Protein-ligand NOE matching: a high-throughput method for binding pose evaluation that does not require protein NMR resonance assignments

Given the three-dimensional (3D) structure of a protein, the binding pose of a ligand can be determined using distance restraints derived from assigned intra-ligand and protein-ligand nuclear Overhauser effects (NOEs). A primary limitation of this approach is the need for resonance assignments of the ligand-bound protein. We have developed an approach that utilizes data from 3D 13C-edited, 13C/15N-filtered HSQC-NOESY spectra for evaluating ligand binding poses without requiring protein NMR resonance assignments. Only the 1H NMR assignments of the bound ligand are essential. Trial ligand binding poses are generated by any suitable method (e.g., computational docking). For each trial binding pose, the 3D 13C-edited, 13C/15N-filtered HSQC-NOESY spectrum is predicted, and the predicted and observed patterns of protein-ligand NOEs are matched and scored using a fast, deterministic bipartite graph matching algorithm. The best scoring (lowest "cost") poses are identified. Our method can incorporate any explicit restraints or protein assignment data that are available, and many extensions of the basic procedure are feasible. Only a single sample is required, and the method can be applied to both slowly and rapidly exchanging ligands. The method was applied to three test cases: one complex involving muscle fatty acid-binding protein (mFABP) and two complexes involving the leukocyte function-associated antigen 1 (LFA-1) I-domain. Without using experimental protein NMR assignments, the method identified the known binding poses with good accuracy. The addition of experimental protein NMR assignments improves the results. Our "NOE matching" approach is expected to be widely applicable; i.e., it does not appear to depend on a fortuitous distribution of binding pocket residues.     

Graphs, networks, and linear unbiased estimates

It is shown how a best linear unbiased estimate (blue) in the additive variety-block setting can be interpreted as a network flow, that is, a function on edges that obeys the Kirkhhoff laws, of minimum square norm. An explicit expression is then obtained for the coefficients of the blue in terms of invariants of the underlying network; specifically, the invariants are: the total number of spanning trees and the number of certain selective yet specific spanning forests with just two trees. The blue is also expressed as a linear combination of bases of paths in a constructive manner. It remains a conjecture as to whether there always exists a basis of paths in which the blue is a convex combination. Consequences to design optimality are explored.     

First principles study of the ground and excited states of FeO, FeO+, and FeO(-)

Through a variety of highly correlated methods combined with large basis sets we have studied the electronic structure of FeO, FeO(+), and FeO(-). In particular, we have constructed complete potential energy curves for 48, 24, and 4 states for the FeO, FeO(+), and FeO(-) species, respectively, at the multireference level of theory. For all states examined we report energetics, common spectroscopic parameters, and dipole moments. Overall our results are in good agreement with experiment, but we have encountered as well interesting differences between experiment and theory deserving further investigation.     

A revisit to the retention mechanism of hydrophilic interaction liquid chromatography using model organic compounds

In this work, a revisit to the retention mechanism of HILIC was attempted to point out critical factors that contribute to the chromatographic regime as well as to bring out subtle details of the relative contribution of partitioning and surface adsorption. In this vein, the retention behaviour of a set of water-soluble vitamins (WSVs) and toluene on three silica based columns was evaluated under varying chromatographic conditions. The data obtained were associated with the hydration degree of the stationary phases and the ability of the organic solvents to disrupt the formation of the water-enriched layer. Moreover, the elution behaviour of toluene at different buffer salt concentrations in the mobile phase, confirmed the preferential partition of salt ions into the stagnant layer, as ACN content was increased. The results from the fitting of partitioning and surface adsorption models indicated differences in the contribution of the two retention mechanisms to both neutral and charged compounds. The occurrence of surface adsorption and the retentivity differences for neutral WSVs depend on the hydration degree and the hydrogen bonding properties of the solutes and the column surface, respectively. For charged solutes experiencing electrostatic repulsion, the contribution of the adsorption mechanism at highly organic mobile phases, emanates from both the weak effect of buffer salt ions on the electrostatic interaction and the strong effect of hydrophilic interactions. On the other hand, the chromatographic retention of electrostatically attracted solutes indicates that the surface adsorption dominates, even at mobile phases rich in water.     

ANNOUNCEMENT

A special issue of Acta Mathematica Scientia, to be published in 2011, will be dedicated to the 85th birthday of Peter D. Lax, who is one of the most promi- nent mathematicians of     

Preface

This special issue of Acta Mathematica Scientia is dedicated to the 85th birthday of Peter D. Lax, one of the most prominent mathematicians of the past hundred years. Peter Lax has made important and seminal contributions in many areas of pure and applied mathematics, including the theory of integrable systems and solitons, the