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Paul PS, Rathnam M, Khalili A, Cortez LM, Srinivasan M, Planel E, Cho JY, Wille H, Sim VL, Mok SA, Kar S. Temperature-Dependent Aggregation of Tau Protein Is Attenuated by Native PLGA Nanoparticles Under in vitro Conditions. Int J Nanomedicine 2025; 20:1999-2019. [PMID: 39968061 PMCID: PMC11834738 DOI: 10.2147/ijn.s494104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2024] [Accepted: 02/01/2025] [Indexed: 02/20/2025] Open
Abstract
Introduction Hyperphosphorylation and aggregation of the microtubule-associated tau protein, which plays a critical role in many neurodegenerative diseases (ie, tauopathies) including Alzheimer's disease (AD), are known to be regulated by a variety of environmental factors including temperature. In this study we evaluated the effects of FDA-approved poly (D,L-lactide-co-glycolic) acid (PLGA) nanoparticles, which can inhibit amyloid-β aggregation/toxicity in cellular/animal models of AD, on temperature-dependent aggregation of 0N4R tau isoforms in vitro. Methods We have used a variety of biophysical (Thioflavin T kinetics, dynamic light scattering and asymmetric-flow field-flow fractionation), structural (fluorescence imaging and transmission electron microscopy) and biochemical (Filter-trap assay and detection of soluble protein) approaches, to evaluate the effects of native PLGA nanoparticles on the temperature-dependent tau aggregation. Results Our results show that the aggregation propensity of 0N4R tau increases significantly in a dose-dependent manner with a rise in temperature from 27°C to 40°C, as measured by lag time and aggregation rate. Additionally, the aggregation of 2N4R tau increases in a dose-dependent manner. Native PLGA significantly inhibits tau aggregation at all temperatures in a concentration-dependent manner, possibly by interacting with the aggregation-prone hydrophobic hexapeptide motifs of tau. Additionally, native PLGA is able to trigger disassembly of preformed 0N4R tau aggregates as a function of temperature from 27°C to 40°C. Conclusion These results, taken together, suggest that native PLGA nanoparticles can not only attenuate temperature-dependent tau aggregation but also promote disassembly of preformed aggregates, which increased with a rise of temperature. Given the evidence that temperature can influence tau pathology, we believe that native PLGA may have a unique potential to regulate tau abnormalities associated with AD-related pathology.
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Affiliation(s)
- Pallabi Sil Paul
- Department of Medicine (Neurology), Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, T6G 2M8, Canada
| | - Mallesh Rathnam
- Department of Medicine (Neurology), Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, T6G 2M8, Canada
| | - Aria Khalili
- Quantum and Nanotechnology Research Centre, National Research Council Canada, Edmonton, Alberta, Canada
| | - Leonardo M Cortez
- Department of Medicine (Neurology), Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, T6G 2M8, Canada
| | - Mahalashmi Srinivasan
- Department of Biochemistry, Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Emmanuel Planel
- Department of Psychiatry and Neurosciences, University of Laval, Quebec, Canada
| | - Jae-Young Cho
- Quantum and Nanotechnology Research Centre, National Research Council Canada, Edmonton, Alberta, Canada
- Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta, Canada
| | - Holger Wille
- Department of Biochemistry, Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Valerie L Sim
- Department of Medicine (Neurology), Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, T6G 2M8, Canada
| | - Sue-Ann Mok
- Department of Biochemistry, Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Satyabrata Kar
- Department of Medicine (Neurology), Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, T6G 2M8, Canada
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Pesce F, Lindorff-Larsen K. Combining Experiments and Simulations to Examine the Temperature-Dependent Behavior of a Disordered Protein. J Phys Chem B 2023. [PMID: 37433228 DOI: 10.1021/acs.jpcb.3c01862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Intrinsically disordered proteins are a class of proteins that lack stable folded conformations and instead adopt a range of conformations that determine their biochemical functions. The temperature-dependent behavior of such disordered proteins is complex and can vary depending on the specific protein and environment. Here, we have used molecular dynamics simulations and previously published experimental data to investigate the temperature-dependent behavior of histatin 5, a 24-residue-long polypeptide. We examined the hypothesis that histatin 5 undergoes a loss of polyproline II (PPII) structure with increasing temperature, leading to more compact conformations. We found that the conformational ensembles generated by the simulations generally agree with small-angle X-ray scattering data for histatin 5, but show some discrepancies with the hydrodynamic radius as probed by pulsed-field gradient NMR spectroscopy, and with the secondary structure information derived from circular dichroism. We attempted to reconcile these differences by reweighting the conformational ensembles against the scattering and NMR data. By doing so, we were in part able to capture the temperature-dependent behavior of histatin 5 and to link the observed decrease in hydrodynamic radius with increasing temperature to a loss of PPII structure. We were, however, unable to achieve agreement with both the scattering and NMR data within experimental errors. We discuss different possible reasons for this including inaccuracies in the force field, differences in conditions of the NMR and scattering experiments, and issues related to the calculation of the hydrodynamic radius from conformational ensembles. Our study highlights the importance of integrating multiple types of experimental data when modeling conformational ensembles of disordered proteins and how environmental factors such as the temperature influence them.
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Affiliation(s)
- Francesco Pesce
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
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Thole JF, Waudby CA, Pielak GJ. Disordered proteins mitigate the temperature dependence of site-specific binding free energies. J Biol Chem 2023; 299:102984. [PMID: 36739945 PMCID: PMC10027511 DOI: 10.1016/j.jbc.2023.102984] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/12/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Biophysical characterization of protein-protein interactions involving disordered proteins is challenging. A common simplification is to measure the thermodynamics and kinetics of disordered site binding using peptides containing only the minimum residues necessary. We should not assume, however, that these few residues tell the whole story. Son of sevenless, a multidomain signaling protein from Drosophila melanogaster, is critical to the mitogen-activated protein kinase pathway, passing an external signal to Ras, which leads to cellular responses. The disordered 55 kDa C-terminal domain of Son of sevenless is an autoinhibitor that blocks guanidine exchange factor activity. Activation requires another protein, Downstream of receptor kinase (Drk), which contains two Src homology 3 domains. Here, we utilized NMR spectroscopy and isothermal titration calorimetry to quantify the thermodynamics and kinetics of the N-terminal Src homology 3 domain binding to the strongest sites incorporated into the flanking disordered sequences. Comparing these results to those for isolated peptides provides information about how the larger domain affects binding. The affinities of sites on the disordered domain are like those of the peptides at low temperatures but less sensitive to temperature. Our results, combined with observations showing that intrinsically disordered proteins become more compact with increasing temperature, suggest a mechanism for this effect.
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Affiliation(s)
- Joseph F Thole
- Department of Chemistry, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Molecular and Cellular Biophysics Program, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Gary J Pielak
- Department of Chemistry, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Molecular and Cellular Biophysics Program, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Department of Biochemistry & Biophysics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Lineberger Cancer Center, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Integrative Program for Biological and Genome Sciences, UNC - Chapel Hill, Chapel Hill, North Carolina, USA.
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Bhuyan AK. Negative Thermal Expansion and Disorder-to-Order Collapse of an Intrinsically Disordered Protein under Marginally Denaturing Conditions. J Phys Chem B 2022; 126:5055-5065. [PMID: 35786899 DOI: 10.1021/acs.jpcb.2c03386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Recent work with intrinsically disordered proteins (IDPs) has projected a myriad of their survival instincts based mainly on the total charge content, the abundance of polar residues, and the paucity of hydrophobic amino acids. This work uses a plant IDP AtPP16-1 (Arabidopsis thaliana phloem protein class 16-1), whose solution NMR structure was determined by us recently, to show legitimate negative thermal expansion (NTE) of the native state. The thermal expansion continues to be negative even as the tertiary structure is perturbed by ultralow levels of urea up to 0.4 M. The NTE of these subdenatured states is called apparent NTE because they are prone to undergo conformational changes with temperature. Hydrodynamic shrinkage of the NTE IDP is also observed by dynamic light scattering (DLS) and NMR-measured global rotational correlation time (τc). The protein with denatured tertiary structure but otherwise preserved native-state secondary structure collapses to a dynamically rigid state. The data are mainly based on thermal coefficients of chemical shift and nuclear relaxation measured by heteronuclear NMR. The hydrodynamic shrinkage and collapse under marginally varying solvent compositions that may arise from unstable tertiary structure and dynamic disorder of chain segments across the backbone could be a generic property of IDPs.
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Affiliation(s)
- Abani K Bhuyan
- School of Chemistry University of Hyderabad, Hyderabad 50046, India
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Nanoscale Phase Separation of Incommensurate and Quasi-Commensurate Spin Stripes in Low Temperature Spin Glass of La2−xSrxNiO4. CONDENSED MATTER 2021. [DOI: 10.3390/condmat6040045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
While spin striped phases in La2−xSrxNiO4+y for 0.25 < x < 0.33 are the archetypal case of a 1D spin density wave (SDW) phase in doped antiferromagnetic strongly correlated perovskites, few information is available on the SDW spatial organization. In this context, we have measured the spatial variation of the wave vector of the SDW reflection profile by scanning micro X-ray diffractions with a coherent beam. We obtained evidence of a SDW order–disorder transition by lowering a high temperature phase (T > 50 K) to a low temperature phase (T < 50 K). We have identified quasi-commensurate spin stripe puddles in the ordered phase at 50 < T < 70 K, while the low temperature spin glassy phase presents a nanoscale phase separation of T = 30 K, with the coexistence of quasi-commensurate and incommensurate spin stripe puddles assigned to the interplay of quantum frustration and strong electronic correlations.
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Functional Nanoscale Phase Separation and Intertwined Order in Quantum Complex Materials. CONDENSED MATTER 2021. [DOI: 10.3390/condmat6040040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Nanoscale phase separation (NPS), characterized by particular types of correlated disorders, plays an important role in the functionality of high-temperature superconductors (HTS). Our results show that multiscale heterogeneity is an essential ingredient of quantum functionality in complex materials. Here, the interactions developing between different structural units cause dynamical spatiotemporal conformations with correlated disorder; thus, visualizing conformational landscapes is fundamental for understanding the physical properties of complex matter and requires advanced methodologies based on high-precision X-ray measurements. We discuss the connections between the dynamical correlated disorder at nanoscale and the functionality in oxygen-doped perovskite superconducting materials.
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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: 451] [Impact Index Per Article: 112.8] [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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A phosphorylation-dependent switch in the disordered p53 transactivation domain regulates DNA binding. Proc Natl Acad Sci U S A 2021; 118:2021456118. [PMID: 33443163 DOI: 10.1073/pnas.2021456118] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The tumor-suppressor p53 is a critical regulator of the cellular response to DNA damage and is tightly regulated by posttranslational modifications. Thr55 in the AD2 interaction motif of the N-terminal transactivation domain functions as a phosphorylation-dependent regulatory switch that modulates p53 activity. Thr55 is constitutively phosphorylated, becomes dephosphorylated upon DNA damage, and is subsequently rephosphorylated to facilitate dissociation of p53 from promoters and inactivate p53-mediated transcription. Using NMR and fluorescence spectroscopy, we show that Thr55 phosphorylation inhibits DNA-binding by enhancing competitive interactions between the disordered AD2 motif and the structured DNA-binding domain (DBD). Nonphosphorylated p53 exhibits positive cooperativity in binding DNA as a tetramer. Upon phosphorylation of Thr55, cooperativity is abolished and p53 binds initially to cognate DNA sites as a dimer. As the concentration of phosphorylated p53 is further increased, a second dimer binds and causes p53 to dissociate from the DNA, resulting in a bell-shaped binding curve. This autoinhibition is driven by favorable interactions between the DNA-binding surface of the DBD and the multiple phosphorylated AD2 motifs within the tetramer. These interactions are augmented by additional phosphorylation of Ser46 and are fine-tuned by the proline-rich domain (PRD). Removal of the PRD strengthens the AD2-DBD interaction and leads to autoinhibition of DNA binding even in the absence of Thr55 phosphorylation. This study reveals the molecular mechanism by which the phosphorylation status of Thr55 modulates DNA binding and controls both activation and termination of p53-mediated transcriptional programs at different stages of the cellular DNA damage response.
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Baul U, Bley M, Dzubiella J. Thermal Compaction of Disordered and Elastin-like Polypeptides: A Temperature-Dependent, Sequence-Specific Coarse-Grained Simulation Model. Biomacromolecules 2020; 21:3523-3538. [DOI: 10.1021/acs.biomac.0c00546] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Upayan Baul
- Applied Theoretical Physics—Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder Strasse 3, D-79104 Freiburg, Germany
| | - Michael Bley
- Applied Theoretical Physics—Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder Strasse 3, D-79104 Freiburg, Germany
| | - Joachim Dzubiella
- Applied Theoretical Physics—Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder Strasse 3, D-79104 Freiburg, Germany
- Cluster of Excellence livMatS@FIT—Freiburg Center for Interactive Materials and Bioinspired Technologies, Albert-Ludwigs-Universität Freiburg, Georges-Köhler-Allee 105, D-79110 Freiburg, Germany
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Di Gioacchino M, Bianconi A, Burghammer M, Ciasca G, Bruni F, Campi G. Myelin basic protein dynamics from out-of-equilibrium functional state to degraded state in myelin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183256. [PMID: 32145283 DOI: 10.1016/j.bbamem.2020.183256] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 02/28/2020] [Accepted: 03/02/2020] [Indexed: 01/15/2023]
Abstract
Living matter is a quasi-stationary out-of-equilibrium system; in this physical condition, structural fluctuations at nano- and meso-scales are needed to understand the physics behind its biological functionality. Myelin has a simple ultrastructure whose fluctuations show correlated disorder in its functional out-of-equilibrium state. However, there is no information on the relationship between this correlated disorder and the dynamics of the intrinsically disordered Myelin Basic Protein (MBP) which is expected to influence the membrane structure and overall functionality. In this work, we have investigated the role of this protein structural dynamics in the myelin ultrastructure fluctuations in various conditions, by using synchrotron Scanning micro X Ray Diffraction and Small Angle X ray Scattering. We have induced the crossover from out-of-equilibrium functional state to in-equilibrium degeneration changing the pH to values far from physiological condition. The observed compression of the cytosolic layer thickness probes that the intrinsic large MBP fluctuations preserve the cytosol structure also in the degraded state. Thus, the transition of myelin ultrastructure from correlated to uncorrelated disordered state, is principally affected by the deformation of the membrane and extracellular domain.
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Affiliation(s)
- Michael Di Gioacchino
- Dipartimento di Scienze, Università degli Studi Roma Tre, Via della Vasca Navale 84, 00146 Roma, Italy; Institute of Crystallography, CNR, via Salaria, Km 29.300, 00015 Monterotondo, Roma, Italy; Rome International Center for Materials Science Superstripes (RICMASS), Via dei Sabelli 119A, 00185 Roma, Italy.
| | - Antonio Bianconi
- Institute of Crystallography, CNR, via Salaria, Km 29.300, 00015 Monterotondo, Roma, Italy; Rome International Center for Materials Science Superstripes (RICMASS), Via dei Sabelli 119A, 00185 Roma, Italy; National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 115409 Moscow, Russia
| | - Manfred Burghammer
- European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, BP220, 38043 Grenoble Cedex, France
| | - Gabriele Ciasca
- Physics Institute, Catholic University of Sacred Heart, Largo F. Vito 1, 00168 Rome, Italy
| | - Fabio Bruni
- Dipartimento di Scienze, Università degli Studi Roma Tre, Via della Vasca Navale 84, 00146 Roma, Italy
| | - Gaetano Campi
- Institute of Crystallography, CNR, via Salaria, Km 29.300, 00015 Monterotondo, Roma, Italy
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Perini G, Ciasca G, Minelli E, Papi M, Palmieri V, Maulucci G, Nardini M, Latina V, Corsetti V, Florenzano F, Calissano P, De Spirito M, Amadoro G. Dynamic structural determinants underlie the neurotoxicity of the N-terminal tau 26-44 peptide in Alzheimer's disease and other human tauopathies. Int J Biol Macromol 2019; 141:278-289. [PMID: 31470053 DOI: 10.1016/j.ijbiomac.2019.08.220] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/10/2019] [Accepted: 08/26/2019] [Indexed: 12/31/2022]
Abstract
The intrinsically disordered tau protein plays a pivotal role in the pathogenesis of Alzheimer's disease (AD) and other human tauopathies. Abnormal post-translational modifications of tau, such as truncation, are causally involved in the onset/development of these neurodegenerative diseases. In this context, the AD-relevant N-terminal fragment mapping between 26 and 44 amino acids of protein (tau26-44) is interesting, being endowed with potent neurotoxic effects in vitro and in vivo. However, the understanding of the mechanism(s) of tau26-44 toxicity is a challenging task because, similarly to the full-length tau, it does not have a unique 3D structure but exists as dynamic ensemble of conformations. Here we use Atomic Force Spectroscopy, Small Angle X-ray Scattering and Molecular Dynamics simulation to gather structural and functional information on the tau26-44. We highlight the presence, the type and the location of its temporary secondary structures and we unveil the occurrence of relevant transient tertiary conformations that could contribute to tau26-44 toxicity. Data are compared with those obtained on the biologically-inactive, reverse-sequence (tau44-26 peptide) which has the same mass, charge, aminoacidic composition as well as the same overall unfolded character of tau26-44.
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Affiliation(s)
- Giordano Perini
- Istituto di Fisica, Università Cattolica del Sacro Cuore, Roma, Italy; Fondazione Policlinico A. Gemelli IRCCS, Roma, Italy
| | - Gabriele Ciasca
- Istituto di Fisica, Università Cattolica del Sacro Cuore, Roma, Italy; Fondazione Policlinico A. Gemelli IRCCS, Roma, Italy.
| | - Eleonora Minelli
- Istituto di Fisica, Università Cattolica del Sacro Cuore, Roma, Italy; Fondazione Policlinico A. Gemelli IRCCS, Roma, Italy
| | - Massimiliano Papi
- Istituto di Fisica, Università Cattolica del Sacro Cuore, Roma, Italy; Fondazione Policlinico A. Gemelli IRCCS, Roma, Italy
| | - Valentina Palmieri
- Istituto di Fisica, Università Cattolica del Sacro Cuore, Roma, Italy; Fondazione Policlinico A. Gemelli IRCCS, Roma, Italy
| | - Giuseppe Maulucci
- Istituto di Fisica, Università Cattolica del Sacro Cuore, Roma, Italy; Fondazione Policlinico A. Gemelli IRCCS, Roma, Italy
| | - Matteo Nardini
- Istituto di Fisica, Università Cattolica del Sacro Cuore, Roma, Italy; Fondazione Policlinico A. Gemelli IRCCS, Roma, Italy
| | - Valentina Latina
- European Brain Research Institute (EBRI), Viale Regina Elena 295, 00161 Rome, Italy
| | - Veronica Corsetti
- European Brain Research Institute (EBRI), Viale Regina Elena 295, 00161 Rome, Italy
| | - Fulvio Florenzano
- European Brain Research Institute (EBRI), Viale Regina Elena 295, 00161 Rome, Italy
| | - Pietro Calissano
- European Brain Research Institute (EBRI), Viale Regina Elena 295, 00161 Rome, Italy
| | - Marco De Spirito
- Istituto di Fisica, Università Cattolica del Sacro Cuore, Roma, Italy; Fondazione Policlinico A. Gemelli IRCCS, Roma, Italy
| | - Giuseppina Amadoro
- European Brain Research Institute (EBRI), Viale Regina Elena 295, 00161 Rome, Italy; Institute of Translational Pharmacology (IFT)-CNR, Via Fosso del Cavaliere 100, 00133 Rome, Italy.
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13
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Proteasome Activation to Combat Proteotoxicity. Molecules 2019; 24:molecules24152841. [PMID: 31387243 PMCID: PMC6696185 DOI: 10.3390/molecules24152841] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/22/2019] [Accepted: 08/01/2019] [Indexed: 12/11/2022] Open
Abstract
Loss of proteome fidelity leads to the accumulation of non-native protein aggregates and oxidatively damaged species: hallmarks of an aged cell. These misfolded and aggregated species are often found, and suggested to be the culpable party, in numerous neurodegenerative diseases including Huntington's, Parkinson's, Amyotrophic Lateral Sclerosis (ALS), and Alzheimer's Diseases (AD). Many strategies for therapeutic intervention in proteotoxic pathologies have been put forth; one of the most promising is bolstering the efficacy of the proteasome to restore normal proteostasis. This strategy is ideal as monomeric precursors and oxidatively damaged proteins, so called "intrinsically disordered proteins" (IDPs), are targeted by the proteasome. This review will provide an overview of disorders in proteins, both intrinsic and acquired, with a focus on susceptibility to proteasomal degradation. We will then examine the proteasome with emphasis on newly published structural data and summarize current known small molecule proteasome activators.
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14
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Narayan A, Bhattacharjee K, Naganathan AN. Thermally versus Chemically Denatured Protein States. Biochemistry 2019; 58:2519-2523. [PMID: 31083972 DOI: 10.1021/acs.biochem.9b00089] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein unfolding thermodynamic parameters are conventionally extracted from equilibrium thermal and chemical denaturation experiments. Despite decades of work, the degree of structure and the compactness of denatured states populated in these experiments are still open questions. Here, building on previous works, we show that thermally and chemically denatured protein states are distinct from the viewpoint of far-ultraviolet circular dichroism experiments that report on the local conformational status of peptide bonds. The differences identified are independent of protein length, structural class, or experimental conditions, highlighting the presence of two sub-ensembles within the denatured states. The sub-ensembles, UT and UD for thermally induced and denaturant-induced unfolded states, respectively, can exclusively exchange populations as a function of temperature at high chemical denaturant concentrations. Empirical analysis suggests that chemically denatured states are ∼50% more expanded than the thermally denatured chains of the same protein. Our observations hint that the strength of protein backbone-backbone interactions and identity versus backbone-solvent/co-solvent interactions determine the conformational distributions. We discuss the implications for protein folding mechanisms, the heterogeneity in relaxation rates, and folding diffusion coefficients.
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Affiliation(s)
- Abhishek Narayan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
| | - Kabita Bhattacharjee
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
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15
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Ilie IM, Caflisch A. Simulation Studies of Amyloidogenic Polypeptides and Their Aggregates. Chem Rev 2019; 119:6956-6993. [DOI: 10.1021/acs.chemrev.8b00731] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Ioana M. Ilie
- Department of Biochemistry, University of Zürich, Zürich CH-8057, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, Zürich CH-8057, Switzerland
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16
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Russo D, de Angelis A, Garvey CJ, Wurm FR, Appavou MS, Prevost S. Effect of Polymer Chain Density on Protein–Polymer Conjugate Conformation. Biomacromolecules 2019; 20:1944-1955. [DOI: 10.1021/acs.biomac.9b00184] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Daniela Russo
- Consiglio Nazionale delle Ricerche & Istituto Officina dei Materiali, Institut Laue Langevin, 38042 Grenoble, France
- Australian Nuclear
Science and Technology Organization, New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | | | - Christopher. J. Garvey
- Australian Nuclear
Science and Technology Organization, New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | - Frederick R. Wurm
- Max-Planck-Institut
für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany
| | - Marie-Sousai Appavou
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich GmbH, Lichtenbergstraße, 185748 Garching, Germany
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17
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Evolution of Complexity in Out-of-Equilibrium Systems by Time-Resolved or Space-Resolved Synchrotron Radiation Techniques. CONDENSED MATTER 2019. [DOI: 10.3390/condmat4010032] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Out-of-equilibrium phenomena are attracting high interest in physics, materials science, chemistry and life sciences. In this state, the study of structural fluctuations at different length scales in time and space are necessary to achieve significant advances in the understanding of the structure-functionality relationship. The visualization of patterns arising from spatiotemporal fluctuations is nowadays possible thanks to new advances in X-ray instrumentation development that combine high-resolution both in space and in time. We present novel experimental approaches using high brilliance synchrotron radiation sources, fast detectors and focusing optics, joint with advanced data analysis based on automated statistical, mathematical and imaging processing tools. This approach has been used to investigate structural fluctuations in out-of-equilibrium systems in the novel field of inhomogeneous quantum complex matter at the crossing point of technology, physics and biology. In particular, we discuss how nanoscale complexity controls the emergence of high-temperature superconductivity (HTS), myelin functionality and formation of hybrid organic-inorganic supramolecular assembly. The emergent complex geometries, opening novel venues to quantum technology and to the development of quantum physics of living systems, are discussed.
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18
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Faust O, Grunhaus D, Shimshon O, Yavin E, Friedler A. Protein Regulation by Intrinsically Disordered Regions: A Role for Subdomains in the IDR of the HIV-1 Rev Protein. Chembiochem 2018; 19:1618-1624. [PMID: 29791766 DOI: 10.1002/cbic.201800192] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Indexed: 11/06/2022]
Abstract
Intrinsically disordered regions (IDRs) in proteins are highly abundant, but they are still commonly viewed as long stretches of polar, solvent-accessible residues. Here we show that the disordered C-terminal domain (CTD) of HIV-1 Rev has two subregions that carry out two distinct complementary roles of regulating protein oligomerization and contributing to stability. We propose that this takes place through a delicate balance between charged and hydrophobic residues within the IDR. This means that mutations in this region, as well as the known mutations in the structured region of the protein, can affect protein function. We suggest that IDRs in proteins should be divided into subdomains similarly to structured regions, rather than being viewed as long flexible stretches.
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Affiliation(s)
- Ofrah Faust
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Dana Grunhaus
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Odelia Shimshon
- The School of Pharmacy, The Hebrew University of Jerusalem, Hadassah Ein Kerem, Jerusalem, 91120, Israel
| | - Eylon Yavin
- The School of Pharmacy, The Hebrew University of Jerusalem, Hadassah Ein Kerem, Jerusalem, 91120, Israel
| | - Assaf Friedler
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
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19
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Rafiee S, Asadollahi K, Riazi G, Ahmadian S, Saboury AA. Vitamin B12 Inhibits Tau Fibrillization via Binding to Cysteine Residues of Tau. ACS Chem Neurosci 2017; 8:2676-2682. [PMID: 28841372 DOI: 10.1021/acschemneuro.7b00230] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Two mechanisms underlie the inhibitory/acceleratory action of chemical compounds on tau aggregation including the regulation of cellular kinases and phosphatases activity and direct binding to tau protein. Vitamin B12 is one of the tau polymerization inhibitors, and its deficiency is linked to inactivation of protein phosphatase 2A and subsequently hyperphosphorylation and aggregation of tau protein. Regarding the structure and function of vitamin B12 and tau protein, we assumed that vitamin B12 is also able to directly bind to tau protein. Hence, we investigated the interaction of vitamin B12 with tau protein in vitro using fluorometry and circular dichrosim. Interaction studies was followed by investigation into the effect of vitamin B12 on tau aggregation using ThT fluorescence, circular dichroism, transmission electron microscopy, and SDS-PAGE. The results indicated that vitamin B12 interacts with tau protein and prevents fibrillization of tau protein. Blocking the cysteine residues of tau confirmed the cysteine-mediated binding of vitamin B12 to tau and showed that binding to cysteine is essential for inhibitory effect of vitamin B12 on tau aggregation. SDS-PAGE analysis indicated that vitamin B12 inhibits tau aggregation and that tau oligomers formed in the presence of vitamin B12 are mostly SDS-soluble. We propose that direct binding of vitamin B12 is another mechanism underlying the inhibitory role of vitamin B12 on tau aggregation and neurodegeneration.
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Affiliation(s)
- Saharnaz Rafiee
- Institute of Biochemistry and Biophysics
(IBB), University of Tehran, Tehran, Iran
| | - Kazem Asadollahi
- Institute of Biochemistry and Biophysics
(IBB), University of Tehran, Tehran, Iran
| | - Gholamhossein Riazi
- Institute of Biochemistry and Biophysics
(IBB), University of Tehran, Tehran, Iran
| | - Shahin Ahmadian
- Institute of Biochemistry and Biophysics
(IBB), University of Tehran, Tehran, Iran
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics
(IBB), University of Tehran, Tehran, Iran
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20
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Florenzano F, Veronica C, Ciasca G, Ciotti MT, Pittaluga A, Olivero G, Feligioni M, Iannuzzi F, Latina V, Maria Sciacca MF, Sinopoli A, Milardi D, Pappalardo G, Marco DS, Papi M, Atlante A, Bobba A, Borreca A, Calissano P, Amadoro G. Extracellular truncated tau causes early presynaptic dysfunction associated with Alzheimer's disease and other tauopathies. Oncotarget 2017; 8:64745-64778. [PMID: 29029390 PMCID: PMC5630290 DOI: 10.18632/oncotarget.17371] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 04/11/2017] [Indexed: 12/14/2022] Open
Abstract
The largest part of tau secreted from AD nerve terminals and released in cerebral spinal fluid (CSF) is C-terminally truncated, soluble and unaggregated supporting potential extracellular role(s) of NH2 -derived fragments of protein on synaptic dysfunction underlying neurodegenerative tauopathies, including Alzheimer's disease (AD). Here we show that sub-toxic doses of extracellular-applied human NH2 tau 26-44 (aka NH 2 htau) -which is the minimal active moiety of neurotoxic 20-22kDa peptide accumulating in vivo at AD synapses and secreted into parenchyma- acutely provokes presynaptic deficit in K+ -evoked glutamate release on hippocampal synaptosomes along with alteration in local Ca2+ dynamics. Neuritic dystrophy, microtubules breakdown, deregulation in presynaptic proteins and loss of mitochondria located at nerve endings are detected in hippocampal cultures only after prolonged exposure to NH 2 htau. The specificity of these biological effects is supported by the lack of any significant change, either on neuronal activity or on cellular integrity, shown by administration of its reverse sequence counterpart which behaves as an inactive control, likely due to a poor conformational flexibility which makes it unable to dynamically perturb biomembrane-like environments. Our results demonstrate that one of the AD-relevant, soluble and secreted N-terminally truncated tau forms can early contribute to pathology outside of neurons causing alterations in synaptic activity at presynaptic level, independently of overt neurodegeneration.
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Affiliation(s)
| | | | - Gabriele Ciasca
- Institute of Physics, Catholic University of the Sacred Heart, Largo F Vito 1, Rome, Italy
| | - Maria Teresa Ciotti
- Institute of Cellular Biology and Neuroscience, CNR, IRCSS Santa Lucia Foundation, Rome, Italy
| | - Anna Pittaluga
- Department of Pharmacy, Pharmacology and Toxicology Section, University of Genoa, Genoa, Viale Cembrano, Italy
| | - Gunedalina Olivero
- Department of Pharmacy, Pharmacology and Toxicology Section, University of Genoa, Genoa, Viale Cembrano, Italy
| | - Marco Feligioni
- European Brain Research Institute, Rome, Italy
- Department of Neurorehabilitation Sciences, Casa Cura Policlinico, Milan, Italy
| | | | | | | | | | - Danilo Milardi
- Institute of Biostructures and Bioimaging, CNR, Catania, Italy
| | | | - De Spirito Marco
- Institute of Physics, Catholic University of the Sacred Heart, Largo F Vito 1, Rome, Italy
| | - Massimiliano Papi
- Institute of Physics, Catholic University of the Sacred Heart, Largo F Vito 1, Rome, Italy
| | - Anna Atlante
- Institute of Biomembranes and Bioenergetics, CNR, Bari, Italy
- Center of Excellence for Biomedical Research, University of Genoa, Genoa, Viale Benedetto XV, Italy
| | - Antonella Bobba
- Institute of Biomembranes and Bioenergetics, CNR, Bari, Italy
- Center of Excellence for Biomedical Research, University of Genoa, Genoa, Viale Benedetto XV, Italy
| | - Antonella Borreca
- Institute of Cellular Biology and Neuroscience, CNR, IRCSS Santa Lucia Foundation, Rome, Italy
| | | | - Giuseppina Amadoro
- European Brain Research Institute, Rome, Italy
- Institute of Translational Pharmacology, CNR, Rome, Italy
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21
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Battisti A, Ciasca G, Grottesi A, Tenenbaum A. Thermal compaction of the intrinsically disordered protein tau: entropic, structural, and hydrophobic factors. Phys Chem Chem Phys 2017; 19:8435-8446. [DOI: 10.1039/c6cp07683a] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The first quantitative assessment of the entropic, hydrophobic, and structural factors producing the thermal compaction of tau, an intrinsically disordered protein.
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Affiliation(s)
- Anna Battisti
- International School for Advanced Studies (SISSA)
- 34136 Trieste
- Italy
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22
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Gorantla NV, Shkumatov AV, Chinnathambi S. Conformational Dynamics of Intracellular Tau Protein Revealed by CD and SAXS. Methods Mol Biol 2017; 1523:3-20. [PMID: 27975241 DOI: 10.1007/978-1-4939-6598-4_1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A native conformation of a protein is essential for its biological role. In certain conditions, some proteins show non-native conformations, leading to aggregation, which in turn may produce severe pathologies. Such physiological conditions are classified as protein misfolding diseases. Alzheimer's disease (AD) is the most common form of dementia. Extracellular senile plaques formed by Amyloid β and intracellular aggregates formed by microtubule-associated protein Tau (MAPT) are the hallmarks of AD. Physiological role of MAPT is to maintain the integrity and stability of microtubules, however it tends to self-aggregate forming intracellular paired helical filaments (PHFs) during AD. MAPT is also subjected to various post-translational modifications such as phosphorylation, glycosylation, truncation, and acetylation. Being natively unfolded, MAPT is prone to full characterization at atomic level. Small-angle X-ray scattering (SAXS) is often applied in combination with other biophysical methods, like nuclear magnetic resonance (NMR), circular dichroism (CD), fluorescence spectroscopy, analytical ultracentrifugation (AUC), or dynamic light scattering (DLS) to characterize natively unfolded systems. Here we describe the practical aspects of MAPT characterization by SAXS and CD in detail as well as outline the inferred structural and functional implications.
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Affiliation(s)
- Nalini Vijay Gorantla
- Neurobiology Group, Division of Biochemical Sciences, National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, 411008, Pune, Maharashtra, India.,Academy of Scientific and Innovative Research (AcSIR), 10025, New Delhi, India
| | | | - Subashchandrabose Chinnathambi
- Neurobiology Group, Division of Biochemical Sciences, National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, 411008, Pune, Maharashtra, India. .,Academy of Scientific and Innovative Research (AcSIR), 10025, New Delhi, India.
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23
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Ciasca G, Papi M, Businaro L, Campi G, Ortolani M, Palmieri V, Cedola A, De Ninno A, Gerardino A, Maulucci G, De Spirito M. Recent advances in superhydrophobic surfaces and their relevance to biology and medicine. BIOINSPIRATION & BIOMIMETICS 2016; 11:011001. [PMID: 26844980 DOI: 10.1088/1748-3190/11/1/011001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
By mimicking naturally occurring superhydrophobic surfaces, scientists can now realize artificial surfaces on which droplets of a few microliters of water are forced to assume an almost spherical shape and an extremely high contact angle. In recent decades, these surfaces have attracted much attention due to their technological applications for anti-wetting and self-cleaning materials. Very recently, researchers have shifted their interest to investigate whether superhydrophobic surfaces can be exploited to study biological systems. This research effort has stimulated the design and realization of new devices that allow us to actively organize, visualize and manipulate matter at both the microscale and nanoscale levels. Such precise control opens up wide applications in biomedicine, as it allows us to directly manipulate objects at the typical length scale of cells and macromolecules. This progress report focuses on recent biological and medical applications of superhydrophobicity. Particular regard is paid to those applications that involve the detection, manipulation and study of extremely small quantities of molecules, and to those that allow high throughput cell and biomaterial screening.
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Affiliation(s)
- G Ciasca
- Istituto di Fisica, Università Cattolica del Sacro Cuore, Largo F Vito 1, 00168 Rome, Italy
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24
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Campi G, Ciasca G, Poccia N, Ricci A, Fratini M, Bianconi A. Controlling photoinduced electron transfer via defects self-organization for novel functional macromolecular systems. Curr Protein Pept Sci 2015; 15:394-9. [PMID: 24678672 PMCID: PMC4030318 DOI: 10.2174/1389203715666140327104023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 11/22/2013] [Accepted: 03/16/2014] [Indexed: 11/22/2022]
Abstract
The electrons transfer (ET) from an atom or a molecule, donor (D), to another, acceptor (A) is the basis of many fundamental chemical and physical processes. The ET mechanism is controlled by spatial arrangements of donor and acceptors: it's the particular spatial arrangement and thus the particular distance and the orientation between the electron donors and acceptors that controls the efficiency in charge separation processes in nature. Here, we stress the importance of this concept reviewing how spatial distribution of atomic and molecular self-assembly can determine the quality and physical features of ET process from biology to material science. In this context, we propose novel lab-on-chip techniques to be used to control spatial distribution of molecules at nanoscale. Synchrotron source brightness jointly to focusing optics fabrication allows one nowadays to monitor and visualize structures with sub-micrometric spatial resolution. This can give us a new powerful tool to set up sophisticated X-ray imaging techniques as well as spectroscopic elemental and chemical mapping to investigate the structure-function relationship controlling the spatial arrangement of the molecules at nanoscale. Finally, we report intriguing recent case studies on the possibility to manipulate and control this spatial distribution and material functionality at nanoscale by using X ray illumination.
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Affiliation(s)
| | | | | | | | | | - Antonio Bianconi
- Institute of Crystallography, Via Salaria Km 29.300, 00015, Monterotondo Roma, Italy.
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25
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Di Poto A, Papi M, Trivedi S, Maiorana A, Gavazzo P, Vassalli M, Lowy FD, De Spirito M, Montanaro L, Imbriani M, Arciola CR, Visai L. In vitro effect of temperature on the conformational structure and collagen binding of SdrF, a Staphylococcus epidermidis adhesin. Appl Microbiol Biotechnol 2015; 99:5593-603. [PMID: 25683665 DOI: 10.1007/s00253-015-6456-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 01/30/2015] [Accepted: 02/02/2015] [Indexed: 12/01/2022]
Abstract
Staphylococcus epidermidis is the leading etiologic agent of device-related infections. S. epidermidis is able to bind, by means of the adhesins of its cell wall, the host matrix proteins filming the artificial surfaces. Thence, bacteria cling to biomaterials and infection develops. The effect of temperature on integrity, structure, and biological activity of the collagen-binding adhesin (SdrF) of S. epidermidis has been here investigated. By cloning in E. coli XL1-Blue, a recombinant of the SdrF binding domain B (rSdrFB), carrying an N-terminal polyhistidine, was obtained. Purification was by HiTrap(TM) Chelating HP columns. Assessment of purity, molecular weight, and integrity was by SDS-PAGE. The rSdrFB-collagen binding was investigated by ELISA. A full three-dimensional reconstruction of rSdrFB was achieved by small-angle X-ray scattering (SAXS). At 25 °C, rSdrFB bound to type I collagen in a dose-dependent, saturable manner, with a Kd of 2.48 × 10(-7) M. When temperature increased from 25 to 37 °C, a strong conformational change occurred, together with the abolition of the rSdrFB-collagen binding. The rSdrFB integrity was not affected by temperature variation. SdrFB-collagen binding is switched on/off depending on the temperature. Implications with the infection pathogenesis are enlightened.
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Affiliation(s)
- Antonella Di Poto
- Department of Molecular Medicine, Center for Tissue Engineering (CIT), INSTM UdR of Pavia, University of Pavia, Viale Taramelli 3/b, 27100, Pavia, Italy
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26
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Colapicchioni V, Palchetti S, Pozzi D, Marini ES, Riccioli A, Ziparo E, Papi M, Amenitsch H, Caracciolo G. Killing cancer cells using nanotechnology: novel poly(I:C) loaded liposome–silica hybrid nanoparticles. J Mater Chem B 2015; 3:7408-7416. [DOI: 10.1039/c5tb01383f] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Synthesized core–shell liposome–silica hybrid nanoparticles (LSH NPs), when loaded with the anti-cancer polyinosinic–polycytidylic acid (poly(I:C)), exhibit high anti-tumoral activity in prostate and breast cancer cells.
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Affiliation(s)
| | - Sara Palchetti
- Department of Molecular Medicine
- ‘Sapienza’ University of Rome
- 00161 Rome
- Italy
| | - Daniela Pozzi
- Department of Molecular Medicine
- ‘Sapienza’ University of Rome
- 00161 Rome
- Italy
| | - Elettra Sara Marini
- Istituto Pasteur-Fondazione Cenci Bolognetti
- Department of Anatomy
- Histology
- Forensic Medicine and Orthopaedics
- Section of Histology and Medical Embryology
| | - Anna Riccioli
- Istituto Pasteur-Fondazione Cenci Bolognetti
- Department of Anatomy
- Histology
- Forensic Medicine and Orthopaedics
- Section of Histology and Medical Embryology
| | - Elio Ziparo
- Istituto Pasteur-Fondazione Cenci Bolognetti
- Department of Anatomy
- Histology
- Forensic Medicine and Orthopaedics
- Section of Histology and Medical Embryology
| | - Massimiliano Papi
- Istituto di Fisica
- Università Cattolica del Sacro Cuore
- 00168 Rome
- Italy
| | - Heinz Amenitsch
- Institute of Inorganic Chemistry
- Graz University of Technology
- 8010 Graz
- Austria
| | - Giulio Caracciolo
- Department of Molecular Medicine
- ‘Sapienza’ University of Rome
- 00161 Rome
- Italy
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27
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Pozzi D, Marchini C, Cardarelli F, Rossetta A, Colapicchioni V, Amici A, Montani M, Motta S, Brocca P, Cantù L, Caracciolo G. Mechanistic understanding of gene delivery mediated by highly efficient multicomponent envelope-type nanoparticle systems. Mol Pharm 2013; 10:4654-65. [PMID: 24188138 DOI: 10.1021/mp400470p] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We packaged condensed DNA/protamine particles in multicomponent envelope-type nanoparticle systems (MENS) combining different molar fractions of the cationic lipids 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) and 3β-[N-(N,N-dimethylaminoethane)-carbamoyl] cholesterol (DC-Chol) and the zwitterionic lipids dioleoylphosphocholine (DOPC) and dioleoylphosphatidylethanolamine (DOPE). Dynamic light scattering (DLS) and microelectrophoresis allowed us to identify the cationic lipid/DNA charge ratio at which MENS are small sized and positively charged, while synchrotron small-angle X-ray scattering (SAXS) and atomic force microscopy (AFM) revealed that MENS are well-shaped DNA/protamine particles covered by a lipid monobilayer. Transfection efficiency (TE) experiments indicate that a nanoparticle formulation, termed MENS-3, was not cytotoxic and highly efficient to transfect Chinese hamster ovary (CHO) cells. To rationalize TE, we performed a quantitative investigation of cell uptake, intracellular trafficking, endosomal escape, and final fate by laser scanning confocal microscopy (LSCM). We found that fluid-phase macropinocytosis is the only endocytosis pathway used by MENS-3. Once taken up by the cell, complexes that are actively transported by microtubules frequently fuse with lysosomes, while purely diffusing systems do not. Indeed, spatiotemporal image correlation spectroscopy (STICS) clarified that MENS-3 mostly exploit diffusion to move in the cytosol of CHO cells, thus explaining the high TE levels observed. Also, MENS-3 exhibited a marked endosomal rupture ability resulting in extraordinary DNA release. The lipid-dependent and structure-dependent TE boost suggests that efficient transfection requires both the membrane-fusogenic activity of the nanocarrier envelope and the employment of lipid species with intrinsic endosomal rupture ability.
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Affiliation(s)
- D Pozzi
- Department of Molecular Medicine, "Sapienza" University of Rome , Viale Regina Elena 291, 00161, Rome, Italy
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28
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Battisti A, Ciasca G, Tenenbaum A. Transient tertiary structures in tau, an intrinsically disordered protein. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.794275] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Barrán-Berdón AL, Pozzi D, Caracciolo G, Capriotti AL, Caruso G, Cavaliere C, Riccioli A, Palchetti S, Laganà A. Time evolution of nanoparticle-protein corona in human plasma: relevance for targeted drug delivery. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:6485-94. [PMID: 23631648 DOI: 10.1021/la401192x] [Citation(s) in RCA: 217] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
When nanoparticles (NPs) enter a biological fluid (e.g., human plasma (HP)), proteins and other biomolecules adsorb on the surface leading to formation of a rich protein shell, referred to as "protein corona". This corona is dynamic in nature and its composition varies over time due to continuous protein association and dissociation events. Understanding the time evolution of the protein corona on the time-scales of a particle's lifetime in blood is fundamental to predict its fate in vivo. In this study, we used lipid NPs, the cationic lipid 3β-[N-(N',N'-dimethylaminoethane)-carbamoyl] (DC-Chol) and the zwitterionic lipid dioleoylphosphatidylethanolamine (DOPE), that are among the most promising nanocarriers both in vitro and in vivo. Here, we investigated the time evolution of DC-Chol-DOPE NPs upon exposure to HP. On time scales between 1 and 60 minutes, nanoliquid tandem mass spectrometry revealed that the protein corona of DC-Chol-DOPE NPs is mainly constituted of apolipoproteins (Apo A-I, Apo C-II, Apo D, and Apo E are the most enriched). Since the total apolipoprotein content is relevant, we exploited the protein corona to target PC3 prostate carcinoma cell line that expresses high levels of scavenger receptor class B type 1 receptor, which mediates the bidirectional lipid transfer between low-density lipoproteins, high-density lipoproteins, and cells. Combining laser scanning confocal microscopy experiments with flow cytometry we demonstrated that DC-Chol-DOPE/HP complexes enter PC3 cells by a receptor-mediated endocytosis mechanism.
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Affiliation(s)
- Ana Lilia Barrán-Berdón
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161 Rome, Italy
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Luo Y, Dinkel P, Yu X, Margittai M, Zheng J, Nussinov R, Wei G, Ma B. Molecular insights into the reversible formation of tau protein fibrils. Chem Commun (Camb) 2013; 49:3582-4. [PMID: 23527380 PMCID: PMC3637047 DOI: 10.1039/c3cc00241a] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We computationally and experimentally showed that tau protein fibrils can be formed at high temperature. When cooled, the fibrils dissociate back to monomers. Heparin promotes tau fibril formation and prevents its reversion. Our results revealed the physicochemical mechanism of reversible formation of tau fibrils.
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Affiliation(s)
- Yin Luo
- Department of Physics, Fudan University, Shanghai, P.R. China
| | - Paul Dinkel
- Department of Chemistry & Biochemistry, University of Denver, Denver, Colorado 80208
| | - Xiang Yu
- Department of Chemical & Biomolecular Engineering, the University of Akron, Akron, Ohio 44325
| | - Martin Margittai
- Department of Chemistry & Biochemistry, University of Denver, Denver, Colorado 80208
| | - Jie Zheng
- Department of Chemical & Biomolecular Engineering, the University of Akron, Akron, Ohio 44325
| | - Ruth Nussinov
- Basic Science Program, SAIC-Frederick, Inc. CCRNP, Frederick National Lab, Frederick, Maryland 21702
- Sackler Inst. of Molecular Medicine. Tel Aviv University, Tel Aviv 69978, Israel
| | - Guanghong Wei
- Department of Physics, Fudan University, Shanghai, P.R. China
| | - Buyong Ma
- Basic Science Program, SAIC-Frederick, Inc. CCRNP, Frederick National Lab, Frederick, Maryland 21702
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