A metadynamics study of simple peptide chains

Palmisano, Vito Federico, VF (2021) A metadynamics study of simple peptide chains. Research Project, Chemistry.

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Abstract

In nature, protein possess the remarkable ability to fold spontaneously into precisely determined three-dimensional structures. Understanding of this process requires the characterization of the driving molecular interactions and intermediate states of the system. At a molecular level, the backbone dihedral angles play an important role for the secondary structure formation, providing crucial informations about the three dimensional structure. Protein conformational energy landscapes are complex, high-dimensional surfaces with many local minima and navigating them requires efficient sampling methods. Molecular dynamics simulations of protein folding can provide high-resolution data on the folding process, but intrinsic limitation of atomistic models render the task extremely difficult. This is where enhanced sampling methods become useful to accelerate the dynamics and sample the conformational space of such systems. In this study, an enhanced sampling method, metadynamics, is employed to describe the behaviour or the torsional angles and in different tripeptide chains. The torsional angles are also evaluated with different force fields. For all the force fields, local minima are commonly shared with small variations along the free energy profiles. The presence of side chains yield to different maxima in the free energy profiles.

Item Type:	Thesis (Research Project)
Supervisor name:	Marrink, S.J.
Degree programme:	Chemistry
Thesis type:	Research Project
Language:	English
Date Deposited:	26 Jan 2021 11:29
Last Modified:	26 Jan 2021 11:29
URI:	https://fse.studenttheses.ub.rug.nl/id/eprint/23827

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