Free Energy of Transition for the Individual Alkaline Conformers of Yeast Iso-1-cytochromec†,‡

Biochemistry ◽  
2007 ◽  
Vol 46 (6) ◽  
pp. 1694-1702 ◽  
Author(s):  
Gianantonio Battistuzzi ◽  
Marco Borsari ◽  
Francesca De Rienzo ◽  
Giulia Di Rocco ◽  
Antonio Ranieri ◽  
...  
Keyword(s):  
Free Energy ◽  
The Individual

Examining sharp restart in a Monte Carlo method for the linearized Poisson–Boltzmann equation

2020 ◽  
Vol 26 (3) ◽  
pp. 223-244
Author(s):  
W. John Thrasher ◽  
Michael Mascagni
Keyword(s):  
Monte Carlo ◽  
Free Energy ◽  
Monte Carlo Algorithm ◽  
Significant Bias ◽  
Poisson Boltzmann ◽  
Electrostatic Free Energy ◽  
Poisson Boltzmann Equation ◽  
The Stability ◽  
Potential Methods ◽  
The Individual

AbstractIt has been shown that when using a Monte Carlo algorithm to estimate the electrostatic free energy of a biomolecule in a solution, individual random walks can become entrapped in the geometry. We examine a proposed solution, using a sharp restart during the Walk-on-Subdomains step, in more detail. We show that the point at which this solution introduces significant bias is related to properties intrinsic to the molecule being examined. We also examine two potential methods of generating a sharp restart point and show that they both cause no significant bias in the examined molecules and increase the stability of the run times of the individual walks.

scholarly journals Intrinsic Dependence of Groundwater Cation Hydraulic and Concentration Features on Negatively Charged Thin Composite Nanofiltration Membrane Rejection and Permeation Behavior

Membranes ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 79
Author(s):  
Miroslav Kukučka ◽  
Nikoleta Kukučka Stojanović
Keyword(s):  
Free Energy ◽  
Gibbs Free Energy ◽  
Membrane Surface ◽  
Transmembrane Pressure ◽  
Nanofiltration Membrane ◽  
Ion Rejection ◽  
Monovalent Ions ◽  
Rejection Coefficient ◽  
The Individual ◽  
Volumetric Flux

Commercial nanofiltration membranes of different molecular weight cut-offs were tested on a pilot plant for the exploration of permeation nature of Ca, Mg, Mn, Fe, Na and ammonium ions. Correlation of transmembrane pressure and rejection quotient versus volumetric flux efficiency on nanofiltration membrane rejection and permeability behavior toward hydrated divalent and monovalent ions separation from the natural groundwater was observed. Membrane ion rejection affinity (MIRA) dimension was established as normalized TMP with regard to permeate solute moiety representing pressure value necessary for solute rejection change of 1%. Ion rejection coefficient (IRC) was introduced to evaluate the membrane rejection capability, and to indicate the prevailed nanofiltration partitioning mechanism near the membrane surface. Positive values of the IRC indicated satisfactory rejection efficiency of the membrane process and its negative values ensigned very low rejection affinity and high permeability of the membranes for the individual solutes. The TMP quotient and the efficiency of rejection for individual cations showed upward and downward trends along with flux utilization increase. Nanofiltration process was observed as an equilibrium. The higher the Gibbs free energy was, cation rejection was more exothermic and valuably enlarged. Low Gibbs free energy values circumferentially closer to endothermic zone indicated expressed ions permeation.

Quantitative Evaluation of the Interfacial Free Energies at A Solid-Liquid Lamellar Eutectic Interface

1981 ◽  
Vol 12 ◽  
Author(s):  
W. F. Kaukler ◽  
J. W. Rutter
Keyword(s):  
Free Energy ◽  
Solid Phase ◽  
Interfacial Free Energy ◽  
Eutectic System ◽  
Liquid Interfaces ◽  
Free Energies ◽  
Two Phases ◽  
Interfacial Free Energies ◽  
The Individual ◽  
Solid Liquid

The solid-liquid interfacial free energies of each of the individual phases comprising the eutectic system, Carbon Tetrabromide-Hexachloroethane, were measured as a function of composition using a “grain boundary groove” technique. Thermodynamic data were combined with groove shape measurements made from high resolution optical photomicrographs of the solid-liquid interfaces to give the interfacial free energy data. An interfacial free energy balance at the eutectic trijunction was performed to obtain all the forces acting on that point. The three interphase interfacial free energies at the eutectic trijunctions as well as a solid-solid phase boundary torque were evaluated.It was found that the solid-liquid interfacial free energies of the two phases of the eutectic could be evaluated from photomicrographs of growing or stationary eutectic interfaces. In addition, it was found that for a substantial range of freezing conditions the eutectic interface shape can be predicted from a knowledge of the interfacial free energies alone.

scholarly journals Dynamic allostery of protein alpha helical coiled-coils

2005 ◽  
Vol 3 (6) ◽  
pp. 125-138 ◽  
Author(s):  
Rhoda J Hawkins ◽  
Tom C.B McLeish
Keyword(s):  
Free Energy ◽  
Ligand Binding ◽  
Molecular Motor ◽  
Coiled Coil ◽  
Coiled Coils ◽  
Coarse Grained ◽  
Static Structure ◽  
Change In The Mean ◽  
The Individual ◽  
Vibrational Free Energy

Alpha helical coiled-coils appear in many important allosteric proteins such as the dynein molecular motor and bacteria chemotaxis transmembrane receptors. As a mechanism for transmitting the information of ligand binding to a distant site across an allosteric protein, an alternative to conformational change in the mean static structure is an induced change in the pattern of the internal dynamics of the protein. We explore how ligand binding may change the intramolecular vibrational free energy of a coiled-coil, using parameterized coarse-grained models, treating the case of dynein in detail. The models predict that coupling of slide, bend and twist modes of the coiled-coil transmits an allosteric free energy of ∼2 k B T , consistent with experimental results. A further prediction is a quantitative increase in the effective stiffness of the coiled-coil without any change in inherent flexibility of the individual helices. The model provides a possible and experimentally testable mechanism for transmission of information through the alpha helical coiled-coil of dynein.

Phase-Separation of B2 Precipitates in an Fe-Ni-Al Alloy

2010 ◽  
Vol 638-642 ◽  
pp. 2274-2278 ◽  
Author(s):  
Yasuhiro Kuno ◽  
Yasuo Nakane ◽  
Takao Kozakai ◽  
Minoru Doi ◽  
Junji Yamanaka ◽  
...  
Keyword(s):  
Free Energy ◽  
Phase Separation ◽  
Volume Fraction ◽  
Heating Temperature ◽  
Phase System ◽  
Al Alloy ◽  
Two Phase ◽  
Chemical Free Energy ◽  
The Difference ◽  
The Individual

When Fe-10.3mol%Ni-14.3mol%Al alloy is heated at 1173 K for 8.64104 s, a number of B2 precipitates are dispersed in the A2 matrix. When the two-phase microstructure of A2+B2 is aged at 973 K, the phase-separation of B2 precipitate particles takes place to form a new A2 phase in each B2 particle. In the course of further ageing at 973 K, the new A2 phase grows but decreases in number, and finally only one A2 particle is left in the individual B2 particles. The appearance of new A2 phase in each B2 precipitate is due to the difference in the volume fraction of A2 phase that should exist in A2+B2 two-phase system depending on the heating temperature: i.e., the phase-separation of B2 precipitates starts with the aid of chemical free energy.

scholarly journals SWOTein: a structure-based approach to predict stability Strengths and Weaknesses of prOTEINs

2021 ◽  
Author(s):  
Qingzhen Hou ◽  
Fabrizio Pucci ◽  
François Ancien ◽  
Jean-Marc Kwasigroch ◽  
Raphaël Bourgeas ◽  
...  
Keyword(s):  
Free Energy ◽  
Conformational Changes ◽  
Large Scale ◽  
Hydrogen Exchange ◽  
Test Cases ◽  
Energy Functions ◽  
Functional Regions ◽  
Large Scale Analysis ◽  
The Individual ◽  
Structured Proteins

Abstract Motivation Although structured proteins adopt their lowest free energy conformation in physiological conditions, the individual residues are generally not in their lowest free energy conformation. Residues that are stability weaknesses are often involved in functional regions, whereas stability strengths ensure local structural stability. The detection of strengths and weaknesses provides key information to guide protein engineering experiments aiming to modulate folding and various functional processes. Results We developed the SWOTein predictor which identifies strong and weak residues in proteins on the basis of three types of statistical energy functions describing local interactions along the chain, hydrophobic forces and tertiary interactions. The large-scale analysis of the different types of strengths and weaknesses demonstrated their complementarity and the enhancement of the information they provide. Moreover, a good average correlation was observed between predicted and experimental strengths and weaknesses obtained from native hydrogen exchange data. SWOTein application to three test cases further showed its suitability to predict and interpret strong and weak residues in the context of folding, conformational changes and protein-protein binding. In summary, SWOTein is both fast and accurate and can be applied at small and large scale to analyze and modulate folding and molecular recognition processes. Availability The SWOTein webserver provides the list of predicted strengths and weaknesses and a protein structure visualization tool that facilitates the interpretation of the predictions. It is freely available for academic use at http://babylone.ulb.ac.be/SWOTein/

scholarly journals An Improved Free Energy Perturbation FEP+ Sampling Protocol for Flexible Ligand-Binding Domains

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Filip Fratev ◽  
Suman Sirimulla
Keyword(s):  
Free Energy ◽  
Ligand Binding ◽  
Structural Changes ◽  
Binding Mode ◽  
Free Energy Perturbation ◽  
Sampling Protocol ◽  
Sampling Schemes ◽  
Energy Perturbation ◽  
The Individual ◽  
Energy Convergence

AbstractRecent improvements to the free energy perturbation (FEP) calculations, especially FEP+ , established their utility for pharmaceutical lead optimization. Herein, we propose a modified version of the FEP/REST (i.e., replica exchange with solute tempering) sampling protocol, based on detail studies on several targets by probing a large number of perturbations with different sampling schemes. Improved FEP+ binding affinity predictions for regular flexible-loop motions and considerable structural changes can be obtained by extending the prior to REST (pre-REST) sampling time from 0.24 ns/λ to 5 ns/λ and 2 × 10 ns/λ, respectively. With this new protocol, much more precise ∆∆G values of the individual perturbations, including the sign of the transformations and decreased error were obtained. We extended the REST simulations from 5 ns to 8 ns to achieve reasonable free energy convergence. Implementing REST to the entire ligand as opposed to solely the perturbed region, and also some important flexible protein residues (pREST region) in the ligand binding domain (LBD) has considerably improved the FEP+ results in most of the studied cases. Preliminary molecular dynamics (MD) runs were useful for establishing the correct binding mode of the compounds and thus precise alignment for FEP+ . Our improved protocol may further increase the FEP+ accuracy.

scholarly journals Thermodynamic vs. Kinetic Basis for Polymorph Selection

Processes ◽  
2019 ◽  
Vol 7 (5) ◽  
pp. 272 ◽  
Author(s):  
Benjamin K. Hodnett ◽  
Vivek Verma
Keyword(s):  
Free Energy ◽  
Intrinsic Properties ◽  
Interfacial Energies ◽  
Upper Limit ◽  
Polymorph Selection ◽  
Metastable Zone ◽  
The Individual ◽  
Stable Polymorph

Ratios of equilibrium solubilities rarely exceed two-fold for polymorph pairs. A model has been developed based on two intrinsic properties of polymorph pairs, namely the ratio of equilibrium solubilities of the individual pairs (C*me/C*st) and the ratio of interfacial energies (γst/γme) and one applied experimental condition, namely the supersaturation identifies which one of a pair of polymorphs nucleates first. A domain diagram has been developed, which identifies the point where the critical free energy of nucleation for the polymorph pair are identical. Essentially, for a system supersaturated with respect to both polymorphs, the model identifies that low supersaturation with respect to the stable polymorph (Sst) leads to an extremely small supersaturation with respect to the metastable polymorph (Sme), radically driving up the critical free energy with respect to the metastable polymorph. Generally, high supersaturations sometimes much higher than the upper limit of the metastable zone, are required to kinetically favour the metastable polymorph.

Sign in / Sign up

Export Citation Format

Share Document