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Krüger M, Mishra A, Spichtinger P, Pöschl U, Berkemeier T. A numerical compass for experiment design in chemical kinetics and molecular property estimation. J Cheminform 2024; 16:34. [PMID: 38520014 PMCID: PMC10960421 DOI: 10.1186/s13321-024-00825-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 03/10/2024] [Indexed: 03/25/2024] Open
Abstract
Kinetic process models are widely applied in science and engineering, including atmospheric, physiological and technical chemistry, reactor design, or process optimization. These models rely on numerous kinetic parameters such as reaction rate, diffusion or partitioning coefficients. Determining these properties by experiments can be challenging, especially for multiphase systems, and researchers often face the task of intuitively selecting experimental conditions to obtain insightful results. We developed a numerical compass (NC) method that integrates computational models, global optimization, ensemble methods, and machine learning to identify experimental conditions with the greatest potential to constrain model parameters. The approach is based on the quantification of model output variance in an ensemble of solutions that agree with experimental data. The utility of the NC method is demonstrated for the parameters of a multi-layer model describing the heterogeneous ozonolysis of oleic acid aerosols. We show how neural network surrogate models of the multiphase chemical reaction system can be used to accelerate the application of the NC for a comprehensive mapping and analysis of experimental conditions. The NC can also be applied for uncertainty quantification of quantitative structure-activity relationship (QSAR) models. We show that the uncertainty calculated for molecules that are used to extend training data correlates with the reduction of QSAR model error. The code is openly available as the Julia package KineticCompass.
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Affiliation(s)
- Matteo Krüger
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Hahn-Meitner-Weg 1, Mainz, 55128, Rhineland Palatinate, Germany
| | - Ashmi Mishra
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Hahn-Meitner-Weg 1, Mainz, 55128, Rhineland Palatinate, Germany
| | - Peter Spichtinger
- Institute for Atmospheric Physics, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 21, Mainz, 55128, Rhineland Palatinate, Germany
| | - Ulrich Pöschl
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Hahn-Meitner-Weg 1, Mainz, 55128, Rhineland Palatinate, Germany
| | - Thomas Berkemeier
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Hahn-Meitner-Weg 1, Mainz, 55128, Rhineland Palatinate, Germany.
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Cook I, Leyh TS. Sterol-activated amyloid beta fibril formation. J Biol Chem 2023; 299:105445. [PMID: 37949224 PMCID: PMC10704437 DOI: 10.1016/j.jbc.2023.105445] [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: 08/27/2023] [Revised: 10/23/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023] Open
Abstract
The metabolic processes that link Alzheimer's disease (AD) to elevated cholesterol levels in the brain are not fully defined. Amyloid beta (Aβ) plaque accumulation is believed to begin decades prior to symptoms and to contribute significantly to the disease. Cholesterol and its metabolites accelerate plaque formation through as-yet-undefined mechanisms. Here, the mechanism of cholesterol (CH) and cholesterol 3-sulfate (CS) induced acceleration of Aβ42 fibril formation is examined in quantitative ligand binding, Aβ42 fibril polymerization, and molecular dynamics studies. Equilibrium and pre-steady-state binding studies reveal that monomeric Aβ42•ligand complexes form and dissociate rapidly relative to oligomerization, that the ligand/peptide stoichiometry is 1-to-1, and that the peptide is likely saturated in vivo. Analysis of Aβ42 polymerization progress curves demonstrates that ligands accelerate polymer synthesis by catalyzing the conversion of peptide monomers into dimers that nucleate the polymerization reaction. Nucleation is accelerated ∼49-fold by CH, and ∼13,000-fold by CS - a minor CH metabolite. Polymerization kinetic models predict that at presumed disease-relevant CS and CH concentrations, approximately half of the polymerization nuclei will contain CS, small oligomers of neurotoxic dimensions (∼12-mers) will contain substantial CS, and fibril-formation lag times will decrease 13-fold relative to unliganded Aβ42. Molecular dynamics models, which quantitatively predict all experimental findings, indicate that the acceleration mechanism is rooted in ligand-induced stabilization of the peptide in non-helical conformations that readily form polymerization nuclei.
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Affiliation(s)
- Ian Cook
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Thomas S Leyh
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA.
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Joshi A, Wang DH, Watterson S, McClean PL, Behera CK, Sharp T, Wong-Lin K. Opportunities for multiscale computational modelling of serotonergic drug effects in Alzheimer's disease. Neuropharmacology 2020; 174:108118. [PMID: 32380022 PMCID: PMC7322519 DOI: 10.1016/j.neuropharm.2020.108118] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 04/13/2020] [Accepted: 04/27/2020] [Indexed: 12/17/2022]
Abstract
Alzheimer's disease (AD) is an age-specific neurodegenerative disease that compromises cognitive functioning and impacts the quality of life of an individual. Pathologically, AD is characterised by abnormal accumulation of beta-amyloid (Aβ) and hyperphosphorylated tau protein. Despite research advances over the last few decades, there is currently still no cure for AD. Although, medications are available to control some behavioural symptoms and slow the disease's progression, most prescribed medications are based on cholinesterase inhibitors. Over the last decade, there has been increased attention towards novel drugs, targeting alternative neurotransmitter pathways, particularly those targeting serotonergic (5-HT) system. In this review, we focused on 5-HT receptor (5-HTR) mediated signalling and drugs that target these receptors. These pathways regulate key proteins and kinases such as GSK-3 that are associated with abnormal levels of Aβ and tau in AD. We then review computational studies related to 5-HT signalling pathways with the potential for providing deeper understanding of AD pathologies. In particular, we suggest that multiscale and multilevel modelling approaches could potentially provide new insights into AD mechanisms, and towards discovering novel 5-HTR based therapeutic targets. Alzheimer's disease (AD) drug treatment is limited, and alternatives are needed. Serotonin (5-HT) mediated signalling pathways may regulate Aβ and tau levels. 5-HT based drugs have the potential to provide as novel therapeutics for AD. Complex 5-HT signalling mechanisms for AD and related drugs hinder understanding. Multiscale models may offer insights into mechanisms and therapeutic targets.
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Affiliation(s)
- Alok Joshi
- Intelligent Systems Research Centre, Ulster University, Derry~Londonderry, Northern Ireland, UK.
| | - Da-Hui Wang
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China; School of System Science, Beijing Normal University, Beijing, China
| | - Steven Watterson
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, Ulster University, Derry~Londonderry, Northern Ireland, UK
| | - Paula L McClean
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, Ulster University, Derry~Londonderry, Northern Ireland, UK
| | - Chandan K Behera
- Intelligent Systems Research Centre, Ulster University, Derry~Londonderry, Northern Ireland, UK
| | - Trevor Sharp
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - KongFatt Wong-Lin
- Intelligent Systems Research Centre, Ulster University, Derry~Londonderry, Northern Ireland, UK.
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Giamblanco N, Fichou Y, Janot JM, Balanzat E, Han S, Balme S. Mechanisms of Heparin-Induced Tau Aggregation Revealed by a Single Nanopore. ACS Sens 2020; 5:1158-1167. [PMID: 32216272 DOI: 10.1021/acssensors.0c00193] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein aggregation is involved in many diseases, including Parkinson's and Alzheimer's. The latter is characterized by intraneuronal deposition of amyloid aggregates composed of the tau protein. Although large and insoluble aggregates are typically found in affected brains, intermediate soluble oligomers are thought to represent crucial species for toxicity and spreading. Nanopore sensors constitute an emerging technology that allows the detection of the size and populations of molecular assembly present in a sample. Here, we employed conical nanopores to obtain the particle distributions during tau aggregation. We identified three distinct populations, monomers, oligomers, and fibrils, which we could quantify along the aggregation process. By comparing tau wild type with a mutant carrying the disease-associated P301L mutation, we showed that the latter mutation promotes the formation of oligomers. We furthermore highlighted that the P301L mutation promotes fibril breakage. This work demonstrates that conical nanopore is a powerful tool to measure and quantify transient protein aggregate intermediates.
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Affiliation(s)
- Nicoletta Giamblanco
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier Cedex
5, France
| | - Yann Fichou
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Jean-Marc Janot
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier Cedex
5, France
| | - Emmanuel Balanzat
- Centre de recherche sur les Ions, les Matériaux et la Photonique, UMR6252 CEA-CNRS-ENSICAEN, 6 Boulevard du Maréchal Juin, 14050 Caen Cedex 4, France
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Sebastien Balme
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier Cedex
5, France
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Kubánková M, Lin X, Albrecht T, Edel JB, Kuimova MK. Rapid Fragmentation during Seeded Lysozyme Aggregation Revealed at the Single Molecule Level. Anal Chem 2019; 91:6880-6886. [PMID: 30999745 DOI: 10.1021/acs.analchem.9b01221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein aggregation is associated with neurodegenerative disorders such as Alzheimer's and Parkinson's diseases. The poorly understood pathogenic mechanism of amyloid diseases makes early stage diagnostics or therapeutic intervention a challenge. Seeded polymerization that reduces the duration of the lag phase and accelerates fibril growth is a widespread model to study amyloid formation. Seeding effects are hypothesized to be important in the "infectivity" of amyloids and are linked to the development of systemic amyloidosis in vivo. The exact mechanism of seeding is unclear yet critical to illuminating the propagation of amyloids. Here we report on the lateral and axial fragmentation of seed fibrils in the presence of lysozyme monomers at short time scales, followed by the generation of oligomers and growth of fibrils.
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Affiliation(s)
- Markéta Kubánková
- Department of Chemistry , Imperial College London , Exhibition Road , London SW7 2AZ , U.K
| | - Xiaoyan Lin
- Department of Chemistry , Imperial College London , Exhibition Road , London SW7 2AZ , U.K
| | - Tim Albrecht
- Department of Chemistry , Imperial College London , Exhibition Road , London SW7 2AZ , U.K.,School of Chemistry, Edgbaston Campus , University of Birmingham , Birmingham B15 2TT , U.K
| | - Joshua B Edel
- Department of Chemistry , Imperial College London , Exhibition Road , London SW7 2AZ , U.K
| | - Marina K Kuimova
- Department of Chemistry , Imperial College London , Exhibition Road , London SW7 2AZ , U.K
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Baughman HER, Clouser AF, Klevit RE, Nath A. HspB1 and Hsc70 chaperones engage distinct tau species and have different inhibitory effects on amyloid formation. J Biol Chem 2018; 293:2687-2700. [PMID: 29298892 DOI: 10.1074/jbc.m117.803411] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 12/15/2017] [Indexed: 11/06/2022] Open
Abstract
The microtubule-associated protein tau forms insoluble, amyloid-type aggregates in various dementias, most notably Alzheimer's disease. Cellular chaperone proteins play important roles in maintaining protein solubility and preventing aggregation in the crowded cellular environment. Although tau is known to interact with numerous chaperones, it remains unclear how these chaperones function mechanistically to prevent tau aggregation and how chaperones from different classes compare in terms of mechanism. Here, we focused on the small heat shock protein HspB1 (also known as Hsp27) and the constitutive chaperone Hsc70 (also known as HspA8) and report how each chaperone interacts with tau to prevent its fibril formation. Using fluorescence and NMR spectroscopy, we show that the two chaperones inhibit tau fibril formation by distinct mechanisms. HspB1 delayed tau fibril formation by weakly interacting with early species in the aggregation process, whereas Hsc70 was highly efficient at preventing tau fibril elongation, possibly by capping the ends of tau fibrils. Both chaperones recognized aggregation-prone motifs within the microtubule-binding repeat region of tau. However, HspB1 binding remained transient in both aggregation-promoting and non-aggregating conditions, whereas Hsc70 binding was significantly tighter under aggregation-promoting conditions. These differences highlight the fact that chaperones from different families play distinct but complementary roles in the prevention of pathological protein aggregation.
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Affiliation(s)
- Hannah E R Baughman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195-7610
| | - Amanda F Clouser
- Department of Biochemistry, University of Washington, Seattle, Washington 98195-7350
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington, Seattle, Washington 98195-7350.
| | - Abhinav Nath
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195-7610.
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