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The amyloid $\beta$ peptide (A$\beta$42), whose aggregation is associated with Alzheimer's disease, is an amphiphatic peptide with a high propensity to self-assemble. A$\beta$42 has a net negative charge at physiological pH and modulations…

Molecular Networks · Quantitative Biology 2020-08-25 Georg Meisl , Xiaoting Yang , Christopher M. Dobson , Sara Linse , Tuomas P. J. Knowles

Cholesterol (CHOL) drives lipid segregation and is thus a key player for the formation of lipid rafts and followingly for the ability of a cell to, e.g., enable selective agglomeration of proteins. The lipid segregation is driven by…

Biological Physics · Physics 2021-03-26 Fabian Keller , Andreas Heuer

Decades after their initial observation in prion-infected brain tissues, the identities of virus-like dense particles, varicose tubules, and oval bodies containing parallel bands and fibrils have remained elusive. Our recent work revealed…

Neurons and Cognition · Quantitative Biology 2025-01-17 Gerold Schmitt-Ulms , Xinzhu Wang , Joel Watts , Stephanie Booth , Holger Wille , Wenda Zhao

Atherosclerosis is a disease characterized by the development of atherosclerotic plaques (APs) in arterial endothelium. The APs in part of an arterial wall are inhomogeneous on size and on distribution. In order to understand this…

Tissues and Organs · Quantitative Biology 2017-09-07 Jicun Wang-Michelitsch , Thomas M. Michelitsch

Being the most commonly known neurodegeneration, Alzheimer's Disease (AD) is annually diagnosed in millions of patients. The present medical scenario still finds the exact diagnosis and classification of AD through neuroimaging data as a…

Image and Video Processing · Electrical Eng. & Systems 2025-03-19 Shravan Venkatraman , Pandiyaraju V , Abeshek A , Pavan Kumar S , Aravintakshan S A

We develop a theory of aggregation using statistical mechanical methods. An example of a complicated aggregation system with several levels of structures is peptide/protein self-assembly. The problem of protein aggregation is important for…

Biomolecules · Quantitative Biology 2023-07-19 John S. Schreck , Jian-Min Yuan

{\alpha}-synuclein ({\alpha}-syn) is an intrinsically disordered protein which is considered to be one of the causes of Parkinson's disease. This protein forms amyloid fibrils when in a highly concentrated solution. The fibril formation of…

Biomolecules · Quantitative Biology 2016-02-09 Nobu C. Shirai , Macoto Kikuchi

Coronary heart disease (CHD) caused by hardening of artery walls due to cholesterol known as atherosclerosis is responsible for large number of deaths world-wide. The disease progression is slow, asymptomatic and may lead to sudden cardiac…

Machine Learning · Computer Science 2015-02-03 V. Sree Hari Rao , M. Naresh Kumar

Alzheimer's disease (AD) is an irreversible brain disease that can dramatically reduce quality of life, most commonly manifesting in older adults and eventually leading to the need for full-time care. Early detection is fundamental to…

Computation and Language · Computer Science 2019-06-14 Flavio Di Palo , Natalie Parde

Neurodegenerative diseases are characterized as the progressive loss of neural cells, e.g. neurons, glial cells. Ageing, monogenic variations, viral infections, and many other factors are determined and speculated as causes for them. While…

Molecular Networks · Quantitative Biology 2019-09-18 Abdulahad Bayraktar , Tugba Onal-Suzek , Baris Ethem Suzek , Omur Baysal

Alzheimer's disease is characterized by dangerous amyloid plaques formed by deposits of the protein Beta-Amyloid aggregates in the brain. The specific amino acid sequence that is responsible for the aggregates of Beta-Amyloid is…

Quantitative Methods · Quantitative Biology 2025-06-18 Ananya Joshi , George Khoury , Christodoulas Floudas

Mild cognitive impairment (MCI) leading to dementia results in a constellation of psychiatric disorders including depression, mood disorders, schizophrenia and others. With increasing age, mild cognitive impairment leads to increased…

Neurons and Cognition · Quantitative Biology 2023-08-10 Sheng Mai

In this perspective we describe the critical role membranes play in modulating the structures of the Amyloid Precursor Proteins to produce the peptides involved in the Alzheimer's disease. Some of the key concepts related to protein…

Soft Condensed Matter · Physics 2014-07-08 John E. Straub , D. Thirumalai

The model for cAMP-dependent synaptic plasticity relates the characterization of a noradrenaline-stimulated adenylyl cyclase with DNA unzipping. Specific proteins condition cAMP insertion in specific sites of the DNA structure to direct…

Biomolecules · Quantitative Biology 2016-06-28 Alfred Bennun

Alzheimer's disease (AD) is a complex, progressive neurodegenerative disorder characterized by extracellular A\b{eta} plaques, neurofibrillary tau tangles, glial activation, and neuronal degeneration, involving multiple cell types and…

Machine Learning · Computer Science 2024-11-19 Anya Chauhan , Ayush Noori , Zhaozhi Li , Yingnan He , Michelle M Li , Marinka Zitnik , Sudeshna Das

Protein aggregates exhibit diverse morphology, exemplified by amyloid fibrils, gel-like structures, and liquid-like condensates. Differences in the morphologies in identical proteins play important functional roles in several diseases.…

Biological Physics · Physics 2024-06-13 Ryota Takaki , Dave Thirumalai

The biological function of protein assemblies was conventionally equated with a unique three-dimensional protein structure and protein-specific interactions. However, in the past 20 years it was found that some assemblies contain long…

Aggregates of misfolded proteins are a hallmark of many age-related diseases. Recently, they have been linked to aging of Escherichia coli (E. coli) where protein aggregates accumulate at the old pole region of the aging bacterium. Because…

Nanoparticles introduced in living cells are capable of strongly promoting the aggregation of peptides and proteins. We use here molecular dynamics simulations to characterise in detail the process by which nanoparticle surfaces catalyse…

Biomolecules · Quantitative Biology 2010-06-08 Stefan Auer , Antonio Trovato , Michele Vendruscolo

The supply of oxygen and nutrients and the disposal of metabolic waste in the organs depend strongly on how blood, especially red blood cells, flow through the microvascular network. Macromolecular plasma proteins such as fibrinogen cause…