Quantification of protein-ligand interactions by mass spectrometry,titration, and H/D exchange: PLIMSTEX

Protein-ligand binding and the concomitant conformational change in the protein are of crucial importance in biophysics and drug design. We report a novel method to quantify protein-ligand interactions in solution by mass spectrometry, titration, and H/D exchange (PLIMSTEX). The approach can determine the conformational change, binding stoichiometry, and affinity in protein-ligand interactions including those that involve small molecules, metal ions, and peptides. Binding constants obtained by PLIMSTEX for four model protein-ligand systems agree with K values measured by conventional methods. At higher protein concentration, the method can be used to determine quickly the binding stoichiometry and possibly the purity of proteins. Taking advantage of concentrating the protein on-column and desalting, we are able to use different concentrations of proteins, buffer systems, salts, and pH in the exchange protocol. High picomole quantities of proteins are sufficient, offering significantly better sensitivity than that of NMR and X-ray crystallography. Automation could make PLIMSTEX a high throughput method for library screening, drug discovery, and proteomics.     

Effects of extending the computational model on DNA-protein T-shaped interactions: the case of adenine-histidine dimers

The MP2/6-31G*(0.25) π-π or π(+)-π T-shaped (edge-to-face) interactions between neutral or protonated histidine and adenine were considered using computational models of varying size to determine the effects of the protein and DNA backbones on the preferred dimer structure and binding strength. The overall consequences of the backbones are reasonably subtle for the neutral adenine-histidine T-shaped dimers. Furthermore, the minor changes in the binding strengths of these dimers upon model extension arise from additional (attractive) backbone-π (bb-π) contacts and changes in the preferred π-π orientations, which is verified by the quantum theory of atoms in molecules (QTAIM). Since the binding strength of the extended dimer equals the sum of the individual backbone-π and π-π contributions, the π-π component is not appreciably affected by polarization of the ring upon inclusion of the biological backbone. In contrast, the larger effect of the backbone on the protonated histidine dimers cannot simply be predicted as the sum of changes in the π-π and bb-π components regardless of the dimer type or model. This suggests, and QTAIM qualitatively supports, that the magnitude of the π(+)-π contribution changes, which is likely due to alterations in the electrostatic landscape of the monomer rings upon inclusion of the biological backbone that largely affect T-shaped dimers. These findings differ from those previously reported for (neutral) π-π stacked and (metallic) cation-π interactions, which highlights the distinct properties of each (π-π, π(+)-π, and cation-π) classification of noncovalent interaction. Furthermore, these results emphasize the importance of considering backbone-π interactions when analyzing contacts that appear in experimental crystal structures and cautions the use of truncated models when evaluating the magnitude of the π(+)-π contribution present in large biological complexes.     

Combining weak affinity chromatography, NMR spectroscopy and molecular simulations in carbohydrate-lysozyme interaction studies

By examining the interactions between the protein hen egg-white lysozyme (HEWL) and commercially available and chemically synthesized carbohydrate ligands using a combination of weak affinity chromatography (WAC), NMR spectroscopy and molecular simulations, we report on new affinity data as well as a detailed binding model for the HEWL protein. The equilibrium dissociation constants of the ligands were obtained by WAC but also by NMR spectroscopy, which agreed well. The structures of two HEWL-disaccharide complexes in solution were deduced by NMR spectroscopy using (1)H saturation transfer difference (STD) effects and transferred (1)H,(1)H-NOESY experiments, relaxation-matrix calculations, molecular docking and molecular dynamics simulations. In solution the two disaccharides β-d-Galp-(1→4)-β-D-GlcpNAc-OMe and β-D-GlcpNAc-(1→4)-β-D-GlcpNAc-OMe bind to the B and C sites of HEWL in a syn-conformation at the glycosidic linkage between the two sugar residues. Intermolecular hydrogen bonding and CH/π-interactions form the basis of the protein-ligand complexes in a way characteristic of carbohydrate-protein interactions. Molecular dynamics simulations with explicit water molecules of both the apo-form of the protein and a ligand-protein complex showed structural change compared to a crystal structure of the protein. The flexibility of HEWL as indicated by a residue-based root-mean-square deviation analysis indicated similarities overall, with some residue specific differences, inter alia, for Arg61 that is situated prior to a flexible loop. The Arg61 flexibility was notably larger in the ligand-complexed form of HEWL. N,N'-Diacetylchitobiose has previously been observed to bind to HEWL at the B and C sites in water solution based on (1)H NMR chemical shift changes in the protein whereas the disaccharide binds at either the B and C sites or the C and D sites in different crystal complexes. The present study thus highlights that protein-ligand complexes may vary notably between the solution and solid states, underscoring the importance of targeting the pertinent binding site(s) for inhibition of protein activity and the advantages of combining different techniques in a screening process.     

Solid-state fluorescence of squarylium dyes

An N-butyl indolenine squarylium dye could include toluene and p-xylene and exhibited the solid-state fluorescence in near-infrared region (F_max=761 nm) in crystalline form due to inhibition of π/π-interactions between the fluorophores.     

FAST-NMR: functional annotation screening technology using NMR spectroscopy

An abundance of protein structures emerging from structural genomics and the Protein Structure Initiative (PSI) are not amenable to ready functional assignment because of a lack of sequence and structural homology to proteins of known function. We describe a high-throughput NMR methodology (FAST-NMR) to annotate the biological function of novel proteins through the structural and sequence analysis of protein-ligand interactions. This is based on basic tenets of biochemistry where proteins with similar functions will have similar active sites and exhibit similar ligand binding interactions, despite global differences in sequence and structure. Protein-ligand interactions are determined through a tiered NMR screen using a library composed of compounds with known biological activity. A rapid co-structure is determined by combining the experimental identification of the ligand binding site from NMR chemical shift perturbations with the protein-ligand docking program AutoDock. Our CPASS (Comparison of Protein Active Site Structures) software and database are then used to compare this active site with proteins of known function. The methodology is demonstrated using unannotated protein SAV1430 from Staphylococcus aureus.     

Intramolecular interactions in crystals of tris(2,6-diisopropylphenoxy)silanethiol and its sodium salts

Hydrolytically stable silanethiol tris(2,6-diisopropylphenoxy)silanethiol (TDST) has been synthesized and reacted with sodium metal. In solid state TDST exhibits π-interactions between the S-H unit and the π-system of the arene, replaced by cation-π interactions in its sodium salts. The interactions are documented by crystal structures and FT-IR spectroscopy.     

High-throughput screening assay for the tunable selection of protein ligands

Here, we describe a new protein-ligand binding assay that is amenable to high-throughput screening applications. The assay involves the use of SUPREX (stability of unpurified proteins from rates of H/D exchange), a new H/D exchange and mass spectrometry-based technique we recently developed for the quantitative analysis of protein-ligand binding interactions. As part of this work, we describe a new high-throughput SUPREX protocol, and we demonstrate that this protocol can be used to efficiently screen peptide ligands in a model combinatorial library for binding to a model protein system, the S-protein. The high-throughput SUPREX protocol developed here is generally applicable to a wide variety of protein ligands, including DNA, small molecules, metals, and other proteins. On the basis of the results of the model study in this work, one person with access to one MALDI mass spectrometer should be able to screen approximately 10 000 compounds per 24-h period using the protocol described here. With full automation and the use of a commercially available MALDI mass spectrometer optimized for high-throughput analyses, we estimate that the SUPREX-based assay described here could be used to screen on the order of 100 000 ligands per day.     

Peculiarities of inclusion complex formation in the 1,4-benzodiazepine-benzene system

5-Phenyl-1-methyl-7-bromo-3-hydroxy-1,2-dihydro-3H-1,4-benzodiazepin-2-one and its 5-(o-chloro)-phenyl analog form 2:1 (host:guest) inclusion compounds with benzene. The crystal structures of the compounds were studied by the single-crystal XRD method and were interpreted as host (H) (benzodiazepine) — guest (G) (benzene solvent molecule) complexes. The studied structures, revealing H-H and H-G interactions as both typical hydrogen bonds and π-π, C-H?π weak interactions, may serve as models for ligand-receptor binding.     

Characterization of protein-ligand interactions by high-resolution solid-state NMR spectroscopy

A novel approach for detection of ligand binding to a protein in solid samples is described. Hydrated precipitates of the anti-apoptotic protein Bcl-xL show well-resolved (13)C-(13)C 2D solid-state NMR spectra that allow site-specific assignment of resonances for many residues in uniformly (13)C-enriched samples. Binding of a small peptide or drug-like organic molecule leads to changes in the chemical shift of resonances from multiple residues in the protein that can be monitored to characterize binding. Differential chemical shifts can be used to distinguish between direct protein-ligand contacts and small conformational changes of the protein induced by ligand binding. The agreement with prior solution-state NMR results indicates that the binding pocket in solid and liquid samples is similar for this protein. Advantages of different labeling schemes involving selective (13)C enrichment of methyl groups of Ala, Val, Leu, and Ile (Cdelta1) for characterizing protein-ligand interactions are also discussed. It is demonstrated that high-resolution solid-state NMR spectroscopy on uniformly or extensively (13)C-enriched samples has the potential to screen proteins of moderate size ( approximately 20 kDa) for ligand binding as hydrated solids. The results presented here suggest the possibility of using solid-state NMR to study ligand binding in proteins not amenable to solution NMR.     

带电组氨酸侧链与DNA碱基间非键作用强度的理论研究

采用MP2方法和6-31+G(d,p)基组优化得到了带有一个正电荷的组氨酸侧链与4个DNA碱基间形成的18个氢键复合物的气相稳定结构, 从文献中获取了组氨酸侧链与DNA碱基间形成的12个堆积和T型复合物的气相稳定结构, 使用包含基组重叠误差(BSSE)校正的MP2方法和aug-cc-pVTZ基组及密度泛函理论M06-2X-D3方法和aug-cc-pVDZ基组计算了这些复合物的结合能. 研究结果表明, 包含BSSE校正的M06-2X-D3方法和aug-cc-pVDZ基组能够给出较准确的结合能; 气相条件下, 组氨酸侧链与同种DNA碱基间的离子氢键作用明显强于堆积作用和T型作用, 组氨酸侧链最易通过离子氢键与胞嘧啶C和鸟嘌呤G作用形成氢键复合物, 组氨酸与胞嘧啶C和鸟嘌呤G间的T型作用强于与腺嘌呤A和胸腺嘧啶T间的离子氢键作用; 水相条件下, 组氨酸侧链与同种DNA碱基间的离子氢键作用仍明显强于堆积作用和T型作用, 组氨酸侧链更易与胞嘧啶C和鸟嘌呤G相互作用形成氢键复合物, 但是最强的组氨酸侧链与胞嘧啶C间的T型作用明显弱于与腺嘌呤A和胸腺嘧啶T间的离子氢键作用, 说明水相条件下组氨酸侧链与DNA碱基间主要通过离子氢键作用形成氢键复合物.     

9-Anthracenyl-substituted pyridyl enones revisited: photoisomerism in ligands and silver(I) complexes

In solution, (E) to (Z)-isomerism is facile both in 3-(9-anthracenyl)-1-(pyridin-4-yl)propenone, 2, and in its silver(I) complex [Ag(2)(2)](+). The crystal structures of (E)-2, (Z)-2 and [Ag{(E)-2}(2)][SbF(6)] are presented, and the roles of edge-to-face and face-to-face π-interactions in the lattice are discussed. Solution NMR spectroscopic data suggest that the driving force for (E) to (Z) isomerization is intramolecular π-stacking of the pyridine and anthracene domains. The reversed enone 3-(9-anthracenyl)-1-(pyridin-4-yl)propen-3-one, (E)-3, and the silver(I) complex [Ag{(E)-3}(2)][SbF(6)] have been prepared and characterized, including a single crystal X-ray determination of the latter. Surprisingly, no π-stacking between anthracene or pyridine domains is observed in the solid state, and the crystal packing is dominated by Ag···F, CH(anthracene)···π-pyridine and CH···F interactions. In contrast to (E)-2 and [Ag{(E)-2}(2)](+), neither (E)-3 nor [Ag{(E)-3}(2)](+) undergoes photoisomerization in solution.     

Tracing kinetic intermediates during ligand binding

Specific protein-ligand interactions are central to biological control. Although structure determination provides important insight into these interactions, it does not address dynamic events that occur during binding. While many biophysical techniques can provide a global view of these dynamics, NMR can be used to derive site-specific dynamics at atomic resolution. Here we show how NMR line shapes can be analyzed to identify long-lived kinetic intermediates for individual amino acids on the reaction pathway for a protein-ligand interaction. Different ligands cause different intermediate states. The lifetimes of these states determine the specificity of binding. This novel approach provides a direct, site-specific visualization of the kinetic mechanism of protein-ligand interactions.     

Combining crystallographic and quantum chemical data to understand DNA-protein π-interactions in nature

Noncovalent interactions are accepted to be prevalent across biochemical systems, including governing interactions between nucleic acids and proteins. The present review summarizes work done to characterize the abundance, structure and strength of DNA–protein π interactions by combining rigorous searches of experimental X-ray crystal structures of DNA–protein complexes and quantum chemical calculations. Focus is placed on interactions that occur between the π-containing amino acids (W, H, F, Y, R, E, and D) and the canonical DNA nucleobases (A, T, G, and C) or 2′-deoxyribose moiety. These studies highlight the considerable frequency of both DNA–protein π–π and sugar–π interactions in nature, which can involve any π-containing amino acid arranged in many unique binding orientations with respect to any DNA component. When combined with the significant strength predicted for the identified DNA–protein π contacts using density functional theory, these works underscore the potential impact of these interactions on critical biological functions. This conclusion is supported by a review of examples from the recent literature that have acknowledged the role of DNA–protein π interactions in binding, specificity, and catalysis.

     

Coverage-dependent adsorption geometry of octithiophene on Au(111)

The adsorption behavior of α-octithiophene (8T) on the Au(111) surface as a function of 8T coverage has been studied with low-temperature scanning tunneling microscopy, high resolution electron energy loss spectroscopy as well as with angle-resolved two-photon photoemission and ultraviolet photoemission spectroscopy. In the sub-monolayer regime 8T adopts a flat-lying adsorption geometry. Upon reaching the monolayer coverage the orientation of 8T molecules changes towards a tilted configuration, with the long molecular axis parallel to the surface plane, facilitating attractive intermolecular π-π-interactions. The photoemission intensity from the highest occupied molecular orbitals (HOMO and HOMO - 1) possesses a strong dependence on the adsorption geometry due to the direction of the involved transition dipole moment for the respective photoemission process. The change in molecular orientation as a function of coverage in the first molecular layer mirrors the delicate balance between intermolecular and molecule/substrate interactions. Fine tuning of these interactions opens up the possibility to control the molecular structure and accordingly the desirable functionality.     

An improved PMF scoring function for universally predicting the interactions of a ligand with protein, DNA, and RNA

An improved potential mean force (PMF) scoring function, named KScore, has been developed by using 23 redefined ligand atom types and 17 protein atom types, as well as 28 newly introduced atom types for nucleic acids (DNA and RNA). Metal ions and water molecules embedded in the binding sites of receptors are considered explicitly by two newly defined atom types. The individual potential terms were devised on the basis of the high-resolution crystal and NMR structures of 2,422 protein-ligand complexes, 300 DNA-ligand complexes, and 97 RNA-ligand complexes. The optimized atom pairwise distances and minima of the potentials overcome some of the disadvantages and ambiguities of current PMF potentials; thus, they more reasonably explain the atomic interaction between receptors and ligands. KScore was validated against five test sets of protein-ligand complexes and two sets of nucleic-acid-ligand complexes. The results showed acceptable correlations between KScore scores and experimentally determined binding affinities (log K i's or binding free energies). In particular, KScore can be used to rank the binding of ligands with metalloproteins; the linear correlation coefficient ( R) for the test set is 0.65. In addition to reasonably ranking protein-ligand interactions, KScore also yielded good results for scoring DNA/RNA--ligand interactions; the linear correlation coefficients for DNA-ligand and RNA-ligand complexes are 0.68 and 0.81, respectively. Moreover, KScore can appropriately reproduce the experimental structures of ligand-receptor complexes. Thus, KScore is an appropriate scoring function for universally ranking the interactions of ligands with protein, DNA, and RNA.     

Fragmentation energetics of the phenol(+)···Ar(3) cation cluster

The various dissociation thresholds of phenol(+)···Ar(3) complexes for the consecutive loss of all three Ar ligands were measured in a molecular beam using resonant photoionization efficiency and mass analyzed threshold ionization spectroscopy via excitation of the first excited singlet state (S(1)). The adiabatic ionization energy is derived as 68077 ± 15 cm(-1). The analysis of the dissociation thresholds demonstrate that all three Ar ligands in the neutral phenol···Ar(3) tetramer are attached to the aromatic ring via π-bonding, denoted phenol···Ar(3)(3π). The value of the dissociation threshold for the loss of one Ar ligand from phenol(+)···Ar(3)(3π), ～190 cm(-1), is significantly lower than the binding energy measured for the π-bonded Ar ligand in the phenol(+)···Ar(π) dimer, D(0) = 535 ± 3 cm(-1). This difference is rationalized by an ionization-induced π → H isomerization process occurring prior to dissociation, that is, one Ar atom in phenol(+)···Ar(3)(3π) moves to the OH binding site, leading to a structure with one H-bonded and 2 π-bonded ligands, denoted phenol(+)···Ar(3)(H/2π). The dissociation thresholds for the loss of two and three Ar atoms are also reported as 860 and 1730 cm(-1). From these values, the binding energy of the H-bound Ar atom can be estimated as 870 cm(-1).     

Limited proteolysis combined with isotope labeling and quantitative LC-MALDI MS for monitoring protein conformational changes: a study on calcium-binding sites of cardiac Troponin C

Studies of protein-protein and protein-ligand interactions are important for understanding biological functions of proteins. A new technique based on the partial proteolysis of proteins combined with quantitative mass spectrometry is developed as a means of tracking structural changes after the formation of a protein-ligand complex. In this technique, a protein of interest with and without the binding of a ligand is digested with an enzyme to generate a set of peptides, followed by separation of the peptides by liquid chromatography. Matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS) is used to identify chromatographically separated peptides, and locate their sequence alignments in the parent protein. Using an isotopically labeled protein as a sample against an unlabeled protein standard, quantitative information can be gathered. This overcomes the inherent lack of quantitative capability of MALDI MS. The utility of the technique to investigate protein-ligand interactions is demonstrated in a model system involving calcium binding to cardiac Troponin C (cTnC). Using this technique, the general location of the three calcium-binding sites of cTnC can be determined by using several different enzymes to generate overlapping peptide maps of cTnC.     

Solvent-induced shifts in electronic spectra of uracil

Highly accurate excitation spectra are predicted for the low-lying n-π* and π-π* states of uracil for both the gas phase and in water employing the complete active space self-consistent field (CASSCF) and multiconfigurational quasidegenerate perturbation theory (MCQDPT) methods. Implementation of the effective fragment potential (EFP) solvent method with CASSCF and MCQDPT enables the prediction of highly accurate solvated spectra, along with a direct interpretation of solvent shifts in terms of intermolecular interactions between solvent and solute. Solvent shifts of the n-π* and π-π* excited states arise mainly from a change in the electrostatic interaction between solvent and solute upon photoexcitation. Polarization (induction) interactions contribute about 0.1 eV to the solvent-shifted excitation. The blue shift of the n-π* state is found to be 0.43 eV and the red shift of the π-π* state is found to be -0.26 eV. Furthermore, the spectra show that in solution the π-π* state is 0.4 eV lower in energy than the n-π* state.     

Facile Processing of Unsubstituted π-Conjugated Aromatic Polymers through Water-solubilization Using Aromatic Micelles

π-Conjugated aromatic polymers (πCAPs) are central components of functional materials yet suffer from insolubility without multiple covalent substituents on their backbones. We herein disclose a new strategy for the facile processing of unsubstituted heterocyclic πCAPs (i.e., poly(para-phenylene-2,6-benzobisoxazole) and poly(benzimidazobenzo-phenanthroline)), independent of the polymer length, via non-covalent encircling with aromatic micelles, composed of bent aromatic amphiphiles, in water. The UV/Visible studies reveal that the efficiencies of the present encircling method are ≈10 to 50-fold higher than those using conventional amphiphiles under the same conditions. The AFM and SEM analyses of the resultant aqueous polymer composites show that otherwise insoluble πCAPs form fine bundles (e.g., ≈1 nm in thickness) in the tubular aromatic micelles, through efficient π-stacking interactions. In the same way, pristine poly(para-phenylene) can be dissolved in water, displaying enhanced fluorescence (10-fold), relative to the polymer solid. Two types of unsubstituted πCAPs are likewise co-encircled in water, indicated by UV/Visible analysis. Importantly, aqueous processing of the encircled πCAPs into free-standing single- or multicomponent films with submicrometer thickness is demonstrated through a simple filtration-annealing protocol.     

π-Hole Interactions Involving Nitro Aromatic Ligands in Protein Structures

Studying noncanonical intermolecular interactions between a ligand and a protein constitutes an emerging research field. Identifying synthetically accessible molecular fragments that can engage in intermolecular interactions is a key objective in this area. Here, it is shown that so-called “π-hole interactions” are present between the nitro moiety in nitro aromatic ligands and lone pairs within protein structures (water and protein carbonyls and sulfurs). Ample structural evidence was found in a PDB analysis and computations reveal interaction energies of about −5 kcal mol⁻¹ for ligand–protein π-hole interactions. Several examples are highlighted for which a π-hole interaction is implicated in the superior binding affinity or inhibition of a nitro aromatic ligand versus a similar non-nitro analogue. The discovery that π-hole interactions with nitro aromatics are significant within protein structures parallels the finding that halogen bonds are biologically relevant. This has implications for the interpretation of ligand–protein complexation phenomena, for example, involving the more than 50 approved drugs that contain a nitro aromatic moiety.