Water-protein interactions in the molten-globule state of carbonic anhydrase b: an NMR spin-diffusion study

We have used the homonuclear Overhauser effect (NOE) to characterize a model protein: carbonic anhydrase B. We have obtained NOE difference spectra for this protein, centering the on-resonance signals either at the methyl-proton or at the water-proton signals. The spin-diffusion spectra obtained as a function of protein concentration and temperature provide direct evidence of much greater protein-water interaction in the molten-globule state than in the native and denatured states. Furthermore, although the protein loses its gross tertiary structure in both the molten-globule and denatured states, it remains almost as compact in its molten-globule state as it is in the native state. The spin-diffusion spectra, obtained as a function of a variable delay time after the saturation pulse, allowed us to measure the relaxation times of several types of proton in the solution. These spectra contain enough information to distinguish between those water molecules solvating the protein and the free ones present as bulk water.     

The relative orientation of the fibronectin 6F11F2 module pair: A 15N NMR relaxation study

The structure of a pair of modules (⁶F1¹F2), that forms part of the collagen-binding region of fibronectin, is refined using heteronuclear relaxation data. A structure of the pair was previously derived from ¹H-¹H NOE and ³ J _HHN data [Bocquier et al. (1999) Structure, 7, 1451–1460] and a weak module–module interface, comprising Leu19 and Leu28, in ⁶F1, and Tyr68 in ²F1, was identified. In this study, the definition of the average relative orientation of the two modules is improved using the dependence of ¹⁵N relaxation on rotational diffusion anisotropy. This structure refinement is based on the selection of a subset of structures from sets calculated with NOE and ³ J _HHN data alone, using the quality of the fits to the relaxation data as the selection criterion. This simple approach is compared to a refinement strategy where ¹⁵N relaxation data are included in the force field as additional restraints [Tjandra et al. (1997) Nat. Struct. Biol., 4, 443–449].     

The Role of Complex Formation and Deleterious Mutations for the Stability of RNA-Like Replicator Systems

In the RNA world hypothesis, RNA(-like) self-replicators are suggested as the central player of prebiotic evolution. However, there is a serious problem in the evolution of complexity in such replicators, i.e., the problem of parasites. Parasites, which are replicated by catalytic replicators (catalysts), but do not replicate the others, can destroy a whole replicator system by exploitation. Recently, a theoretical study underlined complex formation between replicators--an often neglected but realistic process--as a stabilizing factor in a replicator system by demonstrating that complex formation can shift the viable range of diffusion intensity to higher values. In the current study, we extend the previous study of complex formation. Firstly, by investigating a well-mixed replicator system, we establish that complex formation gives parasites an implicit advantage over catalysts, which makes the system significantly more vulnerable to parasites. Secondly, by investigating a spatially extended replicator system, we show that the formation of traveling wave patterns plays a crucial role in the stability of the system against parasites, and that because of this the effect of complex formation is not straightforward; i.e., whether complex formation stabilizes or destabilizes the spatial system is a complex function of other parameters. We give a detailed analysis of the spatial system by considering the pattern dynamics of waves. Furthermore, we investigate the effect of deleterious mutations. Surprisingly, high mutation rates can weaken the exploitation of the catalyst by the parasite.     

Internet of Intelligences Can Be a Platform for Risk Analysis and Management

ABSTRACT

In this article, we clarify the concept of the Internet of Intelligences (IOI) to be a platform for risk analysis. An IOI is a triple consisting of a set of agents, a network, and a model. A process of processing homological information is a layer. An IOI with more than one layer is a Multiple Internet of Intelligences (M-IOI). If agents in an M-IOI not only provide information in response to a question asked by a customer but also review information from other agents and summarize it, we refer to this as a summarizing M-IOI. In this article, a simplest M-IOI is used to answer a question issued by an insurance company considering selling policies in Wenzhou, China, where the level of typhoon risk is high. We employ the normal diffusion model to process the summaries and give an adequate answer.     

Successful amphiphiles as the key to crystallization of membrane proteins: Bridging theory and practice

Background

Membrane proteins constitute a major group of proteins and are of great significance as pharmaceutical targets, but underrepresented in the Protein Data Bank. Particular reasons are their low expression yields and the constant need for cautious and diligent handling in a sufficiently stable hydrophobic environment substituting for the native membrane. When it comes to protein crystallization, such an environment is often established by detergents.

Benthivorous fish bioturbation reduces methane emissions,but increases total greenhouse gas emissions

相似文献   

The degree of macromolecular crowding in the cytoplasm and nucleoplasm of mammalian cells is conserved

Macromolecular crowding provides the cytoplasm and the nucleoplasm with strongly viscoelastic properties and renders the diffusion of soluble proteins in both fluids anomalous. Here, we have determined the nanoscale viscoelasticity of the cytoplasm and the nucleoplasm in different mammalian cell lines. In contrast to the cell-specific response on the macroscale the nanoscale viscoelasticity (i.e. the behavior on length scales about 100-fold smaller than the cell size) only showed minor variations between different cell types. Similarly, the associated anomalous diffusion properties varied only slightly. Our results indicate a conserved state of macromolecular crowding in both compartments for a variety of mammalian cells with the cytoplasm being somewhat more crowded than the nucleus.     

Screening antimicrobial activity of various extracts of Artemisia dracunculus L

The antimicrobial activities of chloroform, acetone and two different concentrations of methanol extracts of Artemisia dracunculus L. were studied. These extracts were tested against nine bacteria and four yeasts strains by the disc diffusion method. The results indicated that the methanol extract of A. dracunculus is more effective against tested microorganisms than chloroform or acetone extracts. The chloroform and acetone extracts were inhibitory only towards Pseudomonas aeruginosa (ATCC 27853). While the methanol extract that was diluted with 10 ml distilled water showed inhibition zones against Shigella (RSHI), Listeria monocytogenes ATCC 7644, P. aeruginosa (ATCC 27853), the methanol extract that was diluted with 5 ml distilled water showed inhibition zones against two different strains of Escherichia coli (RSHI, ATCC 25922), Shigella (RSHI), L. monocytogenes (ATCC 7644), and P. aeruginosa ATCC 27853. The cells of microorganisms treated with plant extracts and normal microorganism cells were observed by scanning electron microscope. It was apparent that cells are damaged after treatment with A. dracunculus.     

A quantitative framework for the design of acellular hemoglobins as blood substitutes: implications of dynamic flow conditions

The delivery of oxygen to tissue by cell-free carriers eliminates intraluminal barriers associated with red blood cells. This is important in arterioles, since arteriolar tone controls capillary perfusion. We describe a mathematical model for O(2) transport by hemoglobin solutions and red blood cells flowing through arteriolar-sized tubes to optimize values of p50, Hill number, hemoglobin molecular diffusivity and concentration. Oxygen release is evaluated by including an extra-luminal resistance term to reflect tissue oxygen consumption. For low consumption (i.e., high resistance to O(2) release) a hemoglobin solution with p50=15 mmHg, n=1, D(HBO2)=3 x 10(-7) cm(2)/s delivers O(2) at a rate similar to that of red blood cells. For high consumption, the p50 must be decreased to 5 mmHg. The model predicts that regardless of size, hemoglobin solutions with higher p50 will present excess O(2) to arteriolar walls. Oversupply of O(2) to arteriolar walls may cause constriction and paradoxically reduced capillary perfusion.