2006
DOI: 10.1143/jpsj.75.064803
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Thermodynamics of Aggregation of Two Proteins

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-selfoverlap-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, … Show more

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Cited by 5 publications
(3 citation statements)
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“…As L decreases, the thermal stability of the complexes increases because of the decrease in the translational entropy of the free states. This result suggests that confinement in a small volume can also induce binding, which is basically the same as the confinement-induced dimerization discussed by Nakanishi and Kikuchi 34 . Increasing the density of the two molecules can also reduce translational entropy of the free states, and stabilize bound states.…”
Section: B Thermal Stability Of the Native Bound Statesupporting
confidence: 79%
See 1 more Smart Citation
“…As L decreases, the thermal stability of the complexes increases because of the decrease in the translational entropy of the free states. This result suggests that confinement in a small volume can also induce binding, which is basically the same as the confinement-induced dimerization discussed by Nakanishi and Kikuchi 34 . Increasing the density of the two molecules can also reduce translational entropy of the free states, and stabilize bound states.…”
Section: B Thermal Stability Of the Native Bound Statesupporting
confidence: 79%
“…We calculated the number of states by using the multiself-overlap ensemble (MSOE) Monte Carlo method 30,31 , which is an extended version of the multicanonical Monte Carlo method 32,33 . The MSOE is a powerful tool in analyzing thermal properties of lattice polymers 28,34 , and is applied for statistical enumeration of self-avoiding walks 35 . The MSOE successfully attained thermal equilibrium between free states and the designed bound state.…”
Section: Model and Methodsmentioning
confidence: 99%
“…When systems comprising up to 40 chains were simulated, some of these conformations were prone to aggregation. Recently, Nakanishi and Kikuchi [136] performed a rigorous thermodynamic analysis on the aggregation of two HP proteins. To overcome problems with the excluded volume, they used multi-self-overlap-ensemble Monte Carlo, which allows chains to move through each other.…”
Section: Lattice Studies Of Aggregationmentioning
confidence: 99%