Elucidating Self-Assembling Peptide Aggregation via Morphoscanner: A New Tool for Protein-Peptide Structural Characterization

Gloria A.A. Saracino, Federico Fontana, Shehrazade Jekhmane, João Medeiros Silva, Markus Weingarth, Fabrizio Gelain

Research output: Contribution to journalArticle

Abstract

Self-assembling and molecular folding are ubiquitous in Nature: they drive the organization of systems ranging from living creatures to DNA molecules. Elucidating the complex dynamics underlying these phenomena is of crucial importance. However, a tool for the analysis of the various phenomena involved in protein/peptide aggregation is still missing. Here, an innovative software is developed and validated for the identification and visualization of b-structuring and b-sheet formation in both simulated systems and crystal structures of proteins and peptides. The novel software suite, dubbed Morphoscanner, is designed to identify and intuitively represent b-structuring and b-sheet formation during molecular dynamics trajectories, paying attention to temporary strand-strand alignment, suboligomer formation and evolution of local order. Self-assembling peptides (SAPs) constitute a promising class of biomaterials and an interesting model to study the spontaneous assembly of molecular systems in vitro. With the help of coarse-grained molecular dynamics the self-assembling of diverse SAPs is simulated into molten aggregates. When applied to these systems, Morphoscanner highlights different b-structuring schemes and kinetics related to SAP sequences. It is demonstrated that Morphoscanner is a novel versatile tool designed to probe the aggregation dynamics of self-assembling systems, adaptable to the analysis of differently coarsened simulations of a variety of biomolecules.

Original languageEnglish
Article number1800471
JournalAdvanced Science
Volume5
Issue number8
DOIs
Publication statusPublished - Aug 1 2018

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assembling
Peptides
peptides
Agglomeration
proteins
Proteins
Molecular Dynamics Simulation
Molecular dynamics
Software
strands
molecular dynamics
computer programs
Biocompatible Materials
Biomolecules
Biomaterials
Molten materials
DNA
Visualization
folding
Crystal structure

Keywords

  • coarse-grained molecular dynamics
  • multilayer graph theory
  • pattern recognition
  • self-assembling peptides
  • β-structures

ASJC Scopus subject areas

  • Medicine (miscellaneous)
  • Chemical Engineering(all)
  • Materials Science(all)
  • Biochemistry, Genetics and Molecular Biology (miscellaneous)
  • Engineering(all)
  • Physics and Astronomy(all)

Cite this

Elucidating Self-Assembling Peptide Aggregation via Morphoscanner : A New Tool for Protein-Peptide Structural Characterization. / Saracino, Gloria A.A.; Fontana, Federico; Jekhmane, Shehrazade; Silva, João Medeiros; Weingarth, Markus; Gelain, Fabrizio.

In: Advanced Science, Vol. 5, No. 8, 1800471, 01.08.2018.

Research output: Contribution to journalArticle

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