Thermodynamics of aggregation of two proteins
Kazuki Nakanishi, Macoto Kikuchi
Abstract
We investigate aggregation mechanism of two proteins in a thermodynamically unambiguous manner by considering the finite size effect of free energy landscape of HP lattice protein model. Multi-Self-Overlap-Ensemble Monte Carlo method is used for numerical calculations. We find that a dimer can be formed spontaneously as a thermodynamically stable state when the system is small enough. It implies the possibility that the aggregation of proteins in a cell is triggered when they are confined in a small region by, for example, being surrounded by other macromolecules.We also find that the dimer exhibits a transition between unstable state and metastable state in the infinite system.
Create a lesson
Related papers
A meta-algorithm for ab initio reconstruction of complex mixtures in cryo-EM
Alkin Kaz, Arda Kaz, Ellen D. Zhong
PHASE: encoding global protein ensembles with local Hamiltonians and all-atom backmapping
Daniele Angioletti, Marco Nobile, Matteo Carli et al.
Analysis of correlations of dwell-times of adjacent kinetic states in the activity of the cold and menthol receptor TRPM8
Ogloblya O. V., Moroz O. F., Zholos A.
Multitask Bayesian Neural Networks for Multiparameter Protein Engineering
Fabio Herrera-Rocha, David Medina-Ortiz, Desiree Wyrzykala et al.
Recovering protein conformations from single-particle cryo-EM data via indirect shape matching gradient flows
Erik Jansson, Jonathan Krook, Ozan Öktem et al.
Is Retrieval All You Need? Assessment and Emergence of Novelty in Protein Structure Generation
Tongyue Xu, Yijie Zhang, Mutian He et al.