Boolean and fuzzy logic implemented at the molecular level

In this work, it is shown how to implement both hard and soft computing by means of two structurally related heterocyclic compounds: flindersine (FL) and 6(5H)-phenanthridinone (PH). Since FL and PH have a carbonyl group in their molecular skeletons, they exhibit Proximity Effects in their photophysics. In other words, they have an emission power that can be modulated through external inputs such as temperature (T) and hydrogen-bonding donation (HBD) ability of solvents. This phenomenology can be exploited to implement both crisp and fuzzy logic. Fuzzy Logic Systems (FLSs) wherein the antecedents of the rules are connected through the AND operator, are built by both the Mamdani’s and Sugeno’s models. Finally, they are adopted as approximators of the proximity effect phenomenon and tested for their prediction capabilities. Moreover, FL as photochromic compound is also a multiply configurable crisp logic molecular element.     

牛血清白蛋白的光损伤和光氧化机理

运用激光闪光光解瞬态吸收技术, 在266 nm激光激励下, 研究了牛血清白蛋白(BSA)光损伤和被SO4-·单电子氧化的反应机理, 表征了反应过程中生成的自由基. 结果表明, 在266 nm激光照射下, BSA可同时发生光电离和光激发, 生成色氨酸阳离子自由基(Trp/NH+·), 由Trp/NH+·快速脱质子形成的色氨酸中性自由基(Trp/N·)及色氨酸三重激发态(3Trp*), 3Trp*再与酪氨酸(Tyr)发生分子内电子转移生成酪氨酸中性自由基(Tyr/O·). 在SO4-·单电子氧化的反应中, 借助减谱技术, 求得BSA中Tyr和色氨酸(Trp)自由基的表观生成速率常数, 但未发现分子内电子转移现象, 阐明了SO4-·自由基是通过与BSA中的Tyr和Trp发生电子转移反应来氧化BSA的, SO4-·氧化BSA的反应速率常数为1.51×10¹⁰ L·mol^-1·s^-1, 从而为进一步研究血清白蛋白的氧化还原代谢过程提供理论基础.     

Fluorescent probe mimicking multiple logic gates and a molecular keypad lock upon interaction with Hg2+ and bovine serum albumin

The output fluorescence exhibited by an intramolecular charge transfer fluorescent probe 1 providing different chemical inputs mimicked multiple logic gates. A molecular keypad lock security device authorizing password entries (logic memory) and capable of solving crossword puzzles has been constructed by computing the output emission of 1 upon chemical inputs of BSA and Hg(2+). Based on logic operations the devised fluorescent keypad lock could be unlocked upon entering a correct sequence of password, 'BHU'.     

Biolocalisation and photochemical properties of two novel macrocyclic photosensitisers: a spectroscopic study

Biolocalisation and photochemical properties of novel macrocyclic photosensitisers, guanidiniocarbonyl-substituted tetraphenylporphyrin (1) and sugar-substituted sapphyrin (2) were investigated by spectroscopic methods. Both photosensitisers absorb in far visible region and showed good tumour localisation. Photosensitiser 2 demonstrated significantly larger absolute and relative to normal tissue (T/N) amount in tumour (330 microg g(-1) wet tissue, T/N=19.0) than photosensitiser 1 did (13 microg g(-1) wet tissue, T/N=2.1). According to iodometric and uric acid assays, compound 1 produced large amount of 1O2 (phidelta=0.60-0.68), while compound 2 showed non-significant 1O2 production (phidelta=0.04). The electronic spectroscopic study confirms that only photosensitiser 1 is able to mediate photooxidation of model compounds (BSA, poly(Trp), Tyr, Trp, and GMP) after light irradiation. Pour photochemical activity of compound 2 was explained by its self-aggregation. Raman spectroscopic study indicated that monomerised photosensitiser 2 effectively damaged BSA and calf thymus DNA after light excitation at the conditions of high excess of these macromolecules.     

Study on the binding of luteolin to bovine serum albumin

Binding of luteolin (LU) to bovine serum albumin (BSA) was investigated at 298, 308 and 318K at pH 7.4 using spectrophotometric techniques such as fluorescence emission, circular dichroism (CD). The data obtained from fluorescence quenching experiments showed that LU was bound to BSA and binding constants and the number of binding sites (n approximately 1) were obtained. The thermodynamic parameters DeltaH(0), DeltaS(0), DeltaG(0) at different temperatures were calculated. They indicated that both hydrophobic forces and hydrogen bonds are the major interactions between LU and BSA. A value of 3.12nm for the average distance r between LU (acceptor) and tryptophan residue (Trp) of BSA (donor) was derived from the fluorescence resonance energy transfer. The effects of some common metal ions on the binding are also considered. Besides, the interaction of BSA with LU led to a change in the conformation of BSA.     

运用模糊神经网络表达和预测链烷烃pVT性质

采用一种基于遗传算法的新型模糊神经网络方法研究链烷烃类化合物的pVT性质。该方法综合神经网络、遗传算法与模糊系统三种柔性智能计算技术的优点,具有良好的学习能力,不易陷入局部最小区域,学习速度较快,网络知识以模糊语言变量的形式加以表达,易于理解。用分子连接性指数对24种链烷烃化合物结构和pVT数据进行学习,进而预测另外14种未知化合物的pVT性质,较好地揭示出化合物分子结构与pVT性质之间的关系,并给出了良好的关联与预测结果。     

Fluorescence probing of albumin-surfactant interaction

Protein-surfactant interactions were studied using bovine serum albumin (BSA) and the three surfactants sodium dodecyl sulfate (SDS), cetyltrimethylammonium bromide (CTAB), and poly(oxyethylene)isooctyl phenyl ether (TX-100). The surfactants used belong to three broad classes, i.e., anionic, cationic, and nonionic. These categories of surfactants were used to elucidate the mechanism of surfactant binding to BSA, at pH 7. The interactions were followed fluorimetrically using both intrinsic tryptophan (Trp) fluorescence and the fluorescence of an external label. The aggregation behavior of the surfactants were studied in the presence of BSA. Steady-state fluorescence studies indicate that all three surfactants bind to BSA in a cooperative manner. This cooperative binding affects the binding of the external label to BSA. All these effects are also manifested in time-resolved fluorescence studies. The effects of surfactants on acrylamide quenching and energy transfer from Trp in BSA to bound dye provided valuable insights into the structural modification of BSA in presence of surfactants. The surfactant-induced conformational change of BSA was also confirmed by circular dichroism studies. However, among the three categories of surfactants, the nonionic surfactant shows the least interaction with BSA.     

槲皮素与酪蛋白和牛血清白蛋白的相互作用及共存碳纳米管的影响

采用荧光猝灭和同步荧光法,研究了磷酸缓冲溶液(PBS, pH=7.4)中有无碳纳米管(CNTs)共存时,荧光活性物质槲皮素(Qct)与牛血清白蛋白(BSA)和酪蛋白(Cas)的相互作用. 推导了方法1(固定蛋白质浓度, 改变Qct浓度, 测量蛋白质荧光改变)和方法2(固定Qct浓度, 改变蛋白质浓度, 测量Qct荧光改变)研究分子间作用的一般方程, 由非线性最小二乘拟合法测算了结合常数K和摩尔结合比n, 并藉此定量评估了“光内滤所致猝灭”效应的影响. 研究了共存CNTs或Qct对BSA或Cas的荧光猝灭效应, 及CNTs对Qct-BSA和Qct-Cas相互作用的影响. 以同步荧光法考察了CNTs或Qct对BSA或Cas构象的影响, 并测算了CNTs或Qct与蛋白质中酪氨酸(Tyr)或色氨酸(Trp)残基相关的K和n. 结果表明, CNTs主要与处于蛋白质分子表面附近的Trp残基作用, 而小分子Qct则还可与处于蛋白质分子内部的Tyr残基作用.     

Energy transfer photophysics from serum albumins to sequestered 3-hydroxy-2-naphthoic acid, an excited state intramolecular proton-transfer probe

The steady-state and time-resolved studies of the sensitized emission of the excited-state proton transfer (ESIPT) probe 3-hydroxy-2-naphthoic acid (3HNA) when bound to bovine serum albumin (BSA) and human serum albumin (HSA) indicate that the nonradiative dipole-dipole F?rster type energy transfer from Trp singlet state of proteins to the ESIPT singlet state of 3HNA is greater in the case of HSA. This is supported by the distance and the orientation of the donor-acceptor pair obtained from the protein-ligand docking studies. The docking studies of the complex of BSA-3HNA also indicate that Trp 134 rather than Trp 213 is involved in the energy transfer process. The local environment of Trp 134 in BSA rather than that of Trp 213 is perturbed because of interaction with 3HNA as revealed by the optical resolution of Trp 134 phosphorescence in the complex at 77 K. Docking studies support the larger rotational correlation time, thetac (approximately 50 ns), observed for Trp residue/residues in the complexes of HSA and BSA compared with that in the free proteins.     

Quenching of tryptophan fluorescence in various proteins by a series of small nickel complexes

A series of twelve anionic, cationic, and neutral nickel(II) complexes have been synthesized and characterized. The interaction of these complexes with bovine serum albumin (BSA), human serum albumin (HSA), lysozyme (Lyso), and tryptophan (Trp) has been studied using steady-state fluorescence spectroscopy. Dynamic and static quenching constants have been calculated, and the role played in quenching by the ligand and complex charge investigated. The nickel complexes showed selectivity towards the different proteins based on the environment surrounding the Trp residue(s). Only small neutral complexes with hydrophobic ligands effectively quenched protein fluorescence via static quenching, with association constants ranging from 10(2) M(-1) (free Trp) to 10(10) M(-1) (lysozyme), indicating a spontaneous and thermodynamically favorable interaction. The number of binding sites, on average, was determined to be one in BSA, HSA and free Trp, and two in lysozyme.     

氧氟沙星与脲诱导牛血清白蛋白结合的机制研究

摘要 利用荧光光谱和紫外光谱研究了脲（Urea）对牛血清白蛋白（BSA）结构的影响以及氧氟沙星（Oflxacin）与脲诱导的BSA结合的情况。结果显示：Urea诱导BSA变性历经两步、三态过程,且伴随中间态的形成。随着Urea浓度的增大,BSA荧光强度降低并先蓝移（344 nm～336 nm）,后又红移至350 nm。Urea浓度在4.6～5.2 mol/L范围时,Oflx对BSA中间态有强的猝灭作用（KQ=10.46×104 L/mol, Urea 4.8 mol/L）和较大的结合常数（KA=3.8807×105 L/mol, Urea 4.8 mol/L）,但是结合位点数小（n=0.76, Urea 5.0 mol/L）,能量传递效率低（E=0.3002, Urea 4.8 mol/L）。同步荧光光谱显示：Urea诱导BSA去折叠时,Trp-212残基微环境并未发生改变,而Tyr的最大荧光发射峰蓝移,Oflx的加入诱导Trp-212的微环境更具疏水性。Oflx加速了Urea对BSA的失活作用。     

三维同步偏振荧光光谱研究蛋白质溶液变性时氨基酸残基的发光行为

将偏振技术、同步技术与三维技术结合起来的三维同步偏振荧光光谱(TDSPS)能分辨蛋白质溶液中的色氨酸(Trp)和酪氨酸(Tyr)残基,具有同步光谱分辨率高、三维技术信息丰富的优点．本文用TDSPS表征牛血清白蛋白(BSA)、人血清白蛋白(HSA)受各种因素影响(酸效应、碱效应、盐效应、猝灭剂等)时Trp,Tyr残基荧光光谱的变化,用于区分HSA和BSA．     

Spectroscopic analyses on interaction of o-Vanillin-D-Phenylalanine, o-Vanillin-L-Tyrosine and o-Vanillin-L-Levodopa Schiff Bases with bovine serum albumin (BSA)

In this work, three o-Vanillin Schiff Bases (o-VSB: o-Vanillin-D-Phenylalanine (o-VDP), o-Vanillin-L-Tyrosine (o-VLT) and o-Vanillin-L-Levodopa (o-VLL)) with alanine constituent were synthesized by direct reflux method in ethanol solution, and then were used to study the interaction to bovine serum albumin (BSA) molecules by fluorescence spectroscopy. Based on the fluorescence quenching calculation, the bimolecular quenching constant (K(q)), apparent quenching constant (K(sv)), effective binding constant (K(A)) and corresponding dissociation constant (K(D)) as well as binding site number (n) were obtained. In addition, the binding distance (r) was also calculated according to Foster's non-radioactive energy transfer theory. The results show that these three o-VSB can efficiently bind to BSA molecules, but the binding array order is o-VDP-BSA>o-VLT-BSA>o-VLL-BSA. Synchronous fluorescence spectroscopy indicates that the o-VDP is more accessibility to tryptophan (Trp) residues of BSA molecules than to tyrosine (Tyr) residues. Nevertheless, the o-VLT and o-VLL are more accessibility to Tyr residues than to Trp residues.     

Simultaneously multiply-configurable or superposed molecular logic systems composed of ICT (internal charge transfer) chromophores and fluorophores integrated with one- or two-ion receptors

Integrated "ICT chromophore-receptor" systems show ion-induced shifts in their electronic absorption spectra. The wavelength of observation can be used to reversibly configure the system to any of the four logic operations permissible with a single input (YES, NOT, PASS 1, PASS 0), under conditions of ion input and transmittance output. We demonstrate these with dyes integrated into Tsien's calcium receptor, 1-2. Applying multiple ion inputs to 1-2 also allows us to perform two- or three-input OR or NOR operations. The weak fluorescence output of 1 also shows YES or NOT logic depending on how it is configured by excitation and emission wavelengths. Integrated "receptor(1)-ICT chromophore-receptor(2)" systems 3-5 selectively target two ions into the receptor terminals. The ion-induced transmittance output of 3-5 can also be configured via wavelength to illustrate several logic types including, most importantly, XOR. The opposite effects of the two ions on the energy of the chromophore excited state is responsible for this behaviour. INHIBIT and REVERSE IMPLICATION are two of the other logic types seen here. Integration of XOR logic with a preceding OR operation can be arranged by using three ion inputs. The fluorescence output of these systems can be configured via wavelength to display INHIBIT or NOR logic under two-input conditions. The superposition or multiplicity of logic gate configurations is an unusual consequence of the ability to simultaneously observe multiple wavelengths.     

Interaction of hypericin with serum albumins: surface-enhanced Raman spectroscopy, resonance Raman spectroscopy and molecular modeling study

Surface-enhanced Raman spectroscopy, resonance Raman spectroscopy and molecular modeling were employed to study the interaction of hypericin (Hyp) with human (HSA), rat (RSA) and bovine (BSA) serum albumins. The identification of the binding site of Hyp in serum albumins as well as the structural model for Hyp/HSA complex are presented. The interactions mainly reflect: (1) a change of the strength of H bonding at the N1-H site of Trp; (2) a change of the Trp side-chain conformation; (3) a change of the hydrophobicity of the Trp environment; and (4) a formation of an H-bond between the carbonyl group of Hyp and a proton donor in HSA and RSA which leads to a protonated-like carbonyl in Hyp. Our results indicate that Hyp is rigidly bound in IIA subdomain of HSA close to Trp214 (distance 5.12 A between the centers of masses). In the model presented the carbonyl group of Hyp is hydrogen bonded to Asn458. Two other candidates for hydrogen bonds have been identified between the bay-region hydroxyl group of Hyp and the carbonyl group of the Trp214 peptidic link and between the peri-region hydroxyl group of Hyp and the Asn458 carbonyl group. It is shown that the structures of the Hyp/HSA and Hyp/RSA complexes are similar to, and in some aspects different from, those found for the Hyp/BSA complex. The role of aminoacid sequence in the IIA subdomains of HSA, RSA and BSA is discussed to explain the observed differences.     

Deciphering the role of pH in the binding of ciprofloxacin hydrochloride to bovine serum albumin

The effect of the added fluoroquinolone, Ciprofloxacin Hydrochloride (CpH), on structural properties of Bovine Serum Albumin (BSA) was investigated by Circular Dichroism (CD), steady-state, time-resolved and Dynamic Light Scattering (DLS) spectroscopic approaches. The intrinsic fluorescence of the Tryptophan (Trp) amino acid residue in the globular protein BSA was made use of and the effect of pH at two different temperatures was thoroughly investigated. CD results indicate that CpH induces some structural changes in BSA and this has been well-supported by steady-state, lifetime and DLS data. The fluorescence intensity of Trp gradually decreases with the rise in concentration of CpH and we have conclusively proved that at pH 7.4 and 9.2, the mechanism of fluorescence quenching is mostly dynamic in nature, whereas at pH 4.5 mainly static quenching is operational. Thermodynamic parameters have been studied to rationalize the nature of binding of CpH to BSA, and we have concluded that hydrophobic and van der Waals forces play an important role in the process of drug-protein interaction at three different pH values. The lifetime of Trp was found to decrease with the rise in CpH concentration and the percentage reduction in lifetime was found to be a function of the pH of the medium under investigation.     

Bovine serum albumin-directed synthesis of biocompatible CdSe quantum dots and bacteria labeling

A simple method was developed for preparing CdSe quantum dots (QDs) using a common protein (bovine serum albumin (BSA)) to sequester QD precursors (Cd(2+)) in situ. Fluorescence (FL) and absorption spectra showed that the chelating time between BSA and Cd(2+), the molar ratio of BSA/Cd(2+), temperature, and pH are the crucial factors for the quality of QDs. The average QD particle size was estimated to be about 5 nm, determined by high-resolution transmission electron microscopy. With FL spectra, Fourier transform infrared spectra, and thermogravimetric analysis, an interesting mechanism was discussed for the formation of the BSA-CdSe QDs. The results indicate that there might be conjugated bonds between CdSe QDs and -OH, -NH, and -SH groups in BSA. In addition, fluorescence imaging suggests that the QDs we designed can successfully label Escherichia coli cells, which gives us a great opportunity to develop biocompatible tools to label bacteria cells.     

Spectroscopic analyses on interaction of Amantadine-Salicylaldehyde, Amantadine-5-Chloro-Salicylaldehyde and Amantadine-o-Vanillin Schiff-Bases with bovine serum albumin (BSA)

In this work, three Tricyclo [3.3.1.1(3,7)] decane-1-amine (Amantadine) Schiff-Bases, Amantadine-Salicylaldehyde (AS), Amantadine-5-Chloro-Salicylaldehyde (AS-5-C) and Amantadine-o-Vanillin (AS-o-V), were synthesized by direct heating reflux method in ethanol solution and characterized by infrared spectrum and elementary analysis. Fluorescence quenching was used to study the interaction of these Amantadine Schiff-Bases (AS, AS-5-C and AS-o-V) with bovine serum albumin (BSA). According to fluorescence quenching calculations the bimolecular quenching constant (K(q)), apparent quenching constant (K(SV)), effective binding constant (K(A)) and corresponding dissociation constant (K(D)), binding site number (n) and binding distance (r) were obtained. The results show that these Amantadine Schiff-Bases can obviously bind to BSA molecules and the binding strength order is AS相似文献   

Spectroscopic studies on the interaction between riboflavin and albumins

The interactions between riboflavin (RF) and human and bovine serum albumin (HSA and BSA) were studied by using absorption and fluorescence spectroscopic methods. Intrinsic fluorescence emission spectra of serum albumin in the presence of RF show that the endogenous photosensitizer acts as a quencher. The decrease of fluorescence intensity at about 350 nm is attributed to changes in the environment of the protein fluorophores caused by the ligand. The quenching mechanisms of albumins by RF were discussed. The binding constants and binding site number were obtained at various temperatures. The distance between albumins and RF in the complexes suggests that the primary binding site for RF is close to tryptophan residue (Trp214) of HSA and Trp212 of BSA. The hydration process of albumins has also been discussed.     

A versatile water soluble fluorescent probe for ratiometric sensing of Hg2+ and bovine serum albumin

A novel tetraazamacrocycle fluorescent sensor (6-(1-(dimethylamino)-5-naphthalene sulfonyl)-3,6,9,15-tetraazabicyclo[9.3.1] pentadeca-1(15),11,13-triene, 1) has been designed and prepared, which can be utilized for selective and ratiometric sensing of Hg(2+) and bovine serum albumin (BSA) with two different responsive modes in aqueous solution at physiological pH (50 mM Tris-HCl, pH 7.6). Above 0.5 ppb Hg(2+) can be discerned by coordination with 1 and the emission color changes enable 1 to be applied to a fast Hg(2+) test paper assay. Sensor 1 has also been demonstrated to be easily cell-penetrable and applicable for Hg(2+) imaging in living cells. Imaging of BSA in the gel using SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis) stained in the medium containing 1 verified that the binding of 1 and BSA was successful in the presence of nonprotein substances. The linear range of 1 towards BSA utilizing ratiometric fluorescent calibration via noncovalent interaction in solution is 0-100 μg mL(-1) with a detection limit of 1 μg mL(-1), and has been successfully employed to determine the albumin concentration in blood serum by means of ratiometric fluorescent measurements for the first time. Finally, sensor 1 behaves as a fluorescent molecular switch composed of triple logic gates upon chemical inputs of Hg(2+) and BSA, which potentially provides intelligent diagnostics for Hg(2+) contaminated serum on the nanoscale.