Formation of hydrophobic contacts across a newly formed interface is energetically favorable. Based on this observation we developed a geometric-hydrophobic docking algorithm that estimates quantitatively the hydrophobic complementarity at protein-protein interfaces. Each molecule to be docked is represented as a grid of complex numbers, storing information regarding the shape of the molecule in the real part and information regarding the hydropathy of the surface in the imaginary part. The grid representations are correlated using fast Fourier transformations. The algorithm is used to compare the extent of hydrophobic complementarity in oligomers (represented by D2 tetramers) and in hetero-dimers of soluble proteins (complexes). We also test the implication of hydrophobic complementarity in distinguishing correct from false docking solutions. We find that hydrophobic complementarity at the interface exists in oligomers and in complexes, and in both groups the extent of such complementarity depends on the size of the interface. Thus, the non-polar portions of large interfaces are more often juxtaposed than non-polar portions of small interfaces. Next we find that hydrophobic complementarity helps to point out correct docking solutions. In oligomers it significantly improves the ranks of nearly correct reassembled and modeled tetramers. Combining geometric, electrostatic and hydrophobic complementarity for complexes gives excellent results, ranking a nearly correct solution < 10 for 5 of 23 tested systems, < 100 for 8 systems and < 1000 for 19 systems.
A scheme enabling the acquisition of high-resolution nuclear magnetic resonance (NMR) spectra within inhomogeneous magnetic fields is introduced and exemplified. The scheme is based on the spatial encoding protocol recently introduced for collecting multidimensional NMR data within a single scan, which retrieves spectral information via interference phenomena between spin packets located at distinct positions within the sample. This in turn enables compensating for field inhomogeneities over the sample as a whole by shifting the phases of the radio-frequency pulses involved in the spatial encoding, rather than by demanding an extreme uniformity in the employed magnetic field. The upper tolerable field inhomogeneity limit thus becomes orders of magnitude higher than that in conventional time-domain acquisitions. No particular spatial dependencies are demanded by the new scheme, which can yield its high-resolution results on a single-scan basis.
We have recently proposed and demonstrated an approach that enables the acquisition of multidimensional nuclear magnetic resonance (NMR) spectra within a single scan. A promising application opened up by this new accelerated form of data acquisition concerns the possibility of monitoring in real time the chemical nature of analytes subject to a continuous flow. The present paper illustrates such potential, with the real-time acquisition of a series of 2D 1H NMR spectra arising from a mixture of compounds subject to a continuous liquid chromatography (LC) separation. This real-time 2D NMR identification of chemicals eluted minutes apart under usual LC-NMR conditions differs from the way in which LC-2D NMR has hitherto been carried out, which relies on stopped-flow modes of operations whereby fractions are first collected and then subject to individual, aliquot-by-aliquot analyses. The real-time LC-2D NMR experiment hereby introduced can be implemented in a straightforward manner using modern commercial LC-NMR hardware, thus opening up immediate possibilities in high-throughput characterizations of complex molecules.
A recently proposed protocol enables the acquisition of two-dimensional nuclear magnetic resonance (2D NMR) spectra within a single scan. A promising application opened up by this new data acquisition mode concerns its combination with active nuclear polarization methods, whereby spectroscopy is carried out on analytes whose spin magnetizations have been significantly enhanced over their Boltzmann thermal values. The present paper explores the potential of such combination, with the acquisition of peptide and protein 2D NMR 1H correlation spectra recorded after the samples had been subject to laser-driven chemically induced dynamic nuclear polarization (CIDNP). It is demonstrated that the speed and sensitivity enhancement afforded by these combined processes enables the acquisition of quality 2D NMR data sets within a fraction of a second, at analyte concentrations that are under 1 mM.
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