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《Biophysical journal》2022,121(13):2503-2513
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, . We find that the native state, N, remains structurally unchanged under crowded conditions, while the size of the unfolded state, U, decreases monotonically with . Hence, for all , 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, , or the free energy of folding. We find, however, that the β-barrel protein is destabilized under low-T, low- conditions. This destabilization can be understood from two characteristics of its folding: 1) a relatively compact U at , 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 , but increasing monotonically with . 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. 相似文献
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《Biophysical journal》2022,121(21):4205-4220
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 (so) and liquid-disordered (ld) 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 so (gel) phase indicated an all-trans rotating chain structure for both lipids. Greater segmental order parameters () were observed in the ld (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 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 () and quadrupolar-order relaxation () measurements. The two acyl-perdeuterated lipids showed distinct differences in relaxation behavior as a function of the order parameter. The R1Z rates had a square-law dependence on , 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. 相似文献
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《Fungal biology》2020,124(12):1058-1067
Fungal growth often appears in a surrounding where water and nutrients are scarce. The impact of this environment during sporogenesis on subsequent growth is often neglected.This study investigates the effect of water availability during sporogenesis on subsequent early growth. Therefore, a carbon-depleted substrate was constructed. Humidity is then the only parameter of interest. The water conditions during sporogenesis, and during subsequent growth, were varied. This is a stressing environment: no carbon source is present, and water provided solely via the vapour.The lag time, , and initial growth rate, , of the germ tubes were monitored.The effect of history on germination and initial growth depends on the of the environment. Only at low do spores produced at low have a smaller and higher compared to those grown at high . This result was remarkably pronounced when the substrate was also made hydrophobic: growth only occurred when spores were developed at low and placed in high .Spores grown on lowered attract more water. It is hypothesized that this attraction affects subsequent growth behaviour, and is the reason why growth on hydrophobic glass only prevails in the condition of high and lowered history.We demonstrate the influence of cultivation conditions on germination, which becomes more pronounced in a more desiccated environment. 相似文献
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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 using multi-echo imaging. B1 distortions were quantified using the double angle method. The relative amplitudes 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 . 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. maps showed strongly varying distortion patterns in the braided stents with the mean intraluminal ranging from in prototype 1 to in prototype 2. Compared to laser-cut stents the braided stents showed a 5 to 9 times higher coefficient of variation of the intraluminal .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. 相似文献
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MR fingerprinting (MRF) is an innovative approach to quantitative MRI. A typical disadvantage of dictionary-based MRF is the explosive growth of the dictionary as a function of the number of reconstructed parameters, an instance of the curse of dimensionality, which determines an explosion of resource requirements. In this work, we describe a deep learning approach for MRF parameter map reconstruction using a fully connected architecture. Employing simulations, we have investigated how the performance of the Neural Networks (NN) approach scales with the number of parameters to be retrieved, compared to the standard dictionary approach. We have also studied optimal training procedures by comparing different strategies for noise addition and parameter space sampling, to achieve better accuracy and robustness to noise. Four MRF sequences were considered: IR-FISP, bSSFP, IR-FISP-, and IR-bSSFP-. A comparison between NN and the dictionary approaches in reconstructing parameter maps as a function of the number of parameters to be retrieved was performed using a numerical brain phantom. Results demonstrated that training with random sampling and different levels of noise variance yielded the best performance. NN performance was at least as good as the dictionary-based approach in reconstructing parameter maps using Gaussian noise as a source of artifacts: the difference in performance increased with the number of estimated parameters because the dictionary method suffers from the coarse resolution of the parameter space sampling. The NN proved to be more efficient in memory usage and computational burden, and has great potential for solving large-scale MRF problems. 相似文献