Probing oligomerization of amyloid beta peptide in silico

Reexamining Alzheimer's Disease: Evidence for a Protective Role for Amyloid-β Protein Precursor and Amyloid-β

(2017) Rudy J. Castellani et al.   JOURNAL OF ALZHEIMERS DISEASE

Trace Copper(II) or Zinc(II) Ions Drastically Modify the Aggregation Behavior of Amyloid-β1–42: An AFM Study

(2017) Massimo Innocenti et al.   JOURNAL OF ALZHEIMERS DISEASE

Amyloid β-Protein Assembly and Alzheimer’s Disease: Dodecamers of Aβ42, but Not of Aβ40, Seed Fibril Formation

(2016) Nicholas J. Economou et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Amyloid β-Protein C-Terminal Fragments: Formation of Cylindrins and β-Barrels

(2016) Thanh D. Do et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Computational Studies of Protein Aggregation: Methods and Applications

(2015) Alex Morriss-Andrews et al.   Annual Review of Physical Chemistry

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

Exploring the Alzheimer amyloid-β peptide conformational ensemble: A review of molecular dynamics approaches

(2015) Linh Tran et al.   PEPTIDES

Peptide dimer structure in an Aβ(1–42) fibril visualized with cryo-EM

(2015) Matthias Schmidt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inhibition of insulin amyloid fibrillization by glyco-acridines: an in vitro and in silico study

(2015) Quan Van Vuong et al.   MedChemComm

Structural Conversion of Aβ17–42 Peptides from Disordered Oligomers to U-Shape Protofilaments via Multiple Kinetic Pathways

(2015) Mookyung Cheon et al.   PLoS Computational Biology

Alzheimer Peptides Aggregate into Transient Nanoglobules That Nucleate Fibrils

(2014) Jinghui Luo et al.   BIOCHEMISTRY

Fibril Elongation by Aβ17–42: Kinetic Network Analysis of Hybrid-Resolution Molecular Dynamics Simulations

(2014) Wei Han et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Understanding Interactions of Functionalized Nanoparticles with Proteins: A Case Study on Lactate Dehydrogenase

(2014) Oliver Stueker et al.   Small

Molecular mechanisms in the selective basal activation of pyrabactin receptor 1: Comparative analysis of mutants

(2014) Lyudmyla Dorosh et al.   FEBS Open Bio

In Silico Cross Seeding of Aβ and Amylin Fibril-like Oligomers

(2013) Workalemahu M. Berhanu et al.   ACS Chemical Neuroscience

Computational Assembly of Polymorphic Amyloid Fibrils Reveals Stable Aggregates

(2013) Mohamed Raef Smaoui et al.   BIOPHYSICAL JOURNAL

Molecular Structure of β-Amyloid Fibrils in Alzheimer’s Disease Brain Tissue

(2013) Jun-Xia Lu et al.   CELL

Insights into Aβ Aggregation: A Molecular Dynamics Perspective

(2013) Joan-Emma Shea et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Conformational Stability of Fibrillar Amyloid-Beta Oligomers via Protofilament Pair Formation – A Systematic Computational Study

(2013) Anna Kahler et al.   PLoS One

Mechanism of IAPP amyloid fibril formation involves an intermediate with a transient  -sheet

(2013) L. E. Buchanan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Free-energy landscape of protein oligomerization from atomistic simulations

(2013) A. Barducci et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploring the essential collective dynamics of interacting proteins: Application to prion protein dimers

(2013) Bilkiss B. Issack et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Copper prevents amyloid-β1–42 from forming amyloid fibrils under near-physiological conditions in vitro

(2013) Matthew Mold et al.   Scientific Reports

Molecular Mechanisms in the Activation of Abscisic Acid Receptor PYR1

(2013) Lyudmyla Dorosh et al.   PLoS Computational Biology

Structural Similarities and Differences between Amyloidogenic and Non-Amyloidogenic Islet Amyloid Polypeptide (IAPP) Sequences and Implications for the Dual Physiological and Pathological Activities of These Peptides

(2013) Chun Wu et al.   PLoS Computational Biology

Investigating How Peptide Length and a Pathogenic Mutation Modify the Structural Ensemble of Amyloid Beta Monomer

(2012) Yu-Shan Lin et al.   BIOPHYSICAL JOURNAL

Metal binding sites in amyloid oligomers: Complexes and mechanisms

(2012) Yifat Miller et al.   COORDINATION CHEMISTRY REVIEWS

Template Induced Conformational Change of Amyloid-β Monomer

(2012) Wenhui Xi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The toxic Aβ oligomer and Alzheimer's disease: an emperor in need of clothes

(2012) Iryna Benilova et al.   NATURE NEUROSCIENCE

Conformational modes in biomolecules: Dynamics and approximate invariance

(2012) Alex Potapov et al.   PHYSICAL REVIEW E

Dimer Formation Enhances Structural Differences between Amyloid β-Protein (1–40) and (1–42): An Explicit-Solvent Molecular Dynamics Study

(2012) Bogdan Barz et al.   PLoS One

Modeling Amyloid-Beta as Homogeneous Dodecamers and in Complex with Cellular Prion Protein

(2012) Steven L. Gallion   PLoS One

Antiparallel  -sheet architecture in Iowa-mutant  -amyloid fibrils

(2012) W. Qiang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role of Water in Protein Aggregation and Amyloid Polymorphism

(2011) D. Thirumalai et al.   ACCOUNTS OF CHEMICAL RESEARCH

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

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

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

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

Distinct Morphologies for Amyloid Beta Protein Monomer: Aβ1–40, Aβ1–42, and Aβ1–40(D23N)

(2011) Sébastien Côté et al.   Journal of Chemical Theory and Computation

Structure and Thermodynamics of Amylin Dimer Studied by Hamiltonian-Temperature Replica Exchange Molecular Dynamics Simulations

(2011) Rozita Laghaei et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the Aβ16–22 dimer and trimer

(2011) Phuong H. Nguyen et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

(2011) Mika Ito et al.   PLoS One

Effects of Temperature on the p53-DNA Binding Interactions and Their Dynamical Behavior: Comparing the Wild Type to the R248Q Mutant

(2011) Khaled Barakat et al.   PLoS One

Effect of Surfaces on Amyloid Fibril Formation

(2011) Bradley Moores et al.   PLoS One

Comparative analysis of essential collective dynamics and NMR-derived flexibility profiles in evolutionarily diverse prion proteins

(2011) Kolattukudy P Santo et al.   Prion

Mapping Conformational Ensembles of Aβ Oligomers in Molecular Dynamics Simulations

(2010) Seongwon Kim et al.   BIOPHYSICAL JOURNAL

Association Thermodynamics and Conformational Stability of β-Sheet Amyloid β(17-42) Oligomers: Effects of E22Q (Dutch) Mutation and Charge Neutralization

(2010) Nikolay Blinov et al.   BIOPHYSICAL JOURNAL

Modulation of Aβ42 fibrillogenesis by glycosaminoglycan structure

(2010) Juan José Valle-Delgado et al.   FASEB JOURNAL

Low molecular weight oligomers of amyloid peptides display β-barrel conformations: A replica exchange molecular dynamics study in explicit solvent

(2010) Alfonso De Simone et al.   JOURNAL OF CHEMICAL PHYSICS

Assessing the Stability of Alzheimer’s Amyloid Protofibrils Using Molecular Dynamics

(2010) Justin A. Lemkul et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Elucidation of Amyloid β-Protein Oligomerization Mechanisms: Discrete Molecular Dynamics Study

(2010) B. Urbanc et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Amyloid-β Oligomers: Possible Roles as Key Neurotoxins in Alzheimer's Disease

(2010) Alex L. Lublin et al.   MOUNT SINAI JOURNAL OF MEDICINE

Preparation and characterization of toxic Aβ aggregates for structural and functional studies in Alzheimer's disease research

(2010) Asad Jan et al.   Nature Protocols

Truncated  -amyloid peptide channels provide an alternative mechanism for Alzheimer's Disease and Down syndrome

(2010) H. Jang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deprotonation of the Asp1Ala2 Peptide Bond Induces Modification of the Dynamic Copper(II) Environment in the Amyloid-β Peptide near Physiological pH

(2009) Christelle Hureau et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Structural Domains and Main-Chain Flexibility in Prion Proteins†

(2009) N. Blinov et al.   BIOCHEMISTRY

The Structure of Aβ42 C-Terminal Fragments Probed by a Combined Experimental and Theoretical Study

(2009) Chun Wu et al.   JOURNAL OF MOLECULAR BIOLOGY

Amyloid-β protein oligomerization and the importance of tetramers and dodecamers in the aetiology of Alzheimer's disease

(2009) Summer L. Bernstein et al.   Nature Chemistry

Dynamics of locking of peptides onto growing amyloid fibrils

(2009) G. Reddy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Structure of the Amyloid-β Peptide High-Affinity Copper II Binding Site in Alzheimer Disease

(2008) Victor A. Streltsov et al.   BIOPHYSICAL JOURNAL

Role of Metal Ions in the Aβ Oligomerization in Alzheimers Disease and in Other Neurological Disorders

(2008) D. Drago et al.   Current Alzheimer Research

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

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

Annular Structures as Intermediates in Fibril Formation of Alzheimer Aβ17−42

(2008) Jie Zheng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Aβ-globulomers are formed independently of the fibril pathway

(2008) Gerald P. Gellermann et al.   NEUROBIOLOGY OF DISEASE

Analysis of the sequence and structural features of the left-handed β-helical fold

(2008) Jay H. Choi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Characterization of Copper Interactions with Alzheimer Amyloid β Peptides

(2003) Craig S. Atwood et al.   JOURNAL OF NEUROCHEMISTRY