Effects of additives on the aggregation of surfactants: binding domination

The effects of electrolytes, alcohols, and urea on the aggregation of SDS, CTAB, and TritonX-100 at 25℃ have been investigated by fluorescence probing of pyrene. Both electrolytes and alcoholsreduce the critical micelle concentration (CMC) of the ionic surfactants, while the effect of the former ismore pronounced. It is shown that the effects of electrolytes mainly depend on the concentrationsand especially the valence of the opposite charge ions, and only slightly depend on the same charge ionsin respect of ion aggregate of micelle. The logarithm of CMC is not linearly correlated with theconcentrations of the counter ion or the electrolytes. The results are rationalized in terms of Hartley'smodel. Propanol increases the CMC of TX-100, while electrolytes and urea do not. In all the threekinds of surfactant micelles the excitation spectrum of pyrene slightly red-shifts (ca. 4 nm) from thatin water, but is not affected by the additives. The micropolarity of the environment in which pyrenemolecule resides in SDS micelle decreases with the increase of the concentrations of electrolytes. Thisis not the case when alcohols and urea were added to SDS or to TX-100. It is suggested that theaddition of electrolytes would result in more orderly orientation of SDS molecules. It is the bindingstrength of the counter ions that dominates the effects of additives on the aggregation of surfactants.     

Importance of inter-residue interactions in ligand—receptor binding

In the present study, the role of inter-residue interactions in ligand binding and the ligand—receptor interactions were examined. Computational chemistry methods of ligand docking and molecular dynamics simulations were used to study the binding of β-funaltrexamine (β-FNA) and N-methyl-β-funaltrexamine (N-methyl-β-FNA) to μ- and κ-opioid receptors and to the μ-receptor with Lys303^6.58Glu mutation. It was found that inter-residue interactions Lys233^5.39—Glu303^6.58 in the mutant receptor and Lys227^5.39—Asp223^5.35 in the κ-receptor are more likely to prevent covalent bond formation between β-FNA and the receptor than the ligand-receptor interactions. This emphasizes the importance of inter-residue interactions in ligand binding as well as the effects of point-mutations.     

Computational prediction of structure-activity relationships for the binding of aminocyclitols to β-glucocerebrosidase

Glucocerebrosidase (GCase, acid β-Glucosidase) hydrolyzes the sphingolipid glucosylceramide into glucose and ceramide. Mutations in this enzyme lead to a lipid metabolism disorder known as Gaucher disease. The design of competitive inhibitors of GCase is a promising field of research for the design of pharmacological chaperones as new therapeutic agents. Using a series of recently reported molecules with experimental binding affinities for GCase in the nanomolar to micromolar range, we here report an extensive theoretical analysis of their binding mode. On the basis of molecular docking, molecular dynamics, and binding free energy calculations using the linear interaction energy method (LIE), we provide details on the molecular interactions supporting ligand binding in the different families of compounds. The applicability of other computational approaches, such as the COMBINE methodology, is also investigated. The results show the robustness of the standard parametrization of the LIE method, which reproduces the experimental affinities with a mean unsigned error of 0.7 kcal/mol. Several structure-activity relationships are established using the computational models here provided, including the identification of hot spot residues in the binding site. The models derived are envisaged as important tools in ligand-design programs for GCase inhibitors.     

Competing binding of metal ions with protein studied by microdialysis

A method has been established to study the competing binding of metal ions with protein by a combined technique of microdialysis with high performance liquid chromatography (HPLC). Ni2+, Cd2+, Zn2+, Cu2+ and human serum albumin (HSA) were chosen as model metal ions and protein. The experimental results show that Ni2+ and Cu2+ share a common primary binding site on HSA, and Zn2+ and Cd2+ share a different common primary binding site from them, but there is a common multi-metal binding site for all of those four metal ions. This method show advantages of fast sampling, easily to be operated and especially to be useful when ideal spectroscopic probes are not available for the study of interaction between protein and metal ions.     

Impact of molecular flexibility on binding strength and self-sorting of chiral π-surfaces

In this work, we have explored for the first time the influence of conformational flexibility of π-core on chiral self-sorting properties of perylene bisimides (PBIs) that are currently one of the most prominent classes of functional dyes. For this purpose, two series of chiral macrocyclic PBIs 3a-c and 4a-c comprising oligoethylene glycol bridges of different lengths at the 1,7 bay positions were synthesized and their atropo-enantiomers (P and M enantiomers) were resolved. Single crystal analysis of atropo-enantiomerically pure (P)-3a not only confirmed the structural integrity of the ethylene glycol bridged macrocycle but also illustrated the formation of π-stacked dimers with left-handed supramolecular helicity. Our detailed studies with the series of highly soluble chiral PBIs 4a-c by 1- and 2-D (1)H NMR techniques, and temperature- and concentration-dependent UV/vis absorption and circular dichroism (CD) spectroscopy revealed that in π-π-stacking dimerization of these PBIs chiral self-recognition (i.e., PP and MM homodimer formation) prevails over self-discrimination (i.e., PM heterodimer formation). Our studies clearly showed that with increasing conformational flexibility of PBI cores imparted by longer bridging units, the binding strength for the dimerization process increases, however, the efficiency for chiral self-recognition decreases. These results are rationalized in terms of an induced-fit mechanism facilitating more planarized π-scaffolds of PBIs containing longer bridging units upon π-π-stacking.     

Thermodynamic characterization of proflavine–DNA binding through microcalorimetric studies

The interaction of an important acridine dye, proflavine hydrochloride, with double stranded DNA was investigated using isothermal titration calorimetry and differential scanning calorimetry. The equilibrium constant for the binding reaction was calculated to be (1.60 ± 0.04) · 10⁵ · M⁻¹ at T = 298.15 K. The binding of proflavine hydrochloride to DNA was favored by both negative enthalpy and positive entropy contributions to the Gibbs energy. The equilibrium constant for the binding reaction decreased with increasing temperature. The standard molar enthalpy change became increasingly negative while the standard molar entropy change became less positive with rise in temperature. However, the standard molar Gibbs free energy change varied marginally suggesting the occurrence of enthalpy–entropy compensation phenomenon. The binding reaction was dominated by non-polyelectrolytic forces which remained virtually unchanged at all the salt concentrations studied. The binding also significantly increased the thermal stability of DNA against thermal denaturation.     

Theoretical studies on the binding energy of β-sheet models

In this paper, B3LYP and MP2 methods are used to investigate the binding energy of seventeen antiparallel and parallel β-sheet models. The results indicate that the binding energy obtained from B3LYP calculations is weaker than that obtained from MP2 calculations but the relative binding energy yielded by B3LYP is almost the same as that by MP2. For the antiparallel β-sheets in which two N-H⋯O=C hydrogen bonds can form either a large hydrogen-bonded ring or a small hydrogen-bonded ring, the binding energy increases obviously when one large ring unit is added, whereas it only changes slightly when one small ring unit is added because of the secondary electrostatic repulsive interaction existing in the small ring unit which is estimated to be about 20 kJ/mol. For the parallel β-sheet models, the binding energy increases almost exactly linearly with the increase of the chain length.     

Synthesis of bisquinoline–pyrrole oligoamide as G-quadruplex binding ligand

A one-pot procedure using ammonium formate under palladium catalysis for the reductive dechlorination and reduction of nitro group of 4-chloro-8-nitro–quinoline derivatives has be successfully carried out. This has lead to the synthesis of bisquinoline–pyrrole oligoamide 1, which show significant G-quadruplex selectivity in preference to duplex DNA. The cooperativity between the bisquinoline and pyrrole oligoamide moieties for good binding affinity to G-quadruplex was proven by synthesizing 2 and 3 lacking a quinoline ring and pyrrole amide, respectively, and both show much reduce affinity to G-quadruplex. Altogether, the results demostrate that the appropriate combination of two chromophores to form the hybride can attenuate binding affinity and selectivity towards G-quadruplex, an important criteria for the rational drug design.     

NMR double resonance study of azide binding to cytochrome c

Equilibrium constants for the binding of azide to ferri-cytochrome c at temperature rangeof 305—325 K were determined at pH=7 by using ~1H double resonance method.Thermodynamicvalues(⊿H~o=-34.5 kJ/mol,⊿S~o=-100 J/mol)were obtained from van't Hoff's relation andwere compared with those for azide binding to other ferric hemeproteins.The reason of loweraffinity of cytochrome c for azide was discussed.     

Microdialysis-liquid chromatographic study on competitive binding of drugs to protein

A new method to determine the interaction between drug and protein has been developed by utilizing the technique of microdialysis sampling with the ketoprofen and the human serum albumin (HSA) as the model of drug and protein.Two kinds of binding sites of HSA to ketoprofen have been observed.The binding constants and number of binding sites obtained by the Scatchard equation are 0.799,3.18×106 mol-1 L and 2.15,2.01×105 mol-1 L,respectively The displacement binding of drugs to HSA has also been studied.The strong displacement of competitive binding of ibuprofen with ketoprofen to HSA was observed,which means that the primary binding site of HSA to ketoprofen and that to ibuprofen are the same.However,only a weaker displacement of warfarin for the association of ketoprofen with HSA was observed,which may suggest that the primary binding site of HSA to ketoprofen is different from that to warfarin.Such a displacement effect for competitive binding of drugs to HSA was explained by the displacement model i     

Quantitative analysis of cation binding to the adenosine nucleotides using the variable ionic strength method: validation of the Debye-Hückel-Onsager theory of electrophoresis in the absence of counterion binding

The free solution mobilities of the adenosine nucleotides 5'-adenosine triphosphate (ATP), 5'-adenosine diphosphate (ADP), 5'-adenosine monophosphate (AMP), and 3'-5'-cyclic AMP (cAMP) have been measured in diethylmalonate buffers containing a wide variety of monovalent cations. The mobilities of all nucleotides increase gradually with the increase in intrinsic conductivity of the cation in the BGE. However, at a given conductivity, the mobilities observed for ATP, ADP, and AMP in BGEs containing alkali metal ions and other cations are lower than these observed in BGEs containing tetraalkylammonium ions. Since the mobility of cAMP is independent of the cation in the BGE, the results suggest that the relatively low mobilities observed for ATP, ADP, and AMP in BGEs containing cations other than a tetraalkylammonium ion are due to cation binding, reducing the effective net charge of the nucleotide and thereby reducing the observed mobility. To measure the binding quantitatively, the mobilities of the nucleotides were measured as a function of ionic strength. The mobilities of ATP, ADP, and AMP decrease nonlinearly with the square root of ionic strength (I(1/2)) in BGEs containing an alkali metal ion or Tris(+). By contrast, the mobilities decrease linearly with I(1/2) in BGEs containing a nonbinding quaternary ammonium ion, as expected from Debye-Hückel-Onsager (DHO) theory. The mobility of cAMP, a nonbinding analyte, decreases linearly with I(1/2), regardless of the cation in the BGE. Hence, a nonlinear decrease of the mobility of an analyte with I(1/2) appears to be a hallmark of counterion binding. The curved mobility profiles observed for ATP, ADP, and AMP in BGEs containing an alkali metal ion or Tris(+) were analyzed by nonlinear curve fitting, using difference mobility profiles to correct for the effect of the physical properties of BGE on the observed mobilities. The calculated apparent dissociation constants range from 22 to 344 mM, depending on the particular cation-nucleotide pair. Similar values have been obtained by other investigators, using different methods. Interestingly, Tris(+) and Li(+) bind to the adenosine nucleotides with approximately equal affinities, suggesting that positively charged Tris(+) buffer ions can compete with alkali metal ions in Tris-buffered solutions.     

Mechanism for binding to the flexible cavity of permethylatedα-cyclodextrin

The cavity of -cyclodextrin (-CDx) is too small to includeo-toluic acid (o-TA) while it is filled byp-toluic acid (p-TA) to form a relatively stable inclusion complex. Such strict selectivity is ascribed to a rigid structure of the -CDx cavity which is stabilized by intramolecular hydrogen bonds between the O(2) hydroxyl groups and the O(3) hydroxyl groups of adjacent glucopyranose units. Meanwhile, the substrate selectivity of hexakis (2,3,6-tri-O-methyl)--CDx (TMe--CDx) remains somewhat obscure because of the flexible nature of its cavity. The absence of the intramolecular hydrogen bonds seems to cause the flexible nature of the TMe--CDx cavity leading to an induced-fit type inclusion. The structures of the inclusion complexes have been presented on the basis of the¹H NMR data. The thermodynamic parameters indicate that the complexation of TMe--CDx witho-TA orp-TA is the entropically favorable process. The entropically favorable complexation of TA with TMe--CDx seems to occur through dehydration from the CO₂H group of TA which is situated at the hydrophobic CDx cavity. The dipole-dipole interaction has been regarded as the force which dominates the orientation of the polar guest molecule in the CDx cavity.     

Validation of the AmpC β-lactamase binding site and identification of inhibitors with novel scaffolds

AmpC β-lactamase confers resistance to β-lactam antibiotics in multiple Gram-negative bacteria. Therefore, identification of non-β-lactam compounds that inhibit the enzyme is considered crucial to the development of novel antibacterial therapies. Given the highly solvent-exposed active site, it is important to study the induced-fit movements and water-mediated interactions to improve docking accuracy and virtual screening enrichments in structure-based design of new AmpC inhibitors. Here, we tested multiple models of the AmpC binding site to investigate the importance of conserved water molecules and binding site plasticity on molecular docking. The results indicate that at least one conserved water molecule greatly improves the binding pose predictions and virtual screening enrichments of known noncovalent AmpC inhibitors. The best model was tested prospectively in the virtual screening of about 6 million commercially available compounds. Sixty-one chemically diverse top-scoring compounds were experimentally tested, which led to the identification of seven previously unknown inhibitors. These findings validate the essential features of the AmpC binding site for molecular recognition and are useful for further optimization of identified inhibitors.     

Thermodynamic stability and retinol binding property of β-lactoglobulin in the presence of cationic surfactants

In this work the stability parameters of bovine β-lactoglobulin, variant A (BLG-A), with regard to their transition curves induced by dodecyltrimethylammonium bromide (C₁₂TAB), tetradecyltrimethylammonium bromide (C₁₄TAB) and hexadecyltrimethylammonium bromide (C₁₆TAB) as cationic surfactants, were determined at 298 K. For each transition curve, the conventional method of analysis which assumes a linear concentration dependence of the pre- and post-transition base lines, gave the most realistic values for ΔG_D(H₂O). The results represent the increase in the denaturating power of surfactants with an increase in hydrocarbon chain length. The value of about 22.27 kJ · mol^?1 was obtained for ΔG_D(H₂O) from transition curves. Subsequently, the retinol binding property of BLG as its functional indicator was investigated in the presence of these surfactants using the spectrofluorimeter titration method. The results represent the substantial enhancement of retinol binding affinity of BLG in the presence of these surfactants.     

Synthesis,DNA binding and topoisomerase inhibition of mononaphthalimide homospermidine derivatives

Two novel mononaphthalimide homospermidine derivatives （2a, 2b） with three or four methylene unit as linkages were synthesized and evaluated for cytotoxicity against human leukemia K562, murine melanoma B 16 and Chinese hamster ovary CHO cell lines. The presence of homospermidine motif could greatly elevate the potency of 1,8-naphthalimide. Conjugate 2b with longer spacer exhibited higher in vitro cytotoxicity than 2a. The DNA binding experiments indicated that conjugates 2b could bind to herring sperm DNA. The topoisomerase Ⅱ poison trials revealed that 2b could inhibit the activity of top. Ⅱ.     

Transient structural disorder as a facilitator of protein-ligand binding: Native H/D exchange—Mass spectrometry study of cellular retinoic acid binding protein I

Binding of all-trans Retinoic Acid (RA) to Cellular Retinoic Acid Binding Protein I (CRABP I) does not result in significant changes of the protein tertiary structure, even though the binding site is inaccessible in a static apo-protein conformation. One of the proposed scenarios for the protein-ligand binding process invokes the notion of a flexible portal region adjacent to the binding site, while another model suggests that the requisite dynamic events are induced by dimerization of the apo-protein in solution. In this work, RA binding to CRABP I is studied in dilute solutions (low micro-molar range), where no dimer and/or oligomer formation occurs. Modulation of backbone dynamics within various segments of the protein by its ligand is assessed using a combination of hydrogen exchange, electrospray ionization mass spectrometry, and collision-induced dissociation of protein ions in the gas phase. Consistent with the portal model of ligand entry, several protein segments (most of them containing residues making hydrophobic contacts to RA in the holo-form of the protein) are flexible in the absence of the ligand. At the same time, the two segments containing arginine residues forming a salt bridge with RA form the least flexible region in the apo-form of the protein. Although the presence of RA in solution reduces flexibility of all protein segments, the largest effect is observed within four strands that form one of the two beta-sheets enveloping a cavity which houses the ligand-binding site. These results are consistent with a model in which ligand binding occurs through a partially unstructured state of the protein with unobstructed access to the ligand-binding site. This intermediate (whose core is formed by the two stable arginine-containing strands) corresponds to a relatively low-energy local minimum on the apo-protein energy surface and is frequently sampled under native conditions.     

Effect of dioxane on the binding of competitive inhibitor proflavin and catalytic activity of bovine pancreatic α-chymotrypsin

The binding of competitive inhibitor proflavin by α-chymotrypsin in water-dioxane mixtures over the entire range of thermodynamic activities of water a _w was studied. The data on the degree of binding of proflavin were compared to the results on the catalytic activity of the enzyme preliminary incubated in water-dioxane mixtures. An analysis of the behavior of the concentration dependences of these characteristics demonstrated that, at low a _w values, the behavior of the interprotein contacts in the enzyme formed during its drying largely governs its functional properties, while at high a _w values, they are determined by the interaction of the enzyme with the organic solvent. Interplay of these two factors is responsible for the observed complex shape of the isotherm of binding of proflavin, with the maximum degree of binding being attained at moderate a _w values.