Study of Interaction Between Tryptophan,Tyrosine, and Phenylalanine Separately with Silver Nanoparticles by Fluorescence Quenching Method

Using the spectroscopic method, the individual interaction of the three biochemically important amino acids, which are constituents of protein, namely, tryptophan, tyrosine, and phenylalanine with biologically synthesized silver nanoparticles has been investigated. The obtained UV-Vis spectra show the formation of ground-state complexes between tryptophan, tyrosine, and phenylalanine with silver nanoparticles. Silver nanoparticles possess the ability to quench the intrinsic fluorescence of the aforesaid amino acids by a dynamic quenching process. The binding constant, number of binding sites, and corresponding thermodynamic parameters (ΔH, ΔS, and ΔG) based on the interaction system were calculated for 293, 303, and 313 K. In the case of tryptophan and phenylalanine, with increase in temperature, the binding constant K was found to decrease; conversely, it was found to increase with increase in temperature in the case of tyrosine. The thermodynamic results revealed that the binding process was spontaneous; hydrogen bonding and van der Waals interaction were the predominant forces responsible for the complex stabilization in the case of tryptophan and phenylalanine, respectively, whereas in the case of tyrosine, hydrophobic interaction was the sole force conferring stability. Moreover, the Förster non-radiation energy transfer theory has been applied to calculate the average binding distance among the above amino acids and silver nanoparticles. The results show a binding distance of <7 nm, which ensures that energy transfer does occur between the said amino acids and silver nanoparticles.     

Assessment of laser-induced thermal load on silicon nanostructures based on ion desorption yields

Experimental assessment of the thermal load induced by fast laser pulses on micro- and nanostructures through IR imaging is currently too slow and lacks the spatial resolution to be useful. In this paper, we introduce a method based on measuring the laser-induced yields of ions to compare the thermal loads on nanofabricated silicon structures, when exposed to nanosecond laser pulses. The laser fluences at which the ion yields of, for example, sodiated and potassiated peptides ions are equal for two different structures correspond to equivalent thermal loads. Using alkalinated peptides is a convenient choice because the corresponding ion intensities are easily measured up to the melting point of silicon. As an example, we compare the nanosecond laser heating of silicon nanopost arrays with diverse post diameters and periodicities. Assessment of the thermal load through ion yield measurements can also be used to verify model assumptions for heat transport regimes in nanostructures.     

Analysis of the local conformation of proteins with two-dimensional fluorescence techniques

Two 2D fluorescence techniques are described which allow the study of conformational changes in proteins in their native form in μM solutions using aromatic amino acids (tryptophan, tyrosine) as intrinsic fluorescence markers. Simultaneous time- and wavelength-resolved fluorescence spectra are measured using a 80 ps laser source in conjunction with streak detection in the exit plane of an astigmatism-corrected spectrometer. This approach allows identification of different photophysical processes by their associated lifetime and spectral intensity distribution; errors due to the more common integration over a wider spectral range are avoided. Time-resolved spectra are sensitive to changes in the collisional environment (dynamic quenching) and can thus be used to monitor local conformation changes close to the respective fluorophors. This is demonstrated for the Ras protein which undergoes a drastic conformation change while binding to different nucleotides. Excitation-emission spectra are two-dimensional fluorescence images with one axis corresponding to the excitation and the other to the emission wavelength. Thus, they contain all conventional excitation and fluorescence spectra of a given substance. The 2D structure facilitates the interpretation of these spectra and allows the direct identification of resonance effects, scattering and the isolation of the contribution of different fluorophors to the complete spectrum. This is demonstrated for mixtures of tyrosine and tryptophan. In this case, both wavelength-resolved spectra and temporal decays are affected by energy transfer processes between the two amino acids. In a last example, both static and time-resolved spectral methods are combined to determine the respective contribution of static and dynamic quenching in calsequestrin. Evaluation of the fluorescence data is in good agreement with a recent crystallographic analysis which shows that all tryptophans are located in a conserved domain of the protein. Addition of Ca²⁺ ions leads to a more compact form of calsequestrin and to polymers. This information would not be obtainable from either of the two techniques alone. Received: 10 February 2000 / Published online: 13 September 2000     

Spectral properties of contact matrix: Application to proteins

A protein can be modelled by a set of points representing its amino acids. Topologically, this set of points is entirely defined by its contact matrix (adjacency matrix in graph theory). The contact matrix characterizing the relation between neighboring amino acids is deduced from Voronoi or Laguerre decomposition. This method allows contact matrices to be defined without any arbitrary cut-off that could induce arbitrary effects. Eigenvalues of these matrices are related with elementary excitations in proteins. We present some spectral properties of these matrices that reflect global properties of proteins. The eigenvectors indicate participation of each amino acids to the excitation modes of the proteins. It is interesting to compare the protein modelled as a close packing of amino acids, with a random close packing of spheres. The main features of the protein are those of a packing, a result that confirms the importance of the dense packing model for proteins. Nevertheless there are some properties, specific to the hierarchical organization of the protein: the primary chain order, the secondary structures and the domain structures.     

疏水表面上吸附态溶菌酶的DSC和FTIR研究

联合差示扫描量热 (DSC)和傅里叶变换红外吸收光谱(FTIR)分别研究了鸡蛋白溶菌酶(Lyz)在适度疏水吸附剂(PEG-600)表面上吸附和折叠时,不同盐(硫酸铵)浓度、表面覆盖度和变性剂(盐酸胍)浓度对无水环境的吸附态天然和变性溶菌酶构象变化及热稳定性的影响。研究发现：随着硫酸铵浓度和溶菌酶表面覆盖度的增加,吸附态天然和变性溶菌酶的吸热峰温度都逐渐降低,同时在较高温度下的微扰也增多。吸附发生后,α-螺旋结构减少,β-折叠和β-转角结构增多。在FTIR图谱中,吸附态变性溶菌酶在1 400～1 425 cm-1处的C—C拉伸振动峰和1 650～1 670 cm-1处的酰胺Ⅰ带特征峰都能明显观测到。但是,与之相比,相同条件下吸附态天然溶菌酶在1 650～1 670 cm-1处特征峰却几乎看不到。吸附态天然溶菌酶发生了结构丢失,表现得更加不稳定。     

EPR investigations of mesoporous silica doped with metal transitions ions

Electron paramagnetic resonance (EPR) experiments were performed on mesoporous silica powders in which (1,4,8,11-tetraazacyclotetradecane) cyclam groups were incorporated. These functionalised groups allow an easy binding with copper and nickel ions. Comparative studies are carried out on samples functionalised by cyclam groups located either inside the pores or in the walls of the mesoporous structures. Copper and nickel EPR parameters, including g-tensors and hyperfine components are determined and relevant electronic, magnetic and structural information are obtained. The EPR spectra intensities and line-widths are investigated on the temperature range [4 K,300 K] to clarify the relative dispersion or agglomeration of the doping ions in the matrices as well as their possible thermally activated mobility and ions pairing. As a support of the experimental EPR investigations, numerical simulations of the geometry of metallic ion environments and their electronic properties are carried out and discussed. The possibility of dynamic Jahn Teller (JT) effect in the temperature range [200, 60 K] is discussed for the nickel doped matrices where the low temperature quenched JT configuration is thought to favour the formation of Ni³⁺ pairs.     

Study of protein-probe complexation equilibria and protein-surfactant interaction using charge transfer fluorescence probe methyl ester of N,N-dimethylamino naphthyl acrylic acid

In this paper, we demonstrate the interaction between intramolecular charge transfer (ICT) probe—Methyl ester of N,N-dimethylamino naphthyl acrylic acid (MDMANA) with bovine serum albumin (BSA) using absorption and fluorescence emission spectroscopy. The nature of probe protein binding interaction, fluorescence resonance energy transfer from protein to probe and time resolved fluorescence decay measurement predict that the probe molecule binds strongly to the hydrophobic cavity of the protein. Furthermore, the interaction of the anionic surfactant sodium dodecyl sulphate (SDS) with water soluble protein BSA has been investigated using MDMANA as fluorescenece probe. The changes in the spectral characteristics of charge transfer fluorescence probe MDMANA in BSA-SDS environment reflects well the nature of the protein-surfactant binding interaction such as specific binding, non-cooperative binding, cooperative binding and saturation binding.     

Synergic approach to XAFS analysis for the identification of most probable binding motifs for mononuclear zinc sites in metalloproteins

In the present work a data analysis approach, based on XAFS data, is proposed for the identification of most probable binding motifs of unknown mononuclear zinc sites in metalloproteins. This approach combines multiple‐scattering EXAFS analysis performed within the rigid‐body refinement scheme, non‐muffin‐tin ab initio XANES simulations, average structural information on amino acids and metal binding clusters provided by the Protein Data Bank, and Debye–Waller factor calculations based on density functional theory. The efficiency of the method is tested by using three reference zinc proteins for which the local structure around the metal is already known from protein crystallography. To show the applicability of the present analysis to structures not deposited in the Protein Data Bank, the XAFS spectra of six mononuclear zinc binding sites present in diverse membrane proteins, for which we have previously proposed the coordinating amino acids by applying a similar approach, is also reported. By comparing the Zn K‐edge XAFS features exhibited by these proteins with those pertaining to the reference structures, key spectral characteristics, related to specific binding motifs, are observed. These case studies exemplify the combined data analysis proposed and further support its validity.     

Analytical laser induced liquid beam desorption mass spectrometry of protonated amino acids and their non-covalently bound aggregates

We have used analytical laser induced liquid beam desorption in combination with high resolution mass spectrometry ( m/Δm≥ 1000) for the study of protonated amino acids (ornithine, citrulline, lysine, arginine) and their non-covalently bound complexes in the gas phase desorbed from water solutions. We report studies in which the desorption mechanism has been investigated. The results imply that biomolecule desorption at our conditions is a single step process involving laser heating of the solvent above its supercritical temperature, a rapid expansion, ion recombination and finally isolation and desorption of only a small fraction of preformed ions and charged aggregates. In addition, we report an investigation of the aqueous solution concentration and pH-dependence of the laser induced desorption of protonated species (monomers and dimers). The experimental findings suggest that the desorption process depends critically upon the proton affinity of the molecules, the concentration of other ions, and of the pH value of the solution. Therefore the ion concentrations measured in the gas phase very likely reflect solution properties (equilibrium concentrations). Arginine self-assembles large non-covalent singly protonated multimers (n = 1...8) when sampled by IR laser induced water beam desorption mass spectrometry. The structures of these aggregates may resemble those of the solid state and may be preformed in solution prior to desorption. A desorption of mixtures of amino acids in water solution enabled us to study (mixed) protonated dimers, one of the various applications of the present technique. Reasons for preferred dimerization - leading to simple cases of molecular recognition - as well as less preferred binding is discussed in terms of the number of specific H-bonds that can be established in the clusters.     

To what extent of ion neutralization can multivalent ion distributions around RNA-like macroions be described by Poisson-Boltzmann theory?

Nucleic acids are negatively charged biomolecules, and metal ions in solutions are important to their folding structures and thermodynamics, especially multivalent ions. However, it has been suggested that the binding of multivalent ions to nucleic acids cannot be quantitatively described by the well-established Poisson-Boltzmann(PB) theory. In this work, we made extensive calculations of ion distributions around various RNA-like macroions in divalent and trivalent salt solutions by PB theory and Monte Carlo(MC) simulations. Our calculations show that PB theory appears to underestimate multivalent ion distributions around RNA-like macroions while can reliably predict monovalent ion distributions. Our extensive comparisons between PB theory and MC simulations indicate that when an RNA-like macroion gets ion neutralization beyond a "critical" value, the multivalent ion distribution around that macroion can be approximately described by PB theory.Furthermore, an empirical formula was obtained to approximately quantify the critical ion neutralization for various RNAlike macroions in multivalent salt solutions, and this empirical formula was shown to work well for various real nucleic acids including RNAs and DNAs.     

Transformational Homologies in Amino Acid Sequences Suggest Memberships in Protein Families

The 20 amino acid monomers composing polymeric proteins are encoded using their individual properties relatable to thermodynamic potentials such as aqueous partial specific volumes, aqueous molar volumes, and free energies of transfer from hydrocarbon to water solvents. These principally hydrophobic solvation, “hydrophobicity”-derived free energies are minimized in protein folding as well as protein–protein and peptide–receptor interactions. Sequential patterns in the one-dimensional distribution of these energies, reflected in dominant wavelengths of amino acid hydrophobicity, and the locations of singular hierarchical, secondary and supersecondary structures are elucidated by orthogonal decomposition and eigenfunction construction followed by continuous wavelet and all poles, maximum entropy power spectral transformations. The resulting graphs discriminate among examples of structural families of proteins.     

Study on variation of thermal image by infrared radiometer influenced by fluctuations of environmental factors

The infrared radiometer (IR) displays the radiation temperature distribution. Frequently, thermal images on a CRT display fluctuate and those radiation temperatures cannot be measured correctly. Therefore, we are frequently faced with the difficult problem of evaluating the detection limits on surface and internal flaws in construction and underground structures, and so on. Those difficulties are considered to be due to fluctuations of the meteorological and environmental factors, mainly influenced by solar radiation, wind velocity, atmospheric temperature, and so on. Our experimental study clarifies the relation between variations of the thermal images on the CRT of IR display and the environmental factors using an analysis of power spectral density.     

Dynamics of alpha helix formation in the CSAW model

We study the folding dynamics of polyalanine (Ala20), a protein fragment with 20 residues whose native state is a single alpha helix. We use the CSAW model (conditioned self-avoiding walk), which treats the protein molecule as a chain in Brownian motion, with interactions that include hydrophobic force and internal hydrogen bonding. We find that large-scale structures form before small-scale structures, and obtain the relevant relaxation times. We find that helix nucleation occurs at two separate points on the protein chain, one near each end. The evolution of small- and large-scale structures involves different mechanisms. While the former can be described by rate equations that govern the growth of helical content, the latter is akin to the relaxation of an elastic solid.     

Structural characterization and angiotensin-converting enzyme (ACE) inhibitory mechanism of Stropharia rugosoannulata mushroom peptides prepared by ultrasound

To reveal the structural characteristics and angiotensin-converting enzyme (ACE) inhibition mechanism of Stropharia rugosoannulata mushroom peptides prepared by multifrequency ultrasound, the peptide distribution, amino acid sequence composition characteristics, formation pathway, and ACE inhibition mechanism of S. rugosoannulata mushroom peptides were studied. It was found that the peptides in S. rugosoannulata mushroom samples treated by multifrequency ultrasound (probe ultrasound and bath ultrasound mode) were mainly octapeptides, nonapeptides, and decapeptides. Hydrophobic amino acids were the primary amino acids in the peptides prepared by ultrasound, and the amino acid dissociation of the peptide bonds at the C-terminal under the action of ultrasound was performed mainly to produce hydrophobic amino acids. Pro and Val (PV), Arg and Pro (RP), Pro and Leu (PL), and Asp (D) combined with hydrophobic amino acids were the characteristic amino acid sequence basis of the active peptides of the S. rugosoannulata mushroom. The docking results of active peptides and ACE showed that hydrogen bond interaction remained the primary mode of interaction between ACE and peptides prepared by ultrasound. The peptides can bind to the amino acid residues in the ACE active pocket, zinc ions, or key amino acids in the domain, and this results in inhibition of ACE activity. Cation–pi interactions also played an important role in the binding of mushroom peptides to ACE. This study explains the structural characteristics and ACE inhibition mechanism used by S. rugosoannulata mushroom peptides prepared by ultrasound, and it will provide a reference for the development and application of S. rugosoannulata mushroom peptides.     

G-SIMS and SMILES: Simulated fragmentation pathways for identification of complex molecules, amino acids and peptides

G-SIMS is a powerful method for the identification of organics and complex molecules at surfaces. We have previously shown that the molecular structure may be reassembled from fragment ions by studying the evolution of G-SIMS intensities as the surface plasma, with effective temperature T_p, is varied, using a method known as G-SIMS-FPM.Here, we develop a novel approach, based on SMILES (Simplified Molecular Input Line Entry Specification), to assist the reassembly process in an automated way through evaluation of the fragmentation pathways for given molecular structures. A computer program takes a parent structure and goes through every possible fragmentation to provide a tree structure of fragmentation products and simulated fragmentation pathways. For any fragment it is then possible to identify the molecular structure, its mass and a pathway to the parent. We find that there is a good correlation with peak evolution in G-SIMS-FPM data and simulated pathways for two amino acids and a simple peptide. This significantly enhances the application of G-SIMS-FPM to unknown materials.     

Proteins: coexistence of stability and flexibility

We introduce an equation for protein native topology based on recent analysis of data from the Protein Data Bank and on a generalization of the Landau-Peierls instability criterion for fractals. The equation relates the protein fractal dimension df, the spectral dimension ds, and the number of amino acids N. Deviations from the equation may render a protein unfolded. The fractal nature of proteins is shown to bridge their seemingly conflicting properties of stability and flexibility. Over 500 proteins have been analyzed (df, ds, and N) and found to obey this equation of state.     

光谱法和分子对接法研究和比较两种全氟羧酸与人血清白蛋白的结合模式

全氟羧酸(PFCAs)由于具有既亲水又疏水的表面活性剂特性,被广泛应用于工业和生活产品中。全氟十一酸(PFUnA)和全氟十三酸(PFTriA)是长链PFCAs类的典型代表,但近年来它们越来越频繁的在人体中检测到,并且发现表现出内分泌干扰效应、发育毒性和致畸性。本文以光谱学和分子对接为基础,探索PFUnA和PFTriA与人体最丰富的蛋白人血清白蛋白(HSA)的结合模式。结果表明,PFUnA和PFTriA均通过动静态猝灭过程猝灭HSA的内源荧光,与HSA只有一个强亲和位点,且PFUnA与HSA的结合比PFTriA更紧密。根据热力学计算结果,可知PFUnA与HSA结合的焓变、熵变分别为-26.32 kJ·mol-1和21.76 J·mol-1·K-1,其结合作用主要依靠静电引力,而PFTriA主要通过范德华力和卤键与HSA结合,是放热熵减过程,其焓变和熵变分别为-39.69 kJ·mol-1和-25.66 J·mol-1·K-1。计算得到的结合距离(r<8 nm)显示从HSA到PFUnA和PFTriA发生了非辐射能量转移。三维荧光光谱和圆二色谱表明,PFUnA和PFTriA与HSA的结合不仅可以改变HSA的构象和微环境,还可以引起α-螺旋稳定性降低。取代实验和分子对接进一步显示PFUnA 和PFTriA通过极性键、疏水作用力和卤键等与HSA的亚域ⅡA疏水腔有高亲和性,且荧光团Trp残基处于结合位置中,进一步证明PFUnA和PFTriA可以猝灭HSA的荧光。本文研究结果为阐明长链PFCAs在机体内与血清蛋白的结合机理提供了完整可靠的数据,并为长链PFCAs的毒性评价和毒理学研究提供了理论依据。     

7-羟基香豆素与三种芳香族氨基酸作用的荧光光谱研究

运用荧光光谱和紫外光谱研究7-羟基香豆素UBM分别与色氨酸Trp,酪氨酸Tyr和苯丙氨酸Phe三种芳香族氨基酸的相互作用。结果表明在模拟人体生理条件下,UMB能引起上述氨基酸发生荧光猝灭,最大猝灭波长依次为347,303和282 nm,猝灭机制均为静态猝灭,相互之间均以摩尔比1：1形成了复合物,且得到两种温度下UMB与Trp,Tyr和Phe反应的表观平衡常数K_c分别为298.15 K时2.993×106,7.858×104和1.186×103 L·mol-1,310.15 K时2.702×104,1.063×105和8.352×103 L·mol-1。热力学函数变化表明UMB与以上三种氨基酸结合作用较强,其中UMB-Trp相互作用力是氢键或范德华力,UMB-Tyr和UMB-Phe相互作用主要以疏水作用为主,同时都可能存在偶极-偶极之间的相互作用。     

20种氨基酸近红外光谱及其分子结构的相关性

旨在研究20种氨基酸的分子结构与其近红外光谱的相关性,为氨基酸近红外光谱在动物科学、食品和医药等方面的推广应用奠定一定的理论基础。应用岛津傅里叶变换红外光谱仪IRPrestige-21及其近红外附件FlexIRTM Near-Infrared Fiber Optics module,采集20种氨基酸标准物质在1 000～2 502 nm波长范围内的近红外光谱,分辨率8 cm-1,每个样品扫描3次,每次扫描50遍,取其平均值为氨基酸标准品的近红外光谱。根据氨基酸侧链基团的不同,分别比较脂肪族氨基酸、芳香族氨基酸和杂环氨基酸中各氨基酸分子结构与其近红外光谱的相关性。研究表明,20种氨基酸在1 000～2 502 nm区域有非常明显的近红外光谱吸收且差异显著。分子量较大的脂肪族氨基酸其近红外光谱受侧链基团的影响较大,而甘氨酸近红外光谱受羧基和氨基的影响较大;两种芳香族氨基酸近红外光谱的差异主要来自于苯环,酪氨酸苯环上的—OH基团降低了苯分子的对称性,导致更多振动吸收峰的出现;杂环氨基酸因其侧链上杂环分子基团构成不同,其近红外光谱在1 600～1 800 nm区域差异较大。综上,20种氨基酸主要存在4个特征光谱区：第1特征光谱区为1 050～1 200 nm主要由C—H基团的二级倍频构成;第2特征光谱区为1 300～1 500 nm主要由C—H基团的组合频构成;因侧链基团分子构成不同,在第3特征光谱区1 600～1 850 nm和第4特征光谱区2 000～2 502 nm表现出差异较大的特征吸收峰。因此,可以利用此4个近红外光谱特征区域对氨基酸进行定量和定性分析,提高氨基酸近红外光谱模型预测的准确性。