Globe-hopping.
Ontology highlight
ABSTRACT:
SUBMITTER: Chistikov D
PROVIDER: S-EPMC7428041 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Biological redox machines require efficient transfer of electrons and holes for function. Reactions involving multiple tunneling steps, termed "hopping," often promote charge separation within and between proteins that is essential for energy storage and conversion. Here we show how semiclassical electron transfer theory can be extended to include hopping reactions: graphical representations (called hopping maps) of the dependence of calculated two-step reaction rate constants on driving force are employed to account for flow in a rhenium-labeled azurin mutant as well as in two structurally characterized redox enzymes, DNA photolyase and MauG. Analysis of the 35 Å radical propagation in ribonucleotide reductases using hopping maps shows that all tyrosines and tryptophans on the radical pathway likely are involved in function. We suggest that hopping maps can facilitate the design and construction of artificial photosynthetic systems for the production of fuels and other chemicals.
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Project description:High-potential iron-oxo species are intermediates in the catalytic cycles of oxygenase enzymes. They can cause heme degradation and irreversible oxidation of nearby amino acids. We have proposed that there are protective mechanisms in which hole hopping from oxidized hemes through tryptophan/tyrosine chains generates a surface-exposed amino-acid oxidant that could be rapidly disarmed by reaction with cellular reductants. In investigations of cytochrome P450BM3, we identified Trp96 as a critical residue that could play such a protective role. This Trp is cation-π paired with Arg398 in 81% of mammalian P450s. Here we report on the effect of the Trp/Arg cation-π interaction on Trp96 formal potentials as well as on electronic coupling strengths between Trp96 and the heme both for wild type cytochrome P450 and selected mutants. Mutation of Arg398 to His, which decreases the Trp96 formal potential, increases Trp-heme electronic coupling; however, surprisingly, the rate of phototriggered electron transfer from a Ru-sensitizer (through Trp96) to the P450BM3 heme was unaffected by the Arg398His mutation. We conclude that Trp96 has moved away from Arg398, suggesting that the protective mechanism for P450s with this Trp-Arg pair is conformationally gated.
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Project description:The general goal of drug discovery is to identify novel compounds that are active against a preselected biological target with acceptable pharmacological properties defined by marketed drugs. Scaffold hopping has been widely applied by medicinal chemists to discover equipotent compounds with novel backbones that have improved properties. In this article we classify scaffold hopping into four major categories, namely heterocycle replacements, ring opening or closure, peptidomimetics and topology-based hopping. We review the structural diversity of original and final scaffolds with respect to each category. We discuss the advantages and limitations of small, medium and large-step scaffold hopping. Finally, we summarize software that is frequently used to facilitate different kinds of scaffold-hopping methods.
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Project description:Alternative models of cardiac rehabilitation (CR) delivery, such as home or community-based programs, have been developed to overcome underutilization. However, their availability and characteristics have never been assessed globally. In this cross-sectional study, a piloted survey was administered online to CR programs globally. CR was available in 111/203 (54.7%) countries globally; data were collected in 93 (83.8% country response rate). 1082 surveys (32.1% program response rate) were initiated. Globally, 85 (76.6%) countries with CR offered supervised programs, and 51 (45.9%; or 25.1% of all countries) offered some alternative model. Thirty-eight (34.2%) countries with CR offered home-based programs, with 106 (63.9%) programs offering some form of electronic CR (eCR). Twenty-five (22.5%) countries with CR offered community-based programs. Where available, programs served a mean of 21.4% ± 22.8% of their patients in home-based programs. The median dose for home-based CR was 3 sessions (Q25-Q75 = 1.0⁻4.0) and for community-based programs was 20 (Q25⁻Q75 = 9.6⁻36.0). Seventy-eight (47.0%) respondents did not perceive they had sufficient capacity to meet demand in their home-based program, for reasons including funding and insufficient staff. Where alternative CR models are offered, capacity is insufficient half the time. Home-based CR dose is insufficient to achieve health benefits. Allocation to program model should be evidence-based.
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Project description:Associative memory Hamiltonian structure prediction potentials are not overly rugged, thereby suggesting their landscapes are like those of actual proteins. In the present contribution we show how basin-hopping global optimization can identify low-lying minima for the corresponding mildly frustrated energy landscapes. For small systems the basin-hopping algorithm succeeds in locating both lower minima and conformations closer to the experimental structure than does molecular dynamics with simulated annealing. For large systems the efficiency of basin-hopping decreases for our initial implementation, where the steps consist of random perturbations to the Cartesian coordinates. We implemented umbrella sampling using basin-hopping to further confirm when the global minima are reached. We have also improved the energy surface by employing bioinformatic techniques for reducing the roughness or variance of the energy surface. Finally, the basin-hopping calculations have guided improvements in the excluded volume of the Hamiltonian, producing better structures. These results suggest a novel and transferable optimization scheme for future energy function development.
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Project description:Photosynthetic reaction centers (PRCs) employ multiple-step tunneling (hopping) to separate electrons and holes that ultimately drive the chemistry required for metabolism. We recently developed hopping maps that can be used to interpret the rates and energetics of electron/hole hopping in three-site (donor-intermediate-acceptor) tunneling reactions, including those in PRCs. Here we analyze several key ET reactions in PRCs, including forward ET in the L-branch, and hopping that could involve thermodynamically uphill intermediates in the M-branch, which is ET-inactive in vivo. We also explore charge recombination reactions, which could involve hopping. Our hopping maps support the view that electron flow in PRCs involves strong electronic coupling between cofactors and reorganization energies that are among the lowest in biology (? 0.4 eV).
| S-EPMC3530024 | biostudies-literature
Project description:The eye is a complex structure composed of several interconnected tissues acting together, across the whole globe, to resist deformation due to intraocular pressure (IOP). However, most work in the ocular biomechanics field only examines the response to IOP over smaller regions of the eye. We used high-field MRI to measure IOP induced ocular displacements and deformations over the whole globe. Seven sheep eyes were obtained from a local abattoir and imaged within 48 h using MRI at multiple levels of IOP. IOP was controlled with a gravity perfusion system and a cannula inserted into the anterior chamber. T2-weighted imaging was performed to the eyes serially at 0 mmHg, 10 mmHg, 20 mmHg and 40 mmHg of IOP using a 9.4 T MRI scanner. Manual morphometry was conducted using 3D visualization software to quantify IOP-induced effects at the globe scale (e.g. axial length and equatorial diameters) or optic nerve head scale (e.g. canal diameter, peripapillary sclera bowing). Measurement sensitivity analysis was conducted to determine measurement precision. High-field MRI revealed an outward bowing of the posterior sclera and anterior bulging of the cornea due to IOP elevation. Increments in IOP from 10 to 40 mmHg caused measurable increases in axial length in 6 of 7 eyes of 7.9 ± 5.7% (mean ± SD). Changes in equatorial diameter were minimal, 0.4 ± 1.2% between 10 and 40 mmHg, and in all cases less than the measurement sensitivity. The effects were nonlinear, with larger deformations at normal IOPs (10-20 mmHg) than at elevated IOPs (20-40 mmHg). IOP also caused measurable increases in the nasal-temporal scleral canal diameter of 13.4 ± 9.7% between 0 and 20 mmHg, but not in the superior-inferior diameter. This study demonstrates that high-field MRI can be used to visualize and measure simultaneously the effects of IOP over the whole globe, including the effects on axial length and equatorial diameter, posterior sclera displacement and bowing, and even changes in scleral canal diameter. The fact that the equatorial diameter did not change with IOP, in agreement with previous studies, indicates that a fixed boundary condition is a reasonable assumption for half globe inflation tests and computational models. Our results demonstrate the potential of high-field MRI to contribute to understanding ocular biomechanics, and specifically of the effects of IOP in large animal models.
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Project description:BackgroundCardiac rehabilitation (CR) is a clinically-effective but complex model of care. The purpose of this study was to characterize the nature of CR programs around the world, in relation to guideline recommendations, and compare this by World Health Organization (WHO) region.MethodsIn this cross-sectional study, a piloted survey was administered online to CR programs globally. Cardiac associations and local champions facilitated program identification. Quality (benchmark of ≥ 75% of programs in a given country meeting each of 20 indicators) was ranked. Results were compared by WHO region using generalized linear mixed models.Findings111/203 (54.7%) countries in the world offer CR; data were collected in 93 (83.8%; N = 1082 surveys, 32.1% program response rate). The most commonly-accepted indications were: myocardial infarction (n = 832, 97.4%), percutaneous coronary intervention (n = 820, 96.1%; 0.10), and coronary artery bypass surgery (n = 817, 95.8%). Most programs were led by physicians (n = 680; 69.1%). The most common CR providers (mean = 5.9 ± 2.8/program) were: nurses (n = 816, 88.1%; low in Africa, p < 0.001), dietitians (n = 739, 80.2%), and physiotherapists (n = 733, 79.3%). The most commonly-offered core components (mean = 8.7 ± 1.9 program) were: initial assessment (n = 939, 98.8%; most commonly for hypertension, tobacco, and physical inactivity), risk factor management (n = 928, 98.2%), patient education (n = 895, 96.9%), and exercise (n = 898, 94.3%; lower in Western Pacific, p < 0.01). All regions met ≥ 16/20 quality indicators, but quality was < 75% for tobacco cessation and return-to-work counseling (lower in Americas, p = < 0.05).InterpretationThis first-ever survey of CR around the globe suggests CR quality is high. However, there is significant regional variation, which could impact patient outcomes.
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Project description:We introduce grand and semigrand canonical global optimization approaches using basin-hopping with an acceptance criterion based on the local contribution of each potential energy minimum to the (semi)grand potential. The method is tested using local harmonic vibrational densities of states for atomic clusters as a function of temperature and chemical potential. The predicted global minima switch from dissociated states to clusters for larger values of the chemical potential and lower temperatures, in agreement with the predictions of a model fitted to heat capacity data for selected clusters. Semigrand canonical optimization allows us to identify particularly stable compositions in multicomponent nanoalloys as a function of increasing temperature, whereas the grand canonical potential can produce a useful survey of favorable structures as a byproduct of the global optimization search.
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