America, America!

This account was written during a four-month stay in Berkeley from May to August 2007. It was partly inspired by a diary published by Simone de Beauvoir after her four-month lecture tour to the US in 1947. We could not resist the temptation of writing a few pages about our impressions. This text is not intended as an essay about anthropological or chemical sciences. We merely tried to understand the conditions of the bubbling creativity that we have so often witnessed in Berkeley. Some of our comments are more or less voluntarily naïve, as if Voltaire's Candide had made a trip to America. Our impressions may appear a bit franchouillardes, and perhaps a trifle rude to our American hosts, whose kindness does not deserve such a harsh treatment

On toxic effects of scientific journals

The advent of online publishing greatly facilitates the dissemination of scientific results. This revolution might have led to the untimely death of many traditional publishing companies, since today's scientists are perfectly capable of writing, formatting and uploading files to appropriate websites that can be consulted by colleagues and the general public alike. They also have the intellectual resources to criticize each other and organize an anonymous peer review system. The Open Access approach appears promising in this respect, but we cannot ignore that it is fraught with editorial and economic problems. A few powerful publishing companies not only managed to survive, but also rake up considerable profits. Moreover, they succeeded in becoming influential ‘trendsetters' since they decide which papers deserve to be published. To make money, one must set novel trends, like Christian Dior or Levi's in fashion, and open new markets, for example in Asia. In doing so, the publishers tend to supplant both national and transnational funding agencies in defining science policy. In many cases, these agencies tend simply to adopt the commercial criteria defined by the journals, forever eager to improve their impact factors. It is not obvious that the publishers of scientific journals, the editorial boards that they appoint, or the people who sift through the vast numbers of papers submitted to a handful of ‘top' journals are endowed with sufficient insight to set the trends of future science. It seems even less obvious that funding agencies should blindly follow the fashion trends set by the publishers. The perverse relationships between private publishers and public funding agencies may have a toxic effect on science polic

Transverse Relaxation of Scalar Coupled Protons in Magnetic Resonance of Non-Deuterated Proteins

The transverse relaxation rates R 2=1/T 2 of protons can be determined by spin-echo sequences with multiple refocusing pulses using moderate radio-frequency field strengths and properly chosen inter-pulse delays so as to suppress echo modulations due to homonuclear scalar couplings. Combination with 2D heteronuclear correlation spectroscopy (HSQC) allows one to measure R 2 of arbitrary protons attached to nitrogen-15 or carbon-13 nuclei. Decays of six amide protons in the protein Ubiquitin that is nitrogen-15 enriched (but not deuterated) were measured at different temperature

Similarities between intra- and intermolecular hydrogen bonds in RNA kissing complexes found by means of cross-correlated relaxation

The bond lengths and dynamics of intra- and intermolecular hydrogen bonds in an RNA kissing complex have been characterized by determining the NMR relaxation rates of various double- and triple-quantum coherences that involve an imino proton and two neighboring nitrogen-15 nuclei belonging to opposite bases. New experiments allow one to determine the chemical shift anisotropy of the imino protons. The bond lengths derived from dipolar relaxation and the lack of modulations of the nitrogen chemical shifts indicate that the intermolecular hydrogen bonds which hold the kissing complex together are very similar to the intramolecular hydrogen bonds in the double-stranded stem of the RN

Cross correlations between 13C-1H dipolar interactions and 15N chemical shift anisotropy in nucleic acids

Two sets of cross-correlated relaxation rates involving chemical shift anisotropy and dipolar interactions have been measured in an RNA kissing complex. In one case, both the CSA and dipolar interaction tensors are located on the same nucleotide base and are rigidly fixed with respect to each other. In the other case, the CSA tensor is located on the nucleotide base whereas the dipolar interaction is located on the adjoining ribose unit. Analysis of the measured rates in terms of isotropic or anisotropic rotational diffusion has been carried out for both cases. A marked difference between the two models is observed for the cross-correlation rates involving rigidly fixed spin interactions. The influence of internal motions about the glycosidic linkage between the nucleotide base and the ribose unit on cross-correlated relaxation rates has been estimated by applying a model of restricted rotational diffusion. Local motions seem to have a more pronounced effect on cross-correlated relaxation rates when the two spin interactions are not rigidly fixed with respect to each othe

Efficient determination of angles subtended by Cα-Hα and N-HN vectors in proteins via dipole-dipole cross-correlation§

The angle ΘCαHα,NHN subtended by the internuclear vectors 13Cα-Hα and 15N-HN in doubly-labeled proteins can be determined by observing the effect of cross-correlation between the dipolar interactions on zero- and double-quantum coherences involving 13Cα and 15N. Two complementary 2D experiments with the appearance of 15N-HN correlation spectra yield signal intensities that depend on the rate of interconversion through cross-correlated relaxation of in-phase and doubly antiphase zero- and double-quantum coherences. The ratio of the signal intensities in the two experiments bears a simple relationship to the cross-correlation rate, and hence to the angle ΘCαHα,NHN. Assuming planarity of the peptide bond, the dihedral angle Ψ (between Cα and C′) can be determined from the knowledge of ΘCαHα,NHN. The experiments are very time-effective and provide good sensitivity and excellent spectral resolutio

Evidence of chemical exchange in recombinant Major Urinary Protein and quenching thereof upon pheromone binding

The internal dynamics of recombinant Major Urinary Protein (rMUP) have been investigated by monitoring transverse nitrogen-15 relaxation using multiple-echo Carr-Purcell-Meiboom-Gill (CPMG) experiments. While the ligand-free protein (APO-rMUP) features extensive evidence of motions on the milliseconds time scale, the complex with 2-methoxy-3-isobutylpyrazine (HOLO-rMUP) appears to be much less mobile on this time scale. At 308K, exchange rates k ex=500-2000s−1 were typically observed in APO-rMUP for residues located adjacent to a β-turn comprising residues 83-87. These residues occlude an entry to the binding pocket and have been proposed to be a portal for ligand entry in other members of the lipocalin family, such as the retinol binding protein and the human fatty-acid binding protein. Exchange rates and populations are largely uncorrelated, suggesting local ‘breathing' motions rather than a concerted global conformational chang

Cross Polarization for Dissolution Dynamic Nuclear Polarization Experiments at Readily Accessible Temperatures 1.2< T <4.2K

Cross polarization can provide significant enhancements with respect to direct polarization of low-γ nuclei such as 13C. Substantial gains in sample throughput (shorter polarization times) can be achieved by exploiting shorter build-up times τDNP(1H)<τDNP(13C). To polarize protons rather than low-γ nuclei, nitroxide radicals with broad ESR resonances such as TEMPO are more appropriate than Trityl and similar carbon-based radicals that have narrow lines. With TEMPO as polarizing agent, the main Dynamic Nuclear Polarization (DNP) mechanism is thermal mixing (TM). Cross polarization makes it possible to attain higher polarization levels at 2.2K than one can obtain with direct DNP of low-γ nuclei with TEMPO at 1.2K, thus avoiding complex cryogenic technolog

Simultaneous determination of Ψ and Φ angles in proteins from measurements of cross-correlated relaxation effects

A method is presented to determine both φ and ψ backbone angles in proteins simultaneously. This is achieved by measuring the effect on two-spin coherences of cross-correlation between 15 N-1HN and 13 $${}^{{\text{13}}}{\text{C}}^\alpha{\text{ - }}{}^{\text{1}}{\text{H}}^\alpha$$ vectors. The cross-correlation rates are obtained by comparing two complementary three-dimensional experiment