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Villanueva ME, Salinas SR, Vico RV, Bianco ID. Surface characterization and interfacial activity of chitinase chi18-5 against chitosan in langmuir monolayers. Colloids Surf B Biointerfaces 2023; 227:113337. [PMID: 37167692 DOI: 10.1016/j.colsurfb.2023.113337] [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: 03/04/2023] [Revised: 04/26/2023] [Accepted: 05/06/2023] [Indexed: 05/13/2023]
Abstract
One of the challenges for producing active chitinase formulations relies on the gap between the laboratory tests and the biological scenarios where the enzyme will perform its function. In this work, we have employed different Langmuir monolayer arrays to evaluate the interfacial behavior of a recently purified recombinant chitinase, Chi18-5. We have demonstrated that two conformations exist for the chitinase at pH values close to its pI, showing very distinct structural properties at the air/aqueous interface. Enzyme activity was assessed by implementing different kinetic approaches and using a chitosan-1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) mixed film as organized substrate model membrane. Combining these strategies, we demonstrated that better catalytic efficiencies can be obtained for Chi18-5 at pH 5. Moreover, the chitinase activity at the air/aqueous interface can be tuned by introducing in situ pH modifications over the surrounding milieu. We also studied the changes in the topography at the mesoscale level using Brewster Angle Microscopy (BAM). We found that Chi18-5 segregated onto the chitosan domains of the membrane, showing differences in homogeneity depending on the pH imposed. Alternatively, pure Chi18-5 was tested for immobilization onto a hydrophilic activated solid support using the Langmuir-Blodgett technique. Atomic Force Microscopy (AFM) analyses showed successfully stabilization and preservation of molecular features attributed to the pH at which the enzyme deposition was performed.
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Affiliation(s)
- M E Villanueva
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - S R Salinas
- Centro de Excelencia en Productos y Procesos de Córdoba (CEPROCOR), CONICET, Córdoba, Argentina
| | - R V Vico
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC-UNC-CONICET), Departamento de Química Orgánica. Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - I D Bianco
- Centro de Excelencia en Productos y Procesos de Córdoba (CEPROCOR), CONICET, Córdoba, Argentina; Universidad Nacional de La Rioja, Departamento de Ciencias Exactas, Físicas y Naturales, La Rioja, Argentina.
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Structural Biology for the Molecular Insight between Aptamers and Target Proteins. Int J Mol Sci 2021; 22:ijms22084093. [PMID: 33920991 PMCID: PMC8071422 DOI: 10.3390/ijms22084093] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 02/07/2023] Open
Abstract
Aptamers are promising therapeutic and diagnostic agents for various diseases due to their high affinity and specificity against target proteins. Structural determination in combination with multiple biochemical and biophysical methods could help to explore the interacting mechanism between aptamers and their targets. Regrettably, structural studies for aptamer–target interactions are still the bottleneck in this field, which are facing various difficulties. In this review, we first reviewed the methods for resolving structures of aptamer–protein complexes and for analyzing the interactions between aptamers and target proteins. We summarized the general features of the interacting nucleotides and residues involved in the interactions between aptamers and proteins. Challenges and perspectives in current methodologies were discussed. Approaches for determining the binding affinity between aptamers and target proteins as well as modification strategies for stabilizing the binding affinity of aptamers to target proteins were also reviewed. The review could help to understand how aptamers interact with their targets and how alterations such as chemical modifications in the structures affect the affinity and function of aptamers, which could facilitate the optimization and translation of aptamers-based theranostics.
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Paudyal S, Sharma SK, da Silva RL, Mintz KJ, Liyanage PY, Al-Youbi AO, Bashammakh AS, El-Shahawi MS, Leblanc RM. Tyrosinase enzyme Langmuir monolayer: Surface chemistry and spectroscopic study. J Colloid Interface Sci 2020; 564:254-263. [DOI: 10.1016/j.jcis.2019.12.118] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/25/2019] [Accepted: 12/26/2019] [Indexed: 02/08/2023]
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Surface chemistry and spectroscopic studies of the native phenylalanine dehydrogenase Langmuir monolayer at the air/aqueous NaCl interface. J Colloid Interface Sci 2020; 560:458-466. [DOI: 10.1016/j.jcis.2019.10.086] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 02/03/2023]
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Khan AY, Kumar GS. Probing the binding of anticancer drug topotecan with human hemoglobin: Structural and thermodynamic studies. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 163:185-93. [DOI: 10.1016/j.jphotobiol.2016.08.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 01/28/2023]
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Abstract
Interactions between ligands and receptors and subsequent "locking" must involve some resistance to unbinding, manifesting itself as an interaction force. At body temperature, spontaneous unbinding will occur, however, external forces are required to accelerate this process. Bearing in mind the potential forces that the receptor-ligand complex is likely to be subjected to in a biological environment, it might be hypothesised that there is some mechanical matching between the receptor and ligand. To test this hypothesis, various receptor and ligand pairs were unfolded in their entirety in order to determine their total unfolding force. In this way, the total force to unfold the protein could be determined, allowing a comparison between ligand and receptor pairs. The interest of this work is to examine the interaction between five proteins and a mica surface by AFM without any modification to preserve the natural elastic properties of the protein molecules during the force measurements. The results showed a mechanical matching between GP120 (ligand) and CD4 (receptor) when analysing the total force required to unfold the same number of domains or events shown by the force distance curves of these proteins.
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Affiliation(s)
- Ana Peñaherrera
- Department of Chemical Engineering and Advanced Materials, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK.
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Whited AM, Park PSH. Atomic force microscopy: a multifaceted tool to study membrane proteins and their interactions with ligands. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:56-68. [PMID: 23603221 DOI: 10.1016/j.bbamem.2013.04.011] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 03/22/2013] [Accepted: 04/09/2013] [Indexed: 01/31/2023]
Abstract
Membrane proteins are embedded in lipid bilayers and facilitate the communication between the external environment and the interior of the cell. This communication is often mediated by the binding of ligands to the membrane protein. Understanding the nature of the interaction between a ligand and a membrane protein is required to both understand the mechanism of action of these proteins and for the development of novel pharmacological drugs. The highly hydrophobic nature of membrane proteins and the requirement of a lipid bilayer for native function have hampered the structural and molecular characterizations of these proteins under physiologically relevant conditions. Atomic force microscopy offers a solution to studying membrane proteins and their interactions with ligands under physiologically relevant conditions and can provide novel insights about the nature of these critical molecular interactions that facilitate cellular communication. In this review, we provide an overview of the atomic force microscopy technique and discuss its application in the study of a variety of questions related to the interaction between a membrane protein and a ligand. This article is part of a Special Issue entitled: Structural and biophysical characterization of membrane protein-ligand binding.
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Affiliation(s)
- Allison M Whited
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
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Pal P, Mahato M, Kamilya T, Talapatra GB. Interaction of glucose with hemoglobin: a study in aqueous solution and at the air–water interface using the Langmuir–Blodgett technique. Phys Chem Chem Phys 2011; 13:9385-96. [DOI: 10.1039/c0cp02277b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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9
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Abstract
Atomic force microscopy (AFM) can directly visualize single molecules in solution, which makes it an extremely powerful technique for carrying out studies of biological complexes and the processes in which they are involved. A recent development, called Recognition Imaging, allows the identification of a specific type of protein in solution AFM images, a capability that greatly enhances the power of the AFM approach for studies of complex biological materials. In this technique, an antibody against the protein of interest is attached to an AFM tip. Scanning a sample with this tip generates a typical topographic image simultaneously and in exact spatial registration with a "recognition image." The latter identifies the locations of antibody-antigen binding events and thus the locations of the protein of interest in the image field. The recognition image can be electronically superimposed on the topographic image, providing a very accurate map of specific protein locations in the topographic image. This technique has been mainly used in in vitro studies of biological complexes and reconstituted chromatin, but has great potential for studying chromatin and protein complexes isolated from nuclei.
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Lohr D, Bash R, Wang H, Yodh J, Lindsay S. Using atomic force microscopy to study chromatin structure and nucleosome remodeling. Methods 2007; 41:333-41. [PMID: 17309844 PMCID: PMC1876669 DOI: 10.1016/j.ymeth.2006.08.016] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2006] [Accepted: 08/16/2006] [Indexed: 10/23/2022] Open
Abstract
Atomic force microscopy (AFM) is a technique that can directly image single molecules in solution and it therefore provides a powerful tool for obtaining unique insights into the basic properties of biological materials and the functional processes in which they are involved. We have used AFM to analyze basic features of nucleosomes in arrays, such as DNA-histone binding strength, cooperativity in template occupation, nucleosome stabilities, nucleosome locations and the effects of acetylation, to compare these features in different types of arrays and to track the response of array nucleosomes to the action of the human Swi-Snf ATP-dependent nucleosome remodeling complex. These experiments required several specific adaptations of basic AFM methods, such as repetitive imaging of the same fields of molecules in liquid, the ability to change the environmental conditions of the sample being imaged and detection of specific types of molecules within compositionally complex samples. Here, we describe the techniques that allowed such analyses to be carried out.
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Affiliation(s)
- D Lohr
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA.
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Zhang W, Barbagallo R, Madden C, Roberts CJ, Woolford A, Allen S. Progressing single biomolecule force spectroscopy measurements for the screening of DNA binding agents. NANOTECHNOLOGY 2005; 16:2325-2333. [PMID: 20818013 DOI: 10.1088/0957-4484/16/10/055] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Recent studies have indicated that the force-extension properties of single molecules of double stranded (ds) DNA are sensitive to the presence of small molecule DNA binding agents, and also to their mode of binding. These observations raise the possibility of using this approach as a highly sensitive tool for the screening of such agents. However, particularly for studies employing the atomic force microscope (AFM), several non-trivial barriers hinder the progress of this approach to the non-specialist arena and hence also the full realization of this possibility. In this paper, we therefore address a series of key reproducibility and metrological issues associated with this type of measurement. Specifically, we present an improved immobilization method that covalently anchors one end (5' end) of a dual labelled (5'-thiol, 3'-biotin) p53 DNA molecule onto a gold substrate via gold-thiol chemistry, whilst the biotinylated 3' end is available for 'pick-up' using a streptavidin modified AFM tip. We also show that co-surface immobilization of DNA with 6-mercapto-1-hexanol (MCH) can also lead to a further increase the measured contour length. We demonstrate the impact of these improved protocols through the observation of the cooperative transition plateau in a DNA fragment of approximately 118 bp, a significantly smaller fragment than previously investigated. The results of a comparative study of the effects of a model minor groove binder (Hoechst 33258) and an intercalating drug (proflavine), alone, as a mixture and under different buffer conditions, are also presented.
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Affiliation(s)
- Wenke Zhang
- Laboratory of Biophysics and Surface Analysis, School of Pharmacy, The University of Nottingham, Nottingham NG7 2RD, UK
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Epand RM. Do proteins facilitate the formation of cholesterol-rich domains? BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2005; 1666:227-38. [PMID: 15519317 DOI: 10.1016/j.bbamem.2004.07.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2004] [Revised: 07/21/2004] [Accepted: 07/23/2004] [Indexed: 01/10/2023]
Abstract
Both biological and model membranes can exhibit the formation of domains. A brief review of some of the diverse methodologies used to identify the presence of domains in membranes is given. Some of these domains are enriched in cholesterol. The segregation of lipids into cholesterol-rich domains can occur in both pure lipid systems as well as membranes containing peptides and proteins. Peptides and proteins can promote the formation of cholesterol-rich domains not only by preferentially interacting with cholesterol and being sequestered into these regions of the membrane, but also indirectly as a consequence of being excluded from cholesterol-rich domains. The redistribution of components is dictated by the thermodynamics of the system. The formation of domains in a biological membrane is a consequence of all of the intermolecular interactions including those among lipid molecules as well as between lipids and proteins.
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Affiliation(s)
- Richard M Epand
- Department of Biochemistry, McMaster University Hamilton, ON L8N 3Z5, Canada.
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Thomasson DM, Gharib A, Li KCP. A primer on molecular biology for imagers: VIII. Equipment for imaging molecular processes. Acad Radiol 2004; 11:1159-70. [PMID: 15530810 DOI: 10.1016/j.acra.2004.07.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2004] [Accepted: 07/19/2004] [Indexed: 01/22/2023]
Affiliation(s)
- David M Thomasson
- National Institutes of Health, Clinical Center, Building 10, 10 Center Drive, MSC 1182, Bethesda, MD 20892-1182, USA
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Epand RF, Martinou JC, Montessuit S, Epand RM, Yip CM. Direct evidence for membrane pore formation by the apoptotic protein Bax. Biochem Biophys Res Commun 2002; 298:744-9. [PMID: 12419316 DOI: 10.1016/s0006-291x(02)02544-5] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Direct imaging of the interaction of the apoptotic protein, Bax, with membrane bilayers shows the presence of toroidal-shaped pores using atomic force microscopy. These pores are sufficiently large to allow passage of proteins from the intermitochondrial space. Both the perturbation of the membrane and the amount of protein bound to the bilayer are increased in the presence of calcium. The results from the imaging are consistent with leakage studies from liposomes of the same composition. The work shows that Bax by itself can form pores in membrane bilayers.
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Affiliation(s)
- Raquel F Epand
- Department of Biochemistry, McMaster University Health Sciences Centre, Hamilton, Ont., Canada.
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Affiliation(s)
- Christopher Yip
- Department of Chemical Engineering and Applied Chemistry, Institute of Biomaterials and Biomedical Engineering, University of Toronto, 407 Rosebrugh Building, 4 Taddle Creek Road, Toronto, Ontario M5S 3G9 Canada.
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