| 1. |
- Chen, Mingzhi, et al.
(författare)
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Predicting protein folding cores by empirical potential functions
- 2009
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Ingår i: Archives of Biochemistry and Biophysics. - New York : Elsevier. - 0003-9861 .- 1096-0384. ; 483:1, s. 16-22
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Tidskriftsartikel (refereegranskat)abstract
- Theoretical and in vitro experiments suggest that protein-folding cores form early in the process of folding, and that proteins may have evolved to optimize both folding speed and native-state stability. In our previous work (Chen et al., Structure, 14, 1401 (2006)), we developed a set of empirical potential functions and used them to analyze interaction energies among secondary-structure elements in two β-sandwich proteins. Our work on this group of proteins demonstrated that the predicted folding core also harbors residues that form native-like interactions early in the folding reaction. In the current work, we have tested our empirical potential functions on structurally-different proteins for which the folding cores have been revealed by protein hydrogen-deuterium exchange experiments. Using a set of 29 unrelated proteins, which have been extensively studied in the literature, we demonstrate that the average prediction result from our method is significantly better than predictions based on other computational methods. Our study is an important step towards the ultimate goal of understanding the correlation between folding cores and native structures.
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| 2. |
- Ma, Chunyan, et al.
(författare)
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Molar enthalpy of mixing and refractive indices of choline chloride-based deep eutectic solvents with water
- 2017
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Ingår i: Journal of Chemical Thermodynamics. - : Elsevier. - 0021-9614 .- 1096-3626. ; 105, s. 30-36
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Tidskriftsartikel (refereegranskat)abstract
- The molar enthalpies of mixing were measured for binary systems of choline chloride-based deep eutectic solvents (glycerol, ethylene glycol and malonic acid) with water at 298.15 K and 308.15 K, and atmospheric pressure with an isothermal calorimeter. Refractive indices were also measured at 303.15 K and atmospheric pressure. The binary mixtures of {chcl/glycerol (1:2) + water, chcl/ethylene glycol (1:2) + water} showed exothermic behaviour over the entire range of composition, while the binary mixture of {chcl/malonic acid (1:1) + water} showed endothermic behaviour at first and then changed to be exothermic with the increasing content of chcl/malonic acid (1:1). Experimental refractive indices were fitted with the Redlich–Kister equation, and experimental molar enthalpies of mixing were correlated with the Redlich–Kister equation and the non-random two-liquid (NRTL) model. The NRTL model with the fitted parameters was used to predict the vapour pressures of these three mixtures. For mixtures of {chcl/glycerol (1:2) + water} and {chcl/ethylene glycol (1:2) + water}, the predicted vapour pressures agreed well with the experimental reults from the literature. While for mixture of {chcl/malonic acid (1:1)+water}, the predicted vapour pressures showed deviation at the high concentration of chcl/malonic acid (1:1), and this was probably because of the complex molecular interaction between chcl/malonic acid (1:1) and water
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| 3. |
- Ma, Chunyan, et al.
(författare)
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Molar Enthalpy of Mixing for Choline Chloride/Urea Deep EutecticSolvent + Water System
- 2016
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Ingår i: Journal of Chemical and Engineering Data. - : American Chemical Society (ACS). - 0021-9568 .- 1520-5134. ; 61:12, s. 4172-4177
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Tidskriftsartikel (refereegranskat)abstract
- The molar enthalpies of mixing for binary systems of choline chloride (chcl)/urea deep eutectic solvents (mole ratios of 1:1.5, 1:2, and 1:2.5) with water were measured at 308.15 and 318.15 K under atmospheric pressure with an isothermal calorimeter. The binary mixture of (chcl/urea (1:2.5) + water) showed endothermic behavior over the entire range of compositions, while the binary mixtures of (chcl/urea (1:1.5) + water) and (chcl/urea (1:2) + water) showed endothermic behavior first and then was changed to be exothermic with increasing content of deep eutectic solvents. The Redlich–Kister (RK) equation and the nonrandom two-liquid (NRTL) model were used to fit experimental molar enthalpies of mixing. The NRTL model with the fitted parameters was further used to predict the vapor pressure for the three systems and was compared with the experimental data from literature. For the binary mixtures of (chcl/urea (1:2) + water), the predicted vapor pressure agreed well with the experimental data only when the temperature was lower than 333.15 K and the mole fraction of chcl/urea (1:2) was lower than 0.1. Otherwise, the deviation increased greatly with an increase of the amount of chcl/urea (1:2).
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