Characterization of a quasicrystalline phase in codispersions of phosphatidylethanolamine and glucocerebroside

Synchrotron x-ray diffraction, differential scanning calorimetry, and electron spin resonance spectroscopy have been employed to characterize a quasicrystalline phase formed in aqueous dispersions of binary mixtures of glucocerebroside and palmitoyloleoylphosphatidylethanolamine. Small- and wide-angle x-ray scattering intensity patterns were recorded during temperature scans between 20 degrees and 90 degrees C from mixtures of composition 2, 5, 10, 20, 30, and 40 mol glucocerebroside per 100 mol phospholipid. The quasicrystalline phase was characterized by a broad lamellar d-spacing of 6.06 nm at 40 degrees C and a broad wide-angle x-ray scattering band centered at approximately 0.438 nm, close to the gel phase centered at approximately 0.425 nm and distinct from a broad peak centered at 0.457 nm observed for a liquid-crystal phase at 80 degrees C. The quasicrystalline phase coexisted with gel and fluid phase of the pure phospholipid. An analysis of the small-angle x-ray scattering intensity profiles indicated a stoichiometry of one glucosphingolipid per two phospholipid molecules in the complex. Structural transitions monitored in cooling scans by synchrotron x-ray diffraction indicated that a cubic phase transforms initially into a lamellar gel. Thermal studies showed that the gel phase subsequently relaxes into the quasicrystalline phase in an exothermic transition. Electron spin resonance spectroscopy using spin labels located at positions 7, 12, and 16 carbons of phospholipid hydrocarbon chains indicated that order and motional constraints at the 7 and 12 positions were indistinguishable between gel and quasicrystalline phases but there was a significant decrease in order and increase in rate of motion at the 16 position on transformation to the quasicrystalline phase. The results are interpreted as an arrangement of polar groups of the complex in a crystalline array and a quasicrystalline packing of the hydrocarbon chains predicated by packing problems in the bilayer core requiring disordering of the highly asymmetric chains. The possible involvement of quasicrystalline phases in formation of membrane rafts is considered.     

A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction

Background  

Current scoring functions are not very successful in protein-ligand binding affinity prediction albeit their popularity in structure-based drug designs. Here, we propose a general knowledge-guided scoring (KGS) strategy to tackle this problem. Our KGS strategy computes the binding constant of a given protein-ligand complex based on the known binding constant of an appropriate reference complex. A good training set that includes a sufficient number of protein-ligand complexes with known binding data needs to be supplied for finding the reference complex. The reference complex is required to share a similar pattern of key protein-ligand interactions to that of the complex of interest. Thus, some uncertain factors in protein-ligand binding may cancel out, resulting in a more accurate prediction of absolute binding constants.     

Probabilistic Prediction of Contacts in Protein-Ligand Complexes

We introduce a statistical method for evaluating atomic level 3D interaction patterns of protein-ligand contacts. Such patterns can be used for fast separation of likely ligand and ligand binding site combinations out of all those that are geometrically possible. The practical purpose of this probabilistic method is for molecular docking and scoring, as an essential part of a scoring function. Probabilities of interaction patterns are calculated conditional on structural x-ray data and predefined chemical classification of molecular fragment types. Spatial coordinates of atoms are modeled using a Bayesian statistical framework with parametric 3D probability densities. The parameters are given distributions a priori, which provides the possibility to update the densities of model parameters with new structural data and use the parameter estimates to create a contact hierarchy. The contact preferences can be defined for any spatial area around a specified type of fragment. We compared calculated contact point hierarchies with the number of contact atoms found near the contact point in a reference set of x-ray data, and found that these were in general in a close agreement. Additionally, using substrate binding site in cathechol-O-methyltransferase and 27 small potential binder molecules, it was demonstrated that these probabilities together with auxiliary parameters separate well ligands from decoys (true positive rate 0.75, false positive rate 0). A particularly useful feature of the proposed Bayesian framework is that it also characterizes predictive uncertainty in terms of probabilities, which have an intuitive interpretation from the applied perspective.     

Hydrophilic/Hydrophobic balance determines morphology of glycolipids with oligolactose headgroups

The morphology of synthetic glycolipids with lactose oligomers (Lac N, the number of lactose units, N = 1, 2, 3) was studied in lamellar phase. By a systematic combination of differential scanning calorimetry and small- and wide-angle x-ray scattering experiments, the effects of hydrophilic/hydrophobic balance on their thermotropic phase behaviors were discussed. The dispersion of Lac 1 exhibited a crystalline-fluid phase transition, dominated by the strong van der Waals interaction between dihexadecyl chains. In the case of Lac 2, the hydrophilic/hydrophobic balance between the headgroup and the alkyl chains is shifted to the hydrophilic side, resulting in a gel-fluid phase transition with a decreased transition temperature and phase transition enthalpy. Different from the first two systems, the differential scanning calorimetry trace of Lac 3 showed much less remarkable peaks. The small- and wide-angle x-ray diffraction patterns did not reveal any transition in the chain ordering, suggesting that the correlation between the hexasaccharide headgroups is so strong that the melting of the alkyl chains was not allowed. Such dominant effects of the hydrophilic/hydrophobic balance on the morphology of Lac N lipids can be attributed to the small sterical mismatch between the alkyl chains and the linear, cylindrical oligolactose groups.     

Analysis of knowledge-based protein-ligand potentials using a self-consistent method

We propose a self-consistent approach to analyze knowledge-based atom-atom potentials used to calculate protein-ligand binding energies. Ligands complexed to actual protein structures were first built using the SMoG growth procedure (DeWitte & Shakhnovich, 1996) with a chosen input potential. These model protein-ligand complexes were used to construct databases from which knowledge-based protein-ligand potentials were derived. We then tested several different modifications to such potentials and evaluated their performance on their ability to reconstruct the input potential using the statistical information available from a database composed of model complexes. Our data indicate that the most significant improvement resulted from properly accounting for the following key issues when estimating the reference state: (1) the presence of significant nonenergetic effects that influence the contact frequencies and (2) the presence of correlations in contact patterns due to chemical structure. The most successful procedure was applied to derive an atom-atom potential for real protein-ligand complexes. Despite the simplicity of the model (pairwise contact potential with a single interaction distance), the derived binding free energies showed a statistically significant correlation (approximately 0.65) with experimental binding scores for a diverse set of complexes.     

Detection of functional ligand-binding events using synchrotron x-ray scattering

Small-molecule ligands that change the structure of a protein are likely to affect its function, whereas those causing no structural change are less likely to be functional. Wide-angle x-ray scattering (WAXS) can be easily carried out on proteins and small molecules in solution in the absence of chemical tags or derivatives. The authors demonstrate that WAXS is a sensitive probe of ligand binding to proteins in solution and can distinguish between nonfunctional and productive binding. Furthermore, similar ligand-binding modes translate into similar scattering patterns. This approach has high potential as a novel, generic, low-throughput assay for functional ligand binding.     

Interpretation of Solution X-Ray Scattering by Explicit-Solvent Molecular Dynamics

Small- and wide-angle x-ray scattering (SWAXS) and molecular dynamics (MD) simulations are complementary approaches that probe conformational transitions of biomolecules in solution, even in a time-resolved manner. However, the structural interpretation of the scattering signals is challenging, while MD simulations frequently suffer from incomplete sampling or from a force-field bias. To combine the advantages of both techniques, we present a method that incorporates solution scattering data as a differentiable energetic restraint into explicit-solvent MD simulations, termed SWAXS-driven MD, with the aim to direct the simulation into conformations satisfying the experimental data. Because the calculations fully rely on explicit solvent, no fitting parameters associated with the solvation layer or excluded solvent are required, and the calculations remain valid at wide angles. The complementarity of SWAXS and MD is illustrated using three biological examples, namely a periplasmic binding protein, aspartate carbamoyltransferase, and a nuclear exportin. The examples suggest that SWAXS-driven MD is capable of refining structures against SWAXS data without foreknowledge of possible reaction paths. In turn, the SWAXS data accelerates conformational transitions in MD simulations and reduces the force-field bias.     

Binding MOAD (Mother Of All Databases)

Binding MOAD (Mother of All Databases) is the largest collection of high-quality, protein-ligand complexes available from the Protein Data Bank. At this time, Binding MOAD contains 5331 protein-ligand complexes comprised of 1780 unique protein families and 2630 unique ligands. We have searched the crystallography papers for all 5000+ structures and compiled binding data for 1375 (26%) of the protein-ligand complexes. The binding-affinity data ranges 13 orders of magnitude. This is the largest collection of binding data reported to date in the literature. We have also addressed the issue of redundancy in the data. To create a nonredundant dataset, one protein from each of the 1780 protein families was chosen as a representative. Representatives were chosen by tightest binding, best resolution, etc. For the 1780 "best" complexes that comprise the nonredundant version of Binding MOAD, 475 (27%) have binding data. This significant collection of protein-ligand complexes will be very useful in elucidating the biophysical patterns of molecular recognition and enzymatic regulation. The complexes with binding-affinity data will help in the development of improved scoring functions and structure-based drug discovery techniques. The dataset can be accessed at http://www.BindingMOAD.org.     

Use of Relibase for retrieving complex three-dimensional interaction patterns including crystallographic packing effects

Relibase is a database system that has been specially designed to handle protein-ligand data. Included within Relibase is a tool that can be used to systematically analyse protein-ligand interaction patterns specified by three-dimensional (3D) constraints, revealing favorable combinations of interacting functional groups and their preferred interaction geometries. This paper describes the Relibase 3D query tools, including novel extensions (Relibase+) for handling crystallographic packing effects. Examples illustrating the broad range of functionality for defining 3D interaction patterns and the application of such queries in drug design comprise carbonyl-carbonyl interactions, zinc binding site environments, and ligand-ligand interactions in the crystal packing.     

Structural evolution of regenerated silk fibroin under shear: combined wide- and small-angle x-ray scattering experiments using synchrotron radiation

The structural evolution of regenerated Bombyx mori silk fibroin during shearing with a Couette cell has been studied in situ by synchrotron radiation small- and wide-angle x-ray scattering techniques. An elongation of fibroin molecules was observed with increasing shear rate, followed by an aggregation phase. The aggregates were found to be amorphous with beta-conformation according to infrared spectroscopy. Scanning x-ray microdiffraction with a 5 microm beam on aggregated material, which had solidified in air, showed silk II reflections and a material with equatorial reflections close to the silk I structure reflections, but with strong differences in reflection intensities. This silk I type material shows up to two low-angle peaks suggesting the presence of water molecules that might be intercalated between hydrogen-bonded sheets.     

Protein-protein and protein-ligand interactions studied by electrospray-ionization mass spectrometry

Preservation of non-covalent interactions in biopolymer mass spectrometry offers new approaches to binding analysis. Recent work from our laboratory is reviewed here and discussed with reference to recent literature in the field. Three issues are considered in particular: hydrophobically stabilized complexes, pH-dependent transitions, and linked protein-ligand and protein-protein binding equilibria.     

A study of apo- and holo-forms of horse liver alcohol dehydrogenase in solution by diffuse x-ray scattering

Apo- and holo-forms of horse liver alcohol dehydrogenase (LADH) in solution were studied by diffuse x-ray scattering. Experimental scattering curves for apo- and holo-forms coincide both with the curves calculated from the crystal structures of apo- and holo-enzymes, and with each other. Thus the “sliding” of catalytical domains in LADH upon substrate binding, which has been shown by x-ray analysis, cannot be detected by diffuse x-ray scattering. Sensitivity of the scattering curves to the domain displacements of sliding and “locking” types has been investigated. It has been shown that the scattering curves of LADH are rather sensitive to the domain “unlocking.” However, these curves change only slightly upon sliding of domains, including the sliding of domains observed in LADH by x-ray analysis.     

Conformation of peptides in lipid membranes studied by x-ray grazing incidence scattering

Although the antimicrobial, fungal peptide alamethicin has been extensively studied, the conformation of the peptide and the interaction with lipid bilayers as well as the mechanism of channel gating are still not completely clear. As opposed to studies of the crystalline state, the polypeptide structures in the environment of fluid bilayers are difficult to probe. We have investigated the conformation of alamethicin in highly aligned stacks of model lipid membranes by synchrotron-based x-ray scattering. The (wide-angle) scattering distribution has been measured by reciprocal space mappings. A pronounced scattering signal is observed in samples of high molar peptide/lipid ratio which is distinctly different from the scattering distribution of an ideal helix in the transmembrane state. Beyond simple models of ideal helices, the data is analyzed in terms of models based on atomic coordinates from the Brookhaven Protein Data Bank, as well as from published molecular dynamics simulations. The results can be explained by assuming a wide distribution of helix tilt angles with respect to the membrane normal and a partial insertion of the N-terminus into the membrane.     

The relationship between zeros and factors of binding polynomials and cooperativity in protein-ligand binding

Cooperativity in the protein-ligand binding process is discussed in terms of the zeros of the binding polynomial and the corresponding possible factorizations of the binding polynomial into polynomials having non-negative coefficients. Particular attention is paid to the case in which the real parts of all zeros are negative (Hurwitz polynomial) and the case in which the binding polynomial admits no positive factorization (positive irreducible polynomial). Such factorizations are then interpreted as site linkage patterns and related to cooperativity. The possible combinations of zeros of the binding polynomials for the MWC and KNF tetrahedral, square and linear models are determined and the corresponding factorization and linkage patterns analyzed. An application and interpretation are then made for data obtained from Trout I hemoglobin.     

Evaluation of site-directed spin labeling for characterizing protein-ligand complexes using simulated restraints

Simulation studies have been performed to evaluate the utility of site-directed spin labeling for determining the structures of protein-ligand complexes, given a known protein structure. Two protein-ligand complexes were used as model systems for these studies: a 1.9-A-resolution x-ray structure of a dihydrofolate reductase mutant complexed with methotrexate, and a 1.5-A-resolution x-ray structure of the V-Src tyrosine kinase SH2 domain complexed with a five-residue phosphopeptide. Nitroxide spin labels were modeled at five dihydrofolate reductase residue positions and at four SH2 domain residue positions. For both systems, after energy minimization, conformational ensembles of the spin-labeled residues were generated by simulated annealing while holding the remainder of the protein-ligand complex fixed. Effective distances, simulating those that could be obtained from (1)H-NMR relaxation measurements, were calculated between ligand protons and the spin labels. These were converted to restraints with several different levels of precision. Restrained simulated annealing calculations were then performed with the aim of reproducing target ligand-binding modes. The effects of incorporating a few supplementary short-range (< or =5.0 A) distance restraints were also examined. For the dihydrofolate reductase-methotrexate complex, the ligand-binding mode was reproduced reasonably well using relatively tight spin-label restraints, but methotrexate was poorly localized using loose spin-label restraints. Short-range and spin-label restraints proved to be complementary. For the SH2 domain-phosphopeptide complex without the short-range restraints, the peptide did not localize to the correct depth in the binding groove; nevertheless, the orientation and internal conformation of the peptide was reproduced moderately well. Use of the spin-label restraints in conjunction with the short-range restraints resulted in relatively well defined structural ensembles. These results indicate that restraints derived from site-directed spin labeling can contribute significantly to defining the orientations and conformations of bound ligands. Accurate ligand localization appears to require either a few supplementary short-range distance restraints, or relatively tight spin-label restraints, with at least one spin label positioned so that some of the restraints draw the ligand into the binding pocket in the latter case.     

Study of binding protein-ligand interaction by ammonium sulfate-assisted adsorption on cellulose esters filters

A technique for the study of neutral carbohydrate binding protein-ligand interaction is described in this report. It is based on filtration on cellulose esters filters of a mixture of the binding protein and the radioactive ligand, following a treatment of this mixture with ammonium sulfate; the technique is described for the galactose binding protein and for the maltose binding protein of Escherichia coli. For the galactose binding protein, an ammonium sulfate concentration far below that required for precipitation of the protein is sufficient to promote an almost complete retention of the protein on the filters. Furthermore, the addition of ammonium sulfate does not modify the amount of preexisting binding protein-ligand complex, and, in much less than one second, leads to a conformation of the protein-ligand complex which does not allow further ligand binding or dissociation. Hence, the technique is not only very useful for the detection of binding proteins in crude extracts and during purification procedures, it is also of value in the determination of the kinetic parameters of protein-ligand interactions.     

Knowledge-based scoring function to predict protein-ligand interactions

The development and validation of a new knowledge-based scoring function (DrugScore) to describe the binding geometry of ligands in proteins is presented. It discriminates efficiently between well-docked ligand binding modes (root-mean-square deviation <2.0 A with respect to a crystallographically determined reference complex) and those largely deviating from the native structure, e.g. generated by computer docking programs. Structural information is extracted from crystallographically determined protein-ligand complexes using ReLiBase and converted into distance-dependent pair-preferences and solvent-accessible surface (SAS) dependent singlet preferences for protein and ligand atoms. Definition of an appropriate reference state and accounting for inaccuracies inherently present in experimental data is required to achieve good predictive power. The sum of the pair preferences and the singlet preferences is calculated based on the 3D structure of protein-ligand binding modes generated by docking tools. For two test sets of 91 and 68 protein-ligand complexes, taken from the Protein Data Bank (PDB), the calculated score recognizes poses generated by FlexX deviating <2 A from the crystal structure on rank 1 in three quarters of all possible cases. Compared to FlexX, this is a substantial improvement. For ligand geometries generated by DOCK, DrugScore is superior to the "chemical scoring" implemented into this tool, while comparable results are obtained using the "energy scoring" in DOCK. None of the presently known scoring functions achieves comparable power to extract binding modes in agreement with experiment. It is fast to compute, regards implicitly solvation and entropy contributions and produces correctly the geometry of directional interactions. Small deviations in the 3D structure are tolerated and, since only contacts to non-hydrogen atoms are regarded, it is independent from assumptions of protonation states.     

Quantification of collagen organization in the peripheral human cornea at micron-scale resolution

The collagen microstructure of the peripheral cornea is important in stabilizing corneal curvature and refractive status. However, the manner in which the predominantly orthogonal collagen fibrils of the central cornea integrate with the circumferential limbal collagen is unknown. We used microfocus wide-angle x-ray scattering to quantify the relative proportion and orientation of collagen fibrils over the human corneolimbal interface at intervals of 50 μm. Orthogonal fibrils changed direction 1–1.5 mm before the limbus to integrate with the circumferential limbal fibrils. Outside the central 6 mm, additional preferentially aligned collagen was found to reinforce the cornea and limbus. The manner of integration and degree of reinforcement varied significantly depending on the direction along which the limbus was approached. We also employed small-angle x-ray scattering to measure the average collagen fibril diameter from central cornea to limbus at 0.5 mm intervals. Fibril diameter was constant across the central 6 mm. More peripherally, fibril diameter increased, indicative of a merging of corneal and scleral collagen. The point of increase varied with direction, consistent with a scheme in which the oblique corneal periphery is reinforced by chords of scleral collagen. The results have implications for the cornea's biomechanical response to ocular surgeries involving peripheral incision.