Multivalent ligand–receptor binding on supported lipid bilayers

Fluid supported lipid bilayers provide an excellent platform for studying multivalent protein–ligand interactions because the two-dimensional fluidity of the membrane allows for lateral rearrangement of ligands in order to optimize binding. Our laboratory has combined supported lipid bilayer-coated microfluidic platforms with total internal reflection fluorescence microscopy (TIRFM) to obtain equilibrium dissociation constant (K_D) data for these systems. This high throughput, on-chip approach provides highly accurate thermodynamic information about multivalent binding events while requiring only very small sample volumes. Herein, we review some of the most salient findings from these studies. In particular, increasing ligand density on the membrane surface can provide a modest enhancement or attenuation of ligand–receptor binding depending upon whether the surface ligands interact strongly with each other. Such effects, however, lead to little more than one order of magnitude change in the apparent K_D values. On the other hand, the lipophilicity and presentation of lipid bilayer-conjugated ligands can have a much greater impact. Indeed, changing the way a particular ligand is conjugated to the membrane can alter the apparent K_D value by at least three orders of magnitude. Such a result speaks strongly to the role of ligand availability for multivalent ligand–receptor binding.     

Kinetics of cooperative ligand–lattice binding: Fast Monte Carlo integration

A fast Monte Carlo integration algorithm with varying time step is described for cooperative binding of ligands of arbitrary length to a one-dimensional lattice. This algorithm is particularly suitable for strongly cooperative or anticooperative systems, i.e., when the time scales for different kinetic events are very different. As an application, the kinetics of a bimodal two-ligand system are briefly discussed.     

Switches of hydrogen bonds during ligand–protein association processes determine binding kinetics

Revealing the processes of ligand–protein associations deepens our understanding of molecular recognition and binding kinetics. Hydrogen bonds (H‐bonds) play a crucial role in optimizing ligand–protein interactions and ligand specificity. In addition to the formation of stable H‐bonds in the final bound state, the formation of transient H‐bonds during binding processes contributes binding kinetics that define a ligand as a fast or slow binder, which also affects drug action. However, the effect of forming the transient H‐bonds on the kinetic properties is little understood. Guided by results from coarse‐grained Brownian dynamics simulations, we used classical molecular dynamics simulations in an implicit solvent model and accelerated molecular dynamics simulations in explicit waters to show that the position and distribution of the H‐bond donor or acceptor of a drug result in switching intermolecular and intramolecular H‐bond pairs during ligand recognition processes. We studied two major types of HIV‐1 protease ligands: a fast binder, xk263, and a slow binder, ritonavir. The slow association rate in ritonavir can be attributed to increased flexibility of ritonavir, which yields multistep transitions and stepwise entering patterns and the formation and breaking of complex H‐bond pairs during the binding process. This model suggests the importance of conversions of spatiotemporal H‐bonds during the association of ligands and proteins, which helps in designing inhibitors with preferred binding kinetics. Copyright © 2014 John Wiley & Sons, Ltd.     

Enhancing ligand–protein binding in affinity thermoprecipitation: Elucidation of spacer effects

Copolymers of N‐isopropylacrylamide and N‐acryloyl amino acid spacers of varying chain length were synthesized. p‐Aminobenzamidine (PABA) was chemically linked to the pendant carboxyl groups of these polymers to obtain thermoprecipitating affinity polymers. The inhibition constant (K_i) of these polymers for trypsin decreased, i.e., the efficiency of PABA–trypsin binding increased with increase in the spacer chain length. The polymer to which PABA was linked through a spacer of five methylene groups exhibited eleven times lower K_i than that of the polymer containing PABA without a spacer. Investigations on model inhibitors N‐acyl‐p‐aminobenzamidines showed that this enhancement in trypsin binding by the polymers was due to the spacer as well as to microenvironmental effects. Recovery and specific activity of the trypsin recovered increased with the spacer chain length. Separation of trypsin from a mixture of trypsin and chymotrypsin was also enhanced with the spacer chain length. The inhibition constants of these affinity polymers were not adversely affected by the crowding effect. © 1999 John Wiley & Sons, Inc. Biotechnol Bioeng 64: 418–425, 1999.     

Investigation of enantioselective ligand–protein binding and displacement interactions using capillary electrophoresis

When a protein such as human serum albumin is added to the separation buffer in capillary electrophoresis, the mobility of solutes which bind to that protein may be altered. The change in mobility of the solute is a function both of the strength of the binding interaction, and the difference in mobility between the free solute and protein additive. By adding other ligands which themselves bind to the protein, the strength of the solute–protein binding may be modified, leading to a measurable change in the mobility of the solute. These effects are particularly striking for chiral compounds, where enantioselectivity may be completely lost on addition of a competitive ligand. Capillary electrophoresis with human serum ablumin as a buffer additive was used to separate the enantiomers of benzoin and three phenothiazine derivatives. A comparison of the binding of (S)-benzoin to human serum albumin as determined by capillary electrophoresis and by ultrafiltration was made. A variety of other ligands were then added to the buffer along with the protein, and the effects on mobility and enantioselectivity were studied. The displacers included (R)- and (S)-oxazepam hemisuccinate, (R)- and (S)-warfarin, nitrazepam, phenylbutazone, and octanoic acid. From the results obtained, it seems that capillary electrophoresis may be a useful, rapid method to screen for drug–drug interactions. There are some advantages of using this technique to study protein–ligand interactions: Only very small amounts of ligand are needed (useful when dealing with metabolites); for chiral compounds, if protein binding is stereoselective, then the method is also stereoselective, so single enantiomers are not needed; finally, measurements are obtained in solution, without the need for immobilization of the protein. A disadvantage is that the ligand and protein must have significantly different electrophoretic mobilities. © 1994 Wiley-Liss, Inc.     

Mapping of ligand‐binding cavities in proteins

The complex interactions between proteins and small organic molecules (ligands) are intensively studied because they play key roles in biological processes and drug activities. Here, we present a novel approach to characterize and map the ligand‐binding cavities of proteins without direct geometric comparison of structures, based on Principal Component Analysis of cavity properties (related mainly to size, polarity, and charge). This approach can provide valuable information on the similarities and dissimilarities, of binding cavities due to mutations, between‐species differences and flexibility upon ligand‐binding. The presented results show that information on ligand‐binding cavity variations can complement information on protein similarity obtained from sequence comparisons. The predictive aspect of the method is exemplified by successful predictions of serine proteases that were not included in the model construction. The presented strategy to compare ligand‐binding cavities of related and unrelated proteins has many potential applications within protein and medicinal chemistry, for example in the characterization and mapping of “orphan structures”, selection of protein structures for docking studies in structure‐based design, and identification of proteins for selectivity screens in drug design programs. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Exploration of human serum albumin binding sites by docking and molecular dynamics flexible ligand–protein interactions

Five‐nanosecond molecular dynamics (MD) simulations were performed on human serum albumin (HSA) to study the conformational features of its primary ligand binding sites (I and II). Additionally, 11 HSA snapshots were extracted every 0.5 ns to explore the binding affinity (K_d) of 94 known HSA binding drugs using a blind docking procedure. MD simulations indicate that there is considerable flexibility for the protein, including the known sites I and II. Movements at HSA sites I and II were evidenced by structural analyses and docking simulations. The latter enabled the study and analysis of the HSA–ligand interactions of warfarin and ketoprofen (ligands binding to sites I and II, respectively) in greater detail. Our results indicate that the free energy values by docking (K_d observed) depend upon the conformations of both HSA and the ligand. The 94 HSA–ligand binding K_d values, obtained by the docking procedure, were subjected to a quantitative structure‐activity relationship (QSAR) study by multiple regression analysis. The best correlation between the observed and QSAR theoretical (K_d predicted) data was displayed at 2.5 ns. This study provides evidence that HSA binding sites I and II interact specifically with a variety of compounds through conformational adjustments of the protein structure in conjunction with ligand conformational adaptation to these sites. These results serve to explain the high ligand‐promiscuity of HSA. © 2009 Wiley Periodicals, Inc. Biopolymers 93: 161–170, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Analysis of derivative binding isotherms. Theoretical considerations

The basic theoretical groundwork for the use of derivative binding isotherms in the analysis of ligand binding is presented. The derivative binding isotherm is defined as Γ (Y) = df/dy where f = fractional degree of saturation and y = natural logarithm of the free ligand concentration. Since Γ (y) is a positive function, which goes to zero as y → ±∞, the mean value of y, 〈y〉, and the second and third moments, μ₂ and μ₃ about 〈y〉 are well defined. For a macromolecular system consisting of N equivalent and independent binding sites, Γ (y) is a symmetrical bell-shaped function with one maximum. The maximum occurs when y = ?ln K_assoc; μ₂ = π²/3, and μ₃ = 0. For multiple sets of independent binding sites, Γ (y) is a superposition of Γ-type functions. If the sets are sufficiently well separated in binding free energy, multiple extrema may be seen at positions corresponding to the logarithms of the dissociation constants for the individual sets. In any case, 〈y〉 is equal to the mean value of the logarithms of the dissociation constants for the sets; μ₂ > π²/3 and equal to π²/3 plus the variance of the logarithms of the dissociation constants about their mean value; and μ₃ is, except by coincidence, not equal to zero and equals the third moment of the distribution of logarithms of the dissociation constants about their mean value. Analysis of Γ(y) for the case of cooperative interactions within a set of binding sites was investigated by examining (1) the Hill model (whose mathematical representation is equivalent to that used to describe antibody heterogeneity except that in the latter case the parameter a, the Sips, constant, is constrained (0 < a ≤1);(2) a common model for cooperativity in which the cooperative free energy is a linear function of the fraction bound; and (3) a general representation of cooperative interactions within a set of sites in terms of ?(f), a smooth function that gives the interaction free energy in units of RT. For the Hill model (or Sips model) Γ(y) is a symmetrical function with one maximum at y = (?1)/a)lnK, μ₂ = π²/3a²; and μ₃ = 0. For the case in which the cooperative free energy is a linear function of f [?(f) = cf], 〈y〉 = ?ln K₀ + (c/2); μ₂ = (π²/3) + c[(c/12) + 1] where c > ?4; and μ₃ = 0. General expressions for the moments in terms of ?(f) are derived. In general, μ₂ < (π²/3) for positive cooperativity and μ₂ > (π₂/3) for negative for negative cooperativity. Γ(y) will be symmetrical if and only if the cooperative free energy is introduced symmetrically about f = 0.5.     

Exhaustive comparison and classification of ligand‐binding surfaces in proteins

Many proteins function by interacting with other small molecules (ligands). Identification of ligand‐binding sites (LBS) in proteins can therefore help to infer their molecular functions. A comprehensive comparison among local structures of LBSs was previously performed, in order to understand their relationships and to classify their structural motifs. However, similar exhaustive comparison among local surfaces of LBSs (patches) has never been performed, due to computational complexity. To enhance our understanding of LBSs, it is worth performing such comparisons among patches and classifying them based on similarities of their surface configurations and electrostatic potentials. In this study, we first developed a rapid method to compare two patches. We then clustered patches corresponding to the same PDB chemical component identifier for a ligand, and selected a representative patch from each cluster. We subsequently exhaustively as compared the representative patches and clustered them using similarity score, PatSim. Finally, the resultant PatSim scores were compared with similarities of atomic structures of the LBSs and those of the ligand‐binding protein sequences and functions. Consequently, we classified the patches into ～2000 well‐characterized clusters. We found that about 63% of these clusters are used in identical protein folds, although about 25% of the clusters are conserved in distantly related proteins and even in proteins with cross‐fold similarity. Furthermore, we showed that patches with higher PatSim score have potential to be involved in similar biological processes.     

Identification of folate binding macromolecule in rabbit choroid plexus.

A macromolecular binder of folic acid and folic acid derivatives has been identified in the particulate fraction of homogenates of rabbit choroid plexus. Within the choroid plexus, there are 2.3 nmol of folate-binding activity (binder) per g of tissue. The molecular weight of the folate binder complex, separated from the particulate fraction after solubilization with Triton X-100, was 340,000 to 400,000 by Sephadex gel filtration. The partially purified binder, when freed of endogenous folates, bound equivalent amounts of both [3H]folic acid and [methyl-14C]methyltetrahydrofolic acid per mg of protein. Folic acid, homofolic acid, 5-methyltetrahydrofolic acid, and to a lesser degree, methotrexate, inhibited the binding of both [3H]folic acid and [14C]methyltetrahydrofolic acid. Binding activity, which decreased below pH = 7.0, was unaffected by pretreatment with ribonuclease but was eliminated completely by papain and a protease (Streptomyces griseus). Although dihydrofolate reductase was present in choroid plexus, the binder was distinct from dihydrofolate reductase as judged by gel filtration and methotrexate sensitivity. This high affinity binder of folates may be responsible, in part, for the rapid, saturable uptake of folic acid and methyltetrahydrofolic acid by rabbit choroid plexus in vitro.     

Crystal structure of afadin PDZ domain–nectin‐3 complex shows the structural plasticity of the ligand‐binding site

Afadin, a scaffold protein localized in adherens junctions (AJs), links nectins to the actin cytoskeleton. Nectins are the major cell adhesion molecules of AJs. At the initial stage of cell–cell junction formation, the nectin–afadin interaction plays an indispensable role in AJ biogenesis via recruiting and tethering other components. The afadin PDZ domain (AFPDZ) is responsible for binding the cytoplasmic C‐terminus of nectins. AFPDZ is a class II PDZ domain member, which prefers ligands containing a class II PDZ‐binding motif, X‐Φ‐X‐Φ (Φ, hydrophobic residues); both nectins and other physiological AFPDZ targets contain this class II motif. Here, we report the first crystal structure of the AFPDZ in complex with the nectin‐3 C‐terminal peptide containing the class II motif. We engineered the nectin‐3 C‐terminal peptide and AFPDZ to produce an AFPDZ–nectin‐3 fusion protein and succeeded in obtaining crystals of this complex as a dimer. This novel dimer interface was created by forming an antiparallel β sheet between β2 strands. A major structural change compared with the known AFPDZ structures was observed in the α2 helix. We found an approximately 2.5 Å‐wider ligand‐binding groove, which allows the PDZ to accept bulky class II ligands. Apparently, the last three amino acids of the nectin‐3 C‐terminus were sufficient to bind AFPDZ, in which the two hydrophobic residues are important.     

Generation of density gradients. Approximations to equivolumetric gradients for zonal rotors

The use of a “density gradient generating function” allows the concentration profile of a density gradient to be written explicitly in terms of the required distribution of sedimentation coefficients in place of the previous implicit formulations. This function, which is easily implemented in a computer program, permits calculation of density gradients for a number of applications. This approach is applied to computation of a variety of equivolumetric gradients of sucrose for zonal rotors and yields a formula for the calibration of such gradients. An accurate approximation has been found which allows the generation of virtually all equivolumetric gradients of sucrose for a given rotor using a single program for the gradient generator employed; the adjustment for different particle densities and for different concentrations at the top of the gradient is made by varying only the initial and final concentrations of sucrose used.     

Expression pattern and ligand‐binding properties of odorant‐binding protein 13 from Monochamus alternatus hope

Odorant‐binding proteins (OBPs) are believed to play an important role in olfactory recognition. In this study, expression pattern and fluorescence binding characteristics of MaltOBP13 from the Japanese pine sawyer beetle, Monochamus alternatus Hope, were investigated via qPCR analysis of MaltOBP13 mRNA level and binding assay of MaltOBP13 and ligands. qPCR monitoring indicated MaltOBP13 mainly expressed in newly emerged males, particularly highly expressed in the last abdominal segment of males, and the expression level was significantly higher in 13‐day‐old mated adults than those of other stages. To further understand the function of the MaltOBP13 protein in odorant reception, the binding affinity of recombinant MaltOBP13 to ligands was tested by fluorescence binding assays with N‐phenyl‐1‐naphthylamine as a fluorescent probe. The results of this assay indicated that MaltOBP13 exhibited a high binding affinity for pine volatiles and binding capacity was higher in acidic conditions than in neutral environment, indicating a possible role in finding host plants.     

Stability of ligand‐binding domain dimer assembly controls kainate receptor desensitization

AMPA and kainate receptors mediate fast synaptic transmission. AMPA receptor ligand‐binding domains form dimers, which are key functional units controlling ion‐channel activation and desensitization. Dimer stability is inversely related to the rate and extent of desensitization. Kainate and AMPA receptors share common structural elements, but functional measurements suggest that subunit assembly and gating differs between these subtypes. To investigate this, we constructed a library of GluR6 kainate receptor mutants and directly measured changes in kainate receptor dimer stability by analytical ultracentrifugation, which, combined with electrophysiological experiments, revealed an inverse correlation between dimer stability and the rate of desensitization. We solved crystal structures for a series of five GluR6 mutants, to understand the molecular mechanisms for dimer stabilization. We demonstrate that the desensitized state of kainate receptors acts as a deep energy well offsetting the stabilizing effects of dimer interface mutants, and that the deactivation of kainate receptor responses is dominated by entry into desensitized states. Our results show how neurotransmitter receptors with similar structures and gating mechanisms can exhibit strikingly different functional properties.     

Comparison analysis of primary ligand‐binding sites in seven‐helix membrane proteins

Seven‐helix transmembrane proteins, including the G‐protein‐coupled receptors (GPCRs), mediate a broad range of fundamental cellular activities through binding to a wide range of ligands. Understanding the structural basis for the ligand‐binding selectivity of these proteins is of significance to their structure‐based drug design. Comparison analysis of proteins' ligand‐binding sites provides a useful way to study their structure‐activity relationships. Various computational methods have been developed for the binding‐site comparison of soluble proteins. In this work, we applied this approach to the analysis of the primary ligand‐binding sites of 92 seven‐helix transmembrane proteins. Results of the studies confirmed that the binding site of bacterial rhodopsins is indeed different from all GPCRs. In the latter group, further comparison of the binding sites indicated a group of residues that could be responsible for ligand‐binding selectivity and important for structure‐based drug design. Furthermore, unexpected binding‐site dissimilarities were observed among adrenergic and adenosine receptors, suggesting that the percentage of the overall sequence identity between a target protein and a template protein alone is not sufficient for selecting the best template for homology modeling of seven‐helix membrane proteins. These results provided novel insight into the structural basis of ligand‐binding selectivity of seven‐helix membrane proteins and are of practical use to the computational modeling of these proteins. © 2010 Wiley Periodicals, Inc. Biopolymers 95: 31–38, 2011.     

Molecular characterization of the ligand–receptor interaction of the neuropeptide Y family

Neuropeptide Y (NPY), peptide YY (PYY) and pancreatic polypeptide (PP) belong to the NPY hormone family and activate a class of receptors called the Y‐receptors, and also belong to the large superfamily of the G‐protein coupled receptors. Structure–affinity and structure–activity relationship studies of peptide analogs, combined with studies based on site‐directed mutagenesis and anti‐receptor antibodies, have given insight into the individual characterization of each receptor subtype relative to its interaction with the ligand, as well as to its biological function. A number of selective antagonists at the Y₁‐receptor are available whose structures resemble that of the C‐terminus of NPY. Some of these compounds, like BIBP3226, BIBO3304 and GW1229, have recently been used for in vivo investigations of the NPY‐induced increase in food intake. Y₂‐receptor selective agonists are the analog cyclo‐(28/32)‐Ac‐[Lys²⁸‐Glu³²]‐(25–36)‐pNPY and the TASP molecule containing two units of the NPY segment 21–36. Now the first antagonist with nanomolar affinity for the Y₂‐receptor is also known, BIIE0246. So far, the native peptide PP has been shown to be the most potent ligand at the Y₄‐receptor. However, by the design of PP/NPY chimera, some analogs have been found that bind not only to the Y₄‐, but also to the Y₅‐receptor with subnanomolar affinities, and are as potent as NPY at the Y₁‐receptor. For the characterization of the Y₅‐receptor in vitro and in vivo, a new class of highly selective agonists is now available. This consists of analogs of NPY and of PP/NPY chimera which all contain the motif Ala³¹‐Aib³². This motif has been shown to induce a 3₁₀‐helical turn in the region 28–31 of NPY and is suggested to be the key motif for high Y₅‐receptor selectivity. The results of feeding experiments in rats treated with the first highly specific Y₅‐receptor agonists support the hypothesis that this receptor plays a role in the NPY‐induced stimulation of food intake. In conclusion, the selective compounds for the different Y‐receptor subtypes known so far are promising tools for a better understanding of the physiological properties of the hormones of the NPY family and related receptors. Copyright © 2000 European Peptide Society and John Wiley & Sons, Ltd.     

Use of the fluorescent weak acid dansylglycine to measure transmembrane proton concentration gradients

The amphiphilic fluorescent dye N-[(5-dimethylamino)naphth-1-ylsulfonyl]glycine (dansylglycine) can be used to monitor the magnitude and stability of transmembrane proton gradients. Although freely soluble in aqueous media, the dye readily adsorbs to the surfaces of lipid vesicles. Because membrane-bound dye fluoresces at a higher frequency, and with greater efficiency, than dye in aqueous solution, it is easy to isolate the fluorescence emission from those dye molecules adsorbed to the lipid surface. When dansylglycine is mixed with phospholipid vesicles, the dye molecules attain a partition equilibrium between buffer and the outer, proximal surface of the vesicles. This is a rapid, diffusion-limited process that is indicated by a fast phase of fluorescence intensity increase monitored at 510 nm. In a second step, the inner, distal surface of each vesicle becomes populated with dye, a process that involves permeation through the lipid bilayer and that is generally much slower than the original adsorption step. Dansylglycine is a weak acid that permeates as an electrically neutral species; the flux of dye across the bilayer is thus strongly dependent on the degree of protonation of the dye's carboxylate moiety. When the external pH is lower than that of the vesicle lumen, the inward flux of dye is greater than that in the opposite direction, and dye accumulates in the lumen. This leads to a local elevation of dansylglycine concentration in the inner membrane monolayer, which in turn results in an elevated fluorescence intensity proportional to the membrane pH gradient.     

Generation and maintenance of concentration gradients between the mesophyll and bundle sheath in maize leaves

(1) Experiments have been carried out to test the proposal that intercellular transport of carbon occurs by diffusion during photosynthesis in C-4 plants. (2) The intercellular distribution of metabolites has been compared in different conditions. A partial separation of the mesophyll and bundle sheath was obtained by homogenisation in liquid N₂, followed by filtration through nylon nets with differing aperture. (3) Concentration gradients between the bundle sheath and mesophyll were found for 3-phosphoglycerate, triose phosphates, malate and pyruvate during photosynthesis. These gradients are shown to be large enough to allow rapid intercellular transport by diffusion. They disappear when photosynthesis is prevented by removal of light or CO₂. (4) The concentration gradients for triose phosphates and 3-phosphoglycerate are due to the differing capacity of the bundle sheath and mesophyll to reduce 3-phosphoglycerate. (5) The distribution of carbon between the malate/pyruvate and 3-phosphoglycerate/triose phosphate shuttles is flexible, and may be controlled by phosphoenolpyruvate carboxylase. (6) The maintenance of these large concentration gradients has consequences for the regulation of sucrose synthesis and the Calvin cycle.