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Katyal N, Sharma S, Deep S. Delving into controversial dichotomy of direct and indirect mechanisms of Trehalose: In search of unanimous consensus. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116656] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Katyal N, Agarwal M, Sen R, Kumar V, Deep S. Paradoxical Effect of Trehalose on the Aggregation of α-Synuclein: Expedites Onset of Aggregation yet Reduces Fibril Load. ACS Chem Neurosci 2018; 9:1477-1491. [PMID: 29601727 DOI: 10.1021/acschemneuro.8b00056] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Aggregation of α-synuclein is closely connected to the pathology of Parkinson's disease. The phenomenon involves multiple steps, commenced by partial misfolding and eventually leading to mature amyloid fibril formation. Trehalose, a widely accepted osmolyte, has been shown previously to inhibit aggregation of various globular proteins owing to its ability to prevent the initial unfolding of protein. In this study, we have examined if it behaves in a similar fashion with intrinsically disordered protein α-synuclein and possesses the potential to act as therapeutic agent against Parkinson's disease. It was observed experimentally that samples coincubated with trehalose fibrillate faster compared to the case in its absence. Molecular dynamics simulations suggested that this initial acceleration is manifestation of trehalose's tendency to perturb the conformational transitions between different conformers of monomeric protein. It stabilizes the aggregation prone "extended" conformer of α-synuclein, by binding to its exposed acidic residues of the C terminus. It also favors the β-rich oligomers once formed. Interestingly, the total fibrils formed are still promisingly less since it accelerates the competing pathway toward formation of amorphous aggregates.
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Affiliation(s)
- Nidhi Katyal
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz-Khas, New Delhi 110016, India
| | - Manish Agarwal
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz-Khas, New Delhi 110016, India
| | - Raktim Sen
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz-Khas, New Delhi 110016, India
| | - Vinay Kumar
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz-Khas, New Delhi 110016, India
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz-Khas, New Delhi 110016, India
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Nakamura Y, Yoshimori A, Akiyama R, Yamaguchi T. Stick boundary condition at large hard sphere arising from effective attraction in binary hard-sphere mixtures. J Chem Phys 2018; 148:124502. [DOI: 10.1063/1.5025202] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yuka Nakamura
- Department of Physics, Kyushu University, Fukuoka 812-0395, Japan
| | - Akira Yoshimori
- Department of Physics, Niigata University, Niigata 950-2181, Japan
| | - Ryo Akiyama
- Department of Chemistry, Kyushu University, Fukuoka 812-0395, Japan
| | - Tsuyoshi Yamaguchi
- Department of Materials Process Engineering, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
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Abstract
Deposition of amyloid fibrils is the seminal event in the pathogenesis of numerous neurodegenerative diseases. The formation of this amyloid assembly is the manifestation of a cascade of structural transitions including toxic oligomer formation in the early stages of aggregation. Thus a viable therapeutic strategy involves the use of small molecular ligands to interfere with this assembly. In this perspective, we have explored the kinetics of aggregate formation of the fibril forming GNNQQNY peptide fragment from the yeast prion protein SUP35 using multiple all atom MD simulations with explicit solvent and provided mechanistic insights into the way trehalose, an experimentally known aggregation inhibitor, modulates the aggregation pathway. The results suggest that the assimilation process is impeded by different barriers at smaller and larger oligomeric sizes: the initial one being easily surpassed at higher temperatures and peptide concentrations. The kinetic profile demonstrates that trehalose delays the aggregation process by increasing both these activation barriers, specifically the latter one. It increases the sampling of small-sized aggregates that lack the beta sheet conformation. Analysis reveals that the barrier in the growth of larger stable oligomers causes the formation of multiple stable small oligomers which then fuse together bimolecularly. The PCA of 26 properties was carried out to deconvolute the events within the temporary lag phases, which suggested dynamism in lags involving an increase in interchain contacts and burial of SASA. The predominant growth route is monomer addition, which changes to condensation on account of a large number of depolymerisation events in the presence of trehalose. The favourable interaction of trehalose specifically with the sidechain of the peptide promotes crowding of trehalose molecules in its vicinity - the combination of both these factors imparts the observed behaviour. Furthermore, increasing trehalose concentration leads to faster expulsion of water molecules than interpeptide interactions. These expelled water molecules have larger translational movement, suggesting an entropy factor to favor the assembly process. Different conformations observed under this condition suggest the role of water molecules in guiding the morphology of the aggregates as well. A similar scenario exists on increasing peptide concentration.
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Affiliation(s)
- Nidhi Katyal
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauzkhas, New Delhi, India.
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauzkhas, New Delhi, India.
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Abstract
This work reports the results of an experimental study where laser techniques are applied to
acoustically levitated droplets of trehalose aqueous solutions in order to perform spectroscopic analyses as a function of concentration and to test the theoretical diameter law. The study of such systems is important in order to better understand the behaviour of trehalose-synthesizing extremophiles that live in extreme environments. In particular, it will be shown how acoustic levitation, combined with optical spectroscopic instruments allows to explore a wide concentration range and to test the validity of the diameter law as a function of levitation lag time, i.e. the D2 vs t law. On this purpose a direct diameter monitoring by a video camera and a laser pointer was first performed; then the diameter was also evaluated by an indirect measure through an OH/CH band area ratio analysis of collected Raman and Infrared spectra. It clearly emerges that D2 vs t follows a linear trend for about 20 minutes, reaching then a plateau at longer time. This result shows how trehalose is able to avoid total water evaporation, this property being essential for the surviving of organisms under extreme environmental conditions.
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Edelman R, Kusner I, Kisiliak R, Srebnik S, Livney YD. Sugar stereochemistry effects on water structure and on protein stability: The templating concept. Food Hydrocoll 2015. [DOI: 10.1016/j.foodhyd.2015.01.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Nakamura Y, Yoshimori A, Akiyama R. Effects of the solvation structure on diffusion of a large particle in a binary mixture studied by perturbation theory. J Mol Liq 2014. [DOI: 10.1016/j.molliq.2014.06.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Migliardo F, Tallima H, El Ridi R. Is there a sphingomyelin-based hydrogen bond barrier at the mammalian host-schistosome parasite interface? Cell Biochem Biophys 2014; 68:359-67. [PMID: 23943053 DOI: 10.1007/s12013-013-9716-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Schistosomes develop, mature, copulate, lay eggs, and live for years in the mammalian host bloodstream, importing nutrients across the tegument, but entirely impervious to the surrounding elements of the immune system. We have hypothesized that sphingomyelin (SM) in the parasite apical lipid bilayer is responsible for these sieving properties via formation of a tight hydrogen bond network with the surrounding water. Here we have used quasi-elastic neutron scattering for characterizing the diffusion of larval and adult Schistosoma mansoni and adult Schistosoma haematobium in the surrounding medium, under various environmental conditions. The results documented the presence of a hydrogen bond barrier around larvae and adult schistosomes. The hydrogen bond network readily collapses if worms are subjected to hypoxic conditions, likely via activation of the parasite tegument-associated neutral sphingomyelinase, and consequent excessive SM hydrolysis. The slower dynamics of lung-stage larvae as compared to adult worms has been related to the existence of hydrogen-bonded networks of different strength and then to their differential resistance to immune attacks.
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Affiliation(s)
- Federica Migliardo
- Department of Physics and Earth Sciences, University of Messina, Messina, 98166, Italy,
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Bousset L, Brewee C, Melki R, Migliardo F. Dynamical properties of α-synuclein in soluble and fibrillar forms by Quasi Elastic Neutron Scattering. Biochim Biophys Acta 2014; 1844:1307-16. [PMID: 24768772 DOI: 10.1016/j.bbapap.2014.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 03/24/2014] [Accepted: 04/14/2014] [Indexed: 10/25/2022]
Abstract
In the present paper, Quasi Elastic Neutron Scattering (QENS) results, gathered at different energy resolution values at the ISIS Facility (RAL, UK), on α-synuclein in soluble and fibrillar forms as a function of temperature and exchanged wave-vector Q are shown. The measurements reveal a different dynamic behavior of the soluble and fibrillar forms of α-synuclein as a function of thermal stress. In more detail, the dynamics of each protein form reflects its own complex conformational heterogeneity. Furthermore, the effect of a well known bioprotectant, trehalose, that influences α-synuclein fibrillation, on both soluble and fibrillar forms of α-synuclein is discussed.
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Affiliation(s)
- Luc Bousset
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Bat 34, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Clémence Brewee
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Bat 34, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Ronald Melki
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Bat 34, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Federica Migliardo
- Department of Physics and Earth Sciences, University of Messina, Viale D'Alcontres 31, 98166 Messina, Italy.
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Migliardo F, Tallima H, El Ridi R. Rigidity and resistance of larval- and adult schistosomes-medium interface. Biochem Biophys Res Commun 2014; 446:255-60. [PMID: 24589739 DOI: 10.1016/j.bbrc.2014.02.100] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 02/21/2014] [Indexed: 11/25/2022]
Abstract
Schistosomiasis is second only to malaria in prevalence and severity, and is still a major health problem in many tropical countries worldwide with about 200-300 million cases and with more than 800 million people at risk of infection. Based on these data, the World Health Organization recommends fostering research efforts for understanding at any level the mechanisms of the infection and then decreasing the social and economical impact of schistosomiasis. A key role is played by the parasite apical lipid membrane, which is entirely impervious to the surrounding elements of the immune system. We have previously demonstrated that the interaction between schistosomes and surrounding medium is governed by a parasite surface membrane sphingomyelin-based hydrogen barrier. In the present article, the elastic contribution to the total motion as a function of the exchanged wave-vector Q and the mean square displacement values for Schistosoma mansoni larvae and worms and Schistosomahaematobium worms have been evaluated by quasi elastic neutron scattering (QENS). The results point out that S. mansoni larvae show a smaller mean square displacement in comparison to S. mansoni and S. haematobium worms. These values increased by repeating the measurements after one day. These differences, which are analogous to those observed for the diffusion coefficient we previously evaluated, are interpreted in terms of rigidity of the parasite-medium interaction. S. mansoni larvae are the most rigid systems, while S. haematobium worms are the most flexible. In addition, temperature and hypoxia induce a weakening of the schistosome-medium interaction. These evidences are related to the strength of the hydrogen-bonded interaction between parasites and environment that we previously determined. We have shown that S. mansoni worms are characterized by a weakened interaction in respect to the larvae, while the S. haematobium worms more weakly interact with the surrounding medium than S. mansoni. The present QENS analysis allowed us to characterize the rigidity of larval- and adult S. mansoni and S. haematobium-host interface and to relate it to the parasite resistance to the hostile elements of the surrounding medium and to the immune effectors attack.
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Affiliation(s)
- Federica Migliardo
- Department of Physics and Earth Sciences, University of Messina, 98166 Messina, Italy.
| | - Hatem Tallima
- Zoology Department, Faculty of Science, Cairo University, Cairo 12613, Egypt
| | - Rashika El Ridi
- Zoology Department, Faculty of Science, Cairo University, Cairo 12613, Egypt
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Kiselev M, Janich M, Hildebrand A, Strunz P, Neubert R, Lombardo D. Structural transition in aqueous lipid/bile salt [DPPC/NaDC] supramolecular aggregates: SANS and DLS study. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.05.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Manukovsky N, Shpigelman A, Edelman R, Livney YD. Hydration-mediated effects of saccharide stereochemistry on poly(N
-isopropylacrylamide) gel swelling. ACTA ACUST UNITED AC 2011. [DOI: 10.1002/polb.22212] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Geerke DP, van Gunsteren WF, Hünenberger PH. Molecular dynamics simulations of the interaction between polyhydroxylated compounds and Lennard-Jones walls: preferential affinity/exclusion effects and their relevance for bioprotection. Molecular Simulation 2010. [DOI: 10.1080/08927021003752804] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Magazù S, Migliardo F. Spectroscopic study of the physical properties making trehalose a stabilizing and shelf life extending compound in food industry. Quality Assurance and Safety of Crops & Foods 2010. [DOI: 10.1111/j.1757-837x.2010.00060.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Magazù S, Migliardo F, Affouard F, Descamps M, Telling MTF. Study of the relaxational and vibrational dynamics of bioprotectant glass-forming mixtures by neutron scattering and molecular dynamics simulation. J Chem Phys 2010. [DOI: 10.1063/1.3407428] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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