A universal thermodynamic approach to analyze biomolecular binding experiments

Probing G-quadruplex-ligand binding using DNA intrinsic fluorescence

G-quadruplexes (G4s) are helical four-stranded nucleic acid structures that can form in guanine-rich sequences, which are mostly found in functional cellular regions, such as telomeres, promoters, and DNA replication origins. Great efforts are being made to target these structures towards the development of specific small molecule G4 binders for novel anti-cancer, neurological, and viral therapies. Here, we introduce an optical assay based on quenching of the intrinsic fluorescence of DNA G-quadruplexes for assessing and comparing the G4 binding affinity of various small molecule ligands in solutions. We show that the approach allows direct quantification of ligand binding to distinctive G4 topologies. We believe that this method will facilitate quick and reliable evaluation of small molecule G4 ligands and support their development.

Biomolecular interactions of ultrasmall metallic nanoparticles and nanoclusters

The use of nanoparticles (NPs) in biomedicine has made a gradual transition from proof-of-concept to clinical applications, with several NP types meeting regulatory approval or undergoing clinical trials. A new type of metallic nanostructures called ultrasmall nanoparticles (usNPs) and nanoclusters (NCs), while retaining essential properties of the larger (classical) NPs, have features common to bioactive proteins. This combination expands the potential use of usNPs and NCs to areas of diagnosis and therapy traditionally reserved for small-molecule medicine. Their distinctive physicochemical properties can lead to unique in vivo behaviors, including improved renal clearance and tumor distribution. Both the beneficial and potentially deleterious outcomes (cytotoxicity, inflammation) can, in principle, be controlled through a judicious choice of the nanocore shape and size, as well as the chemical ligands attached to the surface. At present, the ability to control the behavior of usNPs is limited, partly because advances are still needed in nanoengineering and chemical synthesis to manufacture and characterize ultrasmall nanostructures and partly because our understanding of their interactions in biological environments is incomplete. This review addresses the second limitation. We review experimental and computational methods currently available to understand molecular mechanisms, with particular attention to usNP-protein complexation, and highlight areas where further progress is needed. We discuss approaches that we find most promising to provide relevant molecular-level insight for designing usNPs with specific behaviors and pave the way to translational applications.

A critical view on the analysis of fluorescence quenching data for determining ligand-protein binding affinity

The past decade has seen an increase in the number of research papers on ligand binding to proteins based on fluorescence spectroscopy. In most cases, determination of the binding affinity is made by analyzing the quenching of protein fluorescence induced by the ligand. However, many such articles, even those published in reputed journals, suffer from several mistakes with regard to analysis of fluorescence quenching data. Using the binding of phenylbutazone to human serum albumin as a model, we consider some of these mistakes and show how they affect the values of the association constant. In particular, the failure to correct for the inner filter effect and the use of unsuitable equations are discussed. Ligand binding data presented in these articles should be treated with caution, especially in the absence of data from complementary techniques.

Thermodynamic Analysis of Myelin Basic Protein Adsorbed on Liquid Crystalline Dioleoylphosphatidylcholine Monolayer

To investigate the stability and dynamic characteristics of monolayer adsorbed on unsaturated lipid dioleoylphosphatidylcholine (DOPC) with varying concentrations of myelin basic protein (MBP), the system is studied by applying Langmuir technique and making atomic force microscope (AFM) observation, which is based on the mass conservation equation analysis method referred to in the thermodynamics theory. As indicated by surface pressure-mean molecular area (π - A) and surface pressure-adsorption time (π - T) isotherms, the physical properties of monolayer derived from the interaction of varying concentrations of MBP with liquid crystalline unsaturated lipid DOPC molecules were qualitatively studied. As revealed by surface morphology analysis with AFM, the micro region was expanded as the concentration of MBP in the subphase was on the increase, suggesting that hydrophobic interactions led to the MBP insertion, thus causing accumulation of the MBP on the surface of the monolayer. Experimental results have demonstrated that the partition coefficient of the interaction between MBP and unsaturated phospholipid DOPC and the molecular area of MBP adsorbed on the monolayer film was calculated using the mass conservation equation. In addition, not only does the varying concentration of MBP in the subphase exerts significant effects on the arrangement and conformation of DOPC monolayer, it also has certain guiding significance to exploring the structural changes to biofilm supramolecular aggregates as well as the pathogenesis and treatment of related diseases.

Signal and binding. II. Converting physico-chemical responses to macromolecule-ligand interactions into thermodynamic binding isotherms

Physico-chemical titration techniques are the most commonly used methods in characterizing molecular interactions. These methods are mainly based on spectroscopic, calorimetric, hydrodynamic, etc., measurements. However, truly quantitative physico-chemical methods are absolutely based on the determination of the relationship between the measured signal and the total average degree of binding in order to obtain meaningful interaction parameters. The relationship between the observed physico-chemical signal of whatever nature and the degree of binding must be determined and not assumed, based on some ad hoc intuitive relationship/model, leading to determination of the true binding isotherm. The quantitative methods reviewed and discussed here allow an experimenter to rigorously determine the degree of binding and the free ligand concentration, i.e., they lead to the construction of the thermodynamic binding isotherm in a model-independent fashion from physico-chemical titration curves.

Quantitative analysis of protein-protein interactions

Numerous authors, including contributors to this volume, have described methods to detect protein-protein interactions. Many of these approaches are now accessible to the inexperienced investigator thanks to core facilities and/or affordable instrumentation. This chapter discusses some common design considerations that are necessary to obtain valid measurements, as well as the assumptions and analytical methods that are relevant to the quantitation of these interactions.

Quantitative Thermodynamic Analyses of Spectroscopic Titration Curves

Elucidation of ligand - macromolecule interactions requires detailed knowledge of energetics of the formed complexes. Spectroscopic methods are most commonly used in characterizing molecular interactions in solution. The methods do not require large quantities of material and most importantly, do not perturb the studied reactions. However, spectroscopic methods absolutely require the determination of the relationship between the observed signal and the degree of binding in order to obtain meaningful interaction parameters. In other words, the meaningful, thermodynamic interaction parameters can be only determined if the relationship between the observed signal and the degree of binding is determined and not assumed, based on an ad hoc model of the relationship. The approaches discussed here allow an experimenter to quantitatively determine the degree of binding and the free ligand concentration, i.e., they enable to construct thermodynamic binding isotherms in a model-independent fashion.

Fluorescence spectroscopy and molecular dynamics simulations in studies on the mechanism of membrane destabilization by antimicrobial peptides

Since their initial discovery, 30 years ago, antimicrobial peptides (AMPs) have been intensely investigated as a possible solution to the increasing problem of drug-resistant bacteria. The interaction of antimicrobial peptides with the cellular membrane of bacteria is the key step of their mechanism of action. Fluorescence spectroscopy can provide several structural details on peptide-membrane systems, such as partition free energy, aggregation state, peptide position and orientation in the bilayer, and the effects of the peptides on the membrane order. However, these "low-resolution" structural data are hardly sufficient to define the structural requirements for the pore formation process. Molecular dynamics simulations, on the other hand, provide atomic-level information on the structure and dynamics of the peptide-membrane system, but they need to be validated experimentally. In this review we summarize the information that can be obtained by both approaches, highlighting their versatility and complementarity, suggesting that their synergistic application could lead to a new level of insight into the mechanism of membrane destabilization by AMPs.

Immunological evaluation of SW–HSA conjugate on goats

Locoweeds cause significant livestock poisoning and economic loss all over the world. The purpose of this study was to investigate the immune effects of locoweed toxin, swainsonine (SW) and human serum albumin (HSA) conjugate (SW-HSA), on goats. Twenty-four Sannon goats were randomly separated into immune control group (eight goats), immune poisoning group I (six goats), immune poisoning group II (six goats) and poisoning control group (four goats). Immune control group, immune poisoning groups I and II were first vaccinated with SW-HSA conjugate. The poisoning control group, immune poisoning groups I and II were then fed with 10.0 g/kg BW/day dry powder of Oxytropis kansuensis Bunge everyday morning. The immune control group was supplied with an alfalfa-based diet. Blood samples of these experimental animals were collected at different time interval. Immunoassay was performed using indirect ELISA and E-rosette technique. The results show that, after second booster immunization: (1) anti-SW antibody level in some goats increased to 2(8), which proves that SW-HSA conjugate can induce experimental animals to produce high-level anti-SW antibody in their bodies; (2) the high-level antibody in their bodies could maintain 30 days, and decreased gradually after poisoning experiment (in our experiment, there was a return of the antibody level on day 21 after poisoning experiment); (3) the decreasing of the E-rosette rate of the immune poisoning group was delayed 14 days, which suggests that SW-HSA could low down the loss of the immunity of the goats; (4) swainsonine concentration in the blood was significantly lower (p<0.01) in the immune poisoning groups than that in the poisoning control group, and there was no significant difference (p>0.01) between the two immune poisoning groups within the poisoning experiment.

A thermodynamic and structural study of myelin basic protein in lipid membrane models

Myelin basic protein (MBP) is a major protein of the myelin membrane in the central nervous system. It is believed to play a relevant role in the structure and function of the myelin sheath and is a candidate autoantigen in demyelinating processes such as multiple sclerosis. MBP has many features typical of soluble proteins but is capable of strongly interacting with lipids, probably via a conformation change. Its structure in the lipid membrane as well as the details of its interaction with the lipid membrane are still to be resolved. In this article we study the interaction of MBP with Langmuir films of anionic and neutral phospholipids, used as experimental models of the lipid membrane. By analyzing the equilibrium surface pressure/area isotherms of these films, we measured the protein partition coefficient between the aqueous solution and the lipid membrane, the mixing ratio between protein and lipid, and the area of the protein molecules inserted in the lipid film. The penetration depth of MBP in the lipid monolayer was evaluated by x-ray reflectivity measurements. The mixing ratio and the MBP molecular area decrease as the surface pressure increases, and at high surface pressure the protein is preferentially located at the lipid/water interface for both anionic and neutral lipids. The morphology of MBP adsorbed on lipid films was studied by atomic force microscopy. MBP forms bean-like structures and induces a lateral compaction of the lipid surface. Scattered MBP particles have also been observed. These particles, which are 2.35-nm high, 4.7-nm wide, and 13.3-nm long, could be formed by protein-lipid complexes. On the basis of their size, they could also be either single MBP molecules or pairs of c-shaped interpenetrating molecules.

Model-free analysis of binding at lipid membranes employing micro-calorimetric measurements

Based on universal thermodynamic principles (Schwarz in Biophys Chem 86:119-129, 2000) it is shown how measured enthalpy changes can be utilized to determine the relevant binding isotherm as well as the variation of the molar enthalpy change. This is carried out in a novel way involving multiple titration experiments whose evaluation requires no beforehand assumptions or models whatever. An appropriate specific model mechanism may be discussed afterwards and developed in view of the given experimental results. The pertinent procedure is demonstrated using micro-calorimetric data obtained in the case of the local anesthetic dibucaine as it associates with POPC liposomes. Mutual interactions of the bound ligand molecules could be described in terms of repulsive enthalpic and entropic activity coefficients. Apparently these are induced by electrostatic forces and by the finite size of binding sites, respectively.

Effect of Peptide Lipidation on Membrane Perturbing Activity: A Comparative Study on Two Trichogin Analogues

The effect of lipidation on the membrane perturbing activity of peptaibol antibiotics was investigated by performing a comparative study on two synthetic analogues of the natural peptide trichogin GA IV. Both analogues were labeled with a hydrophobic fluorescent probe, but one of them lacked the N-terminal n-octanoyl chain, present in the natural peptide. Spectroscopic studies show that the fatty acyl chain produces two opposite effects: it increases the affinity of the monomeric peptide for the membrane phase, but, at the same time, it favors peptide aggregation in water, thus inhibiting membrane binding by reducing the effective monomer concentration. In the membrane phase the two analogues exhibit the same aggregation and orientation behavior, indicating that the n-octanoyl chain plays no specific role in determining their orientation or membrane perturbing activity. Indeed, the dependence of peptide-induced membrane leakage on total peptide concentration is basically the same for the two analogues, because the aforementioned opposite effects, caused by peptide lipidation, tend to balance. These findings make questionable the use of lipidation as a general method for increasing the peptide membrane-perturbing activity, as its validity seems to be restricted to parent compounds of limited overall hydrophobicity.

Real-time measurement of solute partitioning to lipid monolayers

The interaction of a peripheral protein with a lipid-water interface can show a pronounced dependence on the composition and two-dimensional packing density of the lipids that comprise the interface. We report a novel optical method for measuring the adsorption of macromolecules, such as proteins and nucleic acids, and smaller solutes, such as drugs, to lipid monolayers at the gas-liquid interface. Using fluorescence emission from proteins and a small molecule, we demonstrate that the emissions from these solutes when in the aqueous phase and when associated with the monolayer can be temporally separated. Such separation allows measurement of the extent of solute adsorption, spectral characterization of the adsorbed solute, and characterization of lipid organization using adsorption kinetics. The method does not require, but is compatible with, the solute having different spectral properties in the bulk and surface phases. Indeed, if optical signals from adsorbed and soluble solute are the same or their relationship is known, absolute surface excess of adsorbed solute can be calculated without independent calibration. With appropriate instrumental configuration, the method should be adaptable for screening solutes for interaction with planar monolayers having both well-defined composition and adjustable lipid packing density.

Negative cooperativity and aggregation in biphasic binding of mastoparan X peptide to membranes with acidic lipids

The change of Trp fluorescence intensity when large vesicles with 10% acidic lipid are added to mastoparan X solutions reflects a fast and a slow binding process. By means of a novel procedure of data analysis that takes advantage of so-called mass conservation plots we have separated association isotherms related to: (i) the apparent fast pre-equilibrium; and (ii) the final equilibrium, respectively. This approach also reveals that the intrinsic fluorescence signal of the slow binding is considerably raised against that of the fast binding, presumably indicating a penetration of bound peptide from the lipid/water interface into the apolar lipid core. The shape of either binding curve discloses a pronounced tendency of aggregation. Furthermore, it turns out that in the slow process the final binding ratio decreases markedly compared with the initial fast binding ratio. Accordingly the occupation of final binding sites must exert a substantial effect of negative cooperativity on the affinity of the interfacial binding states.