Systematic analysis in silico of the critical behavior of amyloid beta peptide and some of its mutants

• Grant number: 16/04176-4
• Support Opportunities: Regular Research Grants
• Start date: June 01, 2016
• End date: May 31, 2018
• Field of knowledge: Physical Sciences and Mathematics - Physics - Condensed Matter Physics
• Principal Investigator: Nelson Augusto Alves
• Grantee: Nelson Augusto Alves
• Host Institution: Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil

Abstract

Molecular dynamics (MD) simulations will be performed to describe intermediate states of amyloid $\beta$-peptides (A$\beta$) with 40 residues (A$\beta_{40}$), 42 residues (A$\beta_{42}$), and a set of peptides obtained by local mutations in the A$\beta$ sequences. A$\beta$ peptides and their mutant variants play a central role in Alzheimer's disease and present different toxicity and aggregation propensities to convert from their soluble forms into insoluble fibrillar aggregates. The ensemble structures will be obtained from MD simulations using the GROMACS package with an all-atom model. The critical properties of these peptides and the features of the conformational transitions will be addressed to describe the mutation effects on the propensities of these peptides. (AU)

Scientific publications

(5)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

FRIGORI, RAFAEL B.; BARROSO DA SILVA, FERNANDO L.; CARVALHO, PATRICIA P. D.; ALVES, NELSON A.. Occurrence of Biased Conformations as Precursors of Assembly States in Fibril Elongation of Amyloid-beta Fibril Variants: An In Silico Study. Journal of Physical Chemistry B, v. 124, n. 14, p. 2798-2805, APR 9 2020. (15/16116-3, 16/04176-4)

ALVES, NELSON A.; DIAS, LUIS G.; FRIGORI, RAFAEL B.. Synergistic long-range effects of mutations underlie aggregation propensities of amylin analogues. Journal of Molecular Modeling, v. 25, n. 9, SEP 2019. (13/08166-5, 17/03204-7, 16/04176-4)

TEIXEIRA, ANDRE L.; ALVES, NELSON A.. The high stability of the three-helix bundle UBA domain of p62 protein as revealed by molecular dynamics simulations. Journal of Molecular Modeling, v. 27, n. 4, APR 2021. (16/04176-4)

ALVES, NELSON A.; FRIGORI, RAFAEL B.. In Silico Comparative Study of Human and Porcine Amylin. Journal of Physical Chemistry B, v. 122, n. 47, p. 10714-10721, NOV 29 2018. (16/04176-4)

ALVES, NELSON A.; FRIGORI, RAFAEL B.. Structural Interconversion in Alzheimer's Amyloid-beta(16-35) Peptide in an Aqueous Solution. Journal of Physical Chemistry B, v. 122, n. 6, p. 1869-1875, FEB 15 2018. (16/04176-4)