Molecular dynamic study of subtilisin Carlsberg in aqueous and nonaqueous solvents

Cruz, Anthony; Ramírez, Eunice; Santana, Alberto; Barletta, Gabriel; López, Gustavo E.

doi:10.1080/08927020802415670

Cited by 16 publications

(29 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Simulations carried out in a mixture of water and ethanol [79], acetonitrile [80] or other organic solvents [81] can determine the degree of destabilization of a protein, leading to possible applications in non-aqueous enzymology. Urea plays a special role because of its widespread use as a denaturing agent.…”

Section: Simulation Of Folding/unfolding Under More Complex Conditmentioning

confidence: 99%

Using simulations to provide the framework for experimental protein folding studies

Rizzuti¹,

Daggett²

2013

Archives of Biochemistry and Biophysics

View full text Add to dashboard Cite

Section: Simulation Of Folding/unfolding Under More Complex Conditmentioning

confidence: 99%

Using simulations to provide the framework for experimental protein folding studies

Rizzuti¹,

Daggett²

2013

Archives of Biochemistry and Biophysics

View full text Add to dashboard Cite

“…This is valuable information for researchers seeking to limit the number of waters when simulating enzymes in organic solvent, such as in studies that probe the effect of water activity on enzyme structure and dynamics. [16,56,63–67] Differences between methods 2 and 3 were more pronounced for CALB protein than for hh-CytC, and in water solvent (where method 2 was notably more effective than method 3 for both proteins).…”

Section: Resultsmentioning

confidence: 99%

To keep or not to keep? the question of crystallographic waters for enzyme simulations in organic solvent

Dahanayake

Gautam

Verma

et al. 2016

Molecular Simulation

View full text Add to dashboard Cite

The use of enzymes in non-aqueous solvents expands the use of biocatalysts to hydrophobic substrates, with the ability to tune selectivity of reactions through solvent selection. Non-aqueous enzymology also allows for fundamental studies on the role of water and other solvents in enzyme structure, dynamics, and function. Molecular dynamics simulations serve as a powerful tool in this area, providing detailed atomic information about the effect of solvents on enzyme properties. However, a common protocol for non-aqueous enzyme simulations does not exist. If you want to simulate enzymes in non-aqueous solutions, how many and which crystallographic waters do you keep? In the present work, this question is addressed by determining which crystallographic water molecules lead most quickly to an equilibrated protein structure. Five different methods of selecting and keeping crystallographic waters are used in order to discover which crystallographic waters lead the protein structure to reach an equilibrated structure more rapidly in organic solutions. It is found that buried waters contribute most to rapid equilibration in organic solvent, with slow-diffusing waters giving similar results.

show abstract

“…This fact makes enzymes in non traditional media a promising basis for various biotechnological applications, and leads to an increasing number of investigations of physical and chemical foundations of the functioning of enzymes in aqueous-organic solvents [4][5][6]. In addition to applied aspects, such studies can provide useful information for understanding the mechanisms of the modifying influence of various low molecular weight organic compounds on the activity of enzymes in living cells [7].…”

Section: Introductionmentioning

confidence: 98%

Effect of dioxane molecules on the hydration shell of polypeptides

2012

View full text Add to dashboard Cite

Our interest in modifying influence of the low-molecular organic compounds on the hydration shell of biopolymers is due to a well-known fact that the former can act as regulators of the enzymatic activity changed the hydration shell of the latter. Dioxane was chosen because of its wide application in non-aqueous biocatalysis. In the present study we investigate the mechanisms of the dioxane influence on water of the first hydration layer of the model polypeptides by FTIR-spectroscopy during simultaneous sorption of water-dioxane vapors into the polypeptide films at low water activity. It was found that modification of the hydration shell of the studied polypeptides was mainly due to the indirect ordering ofpolypeptide secondary structure at penetration of dioxane molecules at these conditions.

show abstract

Molecular dynamic study of subtilisin Carlsberg in aqueous and nonaqueous solvents

Cited by 16 publications

References 39 publications

Using simulations to provide the framework for experimental protein folding studies

Using simulations to provide the framework for experimental protein folding studies

To keep or not to keep? the question of crystallographic waters for enzyme simulations in organic solvent

Effect of dioxane molecules on the hydration shell of polypeptides

Contact Info

Product

Resources

About