Related Experiment Video
Updated: Feb 8, 2026

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
Published on: September 17, 2021
Dynamics and Thermodynamics of Transthyretin Association from Molecular Dynamics Simulations
Cedrix J Dongmo Foumthuim1, Alessandra Corazza1,2, Rodolfo Berni3
1Dipartimento di Area Medica, Università di Udine, Piazzale Kolbe 4, 33100 Udine, Italy.
Abstract:
Molecular dynamics simulations are used in this work to probe the structural stability and the dynamics of engineered mutants of transthyretin (TTR), i.e., the double mutant F87M/L110M (MT-TTR) and the triple mutant F87M/L110M/S117E (3M-TTR), in relation to wild-type. Free energy analysis from end-point simulations and statistical effective energy functions are used to analyze trajectories, revealing that mutations do not have major impact on protein structure but rather on protein association, shifting the equilibria towards dissociated species. The result is confirmed by the analysis of 3M-TTR which shows dissociation within the first 10 ns of the simulation, indicating that contacts are lost at the dimer-dimer interface, whereas dimers (formed by monomers which pair to form two extended β-sheets) appear fairly stable. Overall the simulations provide a detailed view of the dynamics and thermodynamics of wild-type and mutant transthyretins and a rationale of the observed effects.
More Related Videos
15:05Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation
Published on: May 20, 2020
08:54Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid
Published on: January 25, 2020
Related Concept Videos
Dynamic Equilibrium
Third Law of Thermodynamics
Second Law of Thermodynamics
Second Law of Thermodynamics
Dynamics of Circular Motion
Any acceleration must be produced by some force. Therefore, any force or combination of forces can cause centripetal acceleration. A few examples include the tension in the rope on a...
Fermi Level Dynamics
Electron affinity in semiconductors refers to the energy gap between the minimum of its conduction band and the vacuum level and it is a critical parameter in determining how easily a semiconductor can accept additional electrons.
The work...