Compensatory Adaptations of Structural Dynamics in an Intrinsically Disordered Protein Complex

Intrinsically disordered proteins (IDPs) play crucial roles in protein interaction networks and in this context frequently constitute important hubs and interfaces. Here we show by a combination of NMR and EPR spectroscopy that the binding of the cytokine osteopontin (OPN) to its natural ligand, heparin, is accompanied by thermodynamically compensating structural adaptations. The core segment of OPN expands upon binding. This “unfolding‐upon‐binding” is governed primarily through electrostatic interactions between heparin and charged patches along the protein backbone and compensates for entropic penalties due to heparin–OPN binding. It is shown how structural unfolding compensates for entropic losses through ligand binding in IDPs and elucidates the interplay between structure and thermodynamics of rapid substrate‐binding and ‐release events in IDP interaction networks.     

含时密度泛函理论研究低带隙的中性和带电的交替共聚芴的光学特性

用含时的密度泛函（TD—DFT）方法研究了低带隙的中性和带电的交替共聚芴Green 1）,该化合物是由烷染取代芴和（1,2,5-噻吩基-3,4-硫重氮基）喹喔啉噻吩（T—TDQ—T）单元交替重复组成,对他们的激发态特性用二维（2D）和三维（3D）实空间分析方法做了进一步分析．对于中性的Green 1,分别得到其带隙、键能、激子结合能和核驰豫能．用3D跃迁密度方法对中性和带电的Green 1的跃迁偶极矩进行比较可显示出跃迁偶极矩的取向和强度;用3D电荷差异密度方法显示出激发后的中性和带电的Green 1电荷重新分布和比较,用2D实空间分析方法（跃迁密度矩阵）来研究中性和带电的Green 1处于激发态时的电子空穴相干性．中性Green 1的激发态特性分别用TD—DFT和ZINDO两种方法进行了计算,比较得出电子-电子相互作用（在TD—DFT中）对激发态性质的重要影响．     

Interaction of recombinant human interferon-gamma with liposomes

The interaction of recombinant human interferon-gamma (IFN) with egg phosphatidylcholine liposomes was studied. IFN which binds to liposomes was dependent on the liposomal charge and pH, and a preferential binding was observed in negatively charged liposomes at pH 7.4-10. Electron-microscopic observation showed that the increased liposomal turbidity induced by IFN was due to liposomal aggregation, and the increased turbidity could be decreased by the addition of NaCl. Thus, ionic binding may participate in this interaction. But, when the incubation time was longer, the liposomal aggregation was not decreased by the addition of NaCl, and the leakage of the entrapped marker, calcein, was observed. Electron-microscopic analysis showed that this leakage resulted from the morphological change of liposomes. From these findings, ionic binding may participate in the interaction between IFN and liposomes and then develop a morphological change in negatively charged liposomes under the neutral pH condition.     

The effect of charge on the volume change of DNA binding with intercalator DAPP

To study the effect of ligand charge on DNA-ligand binding, we measured the difference in volume change of the noncovalent complex formed between calf thymus DNA and the charged and uncharged form of 3,8-diamino-6-phenylphenanthridine (DAPP). We found that the volume change for binding with the charged DAPPH+ is about 7.8 +/- 1.5 cm3 mol(-1) more positive than with the neutral DAPP. We hypothesize that this large difference in interaction volume originates from partial desolvation of the charge of DAPPH+ when it is bound to DNA.     

Recent developments in the redox-switched binding of organic compounds

This review summarizes and puts into context recent advances in the field of redox-switched binding processes, with particular reference to the interaction between redox-active compounds and organic compounds, both charged and neutral. Simple homogeneous, two-component systems are discussed at first as a precursor to sections on more advanced systems (e.g. multi-component and multi-pole) and binding processes involving components attached to a surface.     

Electrostatic Interactions in Docking a 3D Model of Bovine Testicular Hyaluronidase with a Chondroitin Sulfate Trimer and a Heparin Tetramer

The molecular docking of a 3D-model of bovine testicular hyaluronidase with glycosaminoglycan ligands is performed. A chondroitin sulfate trimer and a heparin tetramer were used as ligands. Methods of computational chemistry are applied to elucidate the regulation of hyaluronidase functioning in an organism when the heparin ligand inactivates the biocatalyst, and the chondroitin sulfate ligand protects the enzyme structure. Eight ligand binding sites are identified on the molecular surface of the enzyme, each of which is equally capable of interacting with chondroitin sulfate trimers and heparin tetramers via electrostatic interactions. It is found that reversible and irreversible conformational changes in the enzyme 3D structure can occur depending on the positioning of negatively charged ligands on its globule (under different conditions, they can either stabilize or inactivate the biocatalyst). Binding sites whose occupancy is sufficient for preventing irreversible deformations of the enzyme conformation upon introducing the heparin ligand into the active site are identified on the molecular surface of hyaluronidase. The interaction of glycosaminoglycan ligands with hyaluronidase is mainly determined by electrostatic forces.     

氯诺昔康与中性及电荷型β-环糊精衍生物的包合作用

采用溶解度法研究了不同pH值下氯诺昔康与中性及电荷型β-环糊精衍生物的包合作用．结果表明,氯诺昔康与3种环糊精都形成了1：1的包合物．以包合常数作为包合作用的量度,在酸性和中性条件下包合能力较碱性强,其中磺丁醚-β-环糊精（SBE移CD）在酸性条件下包合常数最大．电荷型伊环糊精除了通常的疏水作用力为主客体间包合驱动力外,还存在额外的静电包合作用力．     

稀土离子对重组内皮抑素与肝素相互作用的影响

通过荧光光谱法和圆二色谱法研究了重组内皮抑素与稀土离子和肝素的作用.结果表明,稀土离子和肝素都可以与重组内皮抑素结合并引起蛋白的荧光猝灭和二级结构的改变,稀土离子与重组内皮抑素的结合会影响其与肝素的相互作用,并降低重组内皮抑素对人脐静脉内皮细胞的增殖抑制活性.     

Binding Models of Copper(II) Thiosemicarbazone Complexes with Human Serum Albumin: A Speciation Study

Copper(II) complexes of thiosemicarbazones (TSCs) often exhibit anticancer properties, and their pharmacokinetic behavior can be affected by their interaction with blood transport proteins. Interaction of copper(II) complexes of an {N,N,S} donor α-N-pyridyl TSC (Triapine) and an {O,N,S} donor 2-hydroxybenzaldehyde TSC (STSC) with human serum albumin (HSA) was investigated by UV–visible and electron paramagnetic resonance spectroscopy at physiological pH. Asp-Ala-His-Lys and the monodentate N-methylimidazole were also applied as binding models. Conditional formation constants were determined for the ternary copper(II)-TSC complexes formed with HSA, DAHK, and N-methylimidazole based on the spectral changes of both charge transfer and d-d bands. The neutral N-methylimidazole displays a similar binding affinity to both TSC complexes. The partially negatively charged tetrapeptide binds stronger to the positively charged Triapine complex in comparison to the neutral STSC complex, while the opposite trend was observed for HSA, which demonstrates the limitations of the use of simple ligands to model the protein binding. The studied TSC complexes are able to bind to HSA in a fast process, and the conditional constants suggest that their binding strength is only weak-to-moderate.     

中性红与小牛胸腺DNA相互作用机理的电化学和紫外-可见光谱研究

静电作用;嵌插作用;中性红与小牛胸腺DNA相互作用机理的电化学和紫外-可见光谱研究     

A spectrophotometric study on the interaction of neutral red with double-stranded DNA in large excess

With the measurement of molecular absorption, the interaction of neutral red (NR) with double-stranded DNA in large excess was investigated. It was found that the interaction of NR, existing in the acidic state (HNR) at pH 4.56, with double-stranded structure DNA displays different spectral features depending on the molar ratio of HNR/DNA, R. If R>1.33, the binding process is characterized by a binding constant at the 10(6) level with each nucleotide residue of double-stranded DNA binding one HNR molecule. If R<0.67, the binding constant is reduced to the 10(4) level, and the binding number for each nucleotide residue of double-stranded DNA to HNR is less than one.     

Capillary electrophoresis-based analysis of phospholipid and glycosaminoglycan binding by human beta2-glycoprotein I

Human beta2-glycoprotein I (beta2gpI) is a phospholipid and heparin binding plasma glycoprotein involved in autoimmune diseases characterized by blood clotting disturbances (thrombosis) together with the occurrence of autoantibodies against beta2gpI. With the final goal of assessing autoantibody influence on binding interactions of beta2gpI we have studied the development of capillary electrophoresis (CE)-based assays for interactions of negatively charged ligands with beta2gpI. In the development of suitable conditions for analysis at neutral pH of this basic protein (pI about 8) we found the pH hysteresis behavior of fused silica surfaces useful since the protonated surface after an acid pre-wash counteracted protein adsorption efficiently in contrast to more laborious procedures including acrylamide/dimethylacrylamide coatings that did not permit analysis of this particular protein. This simple approach made estimates of heparin-beta2gpI interactions possible and the principle was shown also to work for detection of betagpI binding to anionic phospholipids. Utilizing the pH hysteresis effect may be a simple solution to the adsorption problems often encountered in analyses of proteins by CE.     

Interaction of β‐Cyclodextrin with Cetyltrimethylammonium Bromide in the Presence of Neutral Red and Its Application to the Spectrophotometric Determination of β‐Cyclodextrin

The effects of addition of β‐cyclodextrin (β‐CD) to the neutral red‐cetyltrimethylammonium bromide (CTAB) associates in pH 7 phosphate buffer solutions were investigated. Addition of β‐CD to neutral red‐CTAB association causes decomposition of the associate by displacement of neutral red with β‐CD. The inclusion complex of CTAB with β‐CD is more stable than that with neutral red. The results indicate that formation of inclusion complex of CTAB with β‐CD prevents its association with neutral red, and inclusion complex formation of β‐CD and neutral red in the presence of CTAB takes place after total consumption of CTAB. The competition of β‐CD and neutral red on the interaction with CTAB can be used for the simple, rapid and sensitive spectrophotometric determination of β‐CD.     

肝素与HIV-1膜表面蛋白gp120相互作用的预测和模拟

用分子模拟软件研究肝素与HIV-1膜表面蛋白gp120的相互作用.将肝素中的单糖、二糖和三糖片段作为探针对gp120蛋白进行搜索,统计分析确定肝素结合区域.用肝素六糖片段和结合区域进行反应分子对接,获得两种结合模式.最终建立的模型能够很好地解释肝素体外抑制HIV-1的现象,同时对其机理进行了推测.     

Charged versus Neutral Hydrogen‐Bonded Complexes: Is There a Difference in the Nature of the Hydrogen Bonds?

A theoretical study on some carboxylic acid dimers formed by positively or negatively charged molecules has been carried out by using DFT methods. The resulting dimers possess either a charge of +2 or ?2. In addition, the corresponding neutral complexes have also been considered. The electron density distribution described by the atoms in molecules and the natural bond orbital methods, as well as the electric field maps of the systems, have been analyzed and compared without finding significant differences between the neutral and ionic complexes. The interaction energy along the dissociation path of the charged dimers shows both a local minimum and a local maximum, defining a stability region between them. When this energetic profile is recalculated by removing the repulsion between the charged groups, it resembles to those of the neutral molecules. Hence, the characteristics of the charged dimers are similar to those of the neutral ones: the addition of a repulsion term for the charged groups permits to retrieve the energetic profiles dependence with the distance in the charged system. The interacting quantum atom (IQA) method has been used to calculate the interaction energy terms, including the classic Coulombic term between the whole molecules and the corresponding of the carboxylic acid groups. The IQA results show repulsive electrostatic interactions when the whole molecules are considered in the ionic complexes, but attractive ones between the carboxylic groups in both neutral and ionic complexes.     

Kinetics and mechanism of the reaction between aquacobalamin and isoniazid

Kinetics of the reaction of aquacobalamin (H₂OCbl) with isoniazid (isonicotinic acid hydrazide, INH) in weakly alkaline, neutral, and weakly acidic media was studied using UV–Vis spectroscopy. It is shown that the reversible formation of a complex more stable than those of cobalamin(III) with pyridine and hydrazine occurs during the reaction. A mechanism of the reaction includes reversible stages of binding a neutral INH molecule by cobalamin(III) through an oxygen atom with its subsequent deprotonation, along with the reversible interaction of H₂OCbl and the negatively charged form of INH.     

Hydrogen-bonding interactions in peptide nucleic acid and deoxyribonucleic acid: a comparative study

Peptide nucleic acid (PNA) is a synthetic analogue of deoxyribonucleic acid (DNA) capable of tightly binding to itself and DNA with high specificity. Using hybrid density functional methods, hydrogen-bond (H-bond) strengths have been evaluated for isolated Watson-Crick base pairs, PNA base pairs, and charged as well as neutral DNA base pairs. Heterogeneous base pairs of PNA with charged and neutral DNA have also been investigated. The competing effects of short-range H-bonding and long-range Coulombic repulsions in charged DNA base pairs have been analyzed. Polarizable continuum models have been employed to evaluate solvation effects on the binding energies.     

Effective attraction interactions between like-charge macroions bound to binary fluid lipid membranes

Using integral equation theory of liquids to a binary mixed fluid lipid membrane, the authors study the membrane-mediated interactions between binding macroions and the redistribution of neutral and charged lipids due to the macroions. The authors find that when the concentration of binding macroions is infinitely dilute, the main contribution to the attractive potential between macroions is the line tension between neutral and charged lipids of the membrane. As the relative concentration of charged lipids is increased, the authors observe a repulsive-attractive-repulsive potential transition due to the competition between the line tension of mixed lipids and screened electrostatic macroion-macroion interactions. For the finite concentration of macroions, the main feature of the attraction is similar to the infinite-diluted case. However, the corresponding line tension of binary lipids under single macroion is lowered with the formation of multicomplexes by the charged lipids and the macroions, and the maximum of attractive potential will shift toward the higher values of charged lipid concentration.     

Modulation of lysozyme charge influences interaction with phospholipid vesicles

Lysozyme is a globular protein which is known to bind to negatively charged phospholipid vesicles. In order to study the relationship between charge state of the protein and its interaction with negatively charged phospholipid membranes chemical modifications of the proteins were carried out. Succinylation and carbodiimide modification was used to shift the isoelectric point of lysozyme to lower and higher pH values, respectively. The binding of the modified lysozyme to phospholipid vesicles prepared from phosphatidic acid (PA) was determined using microelectrophoresis and ultracentrifugation. At acidic pH of the solution all lysozyme species reduced the surface charges of PA vesicles. Succinylated lysozyme (succ lysozyme) reduced the electrophoretic mobility (EPM) to nearly zero, whereas native lysozyme and carboxylated lysozyme (carbo lysozyme) changed the surface charge to positive values. At neutral pH, the reduction of surface charges was less for carbo lysozyme and unmodified lysozyme. Succ lysozyme did not change the EPM. Unmodified and carbo lysozyme decreased the magnitude of EPM, but the whole complex was still negatively charged. The bound fraction of all modified lysozyme to PA vesicles at high lysozyme/PA ratios was nearly constant at acidic pH. At low lysozyme/PA ratios the extent of bound lysozyme is changed in the order carbo>unmodified>succ lysozyme. Increasing the pH, the extent of bound lysozyme to PA large unilamellar vesicles (LUV) is reduced, at pH 9.0 only 35% of carbo lysozyme, 23% of unmodified lysozyme is bound, whereas succ lysozyme does not bind at pH 7.4 and 9.0. At low pH, addition of all lysozyme species resulted in a massive aggregation of PA liposomes, at neutral pH aggregation occurs at much higher lysozyme/PA ratios. Lysozyme binding to PA vesicles is accompanied by the penetration of lysozyme into the phospholipid membrane as measured by monolayer techniques. The penetration of lysozyme into the monolayer was modulated by pH and ionic strengths. The interaction of lysozyme with negatively charged vesicles leads to a decrease of the phospholipid vesicle surface hydration as measured by the shift of the maximum of the fluorescence signal of a headgroup labeled phospholipid. The binding of bis-ANS as an additional indicator for the change of surface hydrophobicity is increased at low pH after addition of lysozyme to the vesicles. More hydrophobic patches of the lysozyme-PA complex are exposed at low pH. At low pH the binding process of lysozyme to PA vesicles is followed by an extensive intermixing of phospholipids between the aggregated vesicles, accompanied by a massive leakage of the vesicle aqueous content. The extent of lysozyme interaction with PA LUV at neutral and acidic pH is in the order carbo lysozyme>lysozyme>succ lysozyme.     

Electrocatalytic reaction of hydrogen peroxide and NADH based on poly(neutral red) and FAD hybrid film

A simple method to immobilize poly(neutral red) (PNR) and flavin adenine dinucleotide (FAD) hybrid film (PNR/FAD) by cyclic voltammetry is proposed. The PNR/FAD hybrid film can be easily prepared on an electrode surface involving electropolymerization of neutral red (NR) monomers and the electrostatic interaction between the positively charged PNR and the negatively charged FAD. It exhibits electroactive, stable, surface-confined, pH-dependent, nano-sized, and compatible properties. It provides good electrocatalytic properties to various species. It shows a sensitivity of 5.4 μA mM(-1) cm(-2) and 21.5 μA mM(-1) cm(-2) for hydrogen peroxide (H(2)O(2)) and nicotinamide adenine dinucleotide (NADH) with the linear range of 0.1 μM-39 mM and 5 × 10(-5) to 2.5 × 10(-4) M, respectively. It shows another linear range of 48.8-355.5 mM with the sensitivity of 12.3 μA mM(-1) cm(-2) for H(2)O(2). In particular, the PNR/FAD hybrid film has potential to replace some hemoproteins to be a cathode of biofuel cells and provide the biosensing system for glucose and ethanol.