scholarly journals Protein Unfolding and Aggregation near a Hydrophobic Interface

Polymers ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 156
Author(s):  
David March ◽  
Valentino Bianco ◽  
Giancarlo Franzese
Keyword(s):  
Neurodegenerative Diseases ◽  
Protein Concentration ◽  
Protein Unfolding ◽  
Hydrophobic Surface ◽  
The Other ◽  
Coarse Grained ◽  
Aqueous Environment ◽  
Coarse Grained Model ◽  
Hydrophobic Interface

The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we study how the presence of a hydrophobic surface affects this course of events. To this goal, we use a coarse-grained model of proteins and study by simulations their folding and aggregation near an ideal hydrophobic surface in an aqueous environment by changing parameters such as temperature and hydrophobic strength, related, e.g., to ions concentration. We show that the hydrophobic surface, as well as the other parameters, affect both the protein unfolding and aggregation. We discuss the interpretation of these results and define future lines for further analysis, with their possible implications in neurodegenerative diseases.

scholarly journals Optimal proteome allocation and the temperature dependence of microbial growth laws

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Francis Mairet ◽  
Jean-Luc Gouzé ◽  
Hidde de Jong
Keyword(s):  
Growth Rate ◽  
Stress Responses ◽  
Protein Unfolding ◽  
Microbial Growth ◽  
Coarse Grained ◽  
Effect Of Temperature ◽  
Temperature Sensitive ◽  
Coarse Grained Model ◽  
Proteomic Data ◽  
Growth Laws

AbstractAlthough the effect of temperature on microbial growth has been widely studied, the role of proteome allocation in bringing about temperature-induced changes remains elusive. To tackle this problem, we propose a coarse-grained model of microbial growth, including the processes of temperature-sensitive protein unfolding and chaperone-assisted (re)folding. We determine the proteome sector allocation that maximizes balanced growth rate as a function of nutrient limitation and temperature. Calibrated with quantitative proteomic data for Escherichia coli, the model allows us to clarify general principles of temperature-dependent proteome allocation and formulate generalized growth laws. The same activation energy for metabolic enzymes and ribosomes leads to an Arrhenius increase in growth rate at constant proteome composition over a large range of temperatures, whereas at extreme temperatures resources are diverted away from growth to chaperone-mediated stress responses. Our approach points at risks and possible remedies for the use of ribosome content to characterize complex ecosystems with temperature variation.

The Alteration of the Pore Spaces in Sandstones

1973 ◽  
Vol 31 ◽  
pp. 210-211
Author(s):  
R. E. Ferrell ◽  
G. G. Paulson
Keyword(s):  
Electron Microscope ◽  
Scanning Electron Microscope ◽  
The Other ◽  
Coarse Grained ◽  
Depositional Fabric ◽  
Soluble Components ◽  
Scanning Electron ◽  
Shape And Size

The pore spaces in sandstones are the result of the original depositional fabric and the degree of post-depositional alteration that the rock has experienced. The largest pore volumes are present in coarse-grained, well-sorted materials with high sphericity. The chief mechanisms which alter the shape and size of the pores are precipitation of cementing agents and the dissolution of soluble components. Each process may operate alone or in combination with the other, or there may be several generations of cementation and solution.The scanning electron microscope has ‘been used in this study to reveal the morphology of the pore spaces in a variety of moderate porosity, orthoquartzites.

On the Origin of the Microscystalline Structure in Rapidly Solidified IN-100 Powder

1977 ◽  
Vol 35 ◽  
pp. 260-261
Author(s):  
J. M. Walsh ◽  
K. P. Gumz ◽  
J. C. Whittles ◽  
B. H. Kear
Keyword(s):  
The Other ◽  
Coarse Grained ◽  
Microcrystalline Structure ◽  
Routine Examination ◽  
Atomization Process ◽  
Centrifugal Atomization ◽  
Splat Quenching ◽  
Powder Particles ◽  
Dendritic Microstructures ◽  
Rapidly Solidified

During a routine examination of the microstructure of rapidly solidified IN-100 powder, produced by a newly-developed centrifugal atomization process1, essentially two distinct types of microstructure were identified. When a high melt superheat is maintained during atomization, the powder particles are predominantly coarse-grained, equiaxed or columnar, with distinctly dendritic microstructures, Figs, la and 4a. On the other hand, when the melt superheat is reduced by increasing the heat flow to the disc of the rotary atomizer, the powder particles are predominantly microcrystalline in character, with typically one dendrite per grain, Figs, lb and 4b. In what follows, evidence is presented that strongly supports the view that the unusual microcrystalline structure has its origin in dendrite erosion occurring in a 'mushy zone' of dynamic solidification on the disc of the rotary atomizer.The critical observations were made on atomized material that had undergone 'splat-quenching' on previously solidified, chilled substrate particles.

Insights Into Crowding Effects on Protein Stability From a Coarse-Grained Model

2009 ◽  
Vol 131 (7) ◽  
Author(s):  
Vincent K. Shen ◽  
Jason K. Cheung ◽  
Jeffrey R. Errington ◽  
Thomas M. Truskett
Keyword(s):  
Protein Stability ◽  
Coarse Grained ◽  
Protein Solutions ◽  
Native State ◽  
High Concentration ◽  
Coarse Grained Model ◽  
Excluded Volume Effects ◽  
Thermodynamic Phase ◽  
Broad Interest ◽  
Liquid Liquid Phase Separation

Proteins aggregate and precipitate from high concentration solutions in a wide variety of problems of natural and technological interest. Consequently, there is a broad interest in developing new ways to model the thermodynamic and kinetic aspects of protein stability in these crowded cellular or solution environments. We use a coarse-grained modeling approach to study the effects of different crowding agents on the conformational equilibria of proteins and the thermodynamic phase behavior of their solutions. At low to moderate protein concentrations, we find that crowding species can either stabilize or destabilize the native state, depending on the strength of their attractive interaction with the proteins. At high protein concentrations, crowders tend to stabilize the native state due to excluded volume effects, irrespective of the strength of the crowder-protein attraction. Crowding agents reduce the tendency of protein solutions to undergo a liquid-liquid phase separation driven by strong protein-protein attractions. The aforementioned equilibrium trends represent, to our knowledge, the first simulation predictions for how the properties of crowding species impact the global thermodynamic stability of proteins and their solutions.

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