While metal nanoparticles are being increasingly used in many sectors of the economy, there is growing interest in the biological and environmental safety of their production. The main methods for nanoparticle production are chemical and physical approaches that are often costly and potentially harmful to the environment. The present review is devoted to the possibility of metal nanoparticle synthesis using plant extracts. This approach has been actively pursued in recent years as an alternative, efficient, inexpensive, and environmentally safe method for producing nanoparticles with specified properties. This review provides a detailed analysis of the various factors affecting the morphology, size, and yield of metal nanoparticles. The main focus is on the role of the natural plant biomolecules involved in the bioreduction of metal salts during the nanoparticle synthesis. Examples of effective use of exogenous biomatrices (peptides, proteins, and viral particles) to obtain nanoparticles in plant extracts are discussed.

/pdf/green-nanotechnologies-synthesis-of-metal-nanoparticles-3k69j181mp.pdf

"Green" nanotechnologies: synthesis of metal nanoparticles using plants

Kai proteins globally regulate circadian gene expression of cyanobacteria The KaiC phosphorylation cycle, which persists even without transcription or translation, is assumed to be a basic timing process of the circadian clock We have reconstituted the self-sustainable oscillation of KaiC phosphorylation in vitro by incubating KaiC with KaiA, KaiB, and adenosine triphosphate The period of the in vitro oscillation was stable despite temperature change (temperature compensation), and the circadian periods observed in vivo in KaiC mutant strains were consistent with those measured in vitro The enigma of the circadian clock can now be studied in vitro by examining the interactions between three Kai proteins

https://science.sciencemag.org/content/sci/308/5720/414.full.pdf

Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitro

Small Angle Scattering of X-Rays

Self-assembled cage structures of nanometre dimensions can be used as constrained environments for the preparation of nanostructured materials1,2 and the encapsulation of guest molecules3, with potential applications in drug delivery4 and catalysis5. In synthetic systems the number of subunits contributing to cage structures is typically rather small3,6. But the protein coats of viruses (virions) commonly comprise hundreds of subunits that self-assemble into a cage for transporting viral nucleic acids. Many virions, moreover, can undergo reversible structural changes that open or close gated pores to allow switchable access to their interior7. Here we show that such a virion — that of the cowpea chlorotic mottle virus — can be used as a host for the synthesis of materials. We report the mineralization of two polyoxometalate species (paratungstate and decavanadate) and the encapsulation of an anionic polymer inside this virion, controlled by pH-dependent gating of the virion's pores. The diversity in size and shape of such virus particles make this a versatile strategy for materials synthesis and molecular entrapment.

Host–guest encapsulation of materials by assembled virus protein cages

Phase problems occur in many scientific disciplines, particularly those involving remote sensing using a wave field. Although there has been much interest in phase retrieval in optics and in imaging in general over the past decade, phase retrieval has a much longer history in x-ray crystallography, and a variety of powerful and practical techniques have been developed. The nature of crystallography means that crystallographic phase problems are distinct from those in other imaging contexts, but there are a number of commonalities. Here the principles of phase retrieval in crystallography are outlined and are compared and contrasted with phase retrieval in general imaging. Uniqueness results are discussed, but the emphasis is on phase-retrieval algorithms and areas in which results in one discipline have, and may, contribute to the other.

http://xrm.phys.northwestern.edu/research/pdf_papers/1990/millane_josaa_1990.pdf

Phase retrieval in crystallography and optics

Visualization of protein-nucleic acid interactions in a virus. Refined structure of intact tobacco mosaic virus at 2.9 A resolution by X-ray fiber diffraction.

https://as.vanderbilt.edu/johnsonlab/publications/reprints/pmid15304218.pdf

Visualizing a circadian clock protein: crystal structure of KaiC and functional insights.

In cyanobacteria, KaiC is an essential hexameric clock protein that forms the core of a circadian protein complex. KaiC can be phosphorylated, and the ratio of phospho-KaiC to non-phospho-KaiC is correlated with circadian period. Structural analyses of KaiC crystals identify three potential phosphorylation sites within a 10-A radius of the ATP binding regions that are at the T432, S431, and T426 residues in the KaiCII domains. When these residues are mutated by alanine substitution singly or in combination, KaiC phosphorylation is altered, and circadian rhythmicity is abolished. These alanine substitutions do not prevent KaiC from hexamerizing. Intriguingly, the ability of KaiC overexpression to repress its own promoter is also not prevented by alanine substitutions at these sites, implying that the capability of KaiC to repress its promoter is not sufficient to allow the clockwork to oscillate. The KaiC structure and the mutational analysis suggest that S431 and T426 may share a phosphate that can shuttle between these two residues. Because the phosphorylation status of KaiC oscillates over the daily cycle, and KaiC phosphorylation is essential for clock function as shown here, daily modulations of KaiC activity by phosphorylation at T432 and S431/T426 seem to be key components of the circadian clockwork in cyanobacteria.

https://structbio.vanderbilt.edu/~eglim/journals/95.pdf

Identification of key phosphorylation sites in the circadian clock protein KaiC by crystallographic and mutagenetic analyses.

The cyanobacterial circadian clock can be reconstituted in vitro by mixing recombinant KaiA, KaiB and KaiC proteins with ATP, producing KaiC phosphorylation and dephosphorylation cycles that have a regular rhythm with a ca. 24-h period and are temperature-compensated. KaiA and KaiB are modulators of KaiC phosphorylation, whereby KaiB antagonizes KaiA's action. Here, we present a complete crystallographic model of the Synechococcus elongatus KaiC hexamer that includes previously unresolved portions of the C-terminal regions, and a negative-stain electron microscopy study of S. elongatus and Thermosynechococcus elongatus BP-1 KaiA–KaiC complexes. Site-directed mutagenesis in combination with EM reveals that KaiA binds exclusively to the CII half of the KaiC hexamer. The EM-based model of the KaiA–KaiC complex reveals protein–protein interactions at two sites: the known interaction of the flexible C-terminal KaiC peptide with KaiA, and a second postulated interaction between the apical region of KaiA and the ATP binding cleft on KaiC. This model brings KaiA mutation sites that alter clock period or abolish rhythmicity into contact with KaiC and suggests how KaiA might regulate KaiC phosphorylation.

/pdf/analysis-of-kaia-kaic-protein-interactions-in-the-cyano-36l1hbhcn0.pdf

Analysis of KaiA–KaiC protein interactions in the cyano‐bacterial circadian clock using hybrid structural methods

An experimental rationalization of the structure type encountered in DNA and RNA by systematically investigating the chemical and physical properties of alternative nucleic acids has identified systems with a variety of sugar-phosphate backbones that are capable of Watson-Crick base pairing and in some cases cross-pairing with the natural nucleic acids. The earliest among the model systems tested to date, (4' --> 6')-linked oligo(2',3'-dideoxy-beta-d-glucopyranosyl)nucleotides or homo-DNA, shows stable self-pairing, but the pairing rules for the four natural bases are not the same as those in DNA. However, a complete interpretation and understanding of the properties of the hexapyranosyl (4' --> 6') family of nucleic acids has been impeded until now by the lack of detailed 3D-structural data. We have determined the crystal structure of a homo-DNA octamer. It reveals a weakly twisted right-handed duplex with a strong inclination between the hexose-phosphate backbones and base-pair axes, and highly irregular values for helical rise and twist at individual base steps. The structure allows a rationalization of the inability of allo-, altro-, and glucopyranosyl-based oligonucleotides to form stable pairing systems.

/pdf/crystal-structure-of-homo-dna-and-nature-s-choice-of-pentose-32rbxn69c0.pdf

Rekha Pattanayek

Papers

Visualization of protein-nucleic acid interactions in a virus. Refined structure of intact tobacco mosaic virus at 2.9 A resolution by X-ray fiber diffraction.

Visualizing a circadian clock protein: crystal structure of KaiC and functional insights.

Identification of key phosphorylation sites in the circadian clock protein KaiC by crystallographic and mutagenetic analyses.

Analysis of KaiA–KaiC protein interactions in the cyano‐bacterial circadian clock using hybrid structural methods

Crystal structure of homo-DNA and nature's choice of pentose over hexose in the genetic system.