-cymene complexes of imidazo-pyridine and imidazo quinoline ligands. Dalton Trans 2022; 51:17263-17276. [DOI: 10.1039/d2dt02237k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In recent years, Ru(ii) complexes have gained high importance in medicinal chemistry due to their significant anti-cancer activities, which are directly related to their DNA binding ability.
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Affiliation(s)
- Pravinkumar Selvam
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
| | - Sourav De
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
- Department of Chemical Engineering, National Chung Cheng University, Chia-Yi, Taiwan 62102, Republic of China
| | - Priyankar Paira
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
| | - S. K. Ashok Kumar
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
| | - Selva Kumar R
- Department of Chemistry, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Science (SIMATS), Chennai – 602105, Tamil Nadu, India
| | - Anbalagan Moorthy
- Department of Biotechnology, School of Bioscience & Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Arjita Ghosh
- Department of Biotechnology, School of Bioscience & Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Yung-Chih Kuo
- Department of Chemical Engineering, National Chung Cheng University, Chia-Yi, Taiwan 62102, Republic of China
| | - Subhasis Banerjee
- Department of Pharmaceutical Chemistry, Gupta College of Technological Sciences. Asansol-713301, West Bengal, India
| | - Shantha Kumar Jenifer
- DST Unit of Nanoscience (DST UNS) and Thematic Unit of Excellence (TUE), Department of Chemistry, Indian Institute of Technology Madras, Chennai – 600 036, India
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3
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Frutiger A, Tanno A, Hwu S, Tiefenauer RF, Vörös J, Nakatsuka N. Nonspecific Binding-Fundamental Concepts and Consequences for Biosensing Applications. Chem Rev 2021; 121:8095-8160. [PMID: 34105942 DOI: 10.1021/acs.chemrev.1c00044] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nature achieves differentiation of specific and nonspecific binding in molecular interactions through precise control of biomolecules in space and time. Artificial systems such as biosensors that rely on distinguishing specific molecular binding events in a sea of nonspecific interactions have struggled to overcome this issue. Despite the numerous technological advancements in biosensor technologies, nonspecific binding has remained a critical bottleneck due to the lack of a fundamental understanding of the phenomenon. To date, the identity, cause, and influence of nonspecific binding remain topics of debate within the scientific community. In this review, we discuss the evolution of the concept of nonspecific binding over the past five decades based upon the thermodynamic, intermolecular, and structural perspectives to provide classification frameworks for biomolecular interactions. Further, we introduce various theoretical models that predict the expected behavior of biosensors in physiologically relevant environments to calculate the theoretical detection limit and to optimize sensor performance. We conclude by discussing existing practical approaches to tackle the nonspecific binding challenge in vitro for biosensing platforms and how we can both address and harness nonspecific interactions for in vivo systems.
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Affiliation(s)
- Andreas Frutiger
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Alexander Tanno
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Stephanie Hwu
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Raphael F Tiefenauer
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - János Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
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4
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Reinhard DL, Heinen F, Stoesser J, Engelage E, Huber SM. Tuning the Halogen Bonding Strength of Cyclic Diaryliodonium Salts. Helv Chim Acta 2021. [DOI: 10.1002/hlca.202000221] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Dominik L. Reinhard
- Fakultät für Chemie und Biochemie Ruhr-Universität Bochum Universitätsstraße 150 DE 44801 Bochum Germany
| | - Flemming Heinen
- Fakultät für Chemie und Biochemie Ruhr-Universität Bochum Universitätsstraße 150 DE 44801 Bochum Germany
| | - Julian Stoesser
- Fakultät für Chemie und Biochemie Ruhr-Universität Bochum Universitätsstraße 150 DE 44801 Bochum Germany
| | - Elric Engelage
- Fakultät für Chemie und Biochemie Ruhr-Universität Bochum Universitätsstraße 150 DE 44801 Bochum Germany
| | - Stefan M. Huber
- Fakultät für Chemie und Biochemie Ruhr-Universität Bochum Universitätsstraße 150 DE 44801 Bochum Germany
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5
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Khan MA, Kiser MR, Moradipour M, Nadeau EA, Ghanim RW, Webb BA, Rankin SE, Knutson BL. Effect of Confinement in Nanopores on RNA Interactions with Functionalized Mesoporous Silica Nanoparticles. J Phys Chem B 2020; 124:8549-8561. [PMID: 32881500 DOI: 10.1021/acs.jpcb.0c06536] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Amine-functionalized mesoporous silica nanoparticles (MSNPAs) are ideal carriers for oligonucleotides for gene delivery and RNA interference. This investigation examines the thermodynamic driving force of interactions of double-stranded (ds) RNA with MSNPAs as a function of RNA length (84 and 282 base pair) and particle pore diameter (nonporous, 2.7, 4.3, and 8.1 nm) using isothermal titration calorimetry, extending knowledge of solution-based nucleic acid-polycation interactions to RNA confined in nanopores. Adsorption of RNA follows a two-step process: endothermic interactions driven by entropic contribution from counterion (and water) release and an exothermic regime dominated by short-range interactions within the pores. Evidence of hindered pore loading of the longer RNA and pore size-dependent confinement of RNA in the MSPAs is provided from the relative contributions of the endothermic and exothermic regimes. Reduction of endothermic and exothermic enthalpies in both regimes in the presence of salt for both lengths of RNA indicates the significant contribution of short-range electrostatic interactions, whereas ΔH and ΔG values are consistent with conformation changes and desolvation of nucleic acids upon binding with polycations. Knowledge of the interactions between RNA and functionalized porous nanoparticles will aid in porous nanocarrier design suitable for functional RNA delivery.
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Affiliation(s)
- M Arif Khan
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Maelyn R Kiser
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Mahsa Moradipour
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Emily A Nadeau
- Department of Entomology, University of Kentucky, Lexington, Kentucky 40546, United States
| | - Ramy W Ghanim
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Bruce A Webb
- Department of Entomology, University of Kentucky, Lexington, Kentucky 40546, United States
| | - Stephen E Rankin
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Barbara L Knutson
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States
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Bucaite G, Kang-Pettinger T, Moreira J, Gould HJ, James LK, Sutton BJ, McDonnell JM. Interplay between Affinity and Valency in Effector Cell Degranulation: A Model System with Polcalcin Allergens and Human Patient-Derived IgE Antibodies. THE JOURNAL OF IMMUNOLOGY 2019; 203:1693-1700. [PMID: 31462504 DOI: 10.4049/jimmunol.1900509] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 07/19/2019] [Indexed: 01/10/2023]
Abstract
An allergic reaction is rapidly generated when allergens bind and cross-link IgE bound to its receptor FcεRI on effector cells, resulting in cell degranulation and release of proinflammatory mediators. The extent of effector cell activation is linked to allergen affinity, oligomeric state, valency, and spacing of IgE-binding epitopes on the allergen. Whereas most of these observations come from studies using synthetic allergens, in this study we have used Timothy grass pollen allergen Phl p 7 and birch pollen allergen Bet v 4 to study these effects. Despite the high homology of these polcalcin family allergens, Phl p 7 and Bet v 4 display different binding characteristics toward two human patient-derived polcalcin-specific IgE Abs. We have used native polcalcin dimers and engineered multimeric allergens to test the effects of affinity and oligomeric state on IgE binding and effector cell activation. Our results indicate that polcalcin multimers are required to stimulate high levels of effector cell degranulation when using the humanized RBL-SX38 cell model and that multivalency can overcome the need for high-affinity interactions.
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Affiliation(s)
- Gintare Bucaite
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, United Kingdom.,Asthma UK Centre in Allergic Mechanisms of Asthma, King's College London, London SE1 1UL, United Kingdom
| | - Tara Kang-Pettinger
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, United Kingdom.,Asthma UK Centre in Allergic Mechanisms of Asthma, King's College London, London SE1 1UL, United Kingdom.,Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom; and
| | - Jorge Moreira
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, United Kingdom.,Asthma UK Centre in Allergic Mechanisms of Asthma, King's College London, London SE1 1UL, United Kingdom
| | - Hannah J Gould
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, United Kingdom.,Asthma UK Centre in Allergic Mechanisms of Asthma, King's College London, London SE1 1UL, United Kingdom
| | - Louisa K James
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, United Kingdom.,Asthma UK Centre in Allergic Mechanisms of Asthma, King's College London, London SE1 1UL, United Kingdom.,Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, United Kingdom
| | - Brian J Sutton
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, United Kingdom.,Asthma UK Centre in Allergic Mechanisms of Asthma, King's College London, London SE1 1UL, United Kingdom
| | - James M McDonnell
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, United Kingdom; .,Asthma UK Centre in Allergic Mechanisms of Asthma, King's College London, London SE1 1UL, United Kingdom
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7
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Mondal PK, T A, Rao V, Chopra D. Crystal structure analysis of the biologically active drug mol-ecule riluzole and riluzolium chloride. ACTA CRYSTALLOGRAPHICA SECTION E-CRYSTALLOGRAPHIC COMMUNICATIONS 2019; 75:1084-1089. [PMID: 31417770 PMCID: PMC6690469 DOI: 10.1107/s2056989019009022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 06/24/2019] [Indexed: 11/17/2022]
Abstract
An investigation into the crystallization, crystal structure and packing analysis of the biologically active drug molecule riluzole and its derivative, the riluzolium chloride salt, has been carried out. This study is an investigation into the crystal structure of the biologically active drug molecule riluzole [RZ, 6-(trifluoromethoxy)-1,3-benzothiazol-2-amine], C8H5F3N2OS, and its derivative, the riluzolium chloride salt [RZHCl, 2-amino-6-(trifluoromethoxy)-1,3-benzothiazol-3-ium chloride], C8H6F3N2OS+·Cl−. In spite of repeated efforts to crystallize the drug, its crystal structure has not been reported to date, hence the current study provides a method for obtaining crystals of both riluzole and its corresponding salt, riluzolium hydrochloride. The salt was obtained by grinding HCl with the drug and crystallizing the obtained solid from dichloromethane. The crystals of riluzole were obtained in the presence of l-glutamic acid and d-glutamic acid in separate experiments. In the crystal structure of RZHCl, the –OCF3 moiety is perpendicular to the molecular plane containing the riluzolium ion, as can be seen by the torsion angle of 107.4 (3)°. In the case of riluzole, the torsion angles of the four different molecules in the asymmetric unit show that in three cases the trifluoromethoxy group is perpendicular to the riluzole molecular plane and only in one molecule does the –OCF3 group lie in the same molecular plane. The crystal structure of riluzole primarily consists of strong N—H⋯N hydrogen bonds along with weak C—H⋯F, C—H⋯S, F⋯F, C⋯C and C⋯S interactions, while that of its salt is stabilized by strong [N—H]+⋯Cl− and weak C—H⋯Cl−, N—H⋯S, C—H⋯F, C⋯C, S⋯N and S⋯Cl− interactions.
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Affiliation(s)
- Pradip Kumar Mondal
- Department of Chemistry, Indian Institute of Science Education and Research, Bhopal, Bhauri, Bhopal 462066, India
| | - Athulbabu T
- Department of Chemistry, Indian Institute of Science Education and Research, Bhopal, Bhauri, Bhopal 462066, India
| | - Varun Rao
- Department of Chemistry, Indian Institute of Science Education and Research, Bhopal, Bhauri, Bhopal 462066, India
| | - Deepak Chopra
- Department of Chemistry, Indian Institute of Science Education and Research, Bhopal, Bhauri, Bhopal 462066, India
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8
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Xu X, Angioletti-Uberti S, Lu Y, Dzubiella J, Ballauff M. Interaction of Proteins with Polyelectrolytes: Comparison of Theory to Experiment. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:5373-5391. [PMID: 30095921 DOI: 10.1021/acs.langmuir.8b01802] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We discuss recent investigations of the interaction of polyelectrolytes with proteins. In particular, we review our recent studies on the interaction of simple proteins such as human serum albumin (HSA) and lysozyme with linear polyelectrolytes, charged dendrimers, charged networks, and polyelectrolyte brushes. In all cases discussed here, we combined experimental work with molecular dynamics (MD) simulations and mean-field theories. In particular, isothermal titration calorimetry (ITC) has been employed to obtain the respective binding constants Kb and the Gibbs free energy of binding. MD simulations with explicit counterions but implicit water demonstrate that counterion release is the main driving force for the binding of proteins to strongly charged polyelectrolytes: patches of positive charges located on the surface of the protein become multivalent counterions of the polyelectrolyte, thereby releasing a number of counterions condensed on the polyelectrolyte. The binding Gibbs free energy due to counterion release is predicted to scale with the logarithm of the salt concentration in the system, which is verified by both simulations and experiment. In several cases, namely, for the interaction of proteins with linear polyelectrolytes and highly charged hydrophilic dendrimers, the binding constant could be calculated from simulations to very good approximation. This finding demonstrated that in these cases explicit hydration effects do not contribute to the Gibbs free energy of binding. The Gibbs free energy can also be used to predict the kinetics of protein uptake by microgels for a given system by applying dynamic density functional theory. The entire discussion demonstrates that the direct comparison of theory with experiments can lead to a full understanding of the interaction of proteins with charged polymers. Possible implications for applications, such as drug design, are discussed.
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Affiliation(s)
- Xiao Xu
- School of Chemical Engineering , Nanjing University of Science and Technology , 200 Xiao Ling Wei , Nanjing 210094 , P. R. China
| | - Stefano Angioletti-Uberti
- Department of Materials , Imperial College London , London SW7 2AZ - UK , U.K
- International Research Centre for Soft Matter , Beijing University of Chemical Technology , 100099 Beijing , PR China
| | - Yan Lu
- Soft Matter and Functional Materials , Helmholtz-Zentrum Berlin für Materialien und Energie GmbH , 14109 Berlin , Germany
- Institute of Chemistry , University of Potsdam , 14467 Potsdam , Germany
| | - Joachim Dzubiella
- Soft Matter and Functional Materials , Helmholtz-Zentrum Berlin für Materialien und Energie GmbH , 14109 Berlin , Germany
- Physikalisches Institut , Albert-Ludwigs-Universität , 79104 Freiburg , Germany
| | - Matthias Ballauff
- Soft Matter and Functional Materials , Helmholtz-Zentrum Berlin für Materialien und Energie GmbH , 14109 Berlin , Germany
- Institut für Physik , Humboldt-Universität zu Berlin , 12489 Berlin , Germany
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9
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Rodler A, Ueberbacher R, Beyer B, Jungbauer A. Calorimetry for studying the adsorption of proteins in hydrophobic interaction chromatography. Prep Biochem Biotechnol 2019; 49:1-20. [DOI: 10.1080/10826068.2018.1487852] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Agnes Rodler
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Rene Ueberbacher
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Beate Beyer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Alois Jungbauer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
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10
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Inada M, Kinoshita M, Sumino A, Oiki S, Matsumori N. A concise method for quantitative analysis of interactions between lipids and membrane proteins. Anal Chim Acta 2019; 1059:103-112. [PMID: 30876624 DOI: 10.1016/j.aca.2019.01.042] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 01/31/2023]
Abstract
Although interactions between lipids and membrane proteins (MPs) have been considered crucially important for understanding the functions of lipids, lack of useful and convincing experimental methods has hampered the analysis of the interactions. Here, we developed a surface plasmon resonance (SPR)-based concise method for quantitative analysis of lipid-MP interactions, coating the sensor chip surface with self-assembled monolayer (SAM) with C6-chain. To develop this method, we used bacteriorhodopsin (bR) as an MP, and examined its interaction with various types of lipids. The merits of using C6-SAM-modified sensor chip are as follows: (1) alkyl-chains of SAM confer a better immobilization of MPs because of the efficient preconcentration due to hydrophobic contacts; (2) SAM provides immobilized MPs with a partial membranous environment, which is important for the stabilization of MPs; and (3) a thinner C6-SAM layer (1 nm) compared with MP size forces the MP to bulge outward from the SAM surface, allowing extraneously injected lipids to be accessible to the hydrophobic transmembrane regions. Actually, the amount of bR immobilized on C6-SAM is 10 times higher than that on a hydrophilic CM5 sensor chip, and AFM observations confirmed that bR molecules are exposed on the SAM surface. Of the lipids tested, S-TGA-1, a halobacterium-derived glycolipid, had the highest specificity to bR with a nanomolar dissociation constant. This is consistent with the reported co-crystal structure that indicates the formation of several intermolecular hydrogen bonds. Therefore, we not only reproduced the specific lipid-bR recognition, but also succeeded in its quantitative evaluation, demonstrating the validity and utility of this method.
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Affiliation(s)
- Masataka Inada
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Masanao Kinoshita
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Ayumi Sumino
- Department of Molecular Physiology and Biophysics, Faculty of Medical Sciences, University of Fukui, Fukui, 910-1193, Japan; High-speed AFM for Biological Application Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, 920-1192, Japan; Bio-AFM Frontier Research Center, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Shigetoshi Oiki
- Department of Molecular Physiology and Biophysics, Faculty of Medical Sciences, University of Fukui, Fukui, 910-1193, Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
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11
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Moghadam NH, Salehzadeh S, Tanzadehpanah H, Saidijam M, Karimi J, Khazalpour S. In vitro cytotoxicity and DNA/HSA interaction study of triamterene using molecular modelling and multi-spectroscopic methods. J Biomol Struct Dyn 2018; 37:2242-2253. [PMID: 30043689 DOI: 10.1080/07391102.2018.1489305] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The anticancer activity of triamterene on HCT116 and CT26 colon cancer cells lines was investigated. Furthermore, the mechanism of interaction between triamterene and calf thymus DNA (ct-DNA) and also human serum albumin (HSA) was conducted using spectroscopic and molecular docking techniques. In vitro cytotoxicity of triamterene against HCT116 and CT26 cells showed promising anticancer effects with IC50 values of 31.30 and 24.45 μM, respectively. Competitive studies of the triamterene with NR (neutral red) and MB (methylene blue) as intercalator probes showed that triamterene can be replaced by these probes. The viscosity data also confirmed that triamterene binds to calf-thymus DNA through intercalation binding mode. Binding properties of triamterene with HSA in the presence of warfarin and ibuprofen showed that triamterene competes with warfarin for the site I of human serum albumin (HSA). In addition, the binding modes of triamterene with DNA and HSA were verified by molecular docking technique. Abbreviations ct-DNA calf thymus DNA CV cyclic voltammetry DNA deoxyribonucleic acid DPV differential pulse voltammetry FBS fetal bovine serum HSA human serum albumin NR neutral red MB methylene blue MTT 3-(4,5-dimethylthiazol-2yl)-2,5-diphenyltetrazoliumbromide Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Hamid Tanzadehpanah
- b Research Center for Molecular Medicine , Hamadan University of Medical Sciences , Hamadan , Iran
| | - Massoud Saidijam
- b Research Center for Molecular Medicine , Hamadan University of Medical Sciences , Hamadan , Iran
| | - Jamshid Karimi
- c Department of Biochemistry , Hamadan University of Medical Sciences , Hamadan , Iran
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12
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Limo MJ, Sola-Rabada A, Boix E, Thota V, Westcott ZC, Puddu V, Perry CC. Interactions between Metal Oxides and Biomolecules: from Fundamental Understanding to Applications. Chem Rev 2018; 118:11118-11193. [PMID: 30362737 DOI: 10.1021/acs.chemrev.7b00660] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Metallo-oxide (MO)-based bioinorganic nanocomposites promise unique structures, physicochemical properties, and novel biochemical functionalities, and within the past decade, investment in research on materials such as ZnO, TiO2, SiO2, and GeO2 has significantly increased. Besides traditional approaches, the synthesis, shaping, structural patterning, and postprocessing chemical functionalization of the materials surface is inspired by strategies which mimic processes in nature. Would such materials deliver new technologies? Answering this question requires the merging of historical knowledge and current research from different fields of science. Practically, we need an effective defragmentation of the research area. From our perspective, the superficial accounting of material properties, chemistry of the surfaces, and the behavior of biomolecules next to such surfaces is a problem. This is particularly of concern when we wish to bridge between technologies in vitro and biotechnologies in vivo. Further, besides the potential practical technological efficiency and advantages such materials might exhibit, we have to consider the wider long-term implications of material stability and toxicity. In this contribution, we present a critical review of recent advances in the chemistry and engineering of MO-based biocomposites, highlighting the role of interactions at the interface and the techniques by which these can be studied. At the end of the article, we outline the challenges which hamper progress in research and extrapolate to developing and promising directions including additive manufacturing and synthetic biology that could benefit from molecular level understanding of interactions occurring between inanimate (abiotic) and living (biotic) materials.
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Affiliation(s)
- Marion J Limo
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom.,Interface and Surface Analysis Centre, School of Pharmacy , University of Nottingham , University Park, Nottingham NG7 2RD , United Kingdom
| | - Anna Sola-Rabada
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Estefania Boix
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom.,Department of Bioproducts and Biosystems , Aalto University , P.O. Box 16100, FI-00076 Aalto , Finland
| | - Veeranjaneyulu Thota
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Zayd C Westcott
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Valeria Puddu
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Carole C Perry
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
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13
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Zhang W, Xie F, Liu X, Luo J, Wu J, Wang Z. Pectin from Black Tomato Pomace: Characterization, Interaction with Gallotannin, and Emulsifying Stability Properties. STARCH-STARKE 2018. [DOI: 10.1002/star.201800172] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Wei Zhang
- Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University; NO. 800, Dongchuan Road Shanghai 200240 China
| | - Fan Xie
- Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University; NO. 800, Dongchuan Road Shanghai 200240 China
| | - Xiaohui Liu
- College of Longrun Pu-erh Tea, Yunnan Agriculturual University; Kunming 650201 Yunnan China
| | - Jing Luo
- Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University; NO. 800, Dongchuan Road Shanghai 200240 China
| | - Jinhong Wu
- Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University; NO. 800, Dongchuan Road Shanghai 200240 China
| | - Zhengwu Wang
- Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University; NO. 800, Dongchuan Road Shanghai 200240 China
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14
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Choudhury R, Ramamurthy V. Understanding the complexation of aliphatic and aromatic acids guests with octa acid. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3795] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Rajib Choudhury
- Department of Chemistry; University of Miami; Coral Gables FL USA
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15
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Mirtič J, Ilaš J, Kristl J. Influence of different classes of crosslinkers on alginate polyelectrolyte nanoparticle formation, thermodynamics and characteristics. Carbohydr Polym 2017; 181:93-102. [PMID: 29254056 DOI: 10.1016/j.carbpol.2017.10.040] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 09/22/2017] [Accepted: 10/09/2017] [Indexed: 11/30/2022]
Abstract
Complexation of linear alginate polyanions with different classes of crosslinkers (divalent cations, polycations, positively charged surfactants) was investigated, to unravel their effects on nanoparticle formation. The goal was to define the crosslinker-to-alginate molar ratios at which nanoparticles are formed, and to reveal the underlying thermodynamics and molecular interactions using dynamic and electrophoretic light scattering, isothermal titration calorimetry, and infrared spectroscopy. Alginate nanoparticles were formed across a limited range of molar ratios that was specific for each crosslinker, and had different size and stability. Thermodynamic parameters of alginate complexation with crosslinkers showed that nanoparticle formation was in all cases entropy driven, together with a minor enthalpic contribution. The crosslinking mechanism was based on ionic interactions, with accompanying weaker interactions specific for each crosslinker, and involved characteristic macroscopic association constants (Ka1) for complexation of alginate (range, 104-109M-1). Additionally, the ionic strengths of the media influenced the characteristics and stabilities of the polyelectrolyte nanoparticles.
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Affiliation(s)
- Janja Mirtič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia.
| | - Janez Ilaš
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia.
| | - Julijana Kristl
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia.
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16
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Niroomand H, Mukherjee D, Khomami B. Tuning the photoexcitation response of cyanobacterial Photosystem I via reconstitution into Proteoliposomes. Sci Rep 2017; 7:2492. [PMID: 28559589 PMCID: PMC5449388 DOI: 10.1038/s41598-017-02746-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 04/19/2017] [Indexed: 12/25/2022] Open
Abstract
The role of natural thylakoid membrane housing of Photosystem I (PSI), the transmembrane photosynthetic protein, in its robust photoactivated charge separation with near unity quantum efficiency is not fundamentally understood. To this end, incorporation of suitable protein scaffolds for PSI incorporation is of great scientific and device manufacturing interest. Areas of interest include solid state bioelectronics, and photoelectrochemical devices that require bio-abio interfaces that do not compromise the photoactivity and photostability of PSI. Therefore, the surfactant-induced membrane solubilization of a negatively charged phospholipid (DPhPG) with the motivation of creating biomimetic reconstructs of PSI reconstitution in DPhPG liposomes is studied. Specifically, a simple yet elegant method for incorporation of PSI trimeric complexes into DPhPG bilayer membranes that mimic the natural thylakoid membrane housing of PSI is introduced. The efficacy of this method is demonstrated via absorption and fluorescence spectroscopy measurements as well as direct visualization using atomic force microscopy. This study provides direct evidence that PSI confinements in synthetic lipid scaffolds can be used for tuning the photoexcitation characteristics of PSI. Hence, it paves the way for development of fundamental understanding of microenvironment alterations on photochemical response of light activated membrane proteins.
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Affiliation(s)
- Hanieh Niroomand
- Sustainable Energy Education and Research Center (SEERC), Knoxville, USA.,Department of Chemical and Biomolecular Engineering, Knoxville, USA
| | - Dibyendu Mukherjee
- Sustainable Energy Education and Research Center (SEERC), Knoxville, USA. .,Department of Chemical and Biomolecular Engineering, Knoxville, USA. .,Department of Mechanical, Aerospace and Biomedical Engineering, University of Tennessee, Knoxville, USA.
| | - Bamin Khomami
- Sustainable Energy Education and Research Center (SEERC), Knoxville, USA. .,Department of Chemical and Biomolecular Engineering, Knoxville, USA. .,Department of Mechanical, Aerospace and Biomedical Engineering, University of Tennessee, Knoxville, USA.
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17
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Al-Otaibi JS, EL Gogary TM. Synthesis of novel anthraquinones: Molecular structure, molecular chemical reactivity descriptors and interactions with DNA as antibiotic and anti-cancer drugs. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.10.098] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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Yu S, Schuchardt M, Tölle M, van der Giet M, Zidek W, Dzubiella J, Ballauff M. Interaction of human serum albumin with uremic toxins: a thermodynamic study. RSC Adv 2017. [DOI: 10.1039/c7ra02838e] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Interaction of uremic toxins with HSA is studied by ITC and understood in terms of thermodynamic driving forces.
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Affiliation(s)
- Shun Yu
- Soft Matter and Functional Materials
- Helmholtz-Zentrum Berlin
- 14109 Berlin
- Germany
- Helmholtz Virtual Institute “Multifunctional Biomaterials for Medicine”
| | - Mirjam Schuchardt
- Medizinische Klinik für Nephrologie
- Universitätsmedizin Berlin
- Campus Benjamin Franklin
- 12203 Berlin
- Germany
| | - Markus Tölle
- Medizinische Klinik für Nephrologie
- Universitätsmedizin Berlin
- Campus Benjamin Franklin
- 12203 Berlin
- Germany
| | - Markus van der Giet
- Medizinische Klinik für Nephrologie
- Universitätsmedizin Berlin
- Campus Benjamin Franklin
- 12203 Berlin
- Germany
| | - Walter Zidek
- Medizinische Klinik für Nephrologie
- Universitätsmedizin Berlin
- Campus Benjamin Franklin
- 12203 Berlin
- Germany
| | - Joachim Dzubiella
- Soft Matter and Functional Materials
- Helmholtz-Zentrum Berlin
- 14109 Berlin
- Germany
- Helmholtz Virtual Institute “Multifunctional Biomaterials for Medicine”
| | - Matthias Ballauff
- Soft Matter and Functional Materials
- Helmholtz-Zentrum Berlin
- 14109 Berlin
- Germany
- Helmholtz Virtual Institute “Multifunctional Biomaterials for Medicine”
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19
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Shukla R, Saeed A, Simpson J, Chopra D. Quantitative investigation of C–H⋯π and other intermolecular interactions in a series of crystalline N-(substituted phenyl)-2-naphthamide derivatives. CrystEngComm 2017. [DOI: 10.1039/c7ce01310h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, we have investigated the nature and characteristics of different intermolecular interactions present in a series of sevenN-(substituted phenyl)-2-naphthamides.
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Affiliation(s)
- Rahul Shukla
- Crystallography and Crystal Chemistry Laboratory
- Department of Chemistry
- IISER Bhopal
- Bhopal 462066
- India
| | - Aamer Saeed
- Department of Chemistry
- Quaid-i-Azam University-45320
- Islamabad
- Pakistan
| | - Jim Simpson
- Department of Chemistry
- University of Otago
- Dunedin 9054
- New Zealand
| | - Deepak Chopra
- Crystallography and Crystal Chemistry Laboratory
- Department of Chemistry
- IISER Bhopal
- Bhopal 462066
- India
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20
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Shukla R, Khan I, Ibrar A, Simpson J, Chopra D. Complex electronic interplay of σ-hole and π-hole interactions in crystals of halogen substituted 1,3,4-oxadiazol-2(3H)-thiones. CrystEngComm 2017. [DOI: 10.1039/c7ce00678k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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21
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Interaction of anthraquinone anti-cancer drugs with DNA:Experimental and computational quantum chemical study. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.08.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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22
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Černochová Z, Bogomolova A, Borisova OV, Filippov SK, Černoch P, Billon L, Borisov OV, Štěpánek P. Thermodynamics of the multi-stage self-assembly of pH-sensitive gradient copolymers in aqueous solutions. SOFT MATTER 2016; 12:6788-6798. [PMID: 27451979 DOI: 10.1039/c6sm01105e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The self-assembly thermodynamics of pH-sensitive di-block and tri-block gradient copolymers of acrylic acid and styrene was studied for the first time using isothermal titration calorimetry (ITC) and dynamic light scattering (DLS) performed at varying pH. We were able to monitor each step of micellization as a function of decreasing pH. The growth of micelles is a multi-stage process that is pH dependent with several exothermic and endothermic components. The first step of protonation of the acrylic acid monomer units was accompanied mainly by conformational changes and the beginning of self-assembly. In the second stage of self-assembly, the micelles become larger and the number of micelles becomes smaller. While solution acidity increases, the isothermal calorimetry data show a broad deep minimum corresponding to an exothermic process attributed to an increase in the size of hydrophobic domains and an increase in the structure's hydrophobicity. The minor change in heat capacity (ΔCp) confirms the structural changes during this exothermic process. The exothermic process terminates deionization of acrylic acid. The pH-dependence of the ζ-potential of the block gradient copolymer micelles exhibits a plateau in the regime corresponding to the pH-controlled variation of the micellar dimensions. The onset of micelle formation and the solubility of the gradient copolymers were found to be dependent on the length of the gradient block.
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Affiliation(s)
- Zulfiya Černochová
- Institute of Macromolecular Chemistry AS CR, v.v.i., Heyrovského nám. 2, CZ-162 06 Praha 6, Czech Republic.
| | - Anna Bogomolova
- Institute of Macromolecular Chemistry AS CR, v.v.i., Heyrovského nám. 2, CZ-162 06 Praha 6, Czech Republic.
| | - Olga V Borisova
- UPPA, CNRS UMR 5254 IPREM Equipe de Physique et Chimie des Polymères, Pau, France
| | - Sergey K Filippov
- Institute of Macromolecular Chemistry AS CR, v.v.i., Heyrovského nám. 2, CZ-162 06 Praha 6, Czech Republic.
| | - Peter Černoch
- Institute of Macromolecular Chemistry AS CR, v.v.i., Heyrovského nám. 2, CZ-162 06 Praha 6, Czech Republic.
| | - Laurent Billon
- UPPA, CNRS UMR 5254 IPREM Equipe de Physique et Chimie des Polymères, Pau, France
| | - Oleg V Borisov
- UPPA, CNRS UMR 5254 IPREM Equipe de Physique et Chimie des Polymères, Pau, France and St.Petersburg National Research University of Information Technologies, Mechanics and Optics, 197101, St.Petersburg, Russia
| | - Petr Štěpánek
- Institute of Macromolecular Chemistry AS CR, v.v.i., Heyrovského nám. 2, CZ-162 06 Praha 6, Czech Republic.
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23
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Abstract
On the basis of many literature measurements, a critical overview is given on essential noncovalent interactions in synthetic supramolecular complexes, accompanied by analyses with selected proteins. The methods, which can be applied to derive binding increments for single noncovalent interactions, start with the evaluation of consistency and additivity with a sufficiently large number of different host-guest complexes by applying linear free energy relations. Other strategies involve the use of double mutant cycles, of molecular balances, of dynamic combinatorial libraries, and of crystal structures. Promises and limitations of these strategies are discussed. Most of the analyses stem from solution studies, but a few also from gas phase. The empirically derived interactions are then presented on the basis of selected complexes with respect to ion pairing, hydrogen bonding, electrostatic contributions, halogen bonding, π-π-stacking, dispersive forces, cation-π and anion-π interactions, and contributions from the hydrophobic effect. Cooperativity in host-guest complexes as well as in self-assembly, and entropy factors are briefly highlighted. Tables with typical values for single noncovalent free energies and polarity parameters are in the Supporting Information.
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Affiliation(s)
- Frank Biedermann
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Hans-Jörg Schneider
- FR Organische Chemie der Universität des Saarlandes , D-66041 Saarbrücken, Germany
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24
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Monje-Galvan V, Klauda JB. Peripheral membrane proteins: Tying the knot between experiment and computation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1584-93. [PMID: 26903211 DOI: 10.1016/j.bbamem.2016.02.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/05/2016] [Accepted: 02/12/2016] [Indexed: 01/31/2023]
Abstract
Experimental biology has contributed to answer questions about the morphology of a system and how molecules organize themselves to maintain a healthy functional cell. Single-molecule techniques, optical and magnetic experiments, and fluorescence microscopy have come a long way to probe structural and dynamical information at multiple scales. However, some details are simply too small or the processes are too short-lived to detect by experiments. Computational biology provides a bridge to understand experimental results at the molecular level, makes predictions that have not been seen in vivo, and motivates new fields of research. This review focuses on the advances on peripheral membrane proteins (PMPs) studies; what is known about their interaction with membranes, their role in cell biology, and some limitations that both experiment and computation still have to overcome to gain better structural and functional understanding of these PMPs. As many recent reviews have acknowledged, interdisciplinary efforts between experiment and computation are needed in order to have useful models that lead future directions in the study of PMPs. We present new results of a case study on a PMP that behaves as an intricate machine controlling lipid homeostasis between cellular organelles, Osh4 in yeast Saccharomyces cerevisiae. Molecular dynamics simulations were run to examine the interaction between the protein and membrane models that reflect the lipid diversity of the endoplasmic reticulum and trans-Golgi membranes. Our study is consistent with experimental data showing several residues that interact to smaller or larger extent with the bilayer upon stable binding (~200 ns into the trajectory). We identified PHE239 as a key residue stabilizing the protein-membrane interaction along with two other binding regions, the ALPS-like motif and the β6-β7 loops in the mouth region of the protein. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- Viviana Monje-Galvan
- Department of Chemical and Biomolecular Engineering, College Park, MD 20742, USA
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, College Park, MD 20742, USA; Biophysics Program, University of Maryland, College Park, MD 20742, USA.
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25
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26
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Shukla R, Chopra D. Characterization of N⋯O non-covalent interactions involving σ-holes: “electrostatics” or “dispersion”. Phys Chem Chem Phys 2016; 18:29946-29954. [DOI: 10.1039/c6cp05899j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Exploring the possibility of formation of pnicogen bonds or chalcogen bonds by utilizing the σ-holes present on nitrogen and oxygen atoms in per-halo substituted complexes.
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Affiliation(s)
- Rahul Shukla
- Crystallography and Crystal Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal-462066
- India
| | - Deepak Chopra
- Crystallography and Crystal Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal-462066
- India
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27
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Shukla R, Chopra D. “Pnicogen bonds” or “chalcogen bonds”: exploiting the effect of substitution on the formation of P⋯Se noncovalent bonds. Phys Chem Chem Phys 2016; 18:13820-9. [DOI: 10.1039/c6cp01703g] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A direct comparison of pnicogen bonds and chalcogen bonds in P⋯Se non-covalent interactions.
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Affiliation(s)
- Rahul Shukla
- Crystallography and Crystal Chemistry Laboratory Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal 462066
- India
| | - Deepak Chopra
- Crystallography and Crystal Chemistry Laboratory Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal 462066
- India
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28
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Shukla R, Chopra D. Exploring the Role of Substitution on the Formation of Se···O/N Noncovalent Bonds. J Phys Chem B 2015; 119:14857-70. [DOI: 10.1021/acs.jpcb.5b08684] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Rahul Shukla
- Crystallography
and Crystal
Chemistry Laboratory Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, Madhya Pradesh, India
| | - Deepak Chopra
- Crystallography
and Crystal
Chemistry Laboratory Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, Madhya Pradesh, India
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29
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Zheng W, Li G, Li X. Affinity purification in target identification: the specificity challenge. Arch Pharm Res 2015; 38:1661-85. [DOI: 10.1007/s12272-015-0635-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/07/2015] [Indexed: 12/16/2022]
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30
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Lin D, Lopez-Sanchez P, Gidley MJ. Binding of arabinan or galactan during cellulose synthesis is extensive and reversible. Carbohydr Polym 2015; 126:108-21. [DOI: 10.1016/j.carbpol.2015.03.048] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 03/05/2015] [Accepted: 03/06/2015] [Indexed: 02/05/2023]
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31
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Smith RJ, Beck RW, Prevette LE. Impact of molecular weight and degree of conjugation on the thermodynamics of DNA complexation and stability of polyethylenimine-graft-poly(ethylene glycol) copolymers. Biophys Chem 2015; 203-204:12-21. [DOI: 10.1016/j.bpc.2015.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 04/27/2015] [Accepted: 04/28/2015] [Indexed: 12/13/2022]
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32
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Yu S, Xu X, Yigit C, van der Giet M, Zidek W, Jankowski J, Dzubiella J, Ballauff M. Interaction of human serum albumin with short polyelectrolytes: a study by calorimetry and computer simulations. SOFT MATTER 2015; 11:4630-4639. [PMID: 25959568 DOI: 10.1039/c5sm00687b] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present a comprehensive study of the interaction of human serum albumin (HSA) with poly(acrylic acid) (PAA; number average degree of polymerization: 25) in aqueous solution. The interaction of HSA with PAA is studied in dilute solution as a function of the concentration of added salt (20-100 mM) and temperature (25-37 °C). Isothermal titration calorimetry (ITC) is used to analyze the interaction and to determine the binding constant and related thermodynamic data. It is found that only one PAA chain is bound per HSA molecule. The free energy of binding ΔGb increases with temperature significantly. ΔGb decreases with increasing salt concentration and is dominated by entropic contributions due to the release of bound counterions. Coarse-grained Langevin computer simulations treating the counterions in an explicit manner are used to study the process of binding in detail. These simulations demonstrate that the PAA chains are bound in the Sudlow II site of HSA. Moreover, ΔGb is calculated from the simulations and found to be in very good agreement with the measured data. The simulations demonstrate clearly that the driving force of binding is the release of counterions in full agreement with the ITC-data.
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Affiliation(s)
- Shun Yu
- Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin, Hahn-Meitner Platz 1, 14109 Berlin, Germany.
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33
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Kinoshita M, Kim JY, Kume S, Sakakibara Y, Sugiki T, Kojima C, Kurisu G, Ikegami T, Hase T, Kimata-Ariga Y, Lee YH. Physicochemical nature of interfaces controlling ferredoxin NADP(+) reductase activity through its interprotein interactions with ferredoxin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1200-11. [PMID: 26087388 DOI: 10.1016/j.bbabio.2015.05.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/27/2015] [Accepted: 05/29/2015] [Indexed: 01/27/2023]
Abstract
Although acidic residues of ferredoxin (Fd) are known to be essential for activities of various Fd-dependent enzymes, including ferredoxin NADP(+) reductase (FNR) and sulfite reductase (SiR), through electrostatic interactions with basic residues of partner enzymes, non-electrostatic contributions such as hydrophobic forces remain largely unknown. We herein demonstrated that intermolecular hydrophobic and charge-charge interactions between Fd and enzymes were both critical for enzymatic activity. Systematic site-directed mutagenesis, which altered physicochemical properties of residues on the interfaces of Fd for FNR /SiR, revealed various changes in activities of both enzymes. The replacement of serine 43 of Fd to a hydrophobic residue (S43W) and charged residue (S43D) increased and decreased FNR activity, respectively, while S43W showed significantly lower SiR activity without affecting SiR activity by S43D, suggesting that hydrophobic and electrostatic interprotein forces affected FNR activity. Enzyme kinetics revealed that changes in FNR activity by mutating Fd correlated with Km, but not with kcat or activation energy, indicating that interprotein interactions determined FNR activity. Calorimetry-based binding thermodynamics between Fd and FNR showed different binding modes of FNR to wild-type, S43W, or S43D, which were controlled by enthalpy and entropy, as shown by the driving force plot. Residue-based NMR spectroscopy of (15)N FNR with Fds also revealed distinct binding modes of each complex based on different directions of NMR peak shifts with similar overall chemical shift differences. We proposed that subtle adjustments in both hydrophobic and electrostatic forces were critical for enzymatic activity, and these results may be applicable to protein-based electron transfer systems.
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Affiliation(s)
- Misaki Kinoshita
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Ju Yaen Kim
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Satoshi Kume
- Cellular Function Imaging Team, Division of Bio-function Dynamics Imaging, RIKEN Center for Life Science Technologies, Kobe, Hyogo 650-0047, Japan
| | - Yukiko Sakakibara
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Toshihiko Sugiki
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Chojiro Kojima
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Takahisa Ikegami
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Toshiharu Hase
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Yoko Kimata-Ariga
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan.
| | - Young-Ho Lee
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan.
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Pathak J, Rawat K, Bohidar HB. Charge heterogeneity induced binding and phase stability in β-lacto-globulin–gelatin B gels and coacervates at their common pI. RSC Adv 2015. [DOI: 10.1039/c5ra07195j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
An understanding of the interactions between gelatin B (GB) and β-lacto-globulin (β-Lg) mainly arising from surface selective patch binding occurring at their common pI (≈5.0 ± 0.5) in the absence of added salt.
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Affiliation(s)
- Jyotsana Pathak
- Polymer and Biophysics Laboratory
- School of Physical Sciences
- Jawaharlal Nehru University
- New Delhi 110067
- India
| | - Kamla Rawat
- Special Center for Nanosciences
- Jawaharlal Nehru University
- New Delhi 110067
- India
- Inter University Accelerator Centre (IUAC)
| | - H. B. Bohidar
- Polymer and Biophysics Laboratory
- School of Physical Sciences
- Jawaharlal Nehru University
- New Delhi 110067
- India
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35
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Deleu M, Crowet JM, Nasir MN, Lins L. Complementary biophysical tools to investigate lipid specificity in the interaction between bioactive molecules and the plasma membrane: A review. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:3171-3190. [DOI: 10.1016/j.bbamem.2014.08.023] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 08/05/2014] [Accepted: 08/21/2014] [Indexed: 02/08/2023]
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Estácio SG, Leal SS, Cristóvão JS, Faísca PFN, Gomes CM. Calcium binding to gatekeeper residues flanking aggregation-prone segments underlies non-fibrillar amyloid traits in superoxide dismutase 1 (SOD1). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:118-26. [PMID: 25463043 DOI: 10.1016/j.bbapap.2014.11.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 11/14/2014] [Accepted: 11/18/2014] [Indexed: 12/26/2022]
Abstract
Calcium deregulation is a central feature among neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Calcium accumulates in the spinal and brain stem motor neurons of ALS patients triggering multiple pathophysiological processes which have been recently shown to include direct effects on the aggregation cascade of superoxide dismutase 1 (SOD1). SOD1 is a Cu/Zn enzyme whose demetallated form is implicated in ALS protein deposits, contributing to toxic gain of function phenotypes. Here we undertake a combined experimental and computational study aimed at establishing the molecular details underlying the regulatory effects of Ca(2+) over SOD1 aggregation potential. Isothermal titration calorimetry indicates entropy driven low affinity association of Ca(2+) ions to apo SOD1, at pH7.5 and 37°C. Molecular dynamics simulations denote a noticeable loss of native structure upon Ca(2+) association that is especially prominent at the zinc-binding and electrostatic loops, whose decoupling is known to expose the central SOD1 β-barrel triggering aggregation. Structural mapping of the preferential apo SOD1 Ca(2+) binding locations reveals that among the most frequent ligands for Ca(2+) are negatively-charged gatekeeper residues located in boundary positions with respect to segments highly prone to edge-to-edge aggregation. Calcium interactions thus diminish gatekeeping roles of these residues, by shielding repulsive interactions via stacking between aggregating β-sheets, partly blocking fibril formation and promoting amyloidogenic oligomers such as those found in ALS inclusions. Interestingly, many fALS mutations occur at these positions, disclosing how Ca(2+) interactions recreate effects similar to those of genetic defects, a finding with relevance to understand sporadic ALS pathomechanisms.
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Affiliation(s)
- Sílvia G Estácio
- Centro de Física da Matéria Condensada, Universidade de Lisboa, Lisboa, Portugal; Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.
| | - Sónia S Leal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Joana S Cristóvão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Patrícia F N Faísca
- Centro de Física da Matéria Condensada, Universidade de Lisboa, Lisboa, Portugal; Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.
| | - Cláudio M Gomes
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
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del Rosso MG, Ciesielski A, Colella S, Harrowfield JM, Samorì P. Isothermal titration calorimetry study of a bistable supramolecular system: reversible complexation of cryptand[2.2.2] with potassium ions. Chemphyschem 2014; 15:2743-8. [PMID: 24986754 DOI: 10.1002/cphc.201402296] [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: 05/03/2014] [Indexed: 11/11/2022]
Abstract
Isothermal titration calorimetry (ITC) is used to investigate the thermodynamics of the complexation of potassium ions by 1,10-diaza-4,7,13,16,21,24-hexaoxabicyclo[8.8.8]hexacosane (cryptand[2.2.2]) in aqueous solution. By changing the pH of the solution it was possible to trigger the reversible complexation/decomplexation of the cryptand in consecutive in situ experiments and to assess for the first time the use of ITC to monitor the thermodynamics of a bistable system.
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Affiliation(s)
- Maria G del Rosso
- ISIS & icFRC, Université de Strasbourg & CNRS, 8 allée Gaspard Monge, 67000 Strasbourg (France)
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38
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Fuenzalida JP, Weikert T, Hoffmann S, Vila-Sanjurjo C, Moerschbacher BM, Goycoolea FM, Kolkenbrock S. Affinity protein-based FRET tools for cellular tracking of chitosan nanoparticles and determination of the polymer degree of acetylation. Biomacromolecules 2014; 15:2532-9. [PMID: 24835451 DOI: 10.1021/bm500394v] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Chitosan (CS) is a family of linear polysaccharides with diverse applications in medicine, agriculture, and industry. Its bioactive properties are determined by parameters such as the degree of acetylation (DA), but current techniques to measure the DA are laborious and require large amounts of substrate and sophisticated equipment. It is also challenging to monitor the fate of chitosan-based nanoparticles (CS-NPs) in vitro because current tools cannot measure their enzymatic or chemical degradation. We have developed a method based on the Förster resonance energy transfer (FRET) that occurs between two independent fluorescent proteins fused to a CS-binding domain, who interact with CS polymers or CS-NPs. We used this approach to calibrate a simple and rapid analytical method that can determine the DA of CS substrates. We showed unequivocally that FRET occurs on the surface of CS-NPs and that the FRET signal is quenched by enzymatic degradation of the CS substrate. Finally, we provide in vitro proof-of-concept that these approaches can be used to label CS-NPs and colocalize them following their interactions with mammalian cells.
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Affiliation(s)
- J P Fuenzalida
- IBBP, Westfälische Wilhelms-Universität Münster Schlossgarten 3, 48149, Münster, Germany
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Nasrolahi Shirazi A, Tiwari RK, Oh D, Banerjee A, Yadav A, Parang K. Efficient delivery of cell impermeable phosphopeptides by a cyclic peptide amphiphile containing tryptophan and arginine. Mol Pharm 2013; 10:2008-20. [PMID: 23537165 DOI: 10.1021/mp400046u] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Phosphopeptides are valuable reagent probes for studying protein-protein and protein-ligand interactions. The cellular delivery of phosphopeptides is challenging because of the presence of the negatively charged phosphate group. The cellular uptake of a number of fluorescent-labeled phosphopeptides, including F'-GpYLPQTV, F'-NEpYTARQ, F'-AEEEIYGEFEAKKKK, F'-PEpYLGLD, F'-pYVNVQN-NH2, and F'-GpYEEI (F' = fluorescein), was evaluated in the presence or absence of a [WR]4, a cyclic peptide containing alternative arginine (R) and tryptophan (W) residues, in human leukemia cells (CCRF-CEM) after 2 h incubation using flow cytometry. [WR]4 improved significantly the cellular uptake of all phosphopeptides. PEpYLGLD is a sequence that mimics the pTyr1246 of ErbB2 that is responsible for binding to the Chk SH2 domain. The cellular uptake of F'-PEpYLGLD was enhanced dramatically by 27-fold in the presence of [WR]4 and was found to be time-dependent. Confocal microscopy of a mixture of F'-PEpYLGLD and [WR]4 in live cells exhibited intracellular localization and significantly higher cellular uptake compared to that of F'-PEpYLGLD alone. Transmission electron microscopy (TEM) and isothermal calorimetry (ITC) were used to study the interaction of PEpYLGLD and [WR]4. TEM results showed that the mixture of PEpYLGLD and [WR]4 formed noncircular nanosized structures with width and height of 125 and 60 nm, respectively. ITC binding studies confirmed the interaction between [WR]4 and PEpYLGLD. The binding isotherm curves, derived from sequential binding models, showed an exothermic interaction driven by entropy. These studies suggest that amphiphilic peptide [WR]4 can be used as a cellular delivery tool of cell-impermeable negatively charged phosphopeptides.
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Affiliation(s)
- Amir Nasrolahi Shirazi
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
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40
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Keiser J, Manneck T, Kirchhofer C, Braissant O. Isothermal microcalorimetry to study the activity of triclabendazole and its metabolites on juvenile and adult Fasciola hepatica. Exp Parasitol 2012. [PMID: 23206957 DOI: 10.1016/j.exppara.2012.11.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Isothermal microcalorimetry (IMC) is an analytical tool that continuously measures the heat flow generated by chemical, physical or biological processes. We have demonstrated that IMC is a useful tool to analyze drug effects on helminths, including adult Fasciola hepatica. Here, we used IMC to examine the activity of triclabendazole and its metabolites triclabendazole sulphone and triclabendazole sulphoxide on juvenile and adult F. hepatica. Worms (one adult or 2-3 juveniles) were placed in 4 or 20 ml glass ampoules containing RPMI 1640 and the test compound (25-100 μg/ml) and the heat flow and motility of worms was examined with TAM48 and TAMIII isothermal microcalorimetry instruments. IMC was found to be precisely document drug effects on juvenile F. hepatica and confirmed the pronounced effect of the benzimidazole derivatives on the motor activity of F. hepatica. Juvenile F. hepatica incubated with 100 μg/ml triclabendazole, triclabendazole sulphone and triclabendazole sulphoxide showed no movements 8.3, 35 and 6h post-incubation (all p<0.001). The metabolic heat of triclabendazole sulphoxide treated worms (100 μg/ml) was reduced by 50% and 76% 24 and 120 h post-incubation, respectively. Limitations of calorimetric measurements were observed using adult F. hepatica as only three worms could be measured simultaneously and also control worms showed a considerable decrease in heat flow. Adult F. hepatica exposed to triclabendazole, triclabendazole sulphone and triclabendazole sulphoxide showed no movements after 31 (p=0.009), 49 (p>0.05) and 88 (p>0.05)h. In conclusion, IMC is useful to document drug effects on juvenile F. hepatica and since rapid technological developments in this field are occurring IMC might also hold promise to study adult F. hepatica in the near future.
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Affiliation(s)
- Jennifer Keiser
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, CH-4002 Basel, Switzerland.
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41
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Forrey C, Douglas JF, Gilson MK. The Fundamental Role of Flexibility on the Strength of Molecular Binding. SOFT MATTER 2012; 8:6385-6392. [PMID: 22707976 PMCID: PMC3374587 DOI: 10.1039/c2sm25160d] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Non-covalent molecular association underlies a diverse set of biologically and technologically relevant phenomena, including the action of drugs on their biomolecular targets and self- and supra-molecular assembly processes. Computer models employed to model binding frequently use interaction potentials with atomistic detail while neglecting the thermal molecular motions of the binding species. However, errors introduced by this simplification and, more broadly, the thermodynamic consequences of molecular flexibility on binding, are little understood. Here, we isolate the fundamental relationship of molecular flexibility to binding thermodynamics via simulations of simplified molecules with a wide range of flexibilities but the same interaction potential. Disregarding molecular motion is found to generate large errors in binding entropy, enthalpy and free energy, even for molecules that are nearly rigid. Indeed, small decreases in rigidity markedly reduce affinity for highly rigid molecules. Remarkably, precisely the opposite occurs for more flexible molecules, for which increasing flexibility leads to stronger binding affinity. We also find that differences in flexibility suffice to generate binding specificity: for example, a planar surface selectively binds rigid over flexible molecules. Intriguingly, varying molecular flexibility while keeping interaction potentials constant leads to near-linear enthalpy-entropy compensation over a wide range of flexibilities, with the unexpected twist that increasing flexibility produces opposite changes in entropy and enthalpy for molecules in the flexible versus the rigid regime. Molecular flexibility is thus a crucial determinant of binding affinity and specificity and variations in flexibility can lead to strong yet non-intuitive consequences.
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Affiliation(s)
- Christopher Forrey
- Center for Devices and Radiological Health, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20903, USA
| | - Jack F. Douglas
- Polymers Division, National Institute of Standards and Technology, 1 Bureau Drive, Gaithersburg, MD, 20899, USA
| | - Michael K. Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0736, USA
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42
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Walter SM, Kniep F, Rout L, Schmidtchen FP, Herdtweck E, Huber SM. Isothermal Calorimetric Titrations on Charge-Assisted Halogen Bonds: Role of Entropy, Counterions, Solvent, and Temperature. J Am Chem Soc 2012; 134:8507-12. [DOI: 10.1021/ja2119207] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Sebastian M. Walter
- Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching,
Germany
| | - Florian Kniep
- Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching,
Germany
| | - Laxmidhar Rout
- Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching,
Germany
| | - Franz P. Schmidtchen
- Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching,
Germany
| | - Eberhardt Herdtweck
- Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching,
Germany
| | - Stefan M. Huber
- Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching,
Germany
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43
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Ablinger E, Wegscheider S, Keller W, Prassl R, Zimmer A. Effect of protamine on the solubility and deamidation of human growth hormone. Int J Pharm 2012; 427:209-16. [DOI: 10.1016/j.ijpharm.2012.01.061] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 01/30/2012] [Accepted: 01/31/2012] [Indexed: 11/28/2022]
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44
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45
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Zeng Z, Patel J, Lee SH, McCallum M, Tyagi A, Yan M, Shea KJ. Synthetic polymer nanoparticle-polysaccharide interactions: a systematic study. J Am Chem Soc 2012; 134:2681-90. [PMID: 22229911 PMCID: PMC3275679 DOI: 10.1021/ja209959t] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The interaction between synthetic polymer nanoparticles (NPs) and biomacromolecules (e.g., proteins, lipids, and polysaccharides) can profoundly influence the NPs fate and function. Polysaccharides (e.g., heparin/heparin sulfate) are a key component of cell surfaces and the extracelluar matrix and play critical roles in many biological processes. We report a systematic investigation of the interaction between synthetic polymer nanoparticles and polysaccharides by ITC, SPR, and an anticoagulant assay to provide guidelines to engineer nanoparticles for biomedical applications. The interaction between acrylamide nanoparticles (~30 nm) and heparin is mainly enthalpy driven with submicromolar affinity. Hydrogen bonding, ionic interactions, and dehydration of polar groups are identified to be key contributions to the affinity. It has been found that high charge density and cross-linking of the NP can contribute to high affinity. The affinity and binding capacity of heparin can be significantly diminished by an increase in salt concentration while only slightly decreased with an increase of temperature. A striking difference in binding thermodynamics has been observed when the main component of a polymer nanoparticle is changed from acrylamide (enthalpy driven) to N-isopropylacryalmide (entropy driven). This change in thermodynamics leads to different responses of these two types of polymer NPs to salt concentration and temperature. Select synthetic polymer nanoparticles have also been shown to inhibit protein-heparin interactions and thus offer the potential for therapeutic applications.
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Affiliation(s)
- Zhiyang Zeng
- Department of Chemistry, University of California, Irvine, Irvine, CA, 92697
| | - Jiten Patel
- Department of Chemistry, University of California, Irvine, Irvine, CA, 92697
| | - Shih-Hui Lee
- Department of Chemistry, University of California, Irvine, Irvine, CA, 92697
| | - Monica McCallum
- Department of Chemistry, University of California, Irvine, Irvine, CA, 92697
| | - Anuradha Tyagi
- Department of Chemistry, Portland State University, Portland, Oregon, 97207
| | - Mingdi Yan
- Department of Chemistry, Portland State University, Portland, Oregon, 97207
| | - Kenneth J. Shea
- Department of Chemistry, University of California, Irvine, Irvine, CA, 92697
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46
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Li X, Zhang J, Gu H. Study on the adsorption mechanism of DNA with mesoporous silica nanoparticles in aqueous solution. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:2827-2834. [PMID: 22182067 DOI: 10.1021/la204443j] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Among the numerous adsorption strategies for DNA adsorption into mesopores, the salt-solution-induced adsorption method has a great application potential in nucleic acids science; thus, it is important to understand the adsorption mechanism. This work demonstrates the mechanistic aspects underlying the adsorption behaviors of DNA with mesoporous silica nanoparticles (MSNs) in aqueous solution. The driving forces for the adsorption process can be categorized into three parts: the shielded electrostatic force, the dehydration effect, and the intermolecular hydrogen bonds. Compared to the adsorption behaviors of DNA with a solid silica nanosphere, we find some unique features for DNA adsorption into the mesopores, such as increasing the salt concentration or decreasing the pH value can promote DNA adsorption into the mesoporous silica. Further analysis indicates that the entrance of DNA into mesopores is probably controlled by the Debye length in solution and DNA can generate direct and indirect hydrogen bonds in the pores with different diameters. The following desorption study depicts that such types of hydrogen bonds result in different energy barriers for the desorption process. In summary, our study depicts the mechanism of DNA adsorption within mesopores in aqueous solution and sets the stage for formulating MSNs as carriers of nucleic acids.
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Affiliation(s)
- Xu Li
- Nano Biomedical Research Center, School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
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47
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Yang H, An Q, Zhu W, Li W, Jiang Y, Cui J, Zhang X, Li G. A new strategy for effective construction of protein stacks by using cucurbit[8]uril as a glue molecule. Chem Commun (Camb) 2012; 48:10633-5. [DOI: 10.1039/c2cc33380e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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48
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Lubbers B, Baudenbacher F. Isothermal titration calorimetry in nanoliter droplets with subsecond time constants. Anal Chem 2011; 83:7955-61. [PMID: 21913688 DOI: 10.1021/ac202026a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We reduced the reaction volume in microfabricated suspended-membrane titration calorimeters to nanoliter droplets and improved the sensitivities to below a nanowatt with time constants of around 100 ms. The device performance was characterized using exothermic acid-base neutralizations and a detailed numerical model. The finite element based numerical model allowed us to determine the sensitivities within 1% and the temporal dynamics of the temperature rise in neutralization reactions as a function of droplet size. The model was used to determine the optimum calorimeter design (membrane size and thickness, junction area, and thermopile thickness) and sensitivities for sample volumes of 1 nL for silicon nitride and polymer membranes. We obtained a maximum sensitivity of 153 pW/(Hz)(1/2) for a 1 μm SiN membrane and 79 pW/(Hz)(1/2) for a 1 μm polymer membrane. The time constant of the calorimeter system was determined experimentally using a pulsed laser to increase the temperature of nanoliter sample volumes. For a 2.5 nanoliter sample volume, we experimentally determined a noise equivalent power of 500 pW/(Hz)(1/2) and a 1/e time constant of 110 ms for a modified commercially available infrared sensor with a thin-film thermopile. Furthermore, we demonstrated detection of 1.4 nJ reaction energies from injection of 25 pL of 1 mM HCl into a 2.5 nL droplet of 1 mM NaOH.
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Affiliation(s)
- Brad Lubbers
- Department of Biomedical Engineering, VU Station B 351631, Vanderbilt University, Nashville, Tennessee 37232, USA
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49
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Kizilay E, Kayitmazer AB, Dubin PL. Complexation and coacervation of polyelectrolytes with oppositely charged colloids. Adv Colloid Interface Sci 2011; 167:24-37. [PMID: 21803318 DOI: 10.1016/j.cis.2011.06.006] [Citation(s) in RCA: 284] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 06/10/2011] [Accepted: 06/19/2011] [Indexed: 10/18/2022]
Abstract
Polyelectrolyte-colloid coacervation could be viewed as a sub-category of complex coacervation, but is unique in (1) retaining the structure and properties of the colloid, and (2) reducing the heterogeneity and configurational complexity of polyelectrolyte-polyelectrolyte (PE-PE) systems. Interest in protein-polyelectrolyte coacervates arises from preservation of biofunctionality; in addition, the geometric and charge isotropy of micelles allows for better comparison with theory, taking into account the central role of colloid charge density. In the context of these two systems, we describe critical conditions for complex formation and for coacervation with regard to colloid and polyelectrolyte charge densities, ionic strength, PE molecular weight (MW), and stoichiometry; and effects of temperature and shear, which are unique to the PE-micelle systems. The coacervation process is discussed in terms of theoretical treatments and models, as supported by experimental findings. We point out how soluble aggregates, subject to various equilibria and disproportionation effects, can self-assemble leading to heterogeneity in macroscopically homogeneous coacervates, on multiple length scales.
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Chang Y, McLandsborough L, McClements DJ. Interactions of a cationic antimicrobial (ε-polylysine) with an anionic biopolymer (pectin): an isothermal titration calorimetry, microelectrophoresis, and turbidity study. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2011; 59:5579-5588. [PMID: 21462961 DOI: 10.1021/jf104299q] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
ε-Polylysine (ε-PL) is a food-grade cationic antimicrobial that is highly effective against a range of food pathogens and spoilage organisms. In compositionally complex environments, like those found in most foods and beverages, the antimicrobial activity of cationic ε-PL is likely to be impacted by its interactions with anionic components. The purpose of this study was to characterize the interactions between cationic ε-polylysine and an anionic biopolymer (high methoxyl pectin, HMP) using isothermal titration calorimetry (ITC), microelectrophoresis (ME), and turbidity measurements. ITC and ME measurements indicated that ε-PL bound to pectin, while turbidity measurements indicated that the complexes formed could be either soluble or insoluble depending on solution composition. Ionic strength and pH were also shown to affect the interactions significantly, highlighting their electrostatic origin. This study demonstrates that ε-PL can form either soluble or insoluble complexes with anionic biopolymers depending on the composition of the system. Our study provides basic knowledge that will facilitate the more rational application of ε-PL in complex food systems.
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Affiliation(s)
- Yuhua Chang
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts 01003, United States
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