Conformational effects on the Circular Dichroism of Human Carbonic Anhydrase II: a multilevel computational study

Circular Dichroism (CD) spectroscopy is a powerful method for investigating conformational changes in proteins and therefore has numerous applications in structural and molecular biology. Here a computational investigation of the CD spectrum of the Human Carbonic Anhydrase II (HCAII), with main focus on the near-UV CD spectra of the wild-type enzyme and it seven tryptophan mutant forms, is presented and compared to experimental studies. Multilevel computational methods (Molecular Dynamics, Semiempirical Quantum Mechanics, Time-Dependent Density Functional Theory) were applied in order to gain insight into the mechanisms of interaction between the aromatic chromophores within the protein environment and understand how the conformational flexibility of the protein influences these mechanisms. The analysis suggests that combining CD semi empirical calculations, crystal structures and molecular dynamics (MD) could help in achieving a better agreement between the computed and experimental protein spectra and provide some unique insight into the dynamic nature of the mechanisms of chromophore interactions

Granulomatosis with polyangiitis mimicking infective endocarditis in an adolescent male

Granulomatosis with polyangiitis (GPA) is a rare but serious small vessel vasculitis with heterogeneous clinical presentation ranging from mainly localised disease with a chronic course, to a florid, acute small vessel vasculitic form characterised by severe pulmonary haemorrhage and/or rapidly progressive vasculitis or other severe systemic vasculitic manifestations. Cardiac involvement is, however, uncommon in the paediatric population. We report a case of a 16-year-old male who presented with peripheral gangrene and vegetation with unusual location on the supporting apparatus of the tricuspid valve, initially considered to have infective endocarditis but ultimately diagnosed with GPA. We provide an overview of the limited literature relating to cardiac involvement in GPA, and the diagnostic challenge relating to infective endocarditis in this context, especially focusing on the interpretation of the antineutrophil cytoplasmic antibody (ANCA) and the characteristic clinical features to identify in order to promptly recognise GPA, since timely diagnosis and treatment are essential for this potentially life-threatening condition

From random to rational: improving enzyme design through electric fields, second coordination sphere interactions, and conformational dynamics

Enzymes are versatile and efficient biological catalysts that drive numerous cellular processes, motivating the development of enzyme design approaches to tailor catalysts for diverse applications. In this perspective, we investigate the unique properties of natural, evolved, and designed enzymes, recognizing their strengths and shortcomings. We highlight the challenges and limitations of current enzyme design protocols, with a particular focus on their limited consideration of long-range electrostatic and dynamic effects. We then delve deeper into the impact of the protein environment on enzyme catalysis and explore the roles of preorganized electric fields, second coordination sphere interactions, and protein dynamics for enzyme function. Furthermore, we present several case studies illustrating successful enzyme-design efforts incorporating enzyme strategies mentioned above to achieve improved catalytic properties. Finally, we envision the future of enzyme design research, spotlighting the challenges yet to be overcome and the synergy of intrinsic electric fields, second coordination sphere interactions, and conformational dynamics to push the state-of-the-art boundaries

B=3 Tetrahedrally Symmetric Solitons in the Chiral Quark Soliton Model

In this paper, B=3 soliton solutions with tetrahedral symmetry are obtained numerically in the chiral quark soliton model using the rational map ansatz. The solution exhibits a triply degenerate bound spectrum of the quark orbits in the background of tetrahedrally symmetric pion field configuration. The corresponding baryon density is tetrahedral in shape. Our numerical technique is independent on the baryon number and its application to $B \geq 4$ is straightforward.Comment: 4 pages, 3 figure

Alkaloids from Mongolian species of Peganum multisectum (Maxim) Bobrov

Alkaloids of the aerial parts of P. multisectum (Maxim) Bobrov (Zygophyllaceae) growing in Mongolia have been studied by capillary Gas Chromatography-Mass Spectrometry (GC-MS) and Column Chromatography (CC). Four compounds comprising of 2-methylquinoline (1), 9-amino-2, 3,5,6,7,8-hexahydro-1H-cyclopenta [b] quinoline (2), vasicinone (3) and harmine (4) have been determined by GC-MS, while harmine (4), peganine (5), deoxypeganine (6), deoxyvasicinone (7) and harmane (8) were isolated as pure compounds by the CC. The structures of the five alkaloids 4, 5, 6, 7 and 8 were elucidated by the MS and 1H and 13C NMR analysis. The alkaloids 1, 2 and 8 were identified for the first time from this species.Mongolian Journal of Chemistry 16 (42), 2015, 48-5

Self-Consistent Pushing and Cranking Corrections to the Meson Fields of the Chiral Quark-Loop Soliton

We study translational and spin-isospin symmetry restoration for the two-flavor chiral quark-loop soliton. Instead of a static soliton at rest we consider a boosted and rotating hedgehog soliton. Corrected classical meson fields are obtained by minimizing a corrected energy functional which has been derived by semi-classical methods ('variation after projection'). We evaluate corrected meson fields in the region 300 MeV \le M \le 600 MeV of constituent quark masses M and compare them with the uncorrected fields. We study the effect of the corrections on various expectation values of nuclear observables such as the root-mean square radius, the axial-vector coupling constant, magnetic moments and the delta-nucleon mass splitting.Comment: 19 pages, LaTeX, 7 postscript figures included using 'psfig.sty', to appear in Int.J.Mod.Phys.

Solving Nonlinear Parabolic Equations by a Strongly Implicit Finite-Difference Scheme

We discuss the numerical solution of nonlinear parabolic partial differential equations, exhibiting finite speed of propagation, via a strongly implicit finite-difference scheme with formal truncation error $\mathcal{O}\left[(\Delta x)^2 + (\Delta t)^2 \right]$. Our application of interest is the spreading of viscous gravity currents in the study of which these type of differential equations arise. Viscous gravity currents are low Reynolds number (viscous forces dominate inertial forces) flow phenomena in which a dense, viscous fluid displaces a lighter (usually immiscible) fluid. The fluids may be confined by the sidewalls of a channel or propagate in an unconfined two-dimensional (or axisymmetric three-dimensional) geometry. Under the lubrication approximation, the mathematical description of the spreading of these fluids reduces to solving the so-called thin-film equation for the current's shape $h(x,t)$. To solve such nonlinear parabolic equations we propose a finite-difference scheme based on the Crank--Nicolson idea. We implement the scheme for problems involving a single spatial coordinate (i.e., two-dimensional, axisymmetric or spherically-symmetric three-dimensional currents) on an equispaced but staggered grid. We benchmark the scheme against analytical solutions and highlight its strong numerical stability by specifically considering the spreading of non-Newtonian power-law fluids in a variable-width confined channel-like geometry (a "Hele-Shaw cell") subject to a given mass conservation/balance constraint. We show that this constraint can be implemented by re-expressing it as nonlinear flux boundary conditions on the domain's endpoints. Then, we show numerically that the scheme achieves its full second-order accuracy in space and time. We also highlight through numerical simulations how the proposed scheme accurately respects the mass conservation/balance constraint.Comment: 36 pages, 9 figures, Springer book class; v2 includes improvements and corrections; to appear as a contribution in "Applied Wave Mathematics II

Design of eco-friendly fabric softeners: structure, rheology and interaction with cellulose nanocrystals

Concentrated fabric softeners are water-based formulations containing around 10 - 15 wt. % of double tailed esterquat surfactants primarily synthesized from palm oil. In recent patents, it was shown that a significant part of the surfactant contained in today formulations can be reduced by circa 50 % and replaced by natural guar polymers without detrimental effects on the deposition and softening performances. We presently study the structure and rheology of these softener formulations and identify the mechanisms at the origin of these effects. The polymer additives used are guar gum polysaccharides, one cationic and one modified through addition of hydroxypropyl groups. Formulations with and without guar polymers are investigated using optical and cryo-transmission electron microscopy, small-angle light and Xray scattering and finally rheology. Similar techniques are applied to study the phase behavior of softener and cellulose nanocrystals considered here as a model for cotton. The esterquat surfactants are shown to assemble into micron-sized vesicles in the dilute and concentrated regimes. In the former, guar addition in small amounts does not impair the vesicular structure and stability. In the concentrated regime, cationic guars induce a local crowding associated to depletion interactions and leads to the formation of a local lamellar order. In rheology, adjusting the polymer concentration at one tenth that of the surfactant is sufficient to offset the decrease of the elastic property associated with the surfactant reduction. In conclusion, we have shown that through an appropriate choice of natural additives it is possible to lower the concentration of surfactants in fabric conditioners by about half, a result that could represent a significant breakthrough in current home care formulations.Comment: 10 pages 8 figure