Comparative analysis of essential collective dynamics and NMR-derived flexibility profiles in evolutionarily diverse prion proteins (Q35578781)

9 August 2017

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

1 reference

9 August 2017

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David S Wishart

3

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author name string

Kolattukudy P Santo

series ordinal

1

1 reference

PubMed ID

21869604

9 August 2017

Mark Berjanskii

series ordinal

2

1 reference

PubMed ID

21869604

9 August 2017

Maria Stepanova

series ordinal

4

1 reference

9 August 2017

1 July 2011

1 reference

9 August 2017

1 reference

9 August 2017

5

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9 August 2017

188-200

1 reference

9 August 2017

3

1 reference

Structural organization of brain-derived mammalian prions examined by hydrogen-deuterium exchange

9 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Collective dynamics of periplasmic glutamine binding protein upon domain closure

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Searching for factors that distinguish disease-prone and disease-resistant prions via sequence analysis

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Differential stability of the bovine prion protein upon urea unfolding

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Characterization of cell-surface prion protein relative to its recombinant analogue: insights from molecular dynamics simulations of diglycosylated, membrane-bound human prion protein

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Constraining the loop, releasing prion infectivity

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

De novo generation of a transmissible spongiform encephalopathy by mouse transgenesis

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Algorithmic dimensionality reduction for molecular structure analysis

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Molecular architecture of human prion protein amyloid: a parallel, in-register beta-structure

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Structural and hydration properties of the partially unfolded states of the prion protein

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

NMR: prediction of protein flexibility

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Beta-sheet core of human prion protein amyloid fibrils as determined by hydrogen/deuterium exchange

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Protein-Folding Dynamics: Overview of Molecular Simulation Techniques

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Observation of intermediate states of the human prion protein by high pressure NMR spectroscopy

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Dynamic protein domains: identification, interdependence, and stability

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Toward the understanding of MNEI sweetness from hydration map surfaces

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Chronic wasting disease of elk and deer and Creutzfeldt-Jakob disease: comparative analysis of the scrapie prion protein

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

A simple method to predict protein flexibility using secondary chemical shifts

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

The most infectious prion protein particles.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Prion and water: tight and dynamical hydration sites have a key role in structural stability

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Prion protein NMR structures of cats, dogs, pigs, and sheep

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Prion protein NMR structures of chickens, turtles, and frogs

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Prion protein NMR structures of elk and of mouse/elk hybrids

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Misfolding pathways of the prion protein probed by molecular dynamics simulations

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

12 July 2018

The state of the prion

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Probing the instabilities in the dynamics of helical fragments from mouse PrPC.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Checking the pH-induced conformational transition of prion protein by molecular dynamics simulations: effect of protonation of histidine residues

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Evidence for assembly of prions with left-handed beta-helices into trimers

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Flexibility of beta-sheets: principal component analysis of database protein structures

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Structural studies of the scrapie prion protein by electron crystallography

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Sensitive detection of pathological prion protein by cyclic amplification of protein misfolding

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

NMR structure of the bovine prion protein

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Collective protein dynamics in relation to function

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

NMR solution structure of the human prion protein

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Cellular biology of prion diseases

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Investigating protein dynamics in collective coordinate space

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Solution structure of Syrian hamster prion protein rPrP(90-231).

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

From the globular to the fibrous state: protein structure and structural conversion in amyloid formation.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Common core structure of amyloid fibrils by synchrotron X-ray diffraction.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Solution structure of a 142-residue recombinant prion protein corresponding to the infectious fragment of the scrapie isoform

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Evidence for protein X binding to a discontinuous epitope on the cellular prion protein during scrapie prion propagation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Molecular dynamics study of time-correlated protein domain motions and molecular flexibility: cytochrome P450BM-3

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Scrapie prions: a three-dimensional model of an infectious fragment

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

VMD: visual molecular dynamics

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Essential dynamics of proteins

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Conversion of alpha-helices into beta-sheets features in the formation of the scrapie prion proteins

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Novel proteinaceous infectious particles cause scrapie

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Secondary structure analysis of the scrapie-associated protein PrP 27-30 in water by infrared spectroscopy

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Scrapie infectivity, fibrils and low molecular weight protein.

12 July 2018

1 reference

https://api.crossref.org/works/10.4161%2FPRI.5.3.16097

Molecular dynamics simulation of the unfolding of the human prion protein domain under low pH and high temperature conditions

21 January 2018

1 reference

https://api.crossref.org/works/10.4161%2FPRI.5.3.16097

Metadynamics simulation of prion protein: beta-structure stability and the early stages of misfolding.

21 January 2018

1 reference

https://api.crossref.org/works/10.4161%2FPRI.5.3.16097

Molecular mechanism for low pH triggered misfolding of the human prion protein.

21 January 2018

1 reference

https://api.crossref.org/works/10.4161%2FPRI.5.3.16097

Polymorphism at residue 129 modulates the conformational conversion of the D178N variant of human prion protein 90-231.

21 January 2018

1 reference

https://api.crossref.org/works/10.4161%2FPRI.5.3.16097

Collective variable description of native protein dynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.4161%2FPRI.5.3.16097

Dynamics of essential collective motions in proteins: theory.

21 January 2018

1 reference

https://api.crossref.org/works/10.4161%2FPRI.5.3.16097

PrP (prion) gene expression in sheep may be modulated by alternative polyadenylation of its messenger RNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.4161%2FPRI.5.3.16097

Trans-species amplification of PrP(CWD) and correlation with rigid loop 170N.

21 January 2018

1 reference

https://api.crossref.org/works/10.4161%2FPRI.5.3.16097

Investigation of the effect of glycosylation on human prion protein by molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.4161%2FPRI.5.3.16097

Protofibrillar intermediates of amyloid beta-protein induce acute electrophysiological changes and progressive neurotoxicity in cortical neurons.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3226046

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

26 September 2018

1 reference

https://api.crossref.org/works/10.4161%2FPRI.5.3.16097

Multiple folding pathways for heterologously expressed human prion protein

21 January 2018

1 reference

https://api.crossref.org/works/10.4161%2FPRI.5.3.16097

Structural Domains and Main-Chain Flexibility in Prion Proteins†

21 January 2018

1 reference

https://api.crossref.org/works/10.4161%2FPRI.5.3.16097

Application of the random coil index to studying protein flexibility

21 January 2018

1 reference

https://api.crossref.org/works/10.4161%2FPRI.5.3.16097

GROMACS 3.0: a package for molecular simulation and trajectory analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.4161%2FPRI.5.3.16097

On the limited memory BFGS method for large scale optimization

21 January 2018

1 reference

https://api.crossref.org/works/10.4161%2FPRI.5.3.16097

Assessing the acid-base and conformational properties of histidine residues in human prion protein (125-228) by means of pKa calculations and molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.4161%2FPRI.5.3.16097

The GROMOS Biomolecular Simulation Program Package

21 January 2018

1 reference

https://api.crossref.org/works/10.4161%2FPRI.5.3.16097

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

https://api.crossref.org/works/10.4161%2FPRI.5.3.16097

Flexibility of alpha-helices: results of a statistical analysis of database protein structures

21 January 2018

1 reference

12 December 2020

NMR assignment of the Xenopus laevis prion protein fragment xlPrP (98-226)

1 reference

12 December 2020

NMR assignment of the turtle prion protein fragment tPrP(121-225)

1 reference

12 December 2020

NMR assignment of the chicken prion protein fragments chPrP(128-242) and chPrP(25-242)

1 reference

12 December 2020

Large-amplitude nonlinear motions in proteins

1 reference

12 December 2020

Principal components of the protein dynamical transition

1 reference

12 December 2020

Species barriers in prion diseases--brief review.

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.4161/PRI.5.3.16097

LINCS: A linear constraint solver for molecular simulations

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.4161/PRI.5.3.16097

Identifiers

DOI

10.4161/PRI.5.3.16097

1 reference

9 August 2017

1 reference

9 August 2017

1 reference

PubMed ID

21869604