The use of ion mobility mass spectrometry to assist protein design:A case study on zinc finger fold versus coiled coil interactions

A combination of affinity mass spectrometry, collisional activation and ion mobility analysis coupled with molecular dynamics measurements, are used to probe a zinc finger-coiled coil switching peptide system.</p

Systematic Review on Polyphenol Intake and Health Outcomes: Is there Sufficient Evidence to Define a Health-Promoting Polyphenol-Rich Dietary Pattern?

Growing evidence support association between polyphenol intake and reduced risk for chronic diseases, even if there is a broad debate about the effective amount of polyphenols able to exert such protective effect. The present systematic review provides an overview of the last 10-year literature on the evaluation of polyphenol intake and its association with specific disease markers and/or endpoints. An estimation of the mean total polyphenol intake has been performed despite the large heterogeneity of data reviewed. In addition, the contribution of dietary sources was considered, suggesting tea, coffee, red wine, fruit and vegetables as the main products providing polyphenols. Total flavonoids and specific subclasses, but not total polyphenols, have been apparently associated with a low risk of diabetes, cardiovascular events and all-cause mortality. However, large variability in terms of methods for the evaluation and quantification of polyphenol intake, markers and endpoints considered, makes it still difficult to establish an evidence-based reference intake for the whole class and subclass of compounds. Nevertheless, the critical mass of data available seem to strongly suggest the protective effect of a polyphenol-rich dietary pattern even if further well targeted and methodologically sound research should be encouraged in order to define specific recommendation

Estimated Intakes of Nutrients and Polyphenols in Participants Completing the MaPLE Randomised Controlled Trial and Its Relevance for the Future Development of Dietary Guidelines for the Older Subjects

Abstract: The evaluation of food intake in older subjects is crucial in order to be able to verify adherence to nutritional recommendations. In this context, estimation of the intake of specific dietary bioactives, such as polyphenols, although particularly challenging, is necessary to plan possible intervention strategies to increase their intake. The aims of the present study were to: (i) evaluate the nutritional composition of dietary menus provided in a residential care setting; (ii) estimate the actual intake of nutrients and polyphenols in a group of older subjects participating in the MaPLE study; and (iii) investigate the impact of an eight-week polyphenol-rich dietary pattern, compared to an eight-week control diet, on overall nutrient and polyphenol intake in older participants. The menus served to the participants provided ~770 mg per day of total polyphenols on average with small variations between seasons. The analysis of real consumption, measured using weighed food diaries, demonstrated a lower nutrient (~20%) and polyphenol intake (~15%) compared to that provided by the menus. The feasibility of dietary patterns that enable an increase in polyphenol intake with putative health benefits for age-related conditions is discussed, with a perspective to developing dietary guidelines for this target population. Keywords: nursing home; residential care; aging; menu; flavonoids; phenolic acid

Exploring the topography of free energy surfaces and kinetics of cytochrome c oxidases interacting with small ligands

Free energy landscape explorations have been performed for Cytochrome c Oxidases, aa 3 from Paracoccus denitrificans and ba 3 from Thermus thermophilus, interacting with small gas molecules (CO, NO, O 2), as well as Xe. The calculations were carried out with thermodynamic perturbation theory, the validity of which has been examined by previous molecular dynamics calculations. This approach allows us to bypass the immense computational time required in such problems. The free energy surfaces are constructed as functions of the three Cartesian coordinates of the center of mass of the ligand and averaging over the orientation angles of the molecule. Hydrophilic/hydrophobic cavities and channels around the distal heme-a 3 pocket were detected and the corresponding free energy minima and barriers were estimated. These free energy extrema permit us to extract kinetic parameters and to discuss the biochemical functions of the enzymes in conjunction with experimental results. The conserved cavities found in the two enzymes as well as in previous results of myoglobin demonstrate that topographical characteristics in the distal region of the active sites of the heme oxidase proteins are structurally stable. 2012 The Royal Society of Chemistry

What happens to DNA duplexes in the gas phase?

International audienceIntroduction: DNA duplexes were among the first non-covalent complexes studied by mass spectrometry. Their gas-phase kinetic stability suggested that Watson-Crick base pairing and nearest-neighbor interactions are conserved in vacuo [1,2]. Ion mobility combined with modeling suggested that long duplexes keep a B-helix structure in vacuo, whereas shorter ones (8-16 base pairs) convert into an A-helix [3,4]. Here we challenge this proposal: collision cross sections (CCS) compatible with B-helix or A-helix are indeed obtained at high charge states, but not at the low charge states that predominate in ESI-MS spectra recorded from aqueous solutions at physiological ionic strength. They are much lower. We used extensive molecular dynamics simulations and semi-empirical calculations to understand what happens to DNA duplexes in the gas phase. Methods: Ion mobility spectrometry experiments were carried out on an Agilent 6560 IMS-Q-TOF instrument, and collision cross sections were determined with the drift tube in helium. All molecular dynamics simulations were performed with sander module of AmberTools14 (gas phase) and pmemd module of Amber12 (solution phase), using the parmbsc1 force field (M. Orozco, private communication) which is the latest refinement of parmbsc0, a force field specifically developed for nucleic acids [5]. Semi-empirical calculations were performed with MOPAC software implementing the PM7 method. Preliminary Data: Collision cross sections for [(12-mer)2]5- duplexes range from 700 Ų for a 100%-GC duplex to 750 Ų for a 33%-GC duplex. CCS distributions are broader than the instrumental peak width, indicating that multiple conformations co-exist. The experimental CCSs are all far smaller than that of a B-helix (~900 Ų), and also far smaller than the values reported on more densely charged duplexes of similar size [3,4]. Unbiased MD simulations of protonated duplexes lead to helices which retain some of their initial structural features, but these helices are distorted because hydrogen bonds form between phosphates across the minor groove. Similar gas-phase structures were proposed before [3,6]. Unfortunately, their computed CCS is above 850 Ų, meaning they are far larger than the experimental gas-phase structures of the 5- charge state (although they may represent the structures formed at higher charge states 6- and 7-). For the 5- charge state, the compact structures observed experimentally could be unstructured globular dimers, but this would not explain the persistence of a memory of the sequence in MS/MS experiments [1,2]. We therefore explored biased MD simulation to force the duplex exploring alternative regions on the potential energy surface. In particular, a compaction through hydrogen bond formation between phosphates across the major groove was found to lead the helix to collapse along the longitudinal axis, and the resulting CCSs are now compatible with the experimental ones (even more so when the structures are re-optimized at the semi-empirical level using the PM7 method).Novel Aspect: This work shows that DNA duplexes sprayed in native conditions are actually much more compact than previously thought

Electronic Spectroscopy of Isolated DNA Polyanions

In solution, UV-vis spectroscopy is often used to investigate structural changes in biomolecules (i.e., nucleic acids), owing to changes in the environment of their chromophores (i.e., the nucleobases). Here we address whether action spectroscopy could achieve the same for gas-phase ions, while taking the advantage of additional spectrometric separation of complex mixtures. We therefore systematically studied the action spectroscopy of homo-base 6-mer DNA strands (dG6, dA6, dC6, dT6) and discuss the results in light of gas-phase structures validated by ion mobility spectrometry and infrared ion spectroscopy, of electron binding energies measured by photoelectron spectroscopy, and of calculated electronic photo-absorption spectra. When UV photons interact with oligonucleotide polyanions, two main actions may take place: (1) fragmentation and (2) electron detachment. The action spectra reconstructed from fragmentation follow the absorption spectra well, and result from multiple cycles of absorption and internal conversion. The action spectra reconstructed from the electron photodetachment (ePD) efficiency reveal interesting phenomena: ePD depends on the charge state because it depends on electron binding energies. We illustrate with the G-quadruplex [dTG4T]4 that the ePD action spectrum shifts with the charge state, pointing to possible caveats when comparing the spectra of systems having different charge densities to deduce structural parameters. Moreover, ePD is particularly efficient for purines but not pyrimidines. ePD thus reflects not only absorption, but also particular relaxation pathways of the electronic excited states. As these pathways lead to photo-oxidation, their investigation on model gas-phase systems may prove useful to elucidate mechanisms of photo-oxidative damages, which are linked to mutations and cancers