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Muñoz R, Fuentealba JF, Michea S, Santana PA, Martinez JI, Casanova-Morales N, Salinas-Barrera V. Ultrasonic Sensor: A Fast and Non-Destructive System to Measure the Viscosity and Density of Molecular Fluids. BIOSENSORS 2024; 14:346. [PMID: 39056621 PMCID: PMC11274559 DOI: 10.3390/bios14070346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024]
Abstract
This study presents the design and development of an ultrasonic sensor as a fundamental tool for characterizing the properties of fluids and biofluids. The analysis primarily focuses on measuring the electrical parameters of the system, which correlate with the density and viscosity of the solutions, in sample volumes of microliters and with high temporal resolution (up to 1 data point per second). The use of this sensor allows the fast and non-destructive evaluation of the viscosity and density of fluids deposited on its free surface. The measurements are based on obtaining the impedance versus frequency curve and the phase difference curve (between current and voltage) versus frequency. In this way, characteristic parameters of the transducer, such as the resonance frequency, phase, minimum impedance, and the quality factor of the resonant system, can characterize variations in density and viscosity in the fluid under study. The results obtained revealed the sensor's ability to identify two parameters sensitive to viscosity and two parameters sensitive to density. As a proof of concept, the unfolding of the bovine albumin protein was studied, resulting in a curve that reflects its unfolding kinetics in the presence of urea.
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Affiliation(s)
- Romina Muñoz
- Departamento de Física y Química, Facultad de Ingeniería, Universidad Autónoma de Chile, Av. Pedro de Valdivia 425, Providencia, Santiago 8900000, Chile;
| | - Juan-Francisco Fuentealba
- Escuela de Ingeniería, Universidad Central de Chile, Avda. Santa Isabel 1186, Santiago 8330601, Chile;
| | - Sebastián Michea
- Grupo de Investigación Aplicada en Robótica e Industria 4.0, Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Santiago 7500912, Chile;
| | - Paula A. Santana
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, El Llano Subercaseaux 2801, San Miguel, Santiago 8910060, Chile;
| | - Juan Ignacio Martinez
- Ingeniería Civil Informática, Facultad de Ingeniería, Universidad Autónoma de Chile, Av. Pedro de Valdivia 425, Providencia, Santiago 8900000, Chile;
| | | | - Vicente Salinas-Barrera
- Grupo de Investigación Aplicada en Robótica e Industria 4.0, Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Santiago 7500912, Chile;
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Ha JH, Xu Y, Sekhon H, Zhao W, Wilkens S, Ren D, Loh SN. Mimicking kidney flow shear efficiently induces aggregation of LECT2, a protein involved in renal amyloidosis. J Biol Chem 2024; 300:107231. [PMID: 38537700 PMCID: PMC11040205 DOI: 10.1016/j.jbc.2024.107231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 02/20/2024] [Accepted: 03/15/2024] [Indexed: 04/09/2024] Open
Abstract
Aggregation of leukocyte cell-derived chemotaxin 2 (LECT2) causes ALECT2, a systemic amyloidosis that affects the kidney and liver. Previous studies established that LECT2 fibrillogenesis is accelerated by the loss of its bound zinc ion and stirring/shaking. These forms of agitation create heterogeneous shear conditions, including air-liquid interfaces that denature proteins, that are not present in the body. Here, we determined the extent to which a more physiological form of mechanical stress-shear generated by fluid flow through a network of narrow channels-drives LECT2 fibrillogenesis. To mimic blood flow through the kidney, where LECT2 and other proteins form amyloid deposits, we developed a microfluidic device consisting of progressively branched channels narrowing from 5 mm to 20 μm in width. Shear was particularly pronounced at the branch points and in the smallest capillaries. Aggregation was induced within 24 h by shear levels that were in the physiological range and well below those required to unfold globular proteins such as LECT2. EM images suggested the resulting fibril ultrastructures were different when generated by laminar flow shear versus shaking/stirring. Importantly, results from the microfluidic device showed the first evidence that the I40V mutation accelerated fibril formation and increased both the size and the density of the aggregates. These findings suggest that kidney-like flow shear, in combination with zinc loss, acts in combination with the I40V mutation to trigger LECT2 amyloidogenesis. These microfluidic devices may be of general use for uncovering mechanisms by which blood flow induces misfolding and amyloidosis of circulating proteins.
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Affiliation(s)
- Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Yikang Xu
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York, USA
| | - Harsimranjit Sekhon
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Wenhan Zhao
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York, USA
| | - Stephan Wilkens
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Dacheng Ren
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York, USA; Department of Civil and Environmental Engineering, Syracuse University, Syracuse, New York, USA; Department of Biology, Syracuse University, Syracuse, New York, USA.
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York, USA.
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Ha JH, Xu Y, Sekhon H, Wilkens S, Ren D, Loh SN. Mimicking Kidney Flow Shear Efficiently Induces Aggregation of LECT2, a Protein Involved in Renal Amyloidosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548788. [PMID: 37503176 PMCID: PMC10369975 DOI: 10.1101/2023.07.13.548788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Aggregation of leukocyte cell-derived chemotaxin 2 (LECT2) causes ALECT2, a systemic amyloidosis that affects the kidney and liver. Homozygosity of the I40V LECT2 mutation is believed to be necessary but not sufficient for the disease. Previous studies established that LECT2 fibrillogenesis is greatly accelerated by loss of its single bound zinc ion and stirring or shaking. These forms of agitation are often used to facilitate protein aggregation, but they create heterogeneous shear conditions, including air-liquid interfaces that denature proteins, that are not present in the body. Here, we determined the extent to which a more physiological form of mechanical stress-shear generated by fluid flow through a network of artery and capillary-sized channels-drives LECT2 fibrillogenesis. To mimic blood flow through the human kidney, where LECT2 and other proteins form amyloid deposits, we developed a microfluidic device consisting of progressively branched channels narrowing from 5 mm to 20 μm in width. Flow shear was particularly pronounced at the branch points and in the smallest capillaries, and this induced LECT2 aggregation much more efficiently than conventional shaking methods. EM images suggested the resulting fibril structures were different in the two conditions. Importantly, results from the microfluidic device showed the first evidence that the I40V mutation accelerated fibril formation and increased both size and density of the aggregates. These findings suggest that kidney-like flow shear, in combination with zinc loss, acts in combination with the I40V mutation to trigger LECT2 amyloidogenesis. These microfluidic devices may be of general use for uncovering the mechanisms by which blood flow induces misfolding and amyloidosis of circulating proteins.
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Affiliation(s)
- Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Yikang Xu
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244
| | - Harsimranjit Sekhon
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Stephan Wilkens
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Dacheng Ren
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244
- Department of Civil and Environmental Engineering, Syracuse University, Syracuse, NY 13244
- Department of Biology, Syracuse University, Syracuse, NY 13244
| | - Stewart N. Loh
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
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4
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Trumbore CN, Raghunandan A. An Alzheimer's Disease Mechanism Based on Early Pathology, Anatomy, Vascular-Induced Flow, and Migration of Maximum Flow Stress Energy Location with Increasing Vascular Disease. J Alzheimers Dis 2022; 90:33-59. [PMID: 36155517 DOI: 10.3233/jad-220622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
This paper suggests a chemical mechanism for the earliest stages of Alzheimer's disease (AD). Cerebrospinal fluid (CSF) flow stresses provide the energy needed to induce molecular conformation changes leading to AD by initiating amyloid-β (Aβ) and tau aggregation. Shear and extensional flow stresses initiate aggregation in the laboratory and in natural biophysical processes. Energy-rich CSF flow regions are mainly found in lower brain regions. MRI studies reveal flow stress "hot spots" in basal cisterns and brain ventricles that have chaotic flow properties that can distort molecules such as Aβ and tau trapped in these regions into unusual conformations. Such fluid disturbance is surrounded by tissue deformation. There is strong mapping overlap between the locations of these hot spots and of early-stage AD pathology. Our mechanism creates pure and mixed protein dimers, followed by tissue surface adsorption, and long-term tissue agitation ultimately inducing chemical reactions forming more stable, toxic oligomer seeds that initiate AD. It is proposed that different flow stress energies and flow types in different basal brain regions produce different neurotoxic aggregates. Proliferating artery hardening is responsible for enhanced heart systolic pulses that drive energetic CSF pulses, whose critical maximum systolic pulse energy location migrates further from the heart with increasing vascular disease. Two glymphatic systems, carotid and basilar, are suggested to contain the earliest Aβ and tau AD disease pathologies. A key to the proposed AD mechanism is a comparison of early chronic traumatic encephalopathy and AD pathologies. Experiments that test the proposed mechanism are needed.
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Affiliation(s)
- Conrad N Trumbore
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Aditya Raghunandan
- Department of Mechanical Engineering, University of Rochester, Rochester, NY, USA
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Bogahawaththa D, Vasiljevic T. Shear-induced structural changes and denaturation of bovine immunoglobulin G and serum albumin at different temperatures. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2021.107283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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6
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Krishnamurthy S, Sudhakar S, Mani E. Kinetics of aggregation of amyloid β under different shearing conditions: Experimental and modelling analyses. Colloids Surf B Biointerfaces 2021; 209:112156. [PMID: 34736218 DOI: 10.1016/j.colsurfb.2021.112156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/30/2021] [Accepted: 10/07/2021] [Indexed: 11/16/2022]
Abstract
Amyloid β (Aβ40) is a class of amyloidogenic proteins known to aggregate into a fibrillar network. The rate of aggregation and fibril yield is sensitive to external energy input, such as shear. In this work, simple shear and shaking experiments are performed on Aβ40 solution using a Couette cell and an orbital shaker, respectively. Experiments show that, under uniform shear, both the mass of fibrils and aggregation rate increase with the shear rate. In the case of orbital shaking, the lag time decreases with the rotational speed of the shaker, but the final fibril mass is the same for all agitation speeds. To explain this contrasting behavior of aggregation kinetics, a population balance model is developed to account for the effect of shear on the aggregation of Aβ. The kinetic model includes primary nucleation, secondary nucleation, elongation, fragmentation, and depolymerization steps. The effect of steady uniform shear is encoded in the depolymerization rate constant (kd), and it is shown that kd decreases with shear rate initially and saturates at high shear rates. A competition between elongation and depolymerization rates yields different equilibrium masses of fibril at different shear rates. The model results agree quantitatively well with experimental data on the rate of aggregation and mass of fibrils as a function of shear rate. The modeling framework can be used to explain the shear rate-dependent aggregation of other amyloidogenic proteins.
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Affiliation(s)
- Sriram Krishnamurthy
- Polymer Engineering and Colloid Science Lab, Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai 600036, India
| | - Swathi Sudhakar
- Eberhard Karls Universität Tübingen, ZMBP, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Ethayaraja Mani
- Polymer Engineering and Colloid Science Lab, Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai 600036, India.
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Nguyen PH, Ramamoorthy A, Sahoo BR, Zheng J, Faller P, Straub JE, Dominguez L, Shea JE, Dokholyan NV, De Simone A, Ma B, Nussinov R, Najafi S, Ngo ST, Loquet A, Chiricotto M, Ganguly P, McCarty J, Li MS, Hall C, Wang Y, Miller Y, Melchionna S, Habenstein B, Timr S, Chen J, Hnath B, Strodel B, Kayed R, Lesné S, Wei G, Sterpone F, Doig AJ, Derreumaux P. Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis. Chem Rev 2021; 121:2545-2647. [PMID: 33543942 PMCID: PMC8836097 DOI: 10.1021/acs.chemrev.0c01122] [Citation(s) in RCA: 378] [Impact Index Per Article: 126.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from monomers to fibrils is challenging by experimental and computational means because they involve intrinsically disordered proteins in most diseases. Yet understanding how amyloid species become toxic is the challenge in developing a treatment for these diseases. Here we review what computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, for many years.
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Affiliation(s)
- Phuong H Nguyen
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Bikash R Sahoo
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jie Zheng
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Peter Faller
- Institut de Chimie, UMR 7177, CNRS-Université de Strasbourg, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Laura Dominguez
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Nikolay V Dokholyan
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
- Department of Chemistry, and Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
- Molecular Biology, University of Naples Federico II, Naples 80138, Italy
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Saeed Najafi
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics & Faculty of Applied Sciences, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Mara Chiricotto
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL, U.K
| | - Pritam Ganguly
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - James McCarty
- Chemistry Department, Western Washington University, Bellingham, Washington 98225, United States
| | - Mai Suan Li
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Carol Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yiming Wang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yifat Miller
- Department of Chemistry and The Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | | | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Stepan Timr
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Jiaxing Chen
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Brianna Hnath
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, and Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Sylvain Lesné
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Science, Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200438, China
| | - Fabio Sterpone
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Andrew J Doig
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, U.K
| | - Philippe Derreumaux
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
- Laboratory of Theoretical Chemistry, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
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Trumbore CN. Shear-Induced Amyloid Aggregation in the Brain: V. Are Alzheimer's and Other Amyloid Diseases Initiated in the Lower Brain and Brainstem by Cerebrospinal Fluid Flow Stresses? J Alzheimers Dis 2021; 79:979-1002. [PMID: 33386802 PMCID: PMC7990457 DOI: 10.3233/jad-201025] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2020] [Indexed: 12/13/2022]
Abstract
Amyloid-β (Aβ) and tau oligomers have been identified as neurotoxic agents responsible for causing Alzheimer's disease (AD). Clinical trials using Aβ and tau as targets have failed, giving rise to calls for new research approaches to combat AD. This paper provides such an approach. Most basic AD research has involved quiescent Aβ and tau solutions. However, studies involving laminar and extensional flow of proteins have demonstrated that mechanical agitation of proteins induces or accelerates protein aggregation. Recent MRI brain studies have revealed high energy, chaotic motion of cerebrospinal fluid (CSF) in lower brain and brainstem regions. These and studies showing CSF flow within the brain have shown that there are two energetic hot spots. These are within the third and fourth brain ventricles and in the neighborhood of the circle of Willis blood vessel region. These two regions are also the same locations as those of the earliest Aβ and tau AD pathology. In this paper, it is proposed that cardiac systolic pulse waves that emanate from the major brain arteries in the lower brain and brainstem regions and whose pulse waves drive CSF flows within the brain are responsible for initiating AD and possibly other amyloid diseases. It is further proposed that the triggering of these diseases comes about because of the strengthening of systolic pulses due to major artery hardening that generates intense CSF extensional flow stress. Such stress provides the activation energy needed to induce conformational changes of both Aβ and tau within the lower brain and brainstem region, producing unique neurotoxic oligomer molecule conformations that induce AD.
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Affiliation(s)
- Conrad N. Trumbore
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
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9
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Maruno T, Ohkubo T, Uchiyama S. Stirring rate affects thermodynamics and unfolding kinetics in isothermal titration calorimetry. J Biochem 2020; 168:53-62. [PMID: 32134445 DOI: 10.1093/jb/mvaa028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/10/2020] [Indexed: 11/13/2022] Open
Abstract
Isothermal titration calorimetry (ITC) directly provides thermodynamic parameters depicting the energetics of intermolecular interactions in solution. During ITC experiments, a titration syringe with a paddle is continuously rotating to promote a homogeneous mixing. Here, we clarified that the shape of the paddles (flat, corkscrew and small-pitched corkscrew) and the stirring rates influence on the thermodynamic parameters of protein-ligand interaction. Stirring with the flat paddle at lower and higher rate both yielded a lower exothermic heat due to different reasons. The complete reaction with no incompetent fractions was achieved only when the stirring was performed at 500 or 750 rpm using the small-pitched corkscrew paddle. The evaluation of the protein solution after 1,500 rpm stirring indicated that proteins in the soluble fraction decreased to 94% of the initial amount, among which 6% was at an unfolded state. In addition, a significant increase of micron aggregates was confirmed. Furthermore, a new approach for the determination of the unfolding kinetics based on the time dependence of the total reaction heat was developed. This study demonstrates that a proper stirring rate and paddle shape are essential for the reliable estimation of thermodynamic parameters in ITC experiments.
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Affiliation(s)
- Takahiro Maruno
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tadayasu Ohkubo
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
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10
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Ettah I, Ashton L. Determination of Phosphorylation and Deprotonation Induced Higher Order Structural Transitions in αs-Caseins. Anal Chem 2019; 91:13940-13946. [DOI: 10.1021/acs.analchem.9b03457] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Ilokugbe Ettah
- Department of Chemistry, Lancaster University, Lancaster, Lancashire LA1 4YB, United Kingdom
| | - Lorna Ashton
- Department of Chemistry, Lancaster University, Lancaster, Lancashire LA1 4YB, United Kingdom
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11
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Trumbore CN. Shear-Induced Amyloid Formation in the Brain: III. The Roles of Shear Energy and Seeding in a Proposed Shear Model. J Alzheimers Dis 2019; 65:47-70. [PMID: 30040710 PMCID: PMC6087447 DOI: 10.3233/jad-171003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
If cerebrospinal and interstitial fluids move through very narrow brain flow channels, these restrictive surroundings generate varying levels of fluid shear and different shear rates, and dissolved amyloid monomers absorb different shear energies. It is proposed that dissolved amyloid-β protein (Aβ) and other amyloid monomers undergo shear-induced conformational changes that ultimately lead to amyloid monomer aggregation even at very low brain flow and shear rates. Soluble Aβ oligomers taken from diseased brains initiate in vivo amyloid formation in non-diseased brains. The brain environment is apparently responsible for this result. A mechanism involving extensional shear is proposed for the formation of a seed Aβ monomer molecule that ultimately promotes templated conformational change of other Aβ molecules. Under non-quiescent, non-equilibrium conditions, gentle extensional shear within the brain parenchyma, and perhaps even during laboratory preparation of Aβ samples, may be sufficient to cause subtle conformational changes in these monomers. These result from brain processes that significantly lower the high activation energy predicted for the quiescent Aβ dimerization process. It is further suggested that changes in brain location and changes brought about by aging expose Aβ molecules to different shear rates, total shear, and types of shear, resulting in different conformational changes in these molecules. The consequences of such changes caused by variable shear energy are proposed to underlie formation of amyloid strains causing different amyloid diseases. Amyloid researchers are urged to undertake studies with amyloids, anti-amyloid drugs, and antibodies while all of these are under shear conditions similar to those in the brain.
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Affiliation(s)
- Conrad N Trumbore
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
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12
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Xu Y, Safari MS, Ma W, Schafer NP, Wolynes PG, Vekilov PG. Steady, Symmetric, and Reversible Growth and Dissolution of Individual Amyloid-β Fibrils. ACS Chem Neurosci 2019; 10:2967-2976. [PMID: 31099555 DOI: 10.1021/acschemneuro.9b00179] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Oligomers and fibrils of the amyloid-β (Aβ) peptide are implicated in the pathology of Alzheimer's disease. Here, we monitor the growth of individual Aβ40 fibrils by time-resolved in situ atomic force microscopy and thereby directly measure fibril growth rates. The measured growth rates in a population of fibrils that includes both single protofilaments and bundles of filaments are independent of the fibril thickness, indicating that cooperation between adjacent protofilaments does not affect incorporation of monomers. The opposite ends of individual fibrils grow at similar rates. In contrast to the "stop-and-go" kinetics that has previously been observed for amyloid-forming peptides, growth and dissolution of the Aβ40 fibrils are relatively steady for peptide concentration of 0-10 μM. The fibrils readily dissolve in quiescent peptide-free solutions at a rate that is consistent with the microscopic reversibility of growth and dissolution. Importantly, the bimolecular rate coefficient for the association of a monomer to the fibril end is significantly smaller than the diffusion limit, implying that the transition state for incorporation of a monomer into a fibril is associated with a relatively high free energy.
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Affiliation(s)
- Yuechuan Xu
- Department of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Road, Houston, Texas 77204-4004, United States
| | - Mohammad S. Safari
- Department of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Road, Houston, Texas 77204-4004, United States
| | - Wenchuan Ma
- Department of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Road, Houston, Texas 77204-4004, United States
| | - Nicholas P. Schafer
- Center for Theoretical Biological Physics, Rice University, P.O. Box 1892, MS 654, Houston, Texas 77251-1892, United States
- Department of Chemistry, Rice University, P.O. Box 1892, MS 60, Houston, Texas 77251-1892, United States
| | - Peter G. Wolynes
- Center for Theoretical Biological Physics, Rice University, P.O. Box 1892, MS 654, Houston, Texas 77251-1892, United States
- Department of Chemistry, Rice University, P.O. Box 1892, MS 60, Houston, Texas 77251-1892, United States
| | - Peter G. Vekilov
- Department of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Road, Houston, Texas 77204-4004, United States
- Department of Chemistry, University of Houston, 3585 Cullen Blvd., Houston, Texas 77204-5003, United States
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13
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Park Y, Park Y, Jin S, Kim JW, Jung YM. Formation mechanism of BAMLET by 2D Raman correlation analysis. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.05.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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14
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Bilalis P, Skoulas D, Karatzas A, Marakis J, Stamogiannos A, Tsimblouli C, Sereti E, Stratikos E, Dimas K, Vlassopoulos D, Iatrou H. Self-Healing pH- and Enzyme Stimuli-Responsive Hydrogels for Targeted Delivery of Gemcitabine To Treat Pancreatic Cancer. Biomacromolecules 2018; 19:3840-3852. [PMID: 30095907 DOI: 10.1021/acs.biomac.8b00959] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A novel, multifunctional hydrogel that exhibits a unique set of properties for the effective treatment of pancreatic cancer (PC) is presented. The material is composed of a pentablock terpolypeptide of the type PLys- b-(PHIS- co-PBLG)-PLys- b-(PHIS- co-PBLG)- b-PLys, which is a noncytotoxic polypeptide. It can be implanted via the least invasive route and selectively delivers gemcitabine to efficiently treat PC. Simply mixing the novel terpolypeptide with an aqueous solution of gemcitabine within a syringe results in the facile formation of a hydrogel that has the ability to become liquid under the shear rate of the plunger. Upon injection in the vicinity of cancer tissue, it immediately reforms into a hydrogel due to the unique combination of its macromolecular architecture and secondary structure. Because of its pH responsiveness, the hydrogel only melts close to PC; thus, the drug can be delivered directionally toward the cancerous rather than healthy tissues in a targeted, controlled, and sustained manner. The efficacy of the hydrogel was tested in vivo on human to mouse xenografts using the drug gemcitabine. It was found that the efficacy of the hydrogel loaded with only 40% of the drug delivered in one dose was equal to or slightly better than the peritumoral injection of 100% of the free drug delivered in two doses, the typical chemotherapy used in clinics so far. This result suggests that the hydrogel can direct the delivery of the encapsulated drug effectively in the tumor tissue. Enzymes lead to its biodegradation, avoiding removal by resection of the polypeptidic carrier after cargo delivery. The unique properties of the hydrogel formed can be predetermined through its molecular characteristics, rendering it a promising modular material for many biological applications.
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Affiliation(s)
- Panayiotis Bilalis
- Department of Chemistry , University of Athens , Panepistimiopolis , Zografou , Athens 15771 , Greece
| | - Dimitrios Skoulas
- Department of Chemistry , University of Athens , Panepistimiopolis , Zografou , Athens 15771 , Greece
| | - Anastasios Karatzas
- Department of Chemistry , University of Athens , Panepistimiopolis , Zografou , Athens 15771 , Greece
| | - John Marakis
- FORTH, Institute for Electronic Structure and Laser , Heraklion 70013 , Greece.,Department of Materials Science & Technology , University of Crete , Heraklion 70013 , Greece
| | - Athanasios Stamogiannos
- National Centre for Scientific Research Demokritos, Patriarhou Gregoriou and Neapoleos 27 , Athens , Agia Paraskevi 15341 , Greece
| | - Chrisida Tsimblouli
- Department of Pharmacology, Faculty of Medicine , University of Thessaly , Larissa , Greece
| | - Evangelia Sereti
- Department of Pharmacology, Faculty of Medicine , University of Thessaly , Larissa , Greece
| | - Efstratios Stratikos
- National Centre for Scientific Research Demokritos, Patriarhou Gregoriou and Neapoleos 27 , Athens , Agia Paraskevi 15341 , Greece
| | - Konstantinos Dimas
- Department of Pharmacology, Faculty of Medicine , University of Thessaly , Larissa , Greece
| | - Dimitris Vlassopoulos
- FORTH, Institute for Electronic Structure and Laser , Heraklion 70013 , Greece.,Department of Materials Science & Technology , University of Crete , Heraklion 70013 , Greece
| | - Hermis Iatrou
- Department of Chemistry , University of Athens , Panepistimiopolis , Zografou , Athens 15771 , Greece
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15
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Trumbore CN. Shear-Induced Amyloid Formation in the Brain: II. An Experimental System for Monitoring Amyloid Shear Processes and Investigating Potential Spinal Tap Problems. J Alzheimers Dis 2018; 59:543-557. [PMID: 28671126 PMCID: PMC5523842 DOI: 10.3233/jad-170259] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Liquid sheared amyloid-β (Aβ) initiates amyloid cascade reactions, producing unstable, potentially toxic oligomers. There is a need for new analytical tools with which to study these oligomers. A very small bore capillary flow system is proposed as a tool for studying the effects of liquid shear in amyloid research. This simple system consists of injecting a short cylindrical liquid sample plug containing dissolved amyloid into a liquid mobile phase flowing through an empty, very small internal diameter capillary tube. For liquid samples containing a single protein sample, under conditions in which there is laminar flow and limited sample protein molecular diffusion, chromatograms monitoring the optical protein absorbance of capillary effluent contain either one or two peaks, depending on the mobile phase flow rate. By controlling the sample diffusion times through changes in flow rate and/or capillary diameter, this tool can be used to generate aliquot samples with precise, reproducible amounts of shear for exploring the effects of variable shear on amyloid systems. The tool can be used for producing in-capillary stopped flow spectra of shear-stressed Aβ monomers as well as for kinetic studies of Aβ dimer- and oligomer-forming reactions between shear stressed Aβ monomers. Many other experiments are suggested using this experimental tool for studying the effects of shear on different Aβ and other amyloid systems, including testing for potentially serious amyloid sampling errors in spinal tap quantitative analysis. The technique has potential as both a laboratory research and a clinical tool.
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Affiliation(s)
- Conrad N Trumbore
- Department of Chemistry and Biochemistry, University of Delaware, Kennett Square, PA, USA
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16
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Detecting protein folding by thermal fluctuations of microcantilevers. PLoS One 2017; 12:e0189979. [PMID: 29267316 PMCID: PMC5739453 DOI: 10.1371/journal.pone.0189979] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 12/06/2017] [Indexed: 11/30/2022] Open
Abstract
The accurate characterization of proteins in both their native and denatured states is essential to effectively understand protein function, folding and stability. As a proof of concept, a micro rheological method is applied, based on the characterization of thermal fluctuations of a micro cantilever immersed in a bovine serum albumin solution, to assess changes in the viscosity associated with modifications in the protein’s structure under the denaturant effect of urea. Through modeling the power spectrum density of the cantilever’s fluctuations over a broad frequency band, it is possible to implement a fitting procedure to accurately determine the viscosity of the fluid, even at low volumes. Increases in viscosity during the denaturant process are identified using the assumption that the protein is a hard sphere, with a hydrodynamic radius that increases during unfolding. This is modeled accordingly through the Einstein-Batchelor formula. The Einstein-Batchelor formula estimates are verified through dynamic light scattering, which measures the hydrodynamic radius of proteins. Thus, this methodology is proven to be suitable for the study of protein folding in samples of small size at vanishing shear stresses.
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17
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Antimicrobial Effects of Peptides from Human Beta-Defensin-3 on Planktonic and Biofilm States of Streptococci. Int J Pept Res Ther 2017. [DOI: 10.1007/s10989-017-9634-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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18
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Byington MC, Safari MS, Conrad JC, Vekilov PG. Protein Conformational Flexibility Enables the Formation of Dense Liquid Clusters: Tests Using Solution Shear. J Phys Chem Lett 2016; 7:2339-2345. [PMID: 27267087 DOI: 10.1021/acs.jpclett.6b00822] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
According to recently proposed two-step nucleation mechanisms, crystal nuclei form within preexisting dense liquid clusters. Clusters with radii about 100 nm, which capture from 10(-7) to 10(-3) of the total protein, have been observed with numerous proteins and shown to host crystal nucleation. Theories aiming to understand the mesoscopic size and small protein fraction held in the clusters have proposed that in solutions of single-chain proteins, the clusters consist of partially misfolded protein molecules. To test this conjecture, we perturb the protein conformation by shearing solutions of the protein lysozyme. We demonstrate that shear rates greater than a threshold applied for longer than 1 h reduce the volume of the cluster population. The likely mechanism of the observed response involves enhanced partial unfolding of lysozyme molecules, which exposes hydrophobic surfaces between the constituent domains to the aqueous solution.
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Affiliation(s)
- Michael C Byington
- Department of Chemical and Biomolecular Engineering and ‡Department of Chemistry, University of Houston , 4726 Calhoun Road, Houston, Texas 77204-4004, United States
| | - Mohammad S Safari
- Department of Chemical and Biomolecular Engineering and ‡Department of Chemistry, University of Houston , 4726 Calhoun Road, Houston, Texas 77204-4004, United States
| | - Jacinta C Conrad
- Department of Chemical and Biomolecular Engineering and ‡Department of Chemistry, University of Houston , 4726 Calhoun Road, Houston, Texas 77204-4004, United States
| | - Peter G Vekilov
- Department of Chemical and Biomolecular Engineering and ‡Department of Chemistry, University of Houston , 4726 Calhoun Road, Houston, Texas 77204-4004, United States
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19
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Park Y, Kim Y, Vikram K, Czarnik-Matusewicz B, Jung YM. Two-Dimensional Correlation Analysis of pH-induced Raman Spectral Changes of α-Lactalbumin. B KOREAN CHEM SOC 2016. [DOI: 10.1002/bkcs.10763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yeonju Park
- Department of Chemistry, Institute for Molecular Science and Fusion Technology; Kangwon National University; Chuncheon 24341 Korea
| | - Yeseul Kim
- Department of Chemistry, Institute for Molecular Science and Fusion Technology; Kangwon National University; Chuncheon 24341 Korea
| | - Kunwar Vikram
- Department of Chemistry, Institute for Molecular Science and Fusion Technology; Kangwon National University; Chuncheon 24341 Korea
| | | | - Young Mee Jung
- Department of Chemistry, Institute for Molecular Science and Fusion Technology; Kangwon National University; Chuncheon 24341 Korea
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20
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Ciampi S, Eggers PK, Haworth NL, Darwish N, Wagner P, Coote ML, Wallace GG, Raston CL. Decoloration rates of a photomerocyanine dye as a visual probe into hydrogen bonding interactions. Chem Commun (Camb) 2015; 51:4815-8. [PMID: 25692486 DOI: 10.1039/c4cc09857a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed a visual marker for the investigation of hydrogen bonding (HB) effects. The decoloration rate of a photochromic dye that incorporates a latent intra-molecular HB feature can be linked to the HB character of the media. Kinetic and thermodynamic parameters of this simple decoloration approach for HB sensing are investigated both experimentally and by high level theoretical studies. This principle has been applied for the detection of changes in the HB character of stationary and fluidic systems. A major finding is the observation of a shear-related perturbation of the balance between intra- and inter-molecular HB within a dynamic thin film.
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Affiliation(s)
- Simone Ciampi
- ARC Centre of Excellence for Electromaterials Science, Intelligent Polymer Research Institute, University of Wollongong, Wollongong, NSW 2500, Australia.
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21
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Geitner R, Kötteritzsch J, Siegmann M, Bocklitz TW, Hager MD, Schubert US, Gräfe S, Dietzek B, Schmitt M, Popp J. Two-dimensional Raman correlation spectroscopy reveals molecular structural changes during temperature-induced self-healing in polymers based on the Diels–Alder reaction. Phys Chem Chem Phys 2015; 17:22587-95. [DOI: 10.1039/c5cp02151k] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
For the first time two-dimensional Raman correlation analysis has been used to study self-healing polymers based on the Diels–Alder reaction.
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Affiliation(s)
- R. Geitner
- Institute for Physical Chemistry and Abbe Center of Photonics
- Friedrich Schiller University Jena
- Jena
- Germany
| | - J. Kötteritzsch
- Laboratory for Organic and Macromolecular Chemistry (IOMC)
- Friedrich Schiller University Jena
- Jena
- Germany
- Jena Center of Soft Matter (JCSM)
| | - M. Siegmann
- Institute for Physical Chemistry and Abbe Center of Photonics
- Friedrich Schiller University Jena
- Jena
- Germany
| | - T. W. Bocklitz
- Institute for Physical Chemistry and Abbe Center of Photonics
- Friedrich Schiller University Jena
- Jena
- Germany
| | - M. D. Hager
- Laboratory for Organic and Macromolecular Chemistry (IOMC)
- Friedrich Schiller University Jena
- Jena
- Germany
- Jena Center of Soft Matter (JCSM)
| | - U. S. Schubert
- Laboratory for Organic and Macromolecular Chemistry (IOMC)
- Friedrich Schiller University Jena
- Jena
- Germany
- Jena Center of Soft Matter (JCSM)
| | - S. Gräfe
- Institute for Physical Chemistry and Abbe Center of Photonics
- Friedrich Schiller University Jena
- Jena
- Germany
| | - B. Dietzek
- Institute for Physical Chemistry and Abbe Center of Photonics
- Friedrich Schiller University Jena
- Jena
- Germany
- Jena Center of Soft Matter (JCSM)
| | - M. Schmitt
- Institute for Physical Chemistry and Abbe Center of Photonics
- Friedrich Schiller University Jena
- Jena
- Germany
| | - J. Popp
- Institute for Physical Chemistry and Abbe Center of Photonics
- Friedrich Schiller University Jena
- Jena
- Germany
- Jena Center of Soft Matter (JCSM)
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22
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Orgovan N, Patko D, Hos C, Kurunczi S, Szabó B, Ramsden JJ, Horvath R. Sample handling in surface sensitive chemical and biological sensing: a practical review of basic fluidics and analyte transport. Adv Colloid Interface Sci 2014; 211:1-16. [PMID: 24846752 DOI: 10.1016/j.cis.2014.03.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 03/25/2014] [Indexed: 10/25/2022]
Abstract
This paper gives an overview of the advantages and associated caveats of the most common sample handling methods in surface-sensitive chemical and biological sensing. We summarize the basic theoretical and practical considerations one faces when designing and assembling the fluidic part of the sensor devices. The influence of analyte size, the use of closed and flow-through cuvettes, the importance of flow rate, tubing length and diameter, bubble traps, pressure-driven pumping, cuvette dead volumes, and sample injection systems are all discussed. Typical application areas of particular arrangements are also highlighted, such as the monitoring of cellular adhesion, biomolecule adsorption-desorption and ligand-receptor affinity binding. Our work is a practical review in the sense that for every sample handling arrangement considered we present our own experimental data and critically review our experience with the given arrangement. In the experimental part we focus on sample handling in optical waveguide lightmode spectroscopy (OWLS) measurements, but the present study is equally applicable for other biosensing technologies in which an analyte in solution is captured at a surface and its presence is monitored. Explicit attention is given to features that are expected to play an increasingly decisive role in determining the reliability of (bio)chemical sensing measurements, such as analyte transport to the sensor surface; the distorting influence of dead volumes in the fluidic system; and the appropriate sample handling of cell suspensions (e.g. their quasi-simultaneous deposition). At the appropriate places, biological aspects closely related to fluidics (e.g. cellular mechanotransduction, competitive adsorption, blood flow in veins) are also discussed, particularly with regard to their models used in biosensing.
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23
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Frontiers of two-dimensional correlation spectroscopy. Part 2. Perturbation methods, fields of applications, and types of analytical probes. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.01.016] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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24
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Noda I. Frontiers of Two-Dimensional Correlation Spectroscopy. Part 1. New concepts and noteworthy developments. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.01.025] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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25
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Detection of receptor-induced glycoprotein conformational changes on enveloped virions by using confocal micro-Raman spectroscopy. J Virol 2013; 87:3130-42. [PMID: 23283947 DOI: 10.1128/jvi.03220-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Conformational changes in the glycoproteins of enveloped viruses are critical for membrane fusion, which enables viral entry into cells and the pathological cell-cell fusion (syncytia) associated with some viral infections. However, technological capabilities for identifying viral glycoproteins and their conformational changes on actual enveloped virus surfaces are generally scarce, challenging, and time-consuming. Our model, Nipah virus (NiV), is a syncytium-forming biosafety level 4 pathogen with a high mortality rate (40 to 75%) in humans. Once the NiV attachment glycoprotein (G) (NiV-G) binds the cell receptor ephrinB2 or -B3, G triggers conformational changes in the fusion glycoprotein (F) that result in membrane fusion and viral entry. We demonstrate that confocal micro-Raman spectroscopy can, within minutes, simultaneously identify specific G and F glycoprotein signals and receptor-induced conformational changes in NiV-F on NiV virus-like particles (VLPs). First, we identified reproducible G- and F-specific Raman spectral features on NiV VLPs containing M (assembly matrix protein), G, and/or F or on NiV/vesicular stomatitis virus (VSV) pseudotyped virions via second-derivative transformations and principal component analysis (PCA). Statistical analyses validated our PCA models. Dynamic temperature-induced conformational changes in F and G or receptor-induced target membrane-dependent conformational changes in F were monitored in NiV pseudovirions in situ in real time by confocal micro-Raman spectroscopy. Advantageously, Raman spectroscopy can identify specific protein signals in relatively impure samples. Thus, this proof-of-principle technological development has implications for the rapid identification and biostability characterization of viruses in medical, veterinary, and food samples and for the analysis of virion glycoprotein conformational changes in situ during viral entry.
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26
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Hussain R, Gaiani C, Scher J. From high milk protein powders to the rehydrated dispersions in variable ionic environments: A review. J FOOD ENG 2012. [DOI: 10.1016/j.jfoodeng.2012.06.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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27
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Raudino A, Pannuzzo M. Hydrodynamic-induced enantiomeric enrichment of self-assemblies: Role of the solid-liquid interface in chiral nucleation and seeding. J Chem Phys 2012; 137:134902. [DOI: 10.1063/1.4754434] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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28
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Roy B, Das T, Maiti TK, Chakraborty S. Effect of fluidic transport on the reaction kinetics in lectin microarrays. Anal Chim Acta 2011; 701:6-14. [PMID: 21763802 DOI: 10.1016/j.aca.2011.05.049] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Revised: 05/16/2011] [Accepted: 05/28/2011] [Indexed: 11/16/2022]
Abstract
Lectins are the proteins which can distinguish glycosylation patterns. They are frequently used as biomarkers for progressions of several diseases including cancer. As the lectin microarray based prognosis devices miniaturize the process of glycoprofiling, it is anticipated that their performance can be augmented by integration with microfluidic framework. This is analogous to microfluidics based DNA arrays. However, unlike small oligonucleotide microarrays, it remains uncertain whether the binding reaction-kinetic parameters can be considered invariant of imposed hydrodynamics, for relatively larger and structure sensitive molecules such as lectins. Here we show, using two standard lectins namely Concanavalin A and Abrus Agglutinin, that the steady state binding efficiency unexpectedly declines beyond a critical shear rate magnitude. This observation can be explained only if the associated reaction constants are presumed to be functions of hydrodynamic parameters. We methodically deduce the shear rate dependence of association and dissociation constants from the comparison of experimental and model-simulation trends. The aforementioned phenomena are perceived to be the consequences of strong hydrodynamic perturbations, culminating into molecular structural distortion. The exploration, therefore, reveals a unique coupling between reaction kinetics and hydrodynamics for biomacromolecules and provides a generic scheme towards futuristic microfluidics-coupled biomedical assays.
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Affiliation(s)
- Bibhas Roy
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
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29
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Research Spotlight: Biospectroscopy at the Manchester Interdisciplinary Biocentre. Bioanalysis 2011; 3:1189-94. [DOI: 10.4155/bio.11.95] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The Manchester Interdisciplinary Biocentre (MIB) at The University of Manchester (UK), is a large research facility located in central Manchester. The research undertaken in the MIB is said to address a number of grand challenges, including industrial biotechnology, energy and biofuels, and biomedical healthcare. These are realized via four main research themes: biomolecular mechanism and catalysis; synthetic and chemical biology; systems biology; and enabling technologies. This research spotlight focuses on biospectroscopy in the MIB, namely vibrational spectroscopies. This is just one area of research across just three of the many research groups in the MIB, which could be said to exemplify the fundamental and applied aspects of this field, its interdisciplinary nature and also the way it realizes several of the research themes and grand challenges already mentioned, with cutting edge and innovative research.
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30
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Webster GT, Dusting J, Balabani S, Blanch EW. Detecting the early onset of shear-induced fibril formation of insulin in situ. J Phys Chem B 2011; 115:2617-26. [PMID: 21348502 DOI: 10.1021/jp110367t] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A new approach is presented for detecting the early onset of amyloid fibril formation of insulin in a fluidic environment. The fibrillogenesis of insulin in a well-characterized Taylor-Couette flow cell was analyzed in situ using Raman spectroscopy in combination with principal components analysis (PCA). Raman spectra recorded using a 532.5 nm excitation laser revealed a more rapid fibrillogenesis process during the first 90 min of shearing than previously reported for samples exposed to flow. Bands corresponding to intermolecular H-bonded β-sheet structure of insulin at 1678, 1630, and 1625 cm(-1) observed in the Raman difference spectra between unsheared insulin and sheared insulin show an increase in intensity as a function of shear exposure time, which is characteristic of fibril formation, with the first changes detected after 10 min. Additional analysis of samples removed from the flow cell after specific time periods provided conformation of the flow-enhanced fibrillogenesis process, including the detection of early fibril formation after only 1 min of shearing. FT-IR spectra of the insulin solutions showed evolution of bands at 1673 and 1633 cm(-1) from an increase in H-bonded β-turn and β-sheet structures, respectively, while fluorescence emission spectra detected the presence of a new emission band at 482 nm. TEM images confirmed the early onset of fibril formation at 1 min shear exposure, before a maturation and concentration increase of fibrils with further shearing. This study highlights the ability of fluid flows to accelerate insulin fibril formation, which has important implications for biotechnology applications such as the purification process of insulin therapeutic drugs in the pharmaceutical industry, as well as the use of optical-based methods for detecting fibrillogenesis.
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Affiliation(s)
- Grant T Webster
- Manchester Interdisciplinary Biocentre and Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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31
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Edwards PJB, Kakubayashi M, Dykstra R, Pascal SM, Williams MAK. Rheo-NMR studies of an enzymatic reaction: evidence of a shear-stable macromolecular system. Biophys J 2010; 98:1986-94. [PMID: 20441763 DOI: 10.1016/j.bpj.2010.01.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Revised: 01/07/2010] [Accepted: 01/11/2010] [Indexed: 12/16/2022] Open
Abstract
Understanding the effects of shear forces on biopolymers is key to understanding how biological systems function. Although currently there is good agreement between theoretical predictions and experimental measurements of the behavior of DNA and large multimeric proteins under shear flow, applying the same arguments to globular proteins leads to the prediction that they should only exhibit shear-induced conformational changes at extremely large shear rates. Nevertheless, contradictory experimental evidence continues to appear, and the effect of shear on these biopolymers remains contentious. Here, a custom-built rheo-NMR cell was used to investigate whether shear flow modifies enzyme action compared with that observed quiescently. Specifically, (1)H NMR was used to follow the kinetics of the liberation of methanol from the methylesterified polysaccharide pectin by pectinmethylesterase enzymes. Two different demethylesterifying enzymes, known to have different action patterns, were used. In all experiments performed, Couette flows with shear rates of up to 1570 s(-1) did not generate detectable differences in the rate of methanol liberation compared to unsheared samples. This study provides evidence for a shear-stable macromolecular system consisting of a largely beta-sheet protein and a polysaccharide, in line with current theoretical predictions, but in contrast to some other experimental work on other proteins.
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Affiliation(s)
- Patrick J B Edwards
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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