Protein sequences bound to mineral surfaces persist into deep time.

Proteins persist longer in the fossil record than DNA, but the longevity, survival mechanisms and substrates remain contested. Here, we demonstrate the role of mineral binding in preserving the protein sequence in ostrich (Struthionidae) eggshell, including from the palaeontological sites of Laetoli (3.8 Ma) and Olduvai Gorge (1.3 Ma) in Tanzania. By tracking protein diagenesis back in time we find consistent patterns of preservation, demonstrating authenticity of the surviving sequences. Molecular dynamics simulations of struthiocalcin-1 and -2, the dominant proteins within the eggshell, reveal that distinct domains bind to the mineral surface. It is the domain with the strongest calculated binding energy to the calcite surface that is selectively preserved. Thermal age calculations demonstrate that the Laetoli and Olduvai peptides are 50 times older than any previously authenticated sequence (equivalent to ~16 Ma at a constant 10°C).

Adsorption of poly acrylic acid onto the surface of calcite: an experimental and simulation study.

Macromolecular binding to minerals is of great importance in the formation of biofilms, and carboxylate functional groups have been found to play a pivotal role in the functioning of these macromolecules. Here we present both fluorescence time-resolved anisotropy measurements and simulation data on the conformational behaviour and binding of a poly acrylic acid polymer. In solution the polymer exhibits a pH dependent behaviour, with a coiled conformation at a low pH and extended conformation at higher pH values. The polymer is readily adsorbed on the surface of calcite, preferring to bind in an extended conformation, with the strength of the adsorption dependent on the pH and presence of counter ions. We discuss the reasons why the calculated adsorption free energy differs from that obtained from a Langmuir isotherm analysis, showing that they refer to different quantities. The enhanced binding of the extended conformations shows the importance of flexibility in the binding of macromolecules.

Molecular-level surface structure from nonlinear vibrational spectroscopy combined with simulations.

Vibrational sum-frequency generation spectroscopy is valued for its ability to selectively probe molecules at a variety of interfaces without the use of extrinsic chromophores. The spectra contain valuable information regarding the molecular structure and the interfacial environment through the observation of vibrational resonances associated with specific moieties. Chemical information is obtained by close inspection of the frequencies of these bands and the amplitude of the response under conditions of different beam polarizations. Such sensitivity motivates the development of techniques that can provide structural details. We illustrate several approaches by which various types of calculations and molecular simulations may be used to enhance the sought structural interpretation of experimental data. By applying these techniques to the adsorbate molecules, interfacial water, and the substrate surfaces themselves, we are able to achieve a holistic picture of the adsorption environment.

Combined Stokes vector and Mueller matrix polarimetry for materials characterization.

A robust way of measuring the optical properties of any material is to interrogate it with light of different polarizations. The 16-element Mueller matrix provides the most complete description of the optical properties of a sample based on its ability to alter the polarization state of transmitted or reflected light. This is valuable for ordered and isotropic materials alike. Similarly, the 4-element Stokes vector is the most complete description of the polarization of a light beam, including any depolarization effects. While the Mueller matrix offers the most chemical and physical insight, the Stokes vectors are easier to obtain, and there are more schemes for measuring them quickly in situations where time resolution is important. We describe a method where any Stokes polarimeter may be adapted to obtain Mueller matrices and discuss various approaches for achieving better time resolution.

Towards an improved anti-HIV activity of NRTI via metal-organic frameworks nanoparticles.

Nanoscale mesoporous iron carboxylates metal-organic frameworks (nanoMOFs) have recently emerged as promising platforms for drug delivery, showing biodegradability, biocompatibility and important loading capability of challenging highly water-soluble drugs such as azidothymidine tryphosphate (AZT-TP). In this study, nanoMOFs made of iron trimesate (MIL-100) were able to act as efficient molecular sponges, quickly adsorbing up to 24 wt% AZT-TP with entrapment efficiencies close to 100%, without perturbation of the supramolecular crystalline organization. These data are in agreement with molecular modelling predictions, indicating maximal loadings of 33 wt% and preferential location of the drug in the large cages. Spectrophotometry, isothermal titration calorimetry, and solid state NMR investigations enable to gain insight on the mechanism of interaction of AZT and AZT-TP with the nanoMOFs, pointing out the crucial role of phosphates strongly coordinating with the unsaturated iron(III) sites. Finally, contrarily to the free AZT-TP, the loaded nanoparticles efficiently penetrate and release their cargo of active triphosphorylated AZT inside major HIV target cells, efficiently protecting against HIV infection.

Impact of phosphorylation on the encapsulation of nucleoside analogues within porous iron(iii) metal-organic framework MIL-100(Fe) nanoparticles.

Encapsulation of azidothymidine (AZT) or its phosphorylated derivatives (AZT-MP and AZT-TP) has been performed using nanoparticles of the porous crystalline iron(iii) trimesate metal-organic framework MIL-100(Fe). The number of phosphate groups per nucleoside analogue has a high impact on the drug loading capacity, and their interaction with the Lewis acid sites from the nanoMOFs is also discussed through a combination of techniques such as UV-vis absorption, circular dichroism, isothermal titration calorimetry, HPLC and molecular simulations. Finally, the effect of the differences in terms of host-guest interactions is discussed through the release in physiological buffers of AZT, AZT-MP and AZT-TP. New perspectives for the nanoencapsulation of monophosphorylated nucleoside analogues for effective anti-cancer and anti-viral therapies are then discussed.