Article
Biochemistry & Molecular Biology
Tapojyoti Das, Meraj Ramezani, David Snead, Cristian Follmer, Peter Chung, Ka Yee Lee, David A. A. Holowka, Barbara A. A. Baird, David Eliezer
Summary: Alpha-synuclein plays an important role in regulating synaptic vesicle cycling, exerting both inhibitory and potentiating effects on vesicle release. The binding affinity of alpha-synuclein to isolated vesicles is a key determinant of its ability to potentiate release.
Article
Biochemistry & Molecular Biology
Ana Belen Uceda, Juan Frau, Bartolome Vilanova, Miquel Adrover
Summary: Human alpha-synuclein (α S) is an intrinsically disordered protein highly expressed in dopaminergic neurons. Its amyloid aggregates are considered a hallmark of Parkinson's disease (PD). The oxidation of alpha S's methionine residues (MetO) affects its affinity towards anionic micelles and synaptic-like vesicles, impairing its physiological function as a catalyst of vesicle clustering and fusion.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Ana Belen Uceda, Juan Frau, Bartolome Vilanova, Miquel Adrover
Summary: Parkinson's disease is characterized by the degeneration of dopaminergic neurons and the accumulation of Lewy bodies. Previous studies have examined the molecular mechanism linking nitroxidation, aS aggregation, and PD, but the impact of nitroxidation on the physiological function of aS was unclear. Our research found that nitroxidation of Y39 lengthened the disordered stretch between two consecutive alpha-helices and prevented aS from functioning as a catalyst for the clustering and fusion of synaptic vesicles.
Review
Biochemistry & Molecular Biology
Lennart Brodin, Dragomir Milovanovic, Silvio O. Rizzoli, Oleg Shupliakov
Summary: This review discusses recent data suggesting the protein alpha-synuclein as a component of the synaptic vesicle liquid phase, and considers possible implications of these data for disease.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biology
Manindra Bera, Sathish Ramakrishnan, Jeff Coleman, Shyam S. Krishnakumar, James E. Rothman
Summary: In neurotransmitter release, Complexin regulates rapid vesicle fusion by clamping the SNARE complex, with a fusion delay likely induced by Synaptotagmin-1. The accessory-central domains of Complexin are crucial for its inhibitory function, with specific interactions with SNAREpins enhancing its effectiveness. The C-terminal domain promotes clamping by interacting with membranes to locally elevate Complexin concentration.
Article
Biochemistry & Molecular Biology
Dong-Yan Song, Lin Yuan, Na Cui, Cong Feng, Lanxia Meng, Xin-He Wang, Man Xiang, Di Liu, Chun Wang, Zhentao Zhang, Jia-Yi Li, Wen Li
Summary: Parkinson's disease is an age-related chronic neurological disorder characterized by the aggregation of alpha-synuclein. This study found that over-expression of human alpha-synuclein disrupts synaptic function by interfering with vesicle recycling, but this damage can be alleviated by the re-availment of SYNJ1.
JOURNAL OF NEUROCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Feng Li, Ramalingam Venkat Kalyana Sundaram, Alberto T. Gatta, Jeff Coleman, Sathish Ramakrishnan, Shyam S. Krishnakumar, Frederic Pincet, James E. Rothman
Summary: Munc13-1 forms nano-clusters involving 2 to around 20 copies, with only clusters containing a minimum of 6 copies capable of efficiently capturing and retaining small vesicles. The C-terminal C2C domain is not necessary for clustering, but is crucial for vesicle capture due to electrostatic and hydrophobic interactions.
Article
Clinical Neurology
Gary P. H. Ho, Nagendran Ramalingam, Thibaut Imberdis, Erin C. Wilkie, Ulf Dettmer, Dennis J. Selkoe
Summary: The study demonstrated that inhibiting depalmitoylase acyl-protein-thioesterase-1 (APT1) can reduce alpha-synuclein (αS) cytoplasmic inclusions and alpha S-dependent neurotoxicity, while maintaining the palmitoylation level of the protein MAP6. This reveals a novel link between palmitoylation and αS pathophysiology, suggesting upregulating palmitoylation as a potential therapeutic strategy for synucleinopathies.
MOVEMENT DISORDERS
(2021)
Article
Biochemistry & Molecular Biology
Kathrine Stokholm, Majken Borup Thomsen, Jenny-Ann Phan, Line K. Moller, Cecilie Bay-Richter, Soren H. Christiansen, David P. D. Woldbye, Marina Romero-Ramos, Anne M. Landau
Summary: The overexpression of alpha-synuclein leads to dopaminergic degeneration, resulting in compensatory increases in D2/3 receptor binding and immune activation, recapitulating many of the pathological characteristics of Parkinson's disease.
Review
Biochemistry & Molecular Biology
Li Yang Tan, Kwan Hou Tang, Lynette Yu You Lim, Jia Xin Ong, Hyokeun Park, Sangyong Jung
Summary: alpha-synuclein is a protein strongly associated with the neuropathology observed in Parkinson's disease, dementia with Lewy bodies, and Alzheimer's disease. Mutations and modifications of alpha-syn interfere with its function, leading to abnormalities in presynaptic vesicular dynamics, protein expressions, and mitochondrial profiles. Targeted therapies for alpha-syn are being explored, and the use of novel encapsulation technology may overcome existing challenges.
Article
Cell Biology
Yuxi Lin, Dai Ito, Je Min Yoo, Mi Hee Lim, Wookyung Yu, Yasushi Kawata, Young-Ho Lee
Summary: The aggregation of alpha-synuclein (alpha SN) under different conditions is closely related to synucleinopathies. This study examined the structural changes, binding properties, and amyloidogenicity of alpha SN mutants in two types of membranes. It was found that negatively charged membranes induced dramatic helical folding and amyloid generation of alpha SN, while neutral membranes had minimal effects.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Sophia M. McClain, Moses H. Milchberg, Chad M. Rienstra, Catherine J. Murphy
Summary: The interaction between alpha-synuclein and synaptic vesicle mimics depends on the malleability and rigidity of the mimics, with higher binding affinities observed for rigid mimics. The lipid composition of the mimics also affects the interaction. The study provides insights into the behavior of alpha-synuclein and its relation to membrane properties.
Article
Multidisciplinary Sciences
Rohith K. Nellikka, Bhavya R. Bhaskar, Kinjal Sanghrajka, Swapnali S. Patil, Debasis Das
Summary: Alpha-synuclein plays a crucial role in the pathogenesis of Parkinson's disease by directly regulating individual exocytotic release events, controlling vesicular secretion. It forms an inhibitory complex to decrease the open probability of fusion pores, influenced by various factors. This study reveals the key role of alpha-synuclein in modulating pore properties and highlights its regulatory action in membrane fusion.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Carlos Navarro-Paya, Maximo Sanz-Hernandez, Alfonso De Simone
Summary: This study investigates the membrane binding and conformational changes of alpha-synuclein, shedding light on its biological behavior and the association with Parkinson's disease.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Ana Belen Uceda, Juan Frau, Bartolome Vilanova, Miquel Adrover
Summary: Parkinson's disease is a prevalent neurodegenerative disorder characterized by the accumulation of insoluble Lewy bodies in neurons, leading to neuronal death. The main component of these Lewy bodies, alpha-synuclein, undergoes non-enzymatic post-translational modifications, which affect its aggregation and physiological function. Understanding these modifications is crucial for better understanding the mechanisms underlying diabetes-induced Parkinson's disease.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Michele Vendruscolo, Monika Fuxreiter
Summary: This study investigates the sequence determinants of protein aggregation via the condensation pathway and identifies three relevant features: droplet-promoting propensity, aggregation-promoting propensity, and multimodal interactions quantified by the binding mode entropy. By using this approach, aggregation-promoting mutations in droplet-forming proteins associated with amyotrophic lateral sclerosis (ALS) can be predicted.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Chemistry, Physical
Thomas C. T. Michaels, Alexander J. Dear, Samuel I. A. Cohen, Michele Vendruscolo, Tuomas P. J. Knowles
Summary: Protein self-assembly into amyloid fibrils is crucial for neurodegenerative diseases, with small oligomers formed during this process being neurotoxic species associated with amyloid aggregation. Targeting the formation of oligomers may be a possible therapeutic avenue. Through a kinetic model, researchers have identified key kinetic parameters that effectively control the generation of oligomers, opening up new possibilities for therapeutic strategies against amyloid-related diseases.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Cell Biology
Maria Francesca Palmas, Michela Etzi, Augusta Pisanu, Chiara Camoglio, Claudia Sagheddu, Michele Santoni, Maria Francesca Manchinu, Mauro Pala, Giuliana Fusco, Alfonso De Simone, Luca Picci, Giovanna Mulas, Saturnino Spiga, Maria Scherma, Paola Fadda, Marco Pistis, Nicola Simola, Ezio Carboni, Anna R. Carta
Summary: The study demonstrates that intracerebral infusion of pre-formed human alpha synuclein oligomers (H-alpha SynOs) provides a valid model for studying cognitive symptoms in Parkinson's disease, accompanied by neuroinflammation, shedding light on the mechanisms underlying cognitive impairment.
Article
Biochemistry & Molecular Biology
Giuliana Fusco, Francesco Bemporad, Fabrizio Chiti, Christopher M. M. Dobson, Alfonso De Simone
Summary: Understanding the differences in adaptation between proteins from hyperthermophilic organisms and their mesophilic homologues is crucial for unraveling the mechanisms of biological activity in proteins. Researchers measured NMR residual dipolar couplings and performed additional NMR experiments to study the structural and dynamical properties of a hyperthermophilic acylphosphatase enzyme and a human homologue. The results identified key differences in protein-protein and protein-ligand interactions, shedding light on the structure-dynamics-function relationship associated with the thermal adaptation strategies of protein molecules.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemical Research Methods
Marc Oeller, Ryan Kang, Rosie Bell, Hannes Ausserwoger, Pietro Sormanni, Michele Vendruscolo
Summary: This article describes a computational method that incorporates the effect of pH on protein solubility predictions. The accuracy of these predictions is comparable to experimental methods, as demonstrated on various antibodies and proteins. This method, named CamSol 3.0, is now publicly available at https://www-cohsoftware.ch.cam.ac.uk/index.php/camsolph.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Alyssa Miller, Sean Chia, Zenon Toprakcioglu, Tuuli Hakala, Roman Schmid, Yaduo Feng, Tadas Kartanas, Ayaka Kamada, Michele Vendruscolo, Francesco Simone Ruggeri, Tuomas P. J. Knowles
Summary: In this study, a lab-on-a-chip spray approach was developed to combine rapid sample preparation, mixing, and deposition with nanoanalytical methods in chemistry and biology. This method provides enhanced spectroscopic sensitivity and single-molecule spatial resolution, allowing for multidimensional studies of heterogeneous biomolecular systems.
Review
Chemistry, Multidisciplinary
Ryan Limbocker, Nunilo Cremades, Roberta Cascella, Peter M. Tessier, Michele Vendruscolo, Fabrizio Chiti
Summary: The misfolding and aggregation of peptides and proteins into amyloid aggregates is a common feature of various protein misfolding diseases, including Alzheimer's disease and Parkinson's disease. Misfolded protein oligomers, which can form intermediates in the fibril formation process or be released by mature fibrils, are increasingly recognized as central to the development of these diseases. Despite challenges in studying these oligomers, researchers have developed methods to produce stable and reproducible populations for experimentation. These tools have provided insights into the structural determinants of oligomer toxicity and potential therapeutic strategies.
ACCOUNTS OF CHEMICAL RESEARCH
(2023)
Review
Pharmacology & Pharmacy
Michele Vendruscolo
Summary: Protein misfolding diseases, such as Alzheimer's and Parkinson's diseases, have a major impact on our healthcare systems and societies. This paper discusses drug discovery strategies to target protein misfolding and aggregation, including thermodynamic and kinetic approaches. There is a need for disease-modifying treatments to address the over 50 human disorders associated with protein misfolding and aggregation.
EXPERT OPINION ON DRUG DISCOVERY
(2023)
Review
Clinical Neurology
Mark R. Wilson, Sandeep Satapathy, Michele Vendruscolo
Summary: The proteostasis system regulates cellular processes of protein synthesis, folding, concentration, trafficking, and degradation. The mechanisms of extracellular proteostasis, particularly in the context of neurodegenerative diseases, are not well understood, but growing evidence suggests that impairment of this system may contribute to neuronal death.
NATURE REVIEWS NEUROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Andras Hatos, Joao M. C. Teixeira, Susana Barrera-Vilarmau, Attila Horvath, Silvio C. E. Tosatto, Michele Vendruscolo, Monika Fuxreiter
Summary: Proteins form complex interactions in the cellular environment. The FuzPred server predicts their binding modes based on sequence without specifying the binding partners. The server also estimates the multiplicity of binding modes and visualizes different interaction behaviors on protein structures.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Alyssa Miller, Jiapeng Wei, Sarah Meehan, Christopher M. Dobson, Mark E. Welland, David Klenerman, Michele Vendruscolo, Francesco Simone Ruggeri, Tuomas P. J. Knowles
Summary: Neurodegenerative diseases such as Alzheimer's disease are caused by protein misfolding and aggregation into amyloid fibrils. This study uses atomic force microscopy and statistical theory to characterize amyloid ring structures derived from the brains of AD patients and explains the diversity in the structures formed from protein aggregation. The results show that ex vivo protofibril chains possess greater flexibility than mature amyloid fibrils, allowing them to form end-to-end connections and shedding light on their role in disease.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Multidisciplinary
Mario Gonzalez-Garcia, Giuliana Fusco, Alfonso De Simone
Summary: This study investigated the conformational changes of α-synuclein (aS) upon binding with metal ions using nuclear magnetic resonance (NMR). It was found that binding to calcium and zinc reduced the protection factors in the C-terminal region of the protein, while binding to copper did not affect the amide proton exchange. N-15 relaxation experiments showed conformational perturbations in distinctive regions of the protein upon binding with Cu+ and Zn2+. Overall, these results suggest multiple mechanisms contribute to enhanced aS aggregation through metal binding.
FRONTIERS IN CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Z. Faidon Brotzakis, Thomas Lohr, Steven Truong, Samuel Hoff, Massimiliano Bonomi, Michele Vendruscolo
Summary: In recent years, cryo-electron microscopy has made significant advancements in determining biomolecular structures at the atomic level. However, studying large systems with continuous dynamics using this method has been a challenge. To address this, the metadynamic electron microscopy metainference (MEMMI) method was developed, which combines cryo-EM density maps with prior information to determine the structure and dynamics of large heterogeneous systems. This method was applied to study the amyloid fibril dynamics of the islet amyloid polypeptide (IAPP), revealing interesting characteristics of the fibril's structural variability and liquid-like dynamics in the core region.
Article
Multidisciplinary Sciences
Christine M. Lim, Alicia Gonzalez Diaz, Monika Fuxreiter, Frank W. Pun, Alex Zhavoronkov, Michele Vendruscolo
Summary: This study presents an approach that combines the PandaOmics platform with the FuzDrop method to identify disease-associated proteins prone to protein phase separation (PPS). The validated targets for Alzheimer's disease suggest the potential of this approach in identifying therapeutic targets for diseases involving dysregulation of PPS.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Physics, Applied
Thomas C. T. Michaels, Daoyuan Qian, Andela Saric, Michele Vendruscolo, Sara Linse, Tuomas P. J. Knowles
Summary: This Review discusses the general protein self-assembly behavior of amyloid fibrils, which is associated with functional biology and the development of diseases such as Alzheimer and Parkinson diseases. It summarizes recent progress in describing the biophysical features of amyloid self-assembly as a nucleation-and-growth process, highlighting the role of secondary nucleation. The Review also outlines non-classical aspects of aggregate formation and discusses their implications for understanding and modulating protein assembly pathways.
NATURE REVIEWS PHYSICS
(2023)