(Q34311672)

1 August 2017

title

Mechanism of fiber assembly: treatment of Aβ peptide aggregation with a coarse-grained united-residue force field (English)

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1 August 2017

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4

Harold A Scheraga

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1 August 2017

2

Adam Liwo

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1 August 2017

Ana Rojas

1

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1 August 2017

Dana Browne

series ordinal

3

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1 August 2017

language of work or name

English

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publication date

1 October 2010

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Journal of Molecular Biology

1 August 2017

published in

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1 August 2017

volume

404

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1 August 2017

issue

3

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1 August 2017

page(s)

537-552

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Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field

1 August 2017

cites work

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The importance of hydrogen bonding between the glutamine side chains to the formation of amyloid VQIVYK parallel beta-sheets: an ONIOM DFT/AM1 study

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6 July 2018

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Dynamics of locking of peptides onto growing amyloid fibrils

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Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field

6 July 2018

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6 July 2018

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6 July 2018

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Atomic structures of amyloid cross-beta spines reveal varied steric zippers

6 July 2018

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6 July 2018

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Molecular dynamics with the United-residue force field: ab initio folding simulations of multichain proteins

6 July 2018

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Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins.

6 July 2018

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Monomer adds to preformed structured oligomers of Abeta-peptides by a two-stage dock-lock mechanism.

6 July 2018

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Determining the critical nucleus and mechanism of fibril elongation of the Alzheimer's Abeta(1-40) peptide.

6 July 2018

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Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model alpha-helical systems

6 July 2018

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Molecular dynamics with the united-residue model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode

6 July 2018

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Molecular structure of amyloid fibrils: insights from solid-state NMR.

6 July 2018

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The alpha-to-beta conformational transition of Alzheimer's Abeta-(1-42) peptide in aqueous media is reversible: a step by step conformational analysis suggests the location of beta conformation seeding

6 July 2018

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Experimental constraints on quaternary structure in Alzheimer's beta-amyloid fibrils

6 July 2018

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Molecular dynamics simulations of Alzheimer's beta-amyloid protofilaments

6 July 2018

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Correlation of structural elements and infectivity of the HET-s prion

6 July 2018

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Structure of the cross-beta spine of amyloid-like fibrils

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

On the nucleation of amyloid beta-protein monomer folding

6 July 2018

1 reference

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Theoretical model of prion propagation: a misfolded protein induces misfolding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

Protein folding pathways from replica exchange simulations and a kinetic network model

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

Self-propagating, molecular-level polymorphism in Alzheimer's beta-amyloid fibrils

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

Molecular basis for amyloid fibril formation and stability

6 July 2018

1 reference

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Mechanism of prion propagation: amyloid growth occurs by monomer addition

6 July 2018

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Folding a protein in a computer: An atomic description of the folding/unfolding of protein A

6 July 2018

1 reference

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Multiplexed-replica exchange molecular dynamics method for protein folding simulation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

Solution structure of the Alzheimer amyloid beta-peptide (1-42) in an apolar microenvironment. Similarity with a virus fusion domain

6 July 2018

1 reference

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Naturally secreted oligomers of amyloid beta protein potently inhibit hippocampal long-term potentiation in vivo

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

Alzheimer's disease amyloid propagation by a template-dependent dock-lock mechanism

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

Solution structures of micelle-bound amyloid beta-(1-40) and beta-(1-42) peptides of Alzheimer's disease

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

Solution structure of amyloid beta-peptide(1-40) in a water-micelle environment. Is the membrane-spanning domain where we think it is?

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

New developments of the electrostatically driven Monte Carlo method: test on the membrane-bound portion of melittin

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

Models of amyloid seeding in Alzheimer's disease and scrapie: mechanistic truths and physiological consequences of the time-dependent solubility of amyloid proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

MOLMOL: a program for display and analysis of macromolecular structures

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

On the nucleation and growth of amyloid beta-protein fibrils: detection of nuclei and quantitation of rate constants

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

1H NMR of A beta amyloid peptide congeners in water solution. Conformational changes correlate with plaque competence

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

Structure of amyloid A4-(1-40)-peptide of Alzheimer's disease

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

Amyloid plaque core protein in Alzheimer disease and Down syndrome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

The molecular pathology of Alzheimer's disease

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

Characterization of the nucleation barriers for protein aggregation and amyloid formation

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

The Alzheimer's beta amyloid (Abeta1-39) monomer in an implicit solvent.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

Evidence of fibril-like β-sheet structures in a neurotoxic amyloid intermediate of Alzheimer's β-amyloid.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

Dynamics of Asp23-Lys28 salt-bridge formation in Abeta10-35 monomers

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

Abeta40-Lactam(D23/K28) models a conformation highly favorable for nucleation of amyloid

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

Direct observation of Abeta amyloid fibril growth and inhibition

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

Kinetic analysis of beta-amyloid fibril elongation

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

Kinetic studies of amyloid beta-protein fibril assembly. Differential effects of alpha-helix stabilization

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

Identification and characterization of key kinetic intermediates in amyloid beta-protein fibrillogenesis

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

Amyloid beta interacts with the amyloid precursor protein: a potential toxic mechanism in Alzheimer's disease.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981693

Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin

28 October 2018

1 reference

12 December 2020

Folding time predictions from all-atom replica exchange simulations

1 reference

12 December 2020

The importance of cooperative interactions and a solid-state paradigm to proteins: what Peptide chemists can learn from molecular crystals

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12 December 2020

Solution conformations and aggregational properties of synthetic amyloid beta-peptides of Alzheimer's disease. Analysis of circular dichroism spectra

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12 December 2020

From laws of inference to protein folding dynamics

1 reference

12 December 2020

10.1016/J.JMB.2010.09.057

Identifiers

DOI

1 reference

1 August 2017

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1 August 2017

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