Isolation and grouping of RNA phages by Itaru Watanabe et al. (1967).

I. Watanabe et al. isolated approximately 30 strains of RNA phages from various parts of Japan.

Structure and Function of the T4 Spackle Protein Gp61.3.

The bacteriophage T4 genome contains two genes that code for proteins with lysozyme activity- and . Gene encodes the well-known T4 lysozyme (commonly called T4L) that functions to break the peptidoglycan layer late in the infection cycle, which is required for liberating newly assembled phage progeny. Gene product (gp5) is the tail-associated lysozyme, a component of the phage particle.

Comparison of composition-gradient sedimentation equilibrium and composition-gradient static light scattering as techniques for quantitative characterization of biomolecular interactions: A case study.

The equilibrium hetero-association of NADH oxidase and peroxiredoxin was characterized by means of independently conducted measurements of composition-gradient sedimentation equilibrium and composition-gradient static light scattering. Results obtained from both experiments were quantitatively accounted for by a model according to which a dimer of NADH oxidase forms a 1:1 equilibrium complex with a decamer of peroxiredoxin under the conditions of these experiments. The best-fit equilibrium constants for heteroassociation of the two proteins obtained from the two measurements were found to be identical to well within the uncertainty of estimate of each of the two methods.

Significance of a histone-like protein with its native structure for the diagnosis of asymptomatic tuberculosis.

Tuberculosis causes the highest mortality among all single infections. Asymptomatic tuberculosis, afflicting one third of the global human population, is the major source as 5-10% of asymptomatic cases develop active tuberculosis during their lifetime. Thus it is one of important issues to develop diagnostic tools for accurately detecting asymptomatic infection.

Forty years of research on the assembly and infection process of bacteriophage.

This short biographical note was written as part of the lead-in material for a festschrift kindly organized for me on the occasion of my 70th birthday. The collection of articles assembled in this issue range within the spectrum of the topics covered in the special issue 'Multiscale structural biology-biophysical principles and practice ranging from biomolecules to bionanomachines.' Here I describe some of the high points of my 40 years of research science conducted in the USA, Switzerland and Japan.

Molecular assembly and structure of the bacteriophage T4 tail.

The tail of bacteriophage T4 undergoes large structural changes upon infection while delivering the phage genome into the host cell. The baseplate is located at the distal end of the contractile tail and plays a central role in transmitting the signal to the tail sheath that the tailfibers have been adsorbed by a host bacterium. This then triggers the sheath contraction.

Measurement of amyloid formation by turbidity assay-seeing through the cloud.

Detection of amyloid growth is commonly carried out by measurement of solution turbidity, a low-cost assay procedure based on the intrinsic light scattering properties of the protein aggregate. Here, we review the biophysical chemistry associated with the turbidimetric assay methodology, exploring the reviewed literature using a series of pedagogical kinetic simulations. In turn, these simulations are used to interrogate the literature concerned with in vitro drug screening and the assessment of amyloid aggregation mechanisms.

Crystal structure of a crustacean hyperglycemic hormone (CHH) precursor suggests structural variety in the C-terminal regions of CHH superfamily members.

Unlabelled: The crustacean hyperglycemic hormone (CHH) is one of the major hormones in crustaceans, and peptides belonging to the CHH superfamily have been found in diverse ecdysozoans. Although the basic function of CHH is to control energy metabolism, it also plays various roles in crustacean species, such as in molting and vitellogenesis. Here, we present the crystal structure of Pej-SGP-I-Gly, a partially active precursor of CHH from the kuruma prawn Marsupenaeus japonicus, which has an additional Gly residue in place of the C-terminal amide group of the mature Pej-SGP-I.

Impact of structural polymorphism for the Helicobacter pylori CagA oncoprotein on binding to polarity-regulating kinase PAR1b.

Chronic infection with cagA-positive Helicobacter pylori is the strongest risk factor for atrophic gastritis, peptic ulcers, and gastric cancer. CagA, the product of the cagA gene, is a bacterial oncoprotein, which, upon delivery into gastric epithelial cells, binds to and inhibits the polarity-regulating kinase, partitioning-defective 1b (PAR1b) [also known as microtubule affinity-regulating kinase 2 (MARK2)], via its CagA multimerization (CM) motif. The inhibition of PAR1b elicits junctional and polarity defects, rendering cells susceptible to oncogenesis.

Role of bacteriophage T4 baseplate in regulating assembly and infection.

Bacteriophage T4 consists of a head for protecting its genome and a sheathed tail for inserting its genome into a host. The tail terminates with a multiprotein baseplate that changes its conformation from a "high-energy" dome-shaped to a "low-energy" star-shaped structure during infection. Although these two structures represent different minima in the total energy landscape of the baseplate assembly, as the dome-shaped structure readily changes to the star-shaped structure when the virus infects a host bacterium, the dome-shaped structure must have more energy than the star-shaped structure.

Protein aggregate turbidity: Simulation of turbidity profiles for mixed-aggregation reactions.

Due to their colloidal nature, all protein aggregates scatter light in the visible wavelength region when formed in aqueous solution. This phenomenon makes solution turbidity, a quantity proportional to the relative loss in forward intensity of scattered light, a convenient method for monitoring protein aggregation in biochemical assays. Although turbidity is often taken to be a linear descriptor of the progress of aggregation reactions, this assumption is usually made without performing the necessary checks to provide it with a firm underlying basis.

Development of a Model Protein Interaction Pair as a Benchmarking Tool for the Quantitative Analysis of 2-Site Protein-Protein Interactions.

A significant challenge in the molecular interaction field is to accurately determine the stoichiometry and stepwise binding affinity constants for macromolecules having >1 binding site. The mission of the Molecular Interactions Research Group (MIRG) of the Association of Biomolecular Resource Facilities (ABRF) is to show how biophysical technologies are used to quantitatively characterize molecular interactions, and to educate the ABRF members and scientific community on the utility and limitations of core technologies [such as biosensor, microcalorimetry, or analytic ultracentrifugation (AUC)]. In the present work, the MIRG has developed a robust model protein interaction pair consisting of a bivalent variant of the Bacillus amyloliquefaciens extracellular RNase barnase and a variant of its natural monovalent intracellular inhibitor protein barstar.

Molecular Assembly of Wheat Gliadins into Nanostructures: A Small-Angle X-ray Scattering Study of Gliadins in Distilled Water over a Wide Concentration Range.

Gliadin, one of the major proteins together with glutenin composing gluten, affects the physical properties of wheat flour dough. In this study, nanoscale structures of hydrated gliadins extracted into distilled water were investigated primarily by small-angle X-ray scattering (SAXS) over a wide range of concentrations. Gliadins are soluble in distilled water below 10 wt %.

A multilaboratory comparison of calibration accuracy and the performance of external references in analytical ultracentrifugation.

Analytical ultracentrifugation (AUC) is a first principles based method to determine absolute sedimentation coefficients and buoyant molar masses of macromolecules and their complexes, reporting on their size and shape in free solution. The purpose of this multi-laboratory study was to establish the precision and accuracy of basic data dimensions in AUC and validate previously proposed calibration techniques. Three kits of AUC cell assemblies containing radial and temperature calibration tools and a bovine serum albumin (BSA) reference sample were shared among 67 laboratories, generating 129 comprehensive data sets.

Asymmetrically fused polyoxometalate-silver alkynide composite cluster.

We demonstrate that an asymmetric composite cluster, [Ag25{C≡CC(CH3)3}16(CH3CN)4(P2W15Nb3O62)] (1), consisting of directly fused polyoxometalate and silver alkynide moieties can be facilely synthesized by a one-pot reaction between a Nb-substituted Dawson-type polyoxometalate, H4[α-P2W15Nb3O62](5-), and the mixture of (CH3)3CC≡CAg and CF3SO3Ag. Single-crystal X-ray diffraction revealed the structure of 1, where Ag atoms are selectively attached to the Nb-substituted hemisphere of the pedestal Dawson anion. Its structural integrity in the solution was demonstrated by (31)P NMR spectroscopy and analytical ultracentrifugation.

Conformational stability, reversibility and heat-induced aggregation of α-1-acid glycoprotein.

To investigate the relationship between conformational stability, reversibility of denaturation and aggregation of protein, we determined the conformation, melting temperature (Tm), and reversibility of heat-induced denaturation of α-1-acid glycoprotein (AGP) in aqueous solutions at various pH values using circular dichroism (CD) and differential scanning microcalorimetry. To quantitate and characterize heat-induced AGP aggregation under the same pH conditions, solutions of AGP were incubated at 50°C and then analysed by size exclusion chromatography (SEC), sodium dodecyl sulfate-polyacrylamide gel electrophoresis, CD and SEC in the presence of 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid. The conformational stability of AGP was reduced at lower pH, whereas the reversibility of protein denaturation was reduced at higher pH.

Plasma membrane translocation of a protein needle based on a triple-stranded β-helix motif.

Plasma membrane translocation is challenging due to the barrier of the cell membrane. Contrary to the synthetic cell-penetrating materials, tailed bacteriophages use cell-puncturing protein needles to puncture the cell membranes as an initial step of the DNA injection process. Cell-puncturing protein needles are thought to remain functional in the native phages.

Structure of the 3.3MDa, in vitro assembled, hubless bacteriophage T4 baseplate.

The bacteriophage T4 baseplate is the control center of the virus, where the recognition of an Escherichiacoli host by the long tail fibers is translated into a signal to initiate infection. The short tail fibers unfold from the baseplate for firm attachment to the host, followed by shrinkage of the tail sheath that causes the tail tube to enter and cross the periplasmic space ending with injection of the genome into the host. During this process, the 6.

Cooperative binding of the outer arm-docking complex underlies the regular arrangement of outer arm dynein in the axoneme.

Outer arm dynein (OAD) in cilia and flagella is bound to the outer doublet microtubules every 24 nm. Periodic binding of OADs at specific sites is important for efficient cilia/flagella beating; however, the molecular mechanism that specifies OAD arrangement remains elusive. Studies using the green alga Chlamydomonas reinhardtii have shown that the OAD-docking complex (ODA-DC), a heterotrimeric complex present at the OAD base, functions as the OAD docking site on the doublet.

Structural basis of Sec-independent membrane protein insertion by YidC.

Newly synthesized membrane proteins must be accurately inserted into the membrane, folded and assembled for proper functioning. The protein YidC inserts its substrates into the membrane, thereby facilitating membrane protein assembly in bacteria; the homologous proteins Oxa1 and Alb3 have the same function in mitochondria and chloroplasts, respectively. In the bacterial cytoplasmic membrane, YidC functions as an independent insertase and a membrane chaperone in cooperation with the translocon SecYEG.

Role of positions e and g in the fibrous assembly formation of an amphipathic α-helix-forming polypeptide.

We previously characterized α3, a polypeptide that has a three times repeated sequence of seven amino acids (abcdefg: LETLAKA) and forms fibrous assemblies composed of amphipathic α-helices. Upon comparison of the amino acid sequences of α3 with other α-helix forming polypeptides, we proposed that the fibrous assemblies were formed due to the alanine (Ala) residues at positions e and g. Here, we characterized seven α3 analog polypeptides with serine (Ser), glycine (Gly), or charged residues substituted for Ala at positions e and g.

Structure and properties of the C-terminal β-helical domain of VgrG protein from Escherichia coli O157.

The bacterial Type 6 secretion system (T6SS) translocates protein toxins (also called effectors) from the cytosol of a T6SS-carrying cell to a target cell by a syringe-like supramolecular complex resembling a contractile tail of bacteriophages. Valine-glycine repeat protein G (VgrG) proteins, which are the homologues of the gp27-gp5 (gene product) cell puncturing complex of bacteriophage T4, are considered to be located at the attacking tip of the bacterial T6SS apparatus. Here, we over-expressed six VgrG proteins from pathogenic Escherichia coli O157 and CFT073 strains.