Computational approaches to understanding protein aggregation in neurodegeneration

Structures of the E46K Mutant-Type α-Synuclein Protein and Impact of E46K Mutation on the Structures of the Wild-Type α-Synuclein Protein

(2013) Olivia Wise-Scira et al.   ACS Chemical Neuroscience

Structures and Free Energy Landscapes of the A53T Mutant-Type α-Synuclein Protein and Impact of A53T Mutation on the Structures of the Wild-Type α-Synuclein Protein with Dynamics

(2013) Orkid Coskuner et al.   ACS Chemical Neuroscience

Structures and Free Energy Landscapes of the Wild-Type and A30P Mutant-Type α-Synuclein Proteins with Dynamics

(2013) Olivia Wise-Scira et al.   ACS Chemical Neuroscience

Recent developments in targeting protein misfolding diseases

(2013) Rajiah Aldrin Denny et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Mechanical Resistance in Unstructured Proteins

(2013) Sigurður Ægir Jónsson et al.   BIOPHYSICAL JOURNAL

Discrete Molecular Dynamics Study of Oligomer Formation by N-Terminally Truncated Amyloid β-Protein

(2013) Derya Meral et al.   JOURNAL OF MOLECULAR BIOLOGY

α-Synuclein oligomers and clinical implications for Parkinson disease

(2012) Lorraine V. Kalia et al.   ANNALS OF NEUROLOGY

The Conformational Ensembles of α-Synuclein and Tau: Combining Single-Molecule FRET and Simulations

(2012) Abhinav Nath et al.   BIOPHYSICAL JOURNAL

Direct Observation of the Interconversion of Normal and Toxic Forms of α-Synuclein

(2012) Nunilo Cremades et al.   CELL

Amyloid peptide Aβ40 inhibits aggregation of Aβ42: Evidence from molecular dynamics simulations

(2012) Man Hoang Viet et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

Early Steps in Oxidation-Induced SOD1 Misfolding: Implications for Non-Amyloid Protein Aggregation in Familial ALS

(2012) Vikram Khipple Mulligan et al.   JOURNAL OF MOLECULAR BIOLOGY

Discrete Molecular Dynamics: An Efficient And Versatile Simulation Method For Fine Protein Characterization

(2012) David Shirvanyants et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

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

Distinct phases of free α-synuclein-A Monte Carlo study

(2012) Sigurður AEgir Jónsson et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structure of an Intermediate State in Protein Folding and Aggregation

(2012) P. Neudecker et al.   SCIENCE

Amyloid Structure: Conformational Diversity and Consequences

(2011) Brandon H. Toyama et al.   Annual Review of Biochemistry

Glutathionylation at Cys-111 Induces Dissociation of Wild Type and FALS Mutant SOD1 Dimers

(2011) Rachel L. Redler et al.   BIOCHEMISTRY

Distinct Hydration Properties of Wild-Type and Familial Point Mutant A53T of α-Synuclein Associated with Parkinson's Disease

(2011) E. Hazy et al.   BIOPHYSICAL JOURNAL

Coarse-grained models for protein aggregation

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

Prediction of amyloid aggregation in vivo

(2011) Mattia Belli et al.   EMBO REPORTS

Conformations of the Huntingtin N-term in aqueous solution from atomistic simulations

(2011) Giulia Rossetti et al.   FEBS LETTERS

Structural and Thermodynamic Effects of Post-translational Modifications in Mutant and Wild Type Cu, Zn Superoxide Dismutase

(2011) Elizabeth A. Proctor et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural Basis for Aβ1–42 Toxicity Inhibition by Aβ C-Terminal Fragments: Discrete Molecular Dynamics Study

(2011) B. Urbanc et al.   JOURNAL OF MOLECULAR BIOLOGY

Local Unfolding of Cu, Zn Superoxide Dismutase Monomer Determines the Morphology of Fibrillar Aggregates

(2011) Feng Ding et al.   JOURNAL OF MOLECULAR BIOLOGY

Crystal Structure of the Amyloid-  p3 Fragment Provides a Model for Oligomer Formation in Alzheimer's Disease

(2011) V. A. Streltsov et al.   JOURNAL OF NEUROSCIENCE

Inhibition of Aggregation of Amyloid Peptides by Beta-Sheet Breaker Peptides and Their Binding Affinity

(2011) Man Hoang Viet et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular pathways of motor neuron injury in amyotrophic lateral sclerosis

(2011) Laura Ferraiuolo et al.   Nature Reviews Neurology

Neurochemistry and the non-motor aspects of PD

(2011) I. Ferrer et al.   NEUROBIOLOGY OF DISEASE

How Fast-Folding Proteins Fold

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

Structural and Dynamic Determinants of Protein-Peptide Recognition

(2011) Onur Dagliyan et al.   STRUCTURE

Principles governing oligomer formation in amyloidogenic peptides

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

Mysterious oligomerization of the amyloidogenic proteins

(2010) Vladimir N. Uversky   FEBS Journal

Multiscale investigation of chemical interference in proteins

(2010) Antonios Samiotakis et al.   JOURNAL OF CHEMICAL PHYSICS

β-Barrel Topology of Alzheimer's β-Amyloid Ion Channels

(2010) Hyunbum Jang et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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

Unveiling the unfolding pathway of FALS associated G37R SOD1 mutant: a computational study

(2010) Danilo Milardi et al.   Molecular BioSystems

Exploring the sequence determinants of amyloid structure using position-specific scoring matrices

(2010) Sebastian Maurer-Stroh et al.   NATURE METHODS

Wild-type and mutant SOD1 share an aberrant conformation and a common pathogenic pathway in ALS

(2010) Daryl A Bosco et al.   NATURE NEUROSCIENCE

Structural conversion of neurotoxic amyloid-β1–42 oligomers to fibrils

(2010) Mahiuddin Ahmed et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Polyglutamine Induced Misfolding of Huntingtin Exon1 is Modulated by the Flanking Sequences

(2010) Vinal V. Lakhani et al.   PLoS Computational Biology

Multiscale Modeling of Proteins

(2009) Valentina Tozzini   ACCOUNTS OF CHEMICAL RESEARCH

Computational selection of inhibitors of Aβ aggregation and neuronal toxicity

(2009) Deliang Chen et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Thermodynamics of β-Sheet Formation in Polyglutamine

(2009) Andreas Vitalis et al.   BIOPHYSICAL JOURNAL

Structural Changes to Monomeric CuZn Superoxide Dismutase Caused by the Familial Amyotrophic Lateral Sclerosis-Associated Mutation A4V

(2009) Tom Schmidlin et al.   BIOPHYSICAL JOURNAL

Modifications of Superoxide Dismutase (SOD1) in Human Erythrocytes

(2009) Kyle C. Wilcox et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Effect of β-sheet propensity on peptide aggregation

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

The Predicted Structure of the Headpiece of the Huntingtin Protein and Its Implications on Huntingtin Aggregation

(2009) Nicholas W. Kelley et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural Reorganization of α-Synuclein at Low pH Observed by NMR and REMD Simulations

(2009) Kuen-Phon Wu et al.   JOURNAL OF MOLECULAR BIOLOGY

The Common Architecture of Cross-β Amyloid

(2009) Thomas R. Jahn et al.   JOURNAL OF MOLECULAR BIOLOGY

Recent advances in our understanding of neurodegeneration

(2009) Kurt A. Jellinger   JOURNAL OF NEURAL TRANSMISSION

Determination of the Free Energy Landscape of α-Synuclein Using Spin Label Nuclear Magnetic Resonance Measurements

(2009) Jane R. Allison et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Insights into Structure, Stability, and Toxicity of Monomeric and Aggregated Polyglutamine Models from Molecular Dynamics Simulations

(2008) Luciana Esposito et al.   BIOPHYSICAL JOURNAL

The Zyggregator method for predicting protein aggregation propensities

(2008) Gian Gaetano Tartaglia et al.   CHEMICAL SOCIETY REVIEWS

Huntington’s disease: revisiting the aggregation hypothesis in polyglutamine neurodegenerative diseases

(2008) Ray Truant et al.   FEBS Journal

Probing protein aggregation using discrete molecular dynamics

(2008) Shantanu Sharma   Frontiers in Bioscience-Landmark

Broken Helix in Vesicle and Micelle-Bound α-Synuclein: Insights from Site-Directed Spin Labeling-EPR Experiments and MD Simulations

(2008) Marco Bortolus et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Natural Selection against Protein Aggregation on Self-Interacting and Essential Proteins in Yeast, Fly, and Worm

(2008) Y. Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mechanism of alpha-synuclein oligomerization and membrane interaction: theoretical approach to unstructured proteins studies

(2008) Igor F. Tsigelny et al.   Nanomedicine-Nanotechnology Biology and Medicine

Dynamical roles of metal ions and the disulfide bond in Cu, Zn superoxide dismutase folding and aggregation

(2008) F. Ding et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ab Initio Folding of Proteins with All-Atom Discrete Molecular Dynamics

(2008) Feng Ding et al.   STRUCTURE

Protein Aggregation and Protein Instability Govern Familial Amyotrophic Lateral Sclerosis Patient Survival

(2008) Qi Wang et al.   PLOS BIOLOGY

Aggregation Propensity of the Human Proteome

(2008) Elodie Monsellier et al.   PLoS Computational Biology

Molecular dynamics simulation study on the structural stabilities of polyglutamine peptides

(2007) Hajime Ogawa et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY