TY - CHAP
T1 - Computational modelling of supramolecular metallopeptide assemblies
AU - Martín, Lorena Roldán
AU - Santiago, Luis Rodríguez
AU - Korendovych, Ivan V.
AU - Sodupe, Mariona
AU - Maréchal, Jean Didier
N1 - Copyright © 2024. Published by Elsevier Inc.
PY - 2024
Y1 - 2024
N2 - Among the important questions in supramolecular peptide self-assemblies are their interactions with metallic compounds and ions. In the last decade, intensive efforts have been devoted to understanding the structural properties of these interactions including their dynamical and catalytic impact in natural and de novo systems. Since structural insights from experimental approaches could be particularly challenging, computational chemistry methods are interesting complementary tools. Here, we present the general multiscale strategies we developed and applied for the study of metallopeptide assemblies. These strategies include prediction of metal binding site, docking of metallic moieties, classical and accelerated molecular dynamics and finally QM/MM calculations. The systems of choice for this chapter are, on one side, peptides involved in neurodegenerative diseases and, on the other, de novo fibrillar systems with catalytic properties. Both successes and remaining challenges are highlighted so that the protocol could be apply to other system of this kind.
AB - Among the important questions in supramolecular peptide self-assemblies are their interactions with metallic compounds and ions. In the last decade, intensive efforts have been devoted to understanding the structural properties of these interactions including their dynamical and catalytic impact in natural and de novo systems. Since structural insights from experimental approaches could be particularly challenging, computational chemistry methods are interesting complementary tools. Here, we present the general multiscale strategies we developed and applied for the study of metallopeptide assemblies. These strategies include prediction of metal binding site, docking of metallic moieties, classical and accelerated molecular dynamics and finally QM/MM calculations. The systems of choice for this chapter are, on one side, peptides involved in neurodegenerative diseases and, on the other, de novo fibrillar systems with catalytic properties. Both successes and remaining challenges are highlighted so that the protocol could be apply to other system of this kind.
KW - Amyloid
KW - Catalytic peptides
KW - Molecular modeling
KW - Multiscale approaches
UR - https://www.scopus.com/pages/publications/85190542643
UR - https://www.mendeley.com/catalogue/754d795a-b443-381a-aaa7-3de30861a153/
U2 - 10.1016/bs.mie.2024.03.021
DO - 10.1016/bs.mie.2024.03.021
M3 - Chapter
C2 - 38816124
AN - SCOPUS:85190542643
SN - 9780443236679
VL - 697
T3 - Methods in Enzymology
SP - 211
EP - 245
BT - Peptide Catalysts, Including Catalytic Amyloids
A2 - Korendovych, Ivan V.
ER -