Computational study of ligand binding to protein receptors

We have determined, for the first time, the enthalpic contributions to the energy change associated with ligand reorganization (LR) upon the binding of the same ligand to multiple sites within human serum albumine (HSA). Quantum mechanics based density functional theory (DFT) has been used for the LR calculations, which provides much better accuracy than previously used molecular mechanics methods (MM). Our findings show that for some ligands these enthalpic contributions can be attributed to specific structural and conformational changes.     

A study of ligand binding to protein using resonance energy transfer from the isoindole fluorescent label to ligand

A method for studing the binging of ligands absorbing the light in the region of 350-550 nm to protein is described. The method is based on resonance energy transfer between the fluorescent label covalently bound to the protein and the ligand. The isoindole label, a product of the reaction of the protein with o-phthalaldehyde in the presence of 2-mercaptoethanol, was used as a fluorescent donor. The method was used to determine the binding parameters of a fluorescent probe (a naphthalimide derivative) with human serum albumin. A comparison of the results obtained by the resonance energy and transfer by equilibrium dialysis showed a high accuracy of the resonance energy transfer method.     

UV difference spectroscopy of ligand binding to maltose-binding protein.

We have used UV absorbance spectroscopy to study the binding of linear and circular maltodextrins to maltose-binding protein (MBP). Titrations with maltose yield three isosbestic points in the difference spectrum of MBP, consistent with two protein conformations: ligand-free and ligand-bound. In contrast, titrations with maltotetraose reveal three conformations: ligand-free, a low-affinity liganded state, and a high affinity liganded state. These results confirm and extend the results from tritium NMR spectroscopy, namely, that MBP can bind maltodextrin either by the sugar's anomeric end (high affinity) or by the middle of the maltodextrin chain (low affinity).     

Stabilization of the FK506 binding protein by ligand binding.

Although the rotamase activity of the FK506 binding protein is inhibited by ligand binding, it is hypothesized that the ligand/protein complex itself may be responsible for the immunosuppressive effects of FK506. We have therefore examined the structure of the FK506 binding protein in the presence of an analog of FK506 (FK520) by a combination of fluorescence, CD, FTIR and calorimetry. While only small changes in the overall structure of the protein may be induced by ligand, a large change in thermal stability of the binding protein is observed.     

Sites of binding and orientation in a four-location model for protein stereospecificity

The stereospecificity of the enzyme isocitrate dehydrogenase was examined by steady-state kinetics and x-ray crystallography. The enzyme has the intriguing property that the apoenzyme in the absence of divalent metal showed a selectivity for the inactive l-enantiomer of the substrate isocitrate, whereas the enzyme containing magnesium showed selectivity for the physiologically active d-enantiomer. The hydrogen atom on the C2 carbon that is transferred during the reaction was, in both the d- and l-isocitrate complexes, in an orientation very close to that expected for delivery of a hydride ion to the cosubstrate NADP+. The beta-carboxylate that is eliminated as a CO2 molecule during the reaction occupied the same site on the protein in both the d- and l-isocitrate complexes. In addition, the C3 carbon was in the same protein site in both the d- and l-enantiomers. Only the fourth group, the OH atom, was in a very different position in the apo enzyme and in the metal-containing complexes. A four-location model is necessary to explain the enantiomeric specificity of IDH in contrast to the conventional three-point attachment model. The thermodynamic and kinetic ramifications of this model are explored.     

Tight binding ligand approach to oligosaccharide-grafted protein

A novel type of artificial glycoprotein was developed, by using dihydrofolate reductase (DHFR) and methotrexate (MTX) as a protein-ligand pair. Various oligosaccharides linked to MTX were shown to bind tightly with DHFR and afforded oligosaccharide-grafted protein, which could be isolated easily by lectin beads.     

Fluorescence microscope study of the binding of added C protein to skeletal muscle myofibrils

The binding of extra C protein to rabbit skeletal muscle myofibrils has been investigated by fluorescence microscopy with fluorescein-labeled C protein or unmodified C protein plus fluorescein-labeled anti-C protein. Added C protein binds strongly to the I bands, which is consistent with its binding to F actin in solution (Moos, C., C. M. Mason, J. M. Besterman, I. M. Feng, and J. H. Dubin. 1978. J. Mol. Biol. 124:571-586). Of particular interest, the binding to the I band is calcium regulated: it requires a free calcium ion concentration comparable to that which activates the myofibrillar ATPase. This increases the likelihood that C protein-actin interaction might be physiologically significant. When I band binding is suppressed, binding in the A band becomes evident. It appears to occur particularly near the M line, and possibly at the edges of the A band as well, suggesting that those parts of the thick filaments that lack C protein in vivo may nevertheless be capable of binding added C protein.     

A comprehensive binding study illustrates ligand recognition in the periplasmic binding protein PotF

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Determinants of ligand binding to cAMP-dependent protein kinase

Protein kinases are essential for the regulation of cellular growth and metabolism. Since their dysfunction leads to debilitating diseases, they represent key targets for pharmaceutical research. The rational design of kinase inhibitors requires an understanding of the determinants of ligand binding to these proteins. In the present study, a theoretical model based on continuum electrostatics and a surface-area-dependent nonpolar term is used to calculate binding affinities of balanol derivatives, H-series inhibitors, and ATP analogues toward the catalytic subunit of cAMP-dependent protein kinase (cAPK or protein kinase A). The calculations reproduce most of the experimental trends and provide insight into the driving forces responsible for binding. Nonpolar interactions are found to govern protein-ligand affinity. Hydrogen bonds represent a negligible contribution, because hydrogen bond formation in the complex requires the desolvation of the interacting partners. However, the binding affinity is decreased if hydrogen-bonding groups of the ligand remain unsatisfied in the complex. The disposition of hydrogen-bonding groups in the ligand is therefore crucial for binding specificity. These observations should be valuable guides in the design of potent and specific kinase inhibitors.     

Fluorescence assay for the binding of ribonuclease A to the ribonuclease inhibitor protein

Ribonuclease A (RNase A) and the ribonuclease inhibitor protein (RI) form one of the tightest known protein-protein complexes. RNase A variants and homologues, such as G88R RNase A, that retain ribonucleolytic activity in the presence of RI are toxic to cancer cells. Herein, a new and facile assay is described for measuring the equilibrium dissociation constant (K(d)) and dissociation rate constant (k(d)) for complexes of RI and RNase A. This assay is based on the decrease in fluorescence intensity that occurs when a fluorescein-labeled RNase A binds to RI. To allow time for equilibration, the assay is most readily applied to those complexes with K(d) values in the nanomolar range or higher. Using this assay, the value of K(d) for the complex of RI with fluorescein-labeled G88R RNase A was determined to be 0.55 +/- 0.03 nM. In addition, the value of K(d) was determined for the complex of RI with unlabeled G88R RNase A to be 0.57 +/- 0.05 nM by using a competition assay with fluorescein-labeled G88R RNase A. Finally, the value of k(d) for the complex of RI with fluorescein-labeled G88R RNase A was determined to be (7.5 +/- 0.4) x 10(-3) s(-1) by monitoring the increase in fluorescence intensity upon dissociation. This assay can be used to characterize complexes of RI with a wide variety of RNase A variants and homologues, including those with cytotoxic activity.     

Fluorescence anisotropy assay for pharmacological characterization of ligand binding dynamics to melanocortin 4 receptors

Fluorescence anisotropy assay was implemented for characterization of ligand binding dynamics to melanocortin 4 (MC₄) receptors. This approach enables on-line monitoring of reactions that is essential for estimation of more correct binding parameters, understanding of ligand binding and its regulation mechanisms, and design of new drugs with desirable properties. Two different red-shifted fluorophore-labeled peptide ligands, Cy3B-NDP-α-MSH and TAMRA-NDP-α-MSH, were used and compared in assays that monitored their binding to MC₄ receptors in membranes of Sf9 insect cells. The Cy3B dye-labeled ligand exhibited improved performance in assays when compared with the TAMRA-labeled ligand, having higher photostability, insensitivity to buffer properties, and better signal/noise ratio. The binding of both ligands to membranes of Sf9 cells expressing MC₄ receptors was saturable and with high affinity. All studied MC₄ receptor-specific nonlabeled ligands displaced fluoroligands’ binding in a concentration-dependent manner with potencies in agreement with their pharmacological activities. On-line monitoring of the reactions revealed that equilibrium of peptide binding was not reached even after 3 h. Real-time monitoring of ligand binding dynamics enabled us to find optimal experimental conditions for each particular ligand and an improved estimate of their binding parameters.     

Dynamic fluorescence study of the interaction of lumazine protein with bacterial luciferases

The equilibrium association of lumazine protein from Photobacterium phosphoreum with luciferases from either P. phosphoreum or an aldehyde-requiring dark mutant of Vibrio harveyi is measured from changes of the rotational correlation time which is derived from the decay of the lumazine ligand's fluorescence anisotropy. The rotational correlation time of lumazine protein is 23 ns (2 degrees C, 0.25 M Pi) and is increased on addition of luciferase due to the formation of a higher molecular weight complex. The V. harveyi luciferase exhibits full competence for the association and a 1:1 stoichiometry with a Kd in the range 40-90 microM. At lower ionic strength (0.05 M Pi), the Kd increases but is reduced again by the addition of dodecanol or dimyristoyllecithin. In contrast, tetradecanal, a substrate for the bioluminescence reaction, exerts no influence on the association. The equilibration rate is found to be too slow and for both luciferases the Kd values are too high for the interaction of the native proteins to account quantitatively for the spectral shifting of the bioluminescence by lumazine protein.     

Co-operative response of oligomeric protein receptors coupled to non-co-operative ligand binding.

The biogenesis of 30 S and 50 S ribosomal subunits in exponentially growing Escherichia coli has been studied by following the rate of appearance of pulse-labelled ribosomal proteins on mature subunits. Cells were pulse-labelled for two minutes and for three and a half minutes with radioactive leucine. Ribosomal proteins were extracted and purified by chromatography on carboxymethyl cellulose and analysed by bidimensional gel electrophoresis. All 30 S proteins and most of the 50 S proteins were thus prepared and their radioactivity counted: unequal labelling was obtained. 30 S and 50 S proteins were ordered according to increasing specific radioactivity at both time pulses. The incorporation was greater at three and a half minutes than at two minutes. No major difference in the order at the two labelling times was observed.Only two classes of proteins can be defined in the 30 S and the 50 S subunits, namely early and late proteins. In each class a gradual increase in the radioactivity is apparent from the poorly labelled to the highly labelled proteins. This suggests a definite order of addition.Early 30 S proteins: S17, S16, S15, S19, S18, S8, S4, S20, S10, S6, S9, S12, S7.Late 30 S proteins: S5, S3, S2, S14, S11, S13, S1, S21.Early 50 S proteins: L22, L20, L21, L4, L13, L16, L3, L23, L18, L24, L28, L17, L19, L29, L32, L5, L15, L2, L30, L27.Late 50 S proteins: L25, L11, L7, L12, L1, L9, L8, L10, L33, L14, L6.This order is discussed taking into account the pool size of the proteins measured in the same conditions of cell culture.     

Multivalent ligand binding by serum mannose-binding protein.

The serum-type mannose-binding protein (MBP) is a defense molecule that has carbohydrate-dependent bactericidal effects. It shares with mammalian and chicken hepatic lectins similarity in the primary structure of the carbohydrate-recognition domain, as well as the ligand-binding mode: a high affinity (KD approximately nM) is generated by clustering of approximately 30 terminal target sugar residues on a macromolecule, such as bovine serum albumin, although the individual monosaccharides have low affinity (KD 0.1-1 mM). On the other hand, MBP does not manifest any significant affinity enhancement toward small, di- and trivalent ligands, in contrast to the hepatic lectins whose affinity toward divalent ligands of comparable structures increased from 100- to 1000-fold. Such differences may be explained on the basis of different subunit organization between the hepatic lectins and MBP.     

Saturation transfer difference nuclear magnetic resonance study on the specific binding of ligand to protein

Ligand-based nuclear magnetic resonance (NMR) approaches have shown great promise in the study of ligand-protein interaction. But these approaches suffer from interference from the nonspecific binding. Here a saturation transfer difference (STD) NMR method to map the group epitope and to measure the dissociation constant (K_D) of specific interaction between ligand and protein is presented. The interference from nonspecific binding was corrected by recording STD NMR spectra of ligand-protein solutions with and without inhibitor saturating the mutually specific binding site and subtracting one from the other. The method was examined with l-tryptophan (Trp), naproxen (Nap), and human serum albumin (HSA) as model ligand, inhibitor, and protein, respectively. Results agree well with other reports of Trp-HSA interaction.     

Fluorescence study of ligand binding to potato tuber pyrophosphate-dependent phosphofructokinase: evidence for competitive binding between fructose-1,6-bisphosphate and fructose-2,6-bisphosphate

The intrinsic fluorescence of potato tuber pyrophosphate:fructose-6-phosphate 1-phosphotransferase (PFP) was used as an indicator of conformational changes due to ligand binding. Binding of the substrates and the allosteric activator fructose-2,6-bisphosphate was quantitatively compared to their respective kinetic effects on enzymatic activity. PFP exhibited a relatively high affinity for its isolated substrates, relative to the enzyme's respective K(m) (substrate) values. There are two distinct types of fructose-1,6-bisphosphate interaction with PFP, corresponding to catalytic and activatory binding. Activatory fructose-1,6-bisphosphate binding shares several characteristics with fructose-2,6-bisphosphate binding, indicating that both ligands compete for the same allosteric activator site. Activation by fructose-1,6-bisphosphate or fructose-2,6-bisphosphate was exerted primarily on the forward (glycolytic) reaction by greatly increasing the enzyme's affinity for fructose-6-phosphate. Binding of substrates and effectors to PFP and PFP kinetic properties were markedly influenced by assay pH. Results indicate an increased glycolytic role for PFP during cytosolic acidification that accompanies anoxia stress.     

Analytical expressions for the homotropic binding of ligand to protein dimers and trimers

Cooperative binding of a ligand to multiple subsites on a protein is a common theme among enzymes and receptors. The analysis of cooperative binding data (either positive or negative) often relies on the assumption that free ligand concentration, L, can be approximated by the total ligand concentration, L(T). When this approximation does not hold, such analyses result in inaccurate estimates of dissociation constants. Presented here are exact analytical expressions for equilibrium concentrations of all enzyme and ligand species (in terms of K(d) values and total concentrations of protein and ligand) for homotropic dimeric and trimeric protein-ligand systems. These equations circumvent the need to approximate L and are provided in Excel worksheets suitable for simulation and least-squares fitting. The equations and worksheets are expanded to treat cases where binding signals vary with distinct site occupancy.     

Tritium NMR spectroscopy of ligand binding to maltose-binding protein

Tritium-labeled alpha- and beta-maltodextrins have been used to study their complexes with maltose-binding protein (MBP), a 40-kDa bacterial protein. Five substrates, from maltose to maltohexaose, were labeled at their reducing ends and their binding studied. Tritium NMR spectroscopy of the labeled sugars showed large upfield chemical shift changes upon binding and strong anomeric specificity. At 10 degrees C, MBP bound alpha-maltose with 2.7 +/- 0.5-fold higher affinity than beta-maltose, and, for longer maltodextrins, the ratio of affinities (KD beta/KD alpha) was even larger (between 10 and 30). The maximum chemical shift change was 2.2 ppm, suggesting that the reducing end of bound alpha-maltodextrin makes close contact with an aromatic residue in the MBP-binding site. Experiments with maltotriose (and longer maltodextrins) also revealed the presence of two bound beta-maltotriose resonances in rapid exchange. We interpret these two resonances as arising from two distinct sugar-protein complexes. In one complex, the beta-maltodextrin is bound by its reducing end, and, in the other complex, the beta-maltodextrin is bound by the middle glucose residue(s). This interpretation also suggests how MBP is able to bind both linear and circular maltodextrins.     

Studies on ligand binding to histidine triad nucleotide binding protein 1

Histidine triad nucleotide binding protein (HINT1) is an intracellular protein that binds purine mononucleotides. Strong sequence conservation suggests that these proteins play a fundamental role in cell biology, however its exact cellular function continues to remain elusive. nuclear magnetic resonance (NMR) studies using STD and HSQC were conducted to observe ligand binding to HINT1. These studies were confirmed using fluorescence spectroscopy titrations. We found that AICAR, the first non-phosphate containing ligand, binds to mouse histidine triad nucleotide binding protein 1 (HINT1). Chemical shift perturbations are mapped onto the X-ray structure showing AICAR binds at the same site as GMP. The NMR results demonstrated that this method will be valuable for the future screening of small molecules that can be used to modulate the function of HINT1.