Molecular Simulation Methods to Investigate Protein Adsorption Behavior at the Atomic Level

Latour, Robert A.

doi:10.1016/b978-0-08-055294-1.00097-0

Cited by 7 publications

(2 citation statements)

References 105 publications

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“…The semiempirical method applies a similar computational technique only for the valence electrons; hence, reduces the cost of the computational calculations. DFT method is based on the electron density of the molecular system; hence, it is considered as a greatly rigorous method (Atkins & Friedman, 2011; Gupta, 2015; Latour, 2011). The QM calculations are extensively applied to study the bond rearrangements of the bioreceptors in the presence of the intended target.…”

Section: Computational Methods For Biosensor Designmentioning

confidence: 99%

Recent advances in computational methods for biosensor design

Khoshbin

Housaindokht

Izadyar

et al. 2020

Biotech & Bioengineering

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Biosensors are analytical tools with a great application in healthcare, food quality control, and environmental monitoring. They are of considerable interest to be designed by using cost‐effective and efficient approaches. Designing biosensors with improved functionality or application in new target detection has been converted to a fast‐growing field of biomedicine and biotechnology branches. Experimental efforts have led to valuable successes in the field of biosensor design; however, some deficiencies restrict their utilization for this purpose. Computational design of biosensors is introduced as a promising key to eliminate the gap. A set of reliable structure prediction of the biosensor segments, their stability, and accurate descriptors of molecular interactions are required to computationally design biosensors. In this review, we provide a comprehensive insight into the progress of computational methods to guide the design and development of biosensors, including molecular dynamics simulation, quantum mechanics calculations, molecular docking, virtual screening, and a combination of them as the hybrid methodologies. By relying on the recent advances in the computational methods, an opportunity emerged for them to be complementary or an alternative to the experimental methods in the field of biosensor design.

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Section: Computational Methods For Biosensor Designmentioning

confidence: 99%

Recent advances in computational methods for biosensor design

Khoshbin

Housaindokht

Izadyar

et al. 2020

Biotech & Bioengineering

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show abstract

“…In addition, knowledge on the binding behavior of proteins at liquid–solid interfaces provides valuable insight into the functions of localized proteins in biological systems. Mechanistic aspects of protein adsorption at the molecular level are highly complex − because the adsorption process involves various interactions between proteins and the solid surface or the ligands attached to the surface. ,, …”

Section: Introductionmentioning

confidence: 99%

Microcalorimetric Analysis of the Adsorption of Lysozyme and Cytochrome c onto Cation-Exchange Chromatography Resins: Influence of Temperature on Retention

et al. 2020

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We studied the adsorption mechanism of two basic proteins, equine cytochrome c (Cyt) and chicken egg-white lysozyme (Lys), adsorbing onto negatively charged chromatography surfaces. In liquid chromatography, the retention volume of Lys was larger than that of Cyt on negatively charged ion-exchange resins. When the temperature increased, the retention volume of Cyt increased, whereas that of Lys clearly decreased. Both Lys and Cyt share similar physical characteristics, so the opposite behavior with increasing temperatures was surprising, indicating a more complex mechanism of adsorption may be involved. We analyzed the adsorption of these proteins by using isothermal titration calorimetry (ITC). The change in adsorption enthalpy determined by ITC allowed the understanding of the reason for and underlying driving forces of protein adsorption that resulted in this opposite behavior. Large exothermic enthalpies of adsorption were observed for Lys (−43.95 kJ/mol), and Lys adsorption was found to be enthalpically driven. On the other hand, endothermic enthalpies were dominant for Cyt adsorption (32.41 kJ/mol), which was entropically driven. These results indicate that dehydration and release of counterions play a more important role in Cyt adsorption and ionic interaction and hydrogen bridges are more significant in Lys adsorption. Understanding of the adsorption mechanism of proteins onto chromatography resins is essential for modeling and developing new, efficient chromatographic processes.

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Pore size modulates in vitro osteogenesis of bone marrow mesenchymal stem cells in fibronectin/gelatin coated silk fibroin scaffolds

Liu

Goh

2021

Materials Science and Engineering: C

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Molecular Simulation Methods to Investigate Protein Adsorption Behavior at the Atomic Level

Cited by 7 publications

References 105 publications

Recent advances in computational methods for biosensor design

Recent advances in computational methods for biosensor design

Microcalorimetric Analysis of the Adsorption of Lysozyme and Cytochrome c onto Cation-Exchange Chromatography Resins: Influence of Temperature on Retention

Pore size modulates in vitro osteogenesis of bone marrow mesenchymal stem cells in fibronectin/gelatin coated silk fibroin scaffolds

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