Structural, thermodynamical, and dynamical properties of oligomers formed by the amyloid NNQQ peptide: Insights from coarse-grained simulations

Structural Basis of β-Amyloid-Dependent Synaptic Dysfunctions

(2012) Christian Haupt et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Driving Forces and Structural Determinants of Steric Zipper Peptide Oligomer Formation Elucidated by Atomistic Simulations

(2012) Dirk Matthes et al.   JOURNAL OF MOLECULAR BIOLOGY

Distinct Dimerization for Various Alloforms of the Amyloid-Beta Protein: Aβ1–40, Aβ1–42, and Aβ1–40(D23N)

(2012) Sébastien Côté et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structures of Aβ17–42 Trimers in Isolation and with Five Small-Molecule Drugs Using a Hierarchical Computational Procedure

(2012) Yassmine Chebaro et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Multidimensional View of Amyloid Fibril Nucleation in Atomistic Detail

(2012) Fahimeh Baftizadeh et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Atomic View of a Toxic Amyloid Small Oligomer

(2012) Arthur Laganowsky et al.   SCIENCE

Structural Basis for Inhibiting β-Amyloid Oligomerization by a Non-coded β-Breaker-Substituted Endomorphin Analogue

(2011) Anat Frydman-Marom et al.   ACS Chemical Biology

Spontaneous Formation of Twisted Aβ16-22 Fibrils in Large-Scale Molecular-Dynamics Simulations

(2011) Mookyung Cheon et al.   BIOPHYSICAL JOURNAL

What Drives Amyloid Molecules To Assemble into Oligomers and Fibrils?

(2011) Jeremy D. Schmit et al.   BIOPHYSICAL JOURNAL

Coarse-grained models for protein aggregation

(2011) Chun Wu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

Impact of Thermostats on Folding and Aggregation Properties of Peptides Using the Optimized Potential for Efficient Structure Prediction Coarse-Grained Model

(2011) Yannick G. Spill et al.   Journal of Chemical Theory and Computation

Fibrillization Propensity for Short Designed Hexapeptides Predicted by Computer Simulation

(2011) Victoria A. Wagoner et al.   JOURNAL OF MOLECULAR BIOLOGY

Characteristics of Amyloid-Related Oligomers Revealed by Crystal Structures of Macrocyclic β-Sheet Mimics

(2011) Cong Liu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A New Structural Model of Aβ40Fibrils

(2011) Ivano Bertini et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Small-molecule conversion of toxic oligomers to nontoxic β-sheet–rich amyloid fibrils

(2011) Jan Bieschke et al.   Nature Chemical Biology

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

Mapping the Conformational Dynamics and Pathways of Spontaneous Steric Zipper Peptide Oligomerization

(2011) Dirk Matthes et al.   PLoS One

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

A Multiscale Approach to Characterize the Early Aggregation Steps of the Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35

(2011) Jessica Nasica-Labouze et al.   PLoS Computational Biology

Transformation of amyloid β(1–40) oligomers into fibrils is characterized by a major change in secondary structure

(2010) Rabia Sarroukh et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Principles governing oligomer formation in amyloidogenic peptides

(2010) John E Straub et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Relationship between population of the fibril-prone conformation in the monomeric state and oligomer formation times of peptides: Insights from all-atom simulations

(2010) Hoang Bao Nam et al.   JOURNAL OF CHEMICAL PHYSICS

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

Amyloid Fibril Polymorphism Is under Kinetic Control

(2010) Riccardo Pellarin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Phase Diagram ofα-Helical andβ-Sheet Forming Peptides

(2010) Stefan Auer et al.   PHYSICAL REVIEW LETTERS

Dry amyloid fibril assembly in a yeast prion peptide is mediated by long-lived structures containing water wires

(2010) G. Reddy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evidence for Novel β-Sheet Structures in Iowa Mutant β-Amyloid Fibrils

(2009) Robert Tycko et al.   BIOCHEMISTRY

Effect of β-sheet propensity on peptide aggregation

(2009) Giovanni Bellesia et al.   JOURNAL OF CHEMICAL PHYSICS

Structural diversity of the soluble trimers of the human amylin(20–29) peptide revealed by molecular dynamics simulations

(2009) Yuxiang Mo et al.   JOURNAL OF CHEMICAL PHYSICS

A fast method for large-scaleDe Novopeptide and miniprotein structure prediction

(2009) Julien Maupetit et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Structures and Thermodynamics of Alzheimer’s Amyloid-β Aβ(16−35) Monomer and Dimer by Replica Exchange Molecular Dynamics Simulations: Implication for Full-Length Aβ Fibrillation

(2009) Yassmine Chebaro et al.   JOURNAL OF PHYSICAL CHEMISTRY B

PEP-FOLD: an online resource for de novo peptide structure prediction

(2009) J. Maupetit et al.   NUCLEIC ACIDS RESEARCH

Improved prediction of protein side-chain conformations with SCWRL4

(2009) Georgii G. Krivov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Thermodynamic Selection of Steric Zipper Patterns in the Amyloid Cross-β Spine

(2009) Jiyong Park et al.   PLoS Computational Biology

Insights into Stability and Toxicity of Amyloid-Like Oligomers by Replica Exchange Molecular Dynamics Analyses

(2008) Alfonso De Simone et al.   BIOPHYSICAL JOURNAL

Role of the Region 23-28 in Aβ Fibril Formation: Insights from Simulations of the Monomers and Dimers of Alzheimers Peptides Aβ40 and Aβ42

(2008) Adrien Melquiond et al.   Current Alzheimer Research

The Alzheimer β-amyloid (Aβ1–39) dimer in an implicit solvent

(2008) Priya Anand et al.   JOURNAL OF CHEMICAL PHYSICS

Replica Exchange Molecular Dynamics Simulations of Coarse-grained Proteins in Implicit Solvent

(2008) Yassmine Chebaro et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Thermodynamics and dynamics of amyloid peptide oligomerization are sequence dependent

(2008) Yan Lu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Formation and Growth of Oligomers: A Monte Carlo Study of an Amyloid Tau Fragment

(2008) Da-Wei Li et al.   PLoS Computational Biology