Absorbed weak polyelectrolytes: Impact of confinement, topology, and chemically specific interactions on ionization, conformation free energy, counterion condensation, and absorption equilibrium

2019 ◽  
Vol 57 (9) ◽  
pp. 491-510 ◽  
Author(s):  
Andrea Tagliabue ◽  
Lorella Izzo ◽  
Massimo Mella
Keyword(s):  
Free Energy ◽  
Specific Interactions ◽  
Counterion Condensation ◽  
Weak Polyelectrolytes

scholarly journals Sequence, structure, and cooperativity in folding of elementary protein structural motifs

2015 ◽  
Vol 112 (32) ◽  
pp. 9890-9895 ◽  
Author(s):  
Jason K. Lai ◽  
Ginka S. Kubelka ◽  
Jan Kubelka
Keyword(s):  
Free Energy ◽  
Hydrogen Bonds ◽  
De Novo ◽  
Double Sequence ◽  
Specific Interactions ◽  
Site Specific ◽  
Native Contact ◽  
Energy Profiles ◽  
Mechanical Models ◽  
Free Energy Profiles

Residue-level unfolding of two helix-turn-helix proteins—one naturally occurring and one de novo designed—is reconstructed from multiple sets of site-specific 13C isotopically edited infrared (IR) and circular dichroism (CD) data using Ising-like statistical-mechanical models. Several model variants are parameterized to test the importance of sequence-specific interactions (approximated by Miyazawa–Jernigan statistical potentials), local structural flexibility (derived from the ensemble of NMR structures), interhelical hydrogen bonds, and native contacts separated by intervening disordered regions (through the Wako–Saitô–Muñoz–Eaton scheme, which disallows such configurations). The models are optimized by directly simulating experimental observables: CD ellipticity at 222 nm for model proteins and their fragments and 13C-amide I′ bands for multiple isotopologues of each protein. We find that data can be quantitatively reproduced by the model that allows two interacting segments flanking a disordered loop (double sequence approximation) and incorporates flexibility in the native contact maps, but neither sequence-specific interactions nor hydrogen bonds are required. The near-identical free energy profiles as a function of the global order parameter are consistent with expected similar folding kinetics for nearly identical structures. However, the predicted folding mechanism for the two motifs is different, reflecting the order of local stability. We introduce free energy profiles for “experimental” reaction coordinates—namely, the degree of local folding as sensed by site-specific 13C-edited IR, which highlight folding heterogeneity and contrast its overall, average description with the detailed, local picture.

The Meaning of Component Analysis: Decomposition of the Free Energy in Terms of Specific Interactions

1995 ◽  
Vol 254 (5) ◽  
pp. 801-807 ◽  
Author(s):  
S. Boresch ◽  
M. Karplus
Keyword(s):  
Free Energy ◽  
Component Analysis ◽  
Specific Interactions

scholarly journals Thermophysical Properties of Binary Liquid Systems of Ethanoic Acid, Propanoic Acid, and Butanoic Acid with Benzene or Acetophenone

2013 ◽  
Vol 2013 ◽  
pp. 1-13 ◽  
Author(s):  
R. Ahluwalia ◽  
Ritu Gupta ◽  
J. L. Vashisht ◽  
R. K. Wanchoo
Keyword(s):  
Surface Tension ◽  
Free Energy ◽  
Propanoic Acid ◽  
Specific Interactions ◽  
Butanoic Acid ◽  
Binary Liquid ◽  
Ethanoic Acid ◽  
Volume Viscosity ◽  
Liquid Systems ◽  
Gibb’S Free Energy

The density (), viscosity (), and surface tension () of binary mixtures of carboxylic acids (CAs) (ethanoic acid (EA), propanoic acid (PA), butanoic acid (BA)) + benzene (BEN) or acetophenone (ACT) have been measured at 298.15, 308.15, and 318.15 K. From the experimental results, excess values of molar volume (), viscosity (), Gibb's free energy for the activation of low (), and surface tension () were evaluated and fitted to a Redlich-Kister type of equation. The parameter “” of Grunberg and Nissan expression has also been calculated. From the sign and magnitude of , , , , and “” values, it is concluded that specific interactions are present in CA+ACT system and these interactions are absent in CA + BEN mixtures. Various viscosity and surface tension models have been used to test the consistency of the data.

Specific Interactions versus Counterion Condensation. 1. Nongelling Ions/Polyuronate Systems

2006 ◽  
Vol 7 (1) ◽  
pp. 281-287 ◽  
Author(s):  
Ivan Donati ◽  
Attilio Cesàro ◽  
Sergio Paoletti
Keyword(s):  
Specific Interactions ◽  
Counterion Condensation

Impact of Charge Correlation, Chain Rigidity, and Chemical Specific Interactions on the Behavior of Weak Polyelectrolytes in Solution

2019 ◽  
Vol 123 (42) ◽  
pp. 8872-8888 ◽  
Author(s):  
Andrea Tagliabue ◽  
Lorella Izzo ◽  
Massimo Mella
Keyword(s):  
Specific Interactions ◽  
Chain Rigidity ◽  
Weak Polyelectrolytes

Specific Interactions versus Counterion Condensation. 2. Theoretical Treatment within the Counterion Condensation Theory

2006 ◽  
Vol 7 (5) ◽  
pp. 1587-1596 ◽  
Author(s):  
Ivan Donati ◽  
Julio C. Benegas ◽  
Attilio Cesàro ◽  
Sergio Paoletti
Keyword(s):  
Theoretical Treatment ◽  
Specific Interactions ◽  
Counterion Condensation

Decomposition of the Free Energy of a System in Terms of Specific Interactions

1994 ◽  
Vol 240 (2) ◽  
pp. 167-176 ◽  
Author(s):  
Alan E. Mark ◽  
Wilfred F. van Gunsteren
Keyword(s):  
Free Energy ◽  
Specific Interactions

scholarly journals Inhibition of bacterial transport by uncouplers of oxidative phosphorylation. Effects of pentachlorophenol and analogues in Bacillus subtilis

1978 ◽  
Vol 176 (3) ◽  
pp. 639-647 ◽  
Author(s):  
R A Nicholas ◽  
G W Ordal
Keyword(s):  
Free Energy ◽  
Bacillus Subtilis ◽  
Oxidative Phosphorylation ◽  
Potent Inhibitor ◽  
Bacterial Transport ◽  
Specific Interactions ◽  
Acid Transport ◽  
Competitive Inhibitors ◽  
Glycine Transport ◽  
Energy Of Interaction

Analogues of the potent uncoupler of oxidative phosphorylation pentachlorophenol were tested as inhibitors of proline and glycine transport by Bacillus subtilis. These analogues included less highly substituted chlorophenols and pentachlorothiophenol. Like pentachlorophenol, they are non-competitive inhibitors of proline transport and uncompetitive inhibitors of glycine transport. However, the less highly substituted chlorophenols are weaker acids than pentachlorophenol and also weaker inhibitors. Analysis indicated that the anionic form of the uncouplers is the inhibiting species. Pentachlorothiophenol, a water-insoluble anion, is also a potent inhibitor. These results support previous studies that concluded that uncouplers of oxidative phosphorylation inhibit amino acid transport by binding at specific sites on proteins, the free energy of interaction stabilizing ‘unproductive’ conformations. Such specific interactions of uncoupler with protein are probably commonplace.

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