Characterization of the Conformations of Amyloid Beta 42 in Solution That May Mediate Its Initial Hydrophobic Aggregation

Small Oligomers of Aβ42 Protein in the Bulk Solution with AlphaFold2

(2022) Hubert Santuz et al.   ACS Chemical Neuroscience

Influence of force field choice on the conformational landscape of rat and human islet amyloid polypeptide

(2022) Sandra J. Moore et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer’s Disease, Parkinson’s Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis

(2021) Phuong H. Nguyen et al.   CHEMICAL REVIEWS

Stabilization Effect of Intrinsically Disordered Regions on Multidomain Proteins: The Case of the Methyl-CpG Protein 2, MeCP2

(2021) David Ortega-Alarcon et al.   Biomolecules

Amylin and beta amyloid proteins interact to form amorphous heterocomplexes with enhanced toxicity in neuronal cells

(2020) Prashant Bharadwaj et al.   Scientific Reports

New Insights Into Blood-Brain Barrier Maintenance: The Homeostatic Role of β-Amyloid Precursor Protein in Cerebral Vasculature

(2020) Emma Ristori et al.   Frontiers in Physiology

Role of the cell membrane interface in modulating production and uptake of Alzheimer's beta amyloid protein

(2018) Prashant Bharadwaj et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Characterization of the structural ensembles of p53 TAD2 by molecular dynamics simulations with different force fields

(2018) Yanhua Ouyang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Characterisation of the Structure and Oligomerisation of Islet Amyloid Polypeptides (IAPP): A Review of Molecular Dynamics Simulation Studies

(2018) Sandra Moore et al.   MOLECULES

Amyloidogenicity and toxicity of the reverse and scrambled variants of amyloid-β 1-42

(2017) Devkee M. Vadukul et al.   FEBS LETTERS

Effects of forcefield and sampling method in all-atom simulations of inherently disordered proteins: Application to conformational preferences of human amylin

(2017) Enxi Peng et al.   PLoS One

Monomeric Aβ1–40 and Aβ1–42 Peptides in Solution Adopt Very Similar Ramachandran Map Distributions That Closely Resemble Random Coil

(2016) Julien Roche et al.   BIOCHEMISTRY

Cold denaturation as a tool to measure protein stability

(2016) Domenico Sanfelice et al.   BIOPHYSICAL CHEMISTRY

Analysis of 138 pathogenic mutations in presenilin-1 on the in vitro production of Aβ42 and Aβ40 peptides by γ-secretase

(2016) Linfeng Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparison of force fields for Alzheimer's A β42: A case study for intrinsically disordered proteins

(2016) Martín Carballo-Pacheco et al.   PROTEIN SCIENCE

Amyloid β Protein and Alzheimer’s Disease: When Computer Simulations Complement Experimental Studies

(2015) Jessica Nasica-Labouze et al.   CHEMICAL REVIEWS

Characterization of Aβ Monomers through the Convergence of Ensemble Properties among Simulations with Multiple Force Fields

(2015) David J. Rosenman et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States

(2015) Stefano Piana et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Aβ(1–42) fibril structure illuminates self-recognition and replication of amyloid in Alzheimer's disease

(2015) Yiling Xiao et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Accurate secondary structure prediction and fold recognition for circular dichroism spectroscopy

(2015) András Micsonai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aβ(1–42) fibril structure illuminates self-recognition and replication of amyloid in Alzheimer's disease

(2015) Yiling Xiao et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Secondary Structure of Rat and Human Amylin across Force Fields

(2015) Kyle Quynn Hoffmann et al.   PLoS One

The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments

(2015) Daniele Granata et al.   Scientific Reports

Temperature-dependent solvation modulates the dimensions of disordered proteins

(2014) R. Wuttke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational and Theoretical Methods for Protein Folding

(2013) Mario Compiani et al.   BIOCHEMISTRY

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Aβ Monomers Transiently Sample Oligomer and Fibril-Like Configurations: Ensemble Characterization Using a Combined MD/NMR Approach

(2013) David J. Rosenman et al.   JOURNAL OF MOLECULAR BIOLOGY

Well-Tempered Metadynamics as a Tool for Characterizing Multi-Component, Crystalline Molecular Machines

(2013) Andrew J. Ilott et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Familial Alzheimer A2 V Mutation Reduces the Intrinsic Disorder and Completely Changes the Free Energy Landscape of the Aβ1–28 Monomer

(2013) Phuong H. Nguyen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Motional timescale predictions by molecular dynamics simulations: Case study using proline and hydroxyproline sidechain dynamics

(2013) Abil E. Aliev et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Amyloid β-protein oligomers and Alzheimer’s disease

(2013) Eric Y Hayden et al.   Alzheimers Research & Therapy

Role of Aromatic Side Chains in Amyloid β-Protein Aggregation

(2012) Risto Cukalevski et al.   ACS Chemical Neuroscience

Identification of helix capping and β-turn motifs from NMR chemical shifts

(2012) Yang Shen et al.   JOURNAL OF BIOMOLECULAR NMR

A partially folded structure of amyloid-beta(1–40) in an aqueous environment

(2011) Subramanian Vivekanandan et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Aβ42 oligomers, but not fibrils, simultaneously bind to and cause damage to ganglioside-containing lipid membranes

(2011) Thomas L. Williams et al.   BIOCHEMICAL JOURNAL

Inhibition of amyloid-β aggregation by coumarin analogs can be manipulated by functionalization of the aromatic center

(2011) Deborah D. Soto-Ortega et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Structural Basis for Increased Toxicity of Pathological Aβ42:Aβ40Ratios in Alzheimer Disease

(2011) Kris Pauwels et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution

(2011) Magnus Kjaergaard et al.   JOURNAL OF BIOMOLECULAR NMR

Random coil chemical shift for intrinsically disordered proteins: effects of temperature and pH

(2011) Magnus Kjaergaard et al.   JOURNAL OF BIOMOLECULAR NMR

SHIFTX2: significantly improved protein chemical shift prediction

(2011) Beomsoo Han et al.   JOURNAL OF BIOMOLECULAR NMR

Unfolding of the Amyloid β-Peptide Central Helix: Mechanistic Insights from Molecular Dynamics Simulations

(2011) Mika Ito et al.   PLoS One

Atomic-Level Characterization of the Ensemble of the Aβ(1–42) Monomer in Water Using Unbiased Molecular Dynamics Simulations and Spectral Algorithms

(2010) Nikolaos G. Sgourakis et al.   JOURNAL OF MOLECULAR BIOLOGY

Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins

(2009) D. Nettels et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations

(2009) Fabrizio Marinelli et al.   PLoS Computational Biology

Amyloid β-Protein Monomer Folding: Free-Energy Surfaces Reveal Alloform-Specific Differences

(2008) Mingfeng Yang et al.   JOURNAL OF MOLECULAR BIOLOGY

Role of Water in Mediating the Assembly of Alzheimer Amyloid-β Aβ16−22 Protofilaments

(2008) Mary Griffin Krone et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

(2008) Alessandro Laio et al.   REPORTS ON PROGRESS IN PHYSICS

On the nucleation of amyloid β-protein monomer folding

(2005) Noel D. Lazo et al.   PROTEIN SCIENCE