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Configurational entropy change is a central constituent of the free energy change in non-covalent interactions between biomolecules. Due to both experimental and computational limitations, however, the impact of individual contributions to configurational entropy change remains underexplored. Here, we develop a novel, fully analytical framework to dissect the configurational entropy change of binding into contributions coming from molecular-internal and external degrees of freedom. Importantly, this framework accounts for all coupled and uncoupled contributions in the absence of an external field. We employ our parallel implementation of the maximum-information spanning tree algorithm to provide a comprehensive numerical analysis of the importance of the individual contributions to configurational entropy change on an extensive set of molecular dynamics simulations of protein binding processes. Contrary to commonly accepted assumptions, we show that different coupling terms contribute significantly to the overall configurational entropy change. Finally, while the magnitude of individual terms may be largely unpredictable a priori, the total configurational entropy change can be well approximated by rescaling the sum of uncoupled contributions from internal degrees of freedom only, providing support for NMR-based approaches for configurational entropy change estimation.
This article was published in the following journal.
Name: Journal of chemical theory and computation
A generalization of the Adam-Gibbs model of relaxation in glass-forming liquids is formulated that takes into account fluctuation in the number of molecules inside the cooperative region. The configur...
Coarse-grained (CG) models facilitate efficient simulation of complex systems by integrating out the atomic, or fine-grained (FG), degrees of freedom. Systematically-derived CG models from FG simulati...
A sensitive and visible colorimetric strategy was proposed for Hg detection by thymine-Hg-thymine (T-Hg-T) coordination chemistry and entropy driven catalytic reaction. The entropy driven catalytic re...
Information entropy is generally employed for analysing the complexity of physiological signals. However, most of the entropy definitions estimate the degree of compressibility and thus quantify the r...
Cyclodextrin complexes were used as simple model systems to explore the enthalpy-entropy compensation phenomenon which is often observed in biomolecular processes, e.g. in protein-ligand binding. The ...
Complex patterns of patient-ventilator interactions could be miscalculated by visual observation of mechanical ventilator screens or current algorithms based on physiologic waveforms to de...
The purpose of this study is to learn more about an Entropy monitor that your anesthesiologist will be using.
For verifying the phase lag entropy as the tool for measurement of level of consciousness, the investigators compared phase lag entropy to bispectral index. Using Target-Controlled Infusio...
The main objective of the study is to determine whether depth of anesthesia (DOA) monitoring such as Bispectral Index (BIS) and entropy are accurate in patients with neuro-psychological co...
To compare Bispectral index and entropy during maintenance of anesthesia
The measure of that part of the heat or energy of a system which is not available to perform work. Entropy increases in all natural (spontaneous and irreversible) processes. (From Dorland, 28th ed)
A minichromosome maintenance protein that forms a hexameric complex with MINICHROMSOME MAINTENANCE COMPLEX COMPONENT 9. The MCM8-MCM9 helicase complex is involved in HOMOLOGOUS RECOMBINATION REPAIR following the formation of DNA interstrand cross-links.
A minichromosome maintenance protein that forms a hexameric complex with MINICHROMSOME MAINTENANCE COMPLEX COMPONENT 8. The MCM8-MCM9 helicase complex is involved in HOMOLOGOUS RECOMBINATION REPAIR following the formation of DNA interstrand cross-links.
A dystrophin-associated protein and component of the Biogenesis of Lysosomal Organelles Complex-1 (BLOC-1 complex) which is essential for the formation of LYSOSOME - derived organelles such as platelet dense granules and MELANOSOMES. DTNBP1 is expressed primarily in the brain and neurons, where it functions with ADAPTOR PROTEIN COMPLEX 3 to transport membrane proteins to NEURITES and nerve terminals. It also regulates the release of neurotransmitters, transport of synaptic vesicles, and localization of DOPAMINE D2 RECEPTORS. Mutations in the DTNBP1 gene are associated with Type 7 HERMANSKY-PUDLAK SYNDROME and SCHIZOPHRENIA.
NMR spectroscopy on small- to medium-size biological macromolecules. This is often used for structural investigation of proteins and nucleic acids, and often involves more than one isotope.
Within medicine, nutrition (the study of food and the effect of its components on the body) has many different roles. Appropriate nutrition can help prevent certain diseases, or treat others. In critically ill patients, artificial feeding by tubes need t...