Infrared spectroscopy of proteins.

Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy.

This review deals with current concepts of vibrational spectroscopy for the investigation of protein structure and function. While the focus is on infrared (IR) spectroscopy, some of the general aspects also apply to Raman spectroscopy. Special emphasis is on the amide I vibration of the polypeptide backbone that is used for secondary-structure analysis. Theoretical as well as experimental aspects are covered including transition dipole coupling. Further topics are discussed, namely the absorption of amino-acid side-chains, 1H/2H exchange to study the conformational flexibility and reaction-induced difference spectroscopy for the investigation of reaction mechanisms with a focus on interpretation tools.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0033583502003815

What vibrations tell us about proteins

Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one- fifth of the primary productivity on Earth(1,2). The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology(3-5). Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (similar to 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.

https://hal-cea.archives-ouvertes.fr/cea-00910244/document

The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Janus particles: synthesis, self-assembly, physical properties, and applications.

Bacteriorhodopsin: a light-driven proton pump in Halobacterium Halobium.

Bacteriorhodopsin and the purple membrane of halobacteria

The Photocycle of a Flavin-binding Domain of the Blue Light Photoreceptor Phototropin

A unique gold nanoparticle aggregate (GNA) system has been shown to be an excellent substrate for surface-enhanced Raman scattering (SERS) applications. Rhodamine 6G (R6G), a common molecule used for testing SERS activity on silver, but generally difficult to detect on gold substrates, has been found to readily bind to the GNA and exhibit strong SERS activity due to the unique surface chemistry afforded by sulfur species on the surface. This GNA system has yielded a large SERS enhancement of 107−109 in bulk solution for R6G, on par with or greater than any previously reported gold SERS substrate. SERS activity has also been successfully demonstrated for several biological molecules including adenine, l-cysteine, l-lysine, and l-histidine for the first time on a gold SERS substrate, showing the potential of this GNA as a convenient and powerful SERS substrate for biomolecular detection. In addition, the SERS spectrum of R6G on single aggregates has been measured. We have shown that the special surface prop...

Unique gold nanoparticle aggregates as a highly active surface-enhanced Raman scattering substrate

A photosensitive protein resembling the visual pigments of invertebrates enables phototactic archaebacteria to distinguish colour. This protein exists in two spectrally-distinct forms, one of which is a transient photoproduct of the other and each of which undergoes photochemical reactions controlling the cell's swimming behaviour. Activation of a single pigment molecule in the cell is sufficient to signal the flagellar motor. This signal-transduction mechanism makes evident a colour-sensing capability inherent in the retinal/protein chromophore.

Roberto A. Bogomolni

Papers

Bacteriorhodopsin: a light-driven proton pump in Halobacterium Halobium.

Bacteriorhodopsin and the purple membrane of halobacteria

The Photocycle of a Flavin-binding Domain of the Blue Light Photoreceptor Phototropin

Unique gold nanoparticle aggregates as a highly active surface-enhanced Raman scattering substrate

Mechanism of colour discrimination by a bacterial sensory rhodopsin.