Crowding-induced protein destabilization in the absence of soft attractions

It is generally assumed that volume exclusion by macromolecular crowders universally stabilizes the native states of proteins and destabilization suggests soft attractions between crowders and protein. Here we show that proteins can be destabilized even by crowders that are purely repulsive. With a coarse-grained sequence-based model, we study the folding thermodynamics of two sequences with different native folds, a helical hairpin and a β-barrel, in a range of crowder volume fractions, ${\phi }_{\text{c}}$. We find that the native state, N, remains structurally unchanged under crowded conditions, while the size of the unfolded state, U, decreases monotonically with ${\phi }_{\text{c}}$. Hence, for all ${\phi }_{\text{c}}>0$, U is entropically disfavored relative to N. This entropy-centric view holds for the helical hairpin protein, which is stabilized under all crowded conditions as quantified by changes in either the folding midpoint temperature, $T_{\text{m}}$, or the free energy of folding. We find, however, that the β-barrel protein is destabilized under low-T, low-${\phi }_{\text{c}}$ conditions. This destabilization can be understood from two characteristics of its folding: 1) a relatively compact U at $T<T_{\text{m}}$, such that U is only weakly disfavored entropically by the crowders; and 2) a transient, compact, and relatively low-energy nonnative state that has a maximum population of only a few percent at ${\phi }_{\text{c}}=0$, but increasing monotonically with ${\phi }_{\text{c}}$. Overall, protein destabilization driven by hard-core effects appears possible when a compaction of U leads to even a modest population of compact nonnative states that are energetically competitive with N.     

The mechanisms and process of acephate degradation by hydroxyl radical and hydrated electron

The degradation process of acephate in aqueous solution with OH and ${\text{e}}_{\text{aq}}^{?}$ produced by ⁶⁰Co-γ irradiation and electron pulse radiolysis was studied in the present paper. In the aqueous solution, acephate reacted with ${\text{e}}_{\text{aq}}^{?}$ and transformed to transient species which can absorb weakly in the wavelength range of 300–400?nm and decay very fast. According to the decay of hydrated electron, the reaction rate constant of ${\text{e}}_{\text{aq}}^{?}$ and acephate is (3.51?±?0.076)?×?10⁹?dm³·mol^?1·s^?1. The transient species produced in the reaction of OH and acephate do not distinctly absorb the light in the wavelength range of 300–700?nm, so the decay and kinetics of the transient species cannot determinedirectly. The competing reaction of KSCN oracephate with OH were studied to obtain the reaction rate constant of OH and acephate, which is (9.1?±?0.11)?×?10⁸?dm³·mol^?1·s^?1. Although acetylamide and inorganic ions were determined in the products of the reaction of acephate with OH or ${\text{e}}_{\text{aq}}^{?}$, the concentration of inorganic ions in the products of the reaction of acephate with OH is higher than that in the product of the reaction of acephate with ${\text{e}}_{\text{aq}}^{?}$. Moreover, there were sulfide in the products of the reaction of acephatewith ${\text{e}}_{\text{aq}}^{?}$. The degradation pathways of acephate by OH and ${\text{e}}_{\text{aq}}^{?}$ were also proposed based on the products from GC-MS.     

The effect of tube focal spot size and acquisition mode on task-based image quality performance of a GE revolution HD dual energy CT scanner

PurposeTo assess the task-based performance of images obtained under different focal spot size and acquisition mode on a dual-energy CT scanner.MethodsAxial CT image series of the Catphan phantom were obtained using a tube focus at different sizes. Acquisitions were performed in standard single-energy, high resolution (HR) and dual-energy modes. Images were reconstructed using conventional and high definition (HD) kernels. Task-based transfer function at the 50% level (TTF_50%) for teflon, delrin, low density polyethylene (LDPE) and acrylic, as well as image noise and noise texture, were assessed across all focal spots and acquisition modes using Noise Power Spectrum (NPS) analysis. A non-prewhitening mathematical observer model was used to calculate detectability index ($d_{\mathit{NPW}}^{\prime }$).ResultsTTF_50% degraded with increasing focal spot size. TTF_50% ranged from 0.67 mm⁻¹ for teflon to 0.25 mm⁻¹ for acrylic. For standard kernel, image noise and NPS-determined average spatial frequency were 8.3 HU and 0.29 mm⁻¹, respectively in single-energy, 12.0 HU and 0.37 mm⁻¹ in HR, and 7.9 HU and 0.26 mm⁻¹ in dual-energy mode. For standard kernel, $d_{\mathit{NPW}}^{\prime }$ was 61 in single-energy and HR mode and reduced to 56 in dual-energy mode.ConclusionsThe task-based image quality assessment metrics have shown that spatial resolution is higher for higher image contrast materials and detectability is higher in the standard single-energy mode compared to HR and dual-energy mode. The results of the current study provide CT operators the required knowledge to characterize their CT system towards the optimization of its clinical performance.     

Artifact quantification of venous stents in the MRI environment: Differences between braided and laser-cut designs

PurposeTo quantify B₀- and B₁-induced imaging artifacts of braided venous stents and to compare the artifacts to a set of laser-cut stents used in venous interventions.MethodsThree prototypes of braided venous stents with different geometries were tested in vitro. B₀ field distortion maps were measured via the frequency shift $\mathrm{\Delta }f$ using multi-echo imaging. B₁ distortions were quantified using the double angle method. The relative amplitudes $B_1^{\mathit{rel}}$ were calculated to compare the intraluminal alteration of B₁. Measurements were repeated with the stents in three different orientations: parallel, diagonal and orthogonal to B₀.ResultsAt 1.5 T, the braided stents induced a maximum frequency shift of $\left|\mathrm{\Delta }f\left(\mathit{x}\right)\right|<100\mathrm{H}\mathrm{z}$. Signal voids were limited to a distance of 2 mm to the stent walls at an echo time of 3 ms. No substantial difference in the B₀ field distortions was seen between laser-cut and braided venous stents. $B_1^{\mathit{rel}}$ maps showed strongly varying distortion patterns in the braided stents with the mean intraluminal $B_1^{\mathit{rel}}$ ranging from $\left(63\pm 18\right)\%$ in prototype 1 to $\left(98\pm 38\right)\%$ in prototype 2. Compared to laser-cut stents the braided stents showed a 5 to 9 times higher coefficient of variation of the intraluminal $B_1^{\mathit{rel}}$.ConclusionBraided venous stent prototypes allow for MR imaging of the intraluminal area without substantial signal voids due to B₀-induced artifacts. Whereas B₁ is attenuated homogeneously in laser-cut stents, the B₁ distortion in braided stents is more inhomogeneous and shows areas with enhanced amplitude. This could potentially be used in braided stent designs for intraluminal signal amplification.     

Phospholipid headgroups govern area per lipid and emergent elastic properties of bilayers

Phospholipid bilayers are liquid-crystalline materials whose intermolecular interactions at mesoscopic length scales have key roles in the emergence of membrane physical properties. Here we investigated the combined effects of phospholipid polar headgroups and acyl chains on biophysical functions of membranes with solid-state ²H NMR spectroscopy. We compared the structural and dynamic properties of phosphatidylethanolamine and phosphatidylcholine with perdeuterated acyl chains in the solid-ordered (s_o) and liquid-disordered (l_d) phases. Our analysis of spectral lineshapes of 1,2-diperdeuteriopalmitoyl-sn-glycero-3-phosphoethanolamine (DPPE-d₆₂) and 1,2-diperdeuteriopalmitoyl-sn-glycero-3-phosphocholine (DPPC-d₆₂) in the s_o (gel) phase indicated an all-trans rotating chain structure for both lipids. Greater segmental order parameters ($S_{\text{CD}}$) were observed in the l_d (liquid-crystalline) phase for DPPE-d₆₂ than for DPPC-d₆₂ membranes, while their mixtures had intermediate values irrespective of the deuterated lipid type. Our results suggest the $S_{\text{CD}}$ profiles of the acyl chains are governed by methylation of the headgroups and are averaged over the entire system. Variations in the acyl chain molecular dynamics were further investigated by spin-lattice ($R_{1\text{Z}}$) and quadrupolar-order relaxation ($R_{1\text{Q}}$) measurements. The two acyl-perdeuterated lipids showed distinct differences in relaxation behavior as a function of the order parameter. The R_1Z rates had a square-law dependence on $S_{\text{CD}}$, implying collective mesoscopic dynamics, with a higher bending rigidity for DPPE-d₆₂ than for DPPC-d₆₂ lipids. Remodeling of lipid average and dynamic properties by methylation of the headgroups thus provides a mechanism to control the actions of peptides and proteins in biomembranes.