Survey of Peptide Aggregation Behavior - Medical Science Assignment Help

Assignment Task

A literature study on the different forms of aggregation of free and membrane bound peptides

Summary:

This project investigates the behaviour of peptide aggregates in relation to a cell membrane, using relevant literature on molecular dynamics simulations.

Observations and modelled simulations of peptides relevant for medical research such as the amyloid-beta peptide, playing an important role in neurodegenerative diseases, or peptide drugs show that given the right conditions and sufficient time, peptides aggregate and interact with each other and their environment. Through referencing studies on various peptides, my task is to provide a summary on the major aggregation types and kinetic pathways leading there, as well as how these aggregates affect each other and the membrane of a cell. Results are expected to be a small number of distinct aggregate types regardless of which peptide is studied, alongside some proposed interactions with the cell membrane and how they have a clinical relevance.

Aim:

The aim of this project is to investigate peptide aggregation behaviors in an aqueous solution, within the cell membrane and on the surface of the cell membrane, using currently available literature on computational methods in molecular dynamics simulation. Models on interaction with the cell membrane should give insight into how the aggregating peptides affect each other and the cell membrane itself, extrapolating into potential result in vivo.

My task:

My task is to create a bibliography, primarily from online-published journals, where molecular dynamics simulations, using naturally occurring or synthesi0zed peptides show how they aggregate freely in solution, upon or inside a simulated cell membrane. Comparing observations of various peptides and different studies on the same peptides, a number of peptide aggregate types, roughly classified as amorphous aggregates, beta-sheets and in extension fibril structures and beta barrel nanotubes should be discernible as intermediates and stable endpoints in different circumstances. More importantly, discerning any particular reasons why certain aggregates are favored depending on circumstance. Using the collected data, an analysis is to be performed about the computational protocols that have been used in the different studies, to investigate how simulations are used in different contexts (e.g. simulation length, resolution, methods of analysis) and if possible if this correlates to perceived aggregation pathway, peptide size, charge, amino acid composition etc.

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