Molecular simulations of peptide and protein unfolding: in quest of a molten globule

1993 ◽  
Vol 3 (1) ◽  
pp. 92-98 ◽  
Author(s):  
Charles L. Brooks
Soft Matter ◽  
2020 ◽  
Vol 16 (16) ◽  
pp. 3941-3951
Author(s):  
Aviel Chaimovich ◽  
Christian Leitold ◽  
Christoph Dellago

By computing free energies with molecular simulations, we find a general signature for protein unfolding in force spectroscopy, and in turn, we present a useful formula for experimentalists.


2010 ◽  
Vol 78 (13) ◽  
pp. 2725-2737 ◽  
Author(s):  
Robert L. Baldwin ◽  
Carl Frieden ◽  
George D. Rose

2019 ◽  
Vol 7 (1) ◽  
pp. 35-42
Author(s):  
Ali Es-haghi ◽  
Mahsa Jahedi Moghaddam ◽  
Koorosh Shahpasand

The conversion of a protein from its native conformation to the pathogenic form is a critical event in the pathogenesis of several neurodegenerative disorders such as Alzheimer’s (AD), Parkinson’s, and Huntington’s diseases, along with type II diabetic mellitus. Although there are several reports on the mechanism of protein aggregation, the actual conformation playing a part in the pathogenicity is yet unclear. Accordingly, the present study summarizes the early pathogenic conformation resulting in several protein aggregations. It is well-documented that a pre-molten globule (MG) structure appears at the early stages of some proteins. Pre-MG is one of the intermediate structures, which is formed during some protein unfolding processes. In addition, it is shown that the pre-molten structure is more flexible than the mature MG one and thus, protein easily rearranges to form amyloid fibrils in this conformation. Therefore, protein aggregation is halted by preventing the pre-MG structure. The strategy of protein aggregation prevention has profound implications in fighting the devastating disorder.


2020 ◽  
Author(s):  
Matías R. Machado ◽  
Sergio Pantano

<p> Despite the relevance of properly setting ionic concentrations in Molecular Dynamics (MD) simulations, methods or practical rules to set ionic strength are scarce and rarely documented. Based on a recently proposed thermodynamics method we provide an accurate rule of thumb to define the electrolytic content in simulation boxes. Extending the use of good practices in setting up MD systems is promptly needed to ensure reproducibility and consistency in molecular simulations.</p>


2019 ◽  
Author(s):  
Riccardo Spezia ◽  
Hichem Dammak

<div> <div> <div> <p>In the present work we have investigated the possibility of using the Quantum Thermal Bath (QTB) method in molecular simulations of unimolecular dissociation processes. Notably, QTB is aimed in introducing quantum nuclear effects with a com- putational time which is basically the same as in newtonian simulations. At this end we have considered the model fragmentation of CH4 for which an analytical function is present in the literature. Moreover, based on the same model a microcanonical algorithm which monitor zero-point energy of products, and eventually modifies tra- jectories, was recently proposed. We have thus compared classical and quantum rate constant with these different models. QTB seems to correctly reproduce some quantum features, in particular the difference between classical and quantum activation energies, making it a promising method to study unimolecular fragmentation of much complex systems with molecular simulations. The role of QTB thermostat on rotational degrees of freedom is also analyzed and discussed. </p> </div> </div> </div>


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