Cation-mediated interplay of loops in chaperonin-10

The ubiquitously occurring chaperonins consist of a large tetradecameric Chaperonin-60, forming a cylindrical assembly, and a smaller heptameric Chaperonin-10. For a functional protein folding cycle, Chaperonin-10 caps the cylindrical Chaperonin-60 from one end forming an asymmetric complex. The oligomeric assembly of Chaperonin-10 is known to be highly plastic in nature. In Mycobacterium tuberculosis, the plasticity has been shown to be modulated by reversible binding of divalent cations. Binding of cations confers rigidity to the metal binding loop, and also promotes stability of the oligomeric structure. We have probed the conformational effects of cation binding on the Chaperonin-10 structure through fluorescence studies and molecular dynamics simulations. Fluorescence studies show that cation binding induces reduced exposure and flexibility of the dome loop. The simulations corroborate these results and further indicate a complex landscape of correlated motions between different parts of the molecule. They also show a fascinating interplay between two distantly spaced loops, the metal binding "dome loop" and the GroEL-binding "mobile loop", suggesting an important cation-mediated role in the recognition of Chaperonin-60. In the presence of cations the mobile loop appears poised to dock onto the Chaperonin-60 structure. The divalent metal ions may thus act as key elements in the protein folding cycle, and trigger a conformational switch for molecular recognition.     

Nigro-neostriatal projection

Summary The nigro-neostriatal projection was investigated in albino rats and cats with silver impregnation, fluorescence histochemistry and electron microscopy. After unilateral stereotactic electrolysis in the substantia nigra the dopamine fluorescence of ipsilateral neostriatum is markedly reduced. As shown by silver impregnation and electron microscopy, fine terminals and axons are degenerated in the same region. These observations suggest that the nigro-neostriatal pathway may be composed of the fine dopaminergic axons of the nerve cells of unilateral substantia nigra.Dedicated to Professor K. Goerttler on his 75th birthday. — This work was supported by a research grant from the Ministry of Education, Japan.     

Physical properties of defined lipopolysaccharide salts

The electron spin resonance probes 5-doxylstearate and 4-(dodecyldimethylammonio)-1-oxy-2,2,6,6-tetramethylpiperidine bromide were used to characterize the fluidity of the acyl chain and head-group regions, respectively, of defined salts of lipopolysaccharide (LPS) from Escherichia coli K12. The removal of the weakly bound divalent cations from native LPS by electrodialysis and their replacement by sodium had little effect on the midpoint of the lipid-phase transition or on head-group mobility. In contrast, lipopolysaccharide acyl chain mobility increased following electrodialysis. The replacement of most of the remaining cations with sodium resulted in a further dramatic increase in mobility in both the polar and nonpolar regions of lipopolysaccharide. Head-group mobility of the sodium salt of LPS was shown to be reduced with the addition of divalent cations. Furthermore, evidence is presented which suggests that low magnesium concentrations may induce phase separations in the sodium salt. The magnesium salt of lipopolysaccharide closely resembled the native form in both head-group and acyl chain mobility although the cation charge to phosphorus ratio in the magnesium salt was greater than that detected in the native isolate. Analyses of other lipopolysaccharide salts support our hypothesis that many of the observed differences in the physical and pathological properties of lipopolysaccharide salts may simply be explained by the degree of charge neutralization.     

Modeling interactions between a β‐O‐4 type lignin model compound and 1‐allyl‐3‐methylimidazolium chloride ionic liquid

Aiming at understanding the molecular mechanism of the lignin dissolution in imidazolium‐based ionic liquids (ILs), this work presents a combined quantum chemistry (QC) calculation and molecular dynamics (MD) simulation study on the interaction of the lignin model compound, veratrylglycerol‐β‐guaiacyl ether (VG) with 1‐allyl‐3‐methylimidazolium chloride ([Amim]Cl). The monomer of VG is shown to feature a strong intramolecular hydrogen bond, and its dimer is indicated to present important π‐π stacking and intermolecular hydrogen bonding interactions. The interactions of both the cation and anion of [Amim]Cl with VG are shown to be stronger than that between the two monomers, indicating that [Amim]Cl is capable of dissolving lignin. While Cl^– anion forms a hydrogen‐bonded complex with VG, the imidazolium cation interacts with VG via both the π‐π stacking and intermolecular hydrogen bonding. The calculated interaction energies between VG and the IL or its components (the cation, anion, and ion pair) indicate the anion plays a more important role than the cation for the dissolution of lignin in the IL. Theoretical results provide help for understanding the molecular mechanism of lignin dissolution in imidazolium‐based IL. The theoretical calculations on the interaction between the lignin model compound and [Amim]Cl ionic liquid indicate that the anion of [Amim]Cl plays a more important role for lignin dissolution although the cation also makes a substantial contribution.     

Purification and characterization of the RNA-directed DNA polymerase of a primate type-D retrovirus: Mason-Pfizer virus

The RNA-directed DNA polymerase of the primate type-D retrovirus Mason-Pfizer virus was purified using ion-exchange and affinity chromatography, and molecular sieving. The enzyme was shown to have a molecular weight of approx. 80 000 as determined by sedimentation analysis, molecular sieving and sodium dodecyl sulfate polyacrylamide gel electrophoresis. The purified RNA-directed DNA polymerase retained its ability to use a heteropolymeric RNA as a template. The Mason-Pfizer virus RNA-directed DNA polymerase was also characterized as to its divalent cation preference for several synthetic primertemplates and for heteropolymeric RNA. Mg2+ was preferred as its divalent cation for all primer-templates except oligo(dG).poly(rC)m for which it prefers Mn2+. The Mason-Pfizer virus enzyme was also shown to have a pH optimum of 8-8.5 and a temperature optimum of 37-40 degrees C. The stability of the Mason-Pfizer virus RNA-directed DNA polymerase was shown to differ when measured using different primer-templates.     

Modeling of ion permeation in calcium and sodium channel selectivity filters

Structure-function studies have shown that it is possible to convert a sodium channel to a calcium-selective channel by a single amino acid substitution in the selectivity filter locus. Ion permeation through the "model selectivity filter" was modeled with a reduced set of functional groups representative of the constituent amino acid side chains. Force-field minimizations were conducted to obtain the energy profile of the cations as they get desolvated and bind to the "model selectivity filter." The calculations suggest that the ion selectivity in the calcium channel is due to preferential binding, whereas in the sodium channel it is due to exclusion. Energetics of displacement of a bound cation from the calcium "model selectivity filter" by another cation suggest that "multi-ion mechanism" reduces the activation barrier for ion permeation. Thus, the simple model captures qualitatively most of the conduction characteristics of sodium and calcium channels. However, the computed barriers for permeation are fairly large, suggesting that ion interaction with additional residues along the transport path may be essential to effect desolvation.     

Silver staining of high molecular weight proteins on large-pore polyacrylamide gels

A large-pore gel for electrophoresis in the presence of sodium dodecyl sulfate, composed of 2.55% polyacrylamide crosslinked with 2.75% methylenebisacrylamide, is described. This gel has a resolving power for very high molecular weight proteins and can be stained with silver. The gel is suitable for fractionation of factor VIII/von Willebrand factor directly from plasma samples. Visualization by silver staining revealed a series of covalently bound multimers with molecular weights of up to 8 X 10(6). The procedure described should be useful also for studies on other very high molecular weight proteins and nucleic acids.     

Isolation of choline esters from aqueous solutions by extraction with sodium tetraphenylboron in organic solvents

1. The method is based on the observation that choline esters and sodium tetraphenylboron (Kalignost) form complexes that are insoluble in water but soluble in organic solvents such as nitriles, higher ketones and benzyl alcohol. 2. The extraction procedure is an example of liquid cation exchange where tetraphenylboron is the cation-exchange group. 3. The proportion of choline esters extracted depends on the type and total amount of cation in the aqueous phase and the amount of sodium tetraphenylboron in the organic solvent. 4. The proportion of choline esters extracted is independent of the choline ester concentration, the pH (between 8 and 3) and the relative volumes of the two phases. 5. The affinity of sodium tetraphenylboron for choline esters increases with an increase in the size of the acyl group. 6. The choline ester extracted can be released into an aqueous solution by treatment with strong acids, silver salts and anion-exchange resins.     

Detection of single sequence repeat polymorphisms in denaturing polyacrylamide sequencing gels by silver staining

Large-scale use of molecular markers in plant breeding is limited by the throughput capacity for genotyping. DNA polymorphisms can be detected in denaturing polyacrylamide gels indirectly by nucleotide labeling or directly by staining. Fluorescent-labeling or radiolabeling requires sophisticated infrastructure not always available in developing countries. We present an improved low-cost method for silver staining and compare it to 2 other methods for their ability to detect simple sequence repeat polymorphisms in denaturing polyacrylamide gels bound to glass plates. The 3 procedures differed in their requirement for an oxidation pretreatment, preexposure with formaldehyde during silver nitrate impregnation, inclusion of silver thiosulfate, and by their replacement of sodium carbonate for sodium hydroxide to establish alkaline conditions for silver ion reduction. All methods detected the same banding pattern and alleles. However, important differences in sensitivity, contrast, and background were observed. Two methods gave superior sensitivity, detecting down to 1 μL of loaded amplification products. Our improved method gave lower backgrounds and allowed reutilization of staining solutions. The use of thin (<1 mm) denaturing sequencing gels allows genotyping of 60–96 samples within 4 h. Use of smaller loading sample volumes and reutilization of staining solutions further reduced costs.     

Ad hoc continuum-atomistic thermostat for modeling heat flow in molecular dynamics simulations

An ad hoc thermostating procedure that couples a molecular dynamics (MD) simulation and a numerical solution to the continuum heat flow equation is presented. The method allows experimental thermal transport properties to be modeled without explicitly including electronic degrees of freedom in a MD simulation. The method is demonstrated using two examples, heat flow from a constant temperature silver surface into a single crystal bulk, and a tip sliding along a silver surface. For the former it is shown that frictional forces based on the Hoover thermostat applied locally to grid regions of the simulation are needed for effective feedback between the atomistic and continuum equations. For fast tip sliding the thermostat results in less surface heating, and higher frictional and normal forces compared to the same simulation without the thermostat.     

Cation-Mediated Interplay of Loops in Chaperonin-10

Abstract

The ubiquitously occurring chaperonins consist of a large tetradecameric Chaperonin-60, forming a cylindrical assembly, and a smaller heptameric Chaperonin-10. For a functional protein folding cycle, Chaperonin-10 caps the cylindrical Chaperonin-60 from one end forming an asymmetric complex. The oligomeric assembly of Chaperonin-10 is known to be highly plastic in nature. In Mycobacterium tuberculosis, the plasticity has been shown to be modulated by reversible binding of divalent cations. Binding of cations confers rigidity to the metal binding loop, and also promotes stability of the oligomeric structure. We have probed the conformational effects of cation binding on the Chaperonin-10 structure through fluorescence studies and molecular dynamics simulations. Fluorescence studies show that cation binding induces reduced exposure and flexibility of the dome loop. The simulations corroborate these results and further indicate a complex landscape of correlated motions between different parts of the molecule. They also show a fascinating interplay between two distantly spaced loops, the metal binding “dome loop” and the GroEL-binding “mobile loop”, suggesting an important cation-mediated role in the recognition of Chaperonin-60. In the presence of cations the mobile loop appears poised to dock onto the Chaperonin-60 structure. The divalent metal ions may thus act as key elements in the protein folding cycle, and trigger a conformational switch for molecular recognition.     

Autoradiography method in biological research

The paper deals with data available in literature about the origin and development of the autoradiography method based on the ability of silver halogenides to be reduced under the effect of radioactive radiation and to reconstruct the image of objects which have incorporated the isotope. The evidence are presented on the development and updating of techniques of the above method, as well as on application of combined sets of emulsions and devices. Successful attempts as to the procedure automation and application of computers for quantitative estimation of the autoradiography data are elucidated. Application of different modifications of the autoradiography method in biological tests is shown through examples.     

Identification of a cation transport pathway in Neisseria meningitidis PorB

Neisseria meningitidis is the main causative agent of bacterial meningitis. In its outer membrane, the trimeric Neisserial porin PorB is responsible for the diffusive transport of essential hydrophilic solutes across the bilayer. Previous molecular dynamics simulations based on the recent crystal structure of PorB have suggested the presence of distinct solute translocation pathways through this channel. Although PorB has been electrophysiologically characterized as anion‐selective, cation translocation through nucleotide‐bound PorB during pathogenesis is thought to be instrumental for host cell death. As a result, we were particularly interested in further characterizing cation transport through the pore. We combined a structural approach with additional computational analysis. Here, we present two crystal structures of PorB at 2.1 and 2.65 Å resolution. The new structures display additional electron densities around the protruding loop 3 (L3) inside the pore. We show that these electron densities can be identified as monovalent cations, in our case Cs⁺, which are tightly bound to the inner channel. Molecular dynamics simulations reveal further ion interactions and the free energy landscape for ions inside PorB. Our results suggest that the crystallographically identified locations of Cs⁺ form a cation transport pathway inside the pore. This finding suggests how positively charged ions are translocated through PorB when the channel is inserted into mitochondrial membranes during Neisserial infection, a process which is considered to dissipate the mitochondrial transmembrane potential gradient and thereby induce apoptosis. Proteins 2013. © 2012 Wiley Periodicals, Inc.     

Exciplex formation between silver ions and the lowest MLCT excited state of the tris(bipyrazine)ruthenium(II) cation

The lowest excited MLCT state of the [Ru(bpz)₃]²⁺ cation (1) is shown to react with silver ion in aqueous or acetonitrile solution to form exciplexes with up to six silver ions per excited cation. Lifetime, wavelength data are presented as a function of the [Ag]/[Ru] ratio. An excited state (reductive quenching) potential of 1.55 V is derived from quenching by a range of methoxybenzenes. Data for quenching by metal ions are also presented. There is no ground state interaction between 1 and silver ions.     

An Improved Silver Stain for Developing Nervous Tissue

A reduced silver technique using physical development to stain embryonic nervous tissue is described. Brains are fixed in Bodian's fixative. Paraffin sections are pretreated with 1% chromic acid or 5% formol. They are impregnated with 0.01% silver nitrate dissolved in 0.1 M boric acid/sodium tetraborate buffer of pH 8 or with silver proteinate. Finally they are developed in a special physical developer which contains 0.1% silver nitrate, 0.01-0.l% formol as developed agent, 25% sodium carbonate to buffer the solution at pH 10.3, 0.1% ammonium nitrate to prevent precipitation of silver hydroxide, and 5% tungstosilicic acid as a protective colloid. The development takes several minutes in this solution, thus the intensity of staining can be controlled easily. The method yields uniform, complete and reproducible staining of axons at all developmental stages of the nervous tissue and is easy to handle.     

An improved silver stain for developing nervous tissue.

A reduced silver technique using physical development to stain embryonic nervous tissue is described. Brains are fixed in Bodian's fixative. Paraffin sections are pretreated with 1% chromic acid or 5% formol. They are impregnated with 0.01% silver nitrate dissolved in 0.1 M boric acid/sodium tetraborate buffer of pH 8 or with silver proteinate. Finally they are developed in a special physical developer which contains 0.1% silver nitrate, 0.01-0.1% formol as reducing agent, 2.5% sodium carbonate to buffer the solution at pH 10.3, 0.1% ammonium nitrate to prevent precipitation of silver hydroxide, and 5% tungstosilicic acid as a protective colloid. The development takes several minutes in this solution, thus the intensity of staining can be controlled easily. The method yields uniform, complete and reproducible staining of axons at all developmental stages of the nervous tissue and is easy to handle.     

Mechanism of μ-Opioid Receptor-Magnesium Interaction and Positive Allosteric Modulation

In the era of opioid abuse epidemics, there is an increased demand for understanding how opioid receptors can be allosterically modulated to guide the development of more effective and safer opioid therapies. Among the modulators of the μ-opioid (MOP) receptor, which is the pharmacological target for the majority of clinically used opioid drugs, are monovalent and divalent cations. Specifically, the monovalent sodium cation (Na⁺) has been known for decades to affect MOP receptor signaling by reducing agonist binding, whereas the divalent magnesium cation (Mg²⁺) has been shown to have the opposite effect, notwithstanding the presence of sodium chloride. Although ultra-high-resolution opioid receptor crystal structures have revealed a specific Na⁺ binding site and molecular dynamics (MD) simulation studies have supported the idea that this monovalent ion reduces agonist binding by stabilizing the receptor inactive state, the putative binding site of Mg²⁺ on the MOP receptor, as well as the molecular determinants responsible for its positive allosteric modulation of the receptor, are unknown. In this work, we carried out tens of microseconds of all-atom MD simulations to investigate the simultaneous binding of Mg²⁺ and Na⁺ cations to inactive and active crystal structures of the MOP receptor embedded in an explicit lipid-water environment and confirmed adequate sampling of Mg²⁺ ion binding with a grand canonical Monte Carlo MD method. Analyses of these simulations shed light on 1) the preferred binding sites of Mg²⁺ on the MOP receptor, 2) details of the competition between Mg²⁺ and Na⁺ cations for specific sites, 3) estimates of binding affinities, and 4) testable hypotheses of the molecular mechanism underlying the positive allosteric modulation of the MOP receptor by the Mg²⁺ cation.     

Energy dispersive X-ray analysis of tissue gold after silver amplification by physical development

Summary Rats were treated intraperitoneally with the gold-containing compounds sodium aurothiomalate (Myocrisin), sodium aurothiosulfate (Sanocrysin), and aurothioglucose. Using stem energy dispersive X-ray analysis, gold and silver were shown to be located at the same point in lysosomes of proximal tubular cells of the kidney, in hepatocytes and in macrophages of lymph glands, spleen and liver. This result indicates that, after exposure to ultraviolet radiation, chemically bound tissue gold is transformed to metallic gold that subsequently can catalyze the reduction of silver ions to silver when subjected to physical development, i.e. exposed to a photographic developer containing silver ions in addition to the reducing molecules.     

Cytochemical Localization of Urease in a Rumen Staphylococcus sp. by Electron Microscopy

We describe a technique whereby intracellular urease activity can be localized by transmission electron microscopy. The ammonia produced from the enzymatic hydrolysis of urea is first precipitated with sodium tetraphenylboron and then replaced with silver to produce electron-dense silver tetraphenylboron. This direct reaction product deposition procedure was used to demonstrate the presence of membrane-bound urease of Staphylococcus sp. H3-22, a gram-positive ruminal bacterium.