The role of phosphorylation and dephosphorylation of shell matrix proteins in shell formation : an in vivo and in vitro study

Protein phosphorylation is a fundamental mechanism regulating many aspects of cellular processes. Shell matrix proteins (SMPs) control crystal nucleation, polymorphism, morphology, and organization of calcium carbonate crystallites during shell formation. SMPs phosphorylation is suggested to be important in shell formation but the mechanism is largely unknown. Here, to investigate the mechanism of phosphorylation of SMPs in biomineralization, we performed in vivo and in vitro experiment. By injection of antibody against the anti-phosphoserine/threonine /tyrosine into the extrapallial fluid of the pearl oyster Pinctada fucata, phosphorylation of matrix proteins were significantly reduced after 6 days. Newly formed prismatic layers and nacre tablet were found to grow abnormally with reduced crystallinity and possibly changed crystal orientation shown by Raman spectroscopy. In addition, regeneration of shells is also inhibited in vivo. Then, protein phosphatase was used to dephosphorylate SMPs extracted from the shells. After dephosphorylation, the ability of SMPs to inhibiting calcium carbonate formation have been reduced. Surprisingly, the ability of SMPs to modulate crystal morphology have been largely compromised although phosphorylation extent remained to be at least half of the control. Furthermore, dephosphorylation of SMPs changed the distribution of protein occlusions and decreased the amount of protein occlusions inside crystals shown by confocal imaging, indicating interaction between phosphorylated SMPs and crystals. Taken together, this study provides insight into the mechanism of phosphorylation of SMPs during shell formation

DNA Confinement drives uncoating of the HIV Virus

We present a model for the uncoating of the HIV virus driven by forces exerted on the protein shell of HIV generated by DNA confinement

Synthesis of core/shell quantum dots for diagnostic

In this paper, synthesis of colloidal core and core/shell quantum dots (QDs) was described. First, CdTe QDs capped with glutathione, thioglycolic or mercaptopropionic acid were prepared in aqueous phase, and used for synthesis of colloidal core/shell CdTe/ZnS QDs. Core/shell QDs were used for conjugation with bovine serum albumin (BSA) or immunoglobulin G (IgG) via different crosslinkers (CDI, EDC/NHS, EDC). QDs as well as QDs-protein/antibody conjugates were characterized via UV-Vis spectroscopy and capillary electrophoresis (CE). Based on UV-Vis spectroscopy results it was found that, with increasing concentration of BSA, fluorescence intensity of QDs decreased. CE confirmed formation of QDs-BSA and QDs-IgG conjugates

Terahertz response of dipolar impurities in polar liquids: On anomalous dielectric absorption of protein solutions

A theory of radiation absorption by dielectric mixtures is presented. The coarse-grained formulation is based on the wavevector-dependent correlation functions of molecular dipoles of the host polar liquid and a density-density structure factor of the positions of the solutes. A nonlinear dependence of the absorption coefficient on the solute concentration is predicted and originates from the mutual polarization of the liquid surrounding the solutes by the collective field of the solute dipoles aligned along the radiation field. The theory is applied to terahertz absorption of hydrated saccharides and proteins. While the theory gives an excellent account of the observations for saccharides without additional assumptions and fitting parameters, experimental absorption coefficient of protein solutions significantly exceeds theoretical calculations within standard dielectric models and shows a peak against the protein concentration. A substantial polarization of protein's hydration shell is required to explain the differences between standard theories and experiment. When the correlation function of the total dipole moment of the protein with its hydration shell from numerical simulations is used in the present analytical model an absorption peak similar to that seen is experiment is obtained. The result is sensitive to the specifics of protein-protein interactions in solution. Numerical testing of the theory requires the combination of terahertz dielectric and small-angle scattering measurements.Comment: 11 p

Virus shapes and buckling transitions in spherical shells

We show that the icosahedral packings of protein capsomeres proposed by Caspar and Klug for spherical viruses become unstable to faceting for sufficiently large virus size, in analogy with the buckling instability of disclinations in two-dimensional crystals. Our model, based on the nonlinear physics of thin elastic shells, produces excellent one parameter fits in real space to the full three-dimensional shape of large spherical viruses. The faceted shape depends only on the dimensionless Foppl-von Karman number \gamma=YR^2/\kappa, where Y is the two-dimensional Young's modulus of the protein shell, \kappa is its bending rigidity and R is the mean virus radius. The shape can be parameterized more quantitatively in terms of a spherical harmonic expansion. We also investigate elastic shell theory for extremely large \gamma, 10^3 < \gamma < 10^8, and find results applicable to icosahedral shapes of large vesicles studied with freeze fracture and electron microscopy.Comment: 11 pages, 12 figure

Proteins in solution: Fractal surfaces in solutions

The concept of the surface of a protein in solution, as well of the interface between protein and 'bulk solution', is introduced. The experimental technique of small angle X-ray and neutron scattering is introduced and described briefly. Molecular dynamics simulation, as an appropriate computational tool for studying the hydration shell of proteins, is also discussed. The concept of protein surfaces with fractal dimensions is elaborated. We finish by exposing an experimental (using small angle X-ray scattering) and a computer simulation case study, which are meant as demonstrations of the possibilities we have at hand for investigating the delicate interfaces that connect (and divide) protein molecules and the neighboring electrolyte solution.Comment: 8 pages, 5 figure

Nipah shell disorder, modes of infection, and virulence

The Nipah Virus (NiV) was first isolated during a 1998–9 outbreak in Malaysia. The outbreak initially infected farm pigs and then moved to humans from pigs with a case-fatality rate (CFR) of about 40%. After 2001, regular outbreaks occurred with higher CFRs (~71%, 2001–5, ~93%, 2008–12). The spread arose from drinking virus-laden palm date sap and human-to-human transmission. Intrinsic disorder analysis revealed strong correlation between the percentage of disorder in the N protein and CFR (Regression: r2 = 0.93, p < 0.01, ANOVA: p < 0.01). Distinct disorder and, therefore, genetic differences can be found in all three group of strains. The fact that the transmission modes of the Malaysia strain are different from those of the Bangladesh strains suggests that the correlations may also be linked to the modes of viral transmission. Analysis of the NiV and related viruses suggests links between modes of transmission and disorder of not just the N protein but, also, of M shell protein. The links among shell disorder, transmission modes, and virulence suggest mechanisms by which viruses are attenuated as they passed through different cell hosts from different animal species. These have implications for development of vaccines and epidemiological molecular analytical tools to contain outbreaks

Scrutinizing the protein hydration shell from molecular dynamics simulations against consensus small-angle scattering data

Biological macromolecules in solution are surrounded by a hydration shell, whose structure differs from the structure of bulk solvent. While the importance of the hydration shell for numerous biological functions is widely acknowledged, it remains unknown how the hydration shell is regulated by macromolecular shape and surface composition, mainly because a quantitative probe of the hydration shell structure has been missing. We show that smallangle scattering in solution using X-rays (SAXS) or neutrons (SANS) provide a proteinspecific probe of the protein hydration shell that enables quantitative comparison with molecular simulations. Using explicit-solvent SAXS/SANS predictions, we derived the effect of the hydration shell on the radii of gyration Rg of five proteins using 18 combinations of protein force field and water model. By comparing computed Rg values from SAXS relative to SANS in D2O with consensus SAXS/SANS data from a recent worldwide community effort, we found that several but not all force fields yield a hydration shell contrast in remarkable agreement with experiments. The hydration shell contrast captured by Rg values depends strongly on protein charge and geometric shape, thus providing a protein-specific footprint of protein–water interactions and a novel observable for scrutinizing atomistic hydration shell models against experimental data