Alexander Marchut

Works (5)

Updated: July 5th, 2023 15:57

2006 article

Commentary on: "Assembly of a tetrameric alpha-helical bundle: Computer simulations on an intermediate-resolution protein model" [Proteins 2001;44 : 376-391]

Marchut, A. J., Smith, A. V., & Hall, C. K. (2006, May 15). PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, Vol. 63, pp. 709–710.

By: A. Marchut n, A. Smith & C. Hall n 

MeSH headings : Amino Acids / chemistry; Computer Simulation; Energy Transfer; Hydrogen Bonding; Models, Biological; Models, Molecular; Peptides / chemistry; Polymers / chemistry; Protein Folding; Protein Structure, Secondary
TL;DR: The work of Smith and Hall found two errors in the computer code used to generate results that led to an underestimation of the frequency of amorphous aggregation of the peptides relative to folding into the native states, and an explanation of the effects that the computational errors had on the self-assembly of the model peptides. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2006 journal article

Effects of chain length on the aggregation of model polyglutamine peptides: Molecular dynamics simulations

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 66(1), 96–109.

By: A. Marchut n & C. Hall n 

author keywords: protein aggregation; polyglutamine; amyloid; molecular dynamics; intermediate resolution model
MeSH headings : Computer Simulation; Dimerization; Hydrogen Bonding; Hydrophobic and Hydrophilic Interactions; Models, Molecular; Peptides / chemistry; Peptides / metabolism; Protein Folding; Temperature
TL;DR: The finding that the stability of the ordered aggregates increases as the peptide chain length increases may help to explain the experimentally observed relation between polyglutamine tract length and aggregation in vitro and disease progression in vivo. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2006 journal article

Side-chain interactions determine amyloid formation by model polyglutamine peptides in molecular dynamics simulations

BIOPHYSICAL JOURNAL, 90(12), 4574–4584.

By: A. Marchut n & C. Hall n 

MeSH headings : Amino Acid Sequence; Amyloid / chemical synthesis; Computer Simulation; Dimerization; Models, Chemical; Models, Molecular; Molecular Sequence Data; Motion; Multiprotein Complexes / chemistry; Peptides / chemistry; Protein Conformation; Protein Structure, Tertiary; Structure-Activity Relationship
TL;DR: In these simulations, the spontaneous formation of aggregates and annular structures that are made up of beta-sheets starting from random configurations of random coils are observed, interesting because tubular protofibrils were recently found in experiments on polyglutamine aggregation and because of Perutz's prediction that polyglUTamine would form water-filled nanotubes. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2006 journal article

Spontaneous formation of annular structures observed in molecular dynamics simulations of polyglutamine peptides

COMPUTATIONAL BIOLOGY AND CHEMISTRY, 30(3), 215–218.

By: A. Marchut n & C. Hall n 

author keywords: protein aggregation; polyglutamine; molecular dynamics
MeSH headings : Brain Diseases / etiology; Computer Simulation; Humans; Huntington Disease / etiology; Models, Molecular; Nanotubes; Peptides / chemistry; Protein Conformation; Protein Structure, Secondary
TL;DR: These results are interesting not only because of the recent discovery of tubular protofibrils in experiments on aggregation of mutant huntingtin fragments containing expanded polyglutamine tracts but also because Perutz predicted that polyglUTamine forms water filled nanotubes. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2004 journal article

Solvent effects on the conformational transition of a model polyalanine peptide

Protein Science, 13(11), 2909–2924.

By: H. Nguyen n, A. Marchut n & C. Hall n 

author keywords: polyalanine; alpha-beta transition; secondary structures; solvent conditions; discontinuous molecular dynamics
MeSH headings : Hydrogen Bonding / drug effects; Models, Molecular; Peptides / chemistry; Protein Structure, Secondary / drug effects; Solvents / pharmacology; Temperature
TL;DR: A study of the folding of a single polyalanine‐based peptide is investigated by combining discontinuous molecular dynamics simulation with the newly developed off‐lattice intermediate‐resolution protein model, setting the stage for a study of polyalanines aggregation in a forthcoming paper. (via Semantic Scholar)
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Sources: Web Of Science, Crossref, NC State University Libraries
Added: August 6, 2018

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