Inherent flexibility and protein function: The open/closed conformational transition in the N-terminal domain of calmodulin

The key to understand a protein's function often lies in its conformational dynamics. We develop a coarse-grained variational model to investigate the interplay between structural transitions, conformational flexibility, and function of the N-terminal calmodulin domain (nCaM). In this model, two energy basins corresponding to the "closed" apo conformation and "open" holo conformation of nCaM are coupled by a uniform interpolation parameter. The resulting detailed transition route from our model is largely consistent with the recently proposed EFbeta-scaffold mechanism in EF-hand family proteins. We find that the N-terminal parts of the calcium binding loops shows higher flexibility than the C-terminal parts which form this EFbeta-scaffold structure. The structural transition of binding loops I and II are compared in detail. Our model predicts that binding loop II, with higher flexibility and earlier structural change than binding loop I, dominates the open/closed conformational transition in nCaM.     

Tracking and controlling everything that affects quality is the key to a quality management system

Every laboratory has a need to track and control the variables that drive the quality of the results. However, each laboratory is unique and what one organization deems to be a critical process to track and control will likely differ from other organizations. Furthermore, there is more than just the end product or result that needs to be tracked and controlled. All of the intermediate products and resources play a significant role in producing the final product and each of these needs to be included in the LIMS. At a high level, this article will present ideas and opinions on the following topics in relation to implementing a LIMS process tracking and control system in a laboratory: The difference between tracking and controlling processes; What to track and control in the lab; The "product" of the laboratory; Preventing mistakes in a laboratory; Comprehensive software platform options; The value of seeing a system as opposed to imagining it; The use of barcodes in the laboratory; and an assessment on using the Risk Based Approach in deciding what to include in the tracking system.     

Fluorimetric determination of fluoride in a flow assembly integrated on-line to an open/closed FIA system to remove interference by solid phase extraction

A simple flow injection fluorimetric method for fluoride determination is proposed. The method is based on the enhanced fluorescence of quercitin-Zr(IV) complex when fluoride ion is present in the sample. An open/closed FIA manifold with a mini-column of Dowex 50W X8 resin was used to remove the most important interference (aluminum). The two FIA assemblies were integrated on-line to automate the pretreatment of the water sample and fluoride determination. The calibration graph was linear over the range 0.1-3.0 mug ml(-1) of fluoride with a correlation coefficient of 0.999 and LOD 0.06 mug ml(-1). The relative standard deviation was 2.5% and the sample throughput was 52 h(-1) without pretreatment and 10 h(-1) with pretreatment of the sample. The method was applied to the determination of fluoride in water samples.     

The synthesis of XTT: A new tetrazolium reagent that is bioreducible to a water-soluble formazan

A new tetrazolium salt, XTT, has been synthesized. XTT is reduced by a considerable variety of cell lines to a water-soluble formazan. XTT appears to merit further investigation as a reagent for broader application to cell culture assay systems.     

Imaging the cardiovascular system: seeing is believing.

From the basic light microscope through high-end imaging systems such as multiphoton confocal microscopy and electron microscopes, microscopy has been and will continue to be an essential tool in developing an understanding of cardiovascular development, function, and disease. In this review we briefly touch on a number of studies that illustrate the importance of these forms of microscopy in studying cardiovascular biology. We also briefly review a number of imaging modalities such as computed tomography (CT), magnetic resonance imaging (MRI), ultrasound, and positron emission tomography (PET) that, although they do not fall under the realm of microscopy, are imaging modalities that greatly complement microscopy. Finally we examine the role of proper imaging system calibration and the potential importance of calibration in understanding biological tissues, such as the cardiovascular system, that continually undergo deformation in response to strain.     

Lattice dynamics of polyacetylene as a one-dimensional system: Part I. The case of the trans perfect polymer

In this paper the lattice dynamics of trans-polyacetylene as a perfect one-dimensional crystal is treated. Dispersion curves, density of states and vibrational displacements are calculated. The results of the calculations are used to propose a vibrational assignment for (CH)_x, (CD)_x and (¹³CH)_x. Calculations have been made with a quadratic simplified valence force field (SVFF). The relationship between SVFF and the electron-phonon coupling model for polyacetylene, generally adopted in the literature, is discussed. Comparison with the calculations of other authors is made.     

The open structure of a multi-drug-resistant HIV-1 protease is stabilized by crystal packing contacts

The introduction of HIV-1 protease (HIV-PR) inhibitors has led to a dramatic increase in patient survival; however, these gains are threatened by the emergence of multi-drug-resistant strains. Design of inhibitors that overcome resistance would be greatly facilitated by deeper insight into the mechanistic events associated with binding of substrates and inhibitors, as well as an understanding of the effects of resistance mutations on the structure and dynamic behavior of HIV-PR. We previously reported a series of simulations that provide a model for HIV-PR dynamics, with spontaneous conversions between the bound and unbound crystal forms upon addition or removal of an inhibitor. Importantly, the unbound protease transiently sampled a third fully open state that permits entry to the active site, unlike both crystallographic forms. Recently, a crystal structure of unbound HIV-PR was reported for the MDR 769 isolate (PDB: 1TW7); unlike all previous experimental structures, the binding pocket is open. It is suggested that drug resistance in this strain arises at least in part from the inability of inhibitors to induce closing. We carried out simulations of the MDR 769 HIV-PR mutant and observed that the reported structure is unstable in solution and rapidly adopts the semi-open conformation observed for the unbound wild-type protease in solution. Further analysis suggests that the wide-open structure observed for MDR 769 arises not from sequence variation, but instead is an artifact from crystal packing. Thus, despite being the first experimental structure to reveal flap opening sufficient for substrate access to the active site, this structure may not be directly relevant to studies of inhibitor entry or to the cause of HIV-PR drug resistance.     

Anionic WS-TEMPO-mediatory electrooxidation of alcohols in water: halide-free oxidation directed towards a totally closed system

Electrooxidation of alcohols in water with water-soluble N-oxyl derivatives bearing a sulfonic acid group (anionic WS-TEMPOs) as a mediator proceeded to afford the corresponding ketones and aldehydes in moderate to good yields. The aqueous solution containing WS-TEMPOs could be readily recovered and reused for the electrooxidation of alcohols, thereby providing a totally closed system.     

The interstitial atom of the nitrogenase FeMo-cofactor: ENDOR and ESEEM evidence that it is not a nitrogen

X-ray crystallographic study of the nitrogenase MoFe protein revealed electron density from an atom (denoted X) inside the active-site metal cluster, the [MoFe7S9:homocitrate] FeMo-cofactor. The electron density associated with X is consistent with a single N, O, or C atom. We now have tested whether X is an N or not by comparing the Q-band ENDOR and ESEEM signals from resting-state (S = 3/2) MoFe protein and NMF-extracted FeMo-co from bacteria grown with either 14N or 15N as the exclusive N source. All of the 14N or 15N signals associated with the protein are lost upon extraction of the FeMo-co. We interpret this as strong evidence that X is not an N.     

Water-soluble N-oxyl compounds-mediated electrooxidation of alcohols in water: a prominent access to a totally closed system

Electrooxidation of alcohols in water involving water-soluble N-oxyl compounds (WS-TEMPOs) proceeded smoothly to afford the corresponding ketones and aldehydes in good yields. Notably, most of WS-TEMPOs in water remained intact after the electrolysis. The aqueous solution containing WS-TEMPOs was recovered easily and repeatedly used for the electrooxidation of alcohols, offering a totally closed system.     

A case study on biological activity in a surface-bound multicomponent system: the biotin-streptavidin-peroxidase system

The adsorption of multiple protein layers on biotinylated organic surfaces has been characterized using surface plasmon resonance (SPR) and atomic force microscopy (AFM). Diffusion-limited loading of the biotinylated self-assembled monolayers (SAMs) ensures a precise control of the streptavidin surface density. For the subsequent interaction with biotinylated peroxidase, SPR data hint at a streptavidin density dependent orientation during peroxidase adsorption. Microcontact printed well-defined two-dimensional patterned surfaces of biotinylated organothiols and protein-resistant OEG-thiols allow an in-situ differentiation of specific and nonspecific adsorption (e.g., mono- vs multilayer adsorption). Additionally, the very important issue of biological activity of surface-bound enzymes is addressed by comparing the enzyme activities in solution with that for surface-bound species.     

Systematic exploration of a rutile-type zinc(II)-phosphonocarboxylate open framework: the factors that influence the structure

To systematically explore the assembly mechanism of a rutile-type open framework of {[Zn(3)(pbdc)(2)]·2H(3)O}(n) (3) (H(4)pbdc = 5-phosphonobenzene-1,3-dicarboxylic acid) constructed by 3-connected pbdc ligands and 6-connected Zn(3)(CO(2))(4)(PO(3))(2) secondary building units (Zn(3)-SBUs), three major factors including solvothermal procedures, types of solvents and amines, are taken into consideration. Seven novel structures, namely {[Zn(5)(pbdc)(2)(OH)(2)(H(2)O)(4)]·4H(2)O}(n) (1), {[Zn(3)(pbdc)(2)·H(2)O]·(Htea)·H(3)O·2-5(H(2)O)}(n) (2), {[Zn(3)(pbdc)(2)](H(3)O)(2)(dma)}(n) (4), {[Zn(2)(pbdc)(taea)]·3H(2)O}(n) (5), {[Zn(3)(pbdc)(2)(Hpda)(2)]·2H(2)O}(n) (6), {[Zn(5)(pbdc)(2)(Hpbdc)(2)]·2H(2)pz·9H(2)O}(n) (7), {[Zn(3)(pbdc)(2)]·Hpd·H(3)O·4H(2)O}(n) (8) are obtained. The results indicate that the layered-solvothermal method and the isopropanol solvent play crucial roles in the construction of the special anionic open framework of [Zn(3)(pbdc)(2)](2-). Changing these two factors led molecular assembly away from the rutile-type open framework. However, amines play a variable role in the framework, which means that by using appropriate amines, molecular assembly could generate the open framework of [Zn(3)(pbdc)(2)](2-) with pores decorated by amines. These results suggest a different approach towards decorating pores in anionic frameworks with precise structural information.     

Ni-catalyzed ketene cycloaddition: a system that resists the formation of decarbonylation side products

Ni-phosphine complexes were used as catalysts for the cycloaddition of various ketenes and diynes. In general, 2,4-cyclohexadienones were formed instead of products arising from decarbonylation of the ketenes.     

The pseudouridine synthases: revisiting a mechanism that seemed settled

RNA containing 5-fluorouridine, [f 5U]RNA, has been used as a mechanistic probe for the pseudouridine synthases, which convert uridine in RNA to its C-glycoside isomer, pseudouridine. Hydrated products of f 5U were attributed to ester hydrolysis of a covalent complex between an essential aspartic acid residue and f 5U, and the results were construed as strong support for a mechanism involving Michael addition by the aspartic acid residue. Labeling studies with [18O]water are now reported that rule out such ester hydrolysis in one pseudouridine synthase, TruB. The aspartic acid residue does not become labeled, and the hydroxyl group in the hydrated product of f 5U derives directly from solvent. The hydrated product, therefore, cannot be construed to support Michael addition during the conversion of uridine to pseudouridine, but the results do not rule out such a mechanism. A hypothesis is offered for the seemingly disparate behavior of different pseudouridine synthases toward [f 5U]RNA.     

The SON2 mechanism : A non-oxidative reaction that is initiated by electron transfer oxidation

Under oxidizing conditions, aromatic chloro and fluoro compounds undergo what formally are typical nucleophilic substitution reactions with surprising ease. As an example, 4-fluoroanisole is converted the 4-acetoxyanisole by anodic or metal ion oxidative initiation, and the reaction is shown to be a chain process. It is proposed that a mechanism analogous to that of the reductively initiated S_RN1 mechanism operates: The substrate is oxidized to a radical cation by the initiator system, and the radical cation then undergoes ipso attack by the nucleophile. In the third step, the leaving group leaves as a species at the same oxidation level as the nucleophile, giving the radical cation of the product to be formed. A chain transfer step involving this ion and a new substrate molecule then completes the propagation sequence.Previously reported cases of this phenomenon are discussed and the individual steps of the chain reaction are considered in terms of their thermochemistry. It is concluded that the S_ON2 mechanism should be more favoured with easily oxidizable substrates.     

Repetitive determination of calcium ion and regeneration of a chromogenic reagent using chlorophosphonazo III and an ion exchanger in a circulatory flow injection system.

The spectrophotometric determination of Ca2+ with chlorophosphonazo III (CPN) has been carried out by a circulatory flow injection (FI) method. A cation-exchange mini-column for the on-line regeneration of the main reagent was incorporated in this FT system, allowing a repetitive determination of Ca2+. A solution of 4.0 x 10(-5) M CPN in a 0.05 M acetate buffer (pH 5.0) in a single reservoir (50 ml) was continuously circulated at a constant flow rate of 1.5 ml min(-1). Into the stream, an aliquot (20 microl) of a sample containing Ca2+ was quickly injected by means of a 6-way valve. The complex formed was monitored spectrophotometrically at 670 nm in the flow system. Then, the stream passed through a cation-exchange column, which was introduced after the flow-through cell. A successful ligand-exchange reaction of Ca2+ between the CPN reagent and a cation exchanger, as well as a simultaneous regeneration of the free reagent took place. The stream then returned to the reservoir. The regeneration and recycling of the CPN reagent allowed as many as 300 repetitive determinations of 2.5 mg l(-1) Ca2+ solutions with the same 50 ml circulating solution.     

The de novo methylation activity of Dnmt3a is distinctly different than that of Dnmt1

Background  

Though Dnmt1 is considered the primary maintenance methyltransferase and Dnmt3a and Dnmt3b are considered de novo methyltransferases in mammals, these three enzymes may work together in maintaining as well as establishing DNA methylation patterns. It has been proposed that Dnmt1 may carry out de novo methylation at sites in the genome with transient single-stranded regions, such as replication origins, and then spread methylation from these nucleation sites in vivo, even though such activity has not been reported.