Fret Studies of Conformational Changes in Heparin-Binding Peptides

FRET (Förster Resonance Energy Transfer) was applied to study structural properties of heparin-binding peptides containing the sequence XBBBXXBX where ‘X’ represents hydropathic or uncharged and ‘B’ represents basic amino acids. Internally quenched fluorogenic peptides were synthesized containing the fluorescent donor oaminobenzoic acid (o-Abz) and the acceptor dinitrophenyl ethylenediamine (Eddnp) group. Using the CONTIN computational package, distance distributions were recovered from time resolved fluorescence data, associated to end-to-end distances of the peptides. The peptides containing three or four repeat units have random structure in aqueous medium, and the interaction with low molecular weight heparin stabilized short end-to end distances. Experiments in water/trifluoroethanol (TFE) mixtures showed changes in distance distributions compatible with compact conformations stabilized above 40 % volume content of TFE in the mixture. Similar changes in distance distributions were also observed for the peptides in interaction with SDS micelles in aqueous suspensions and circular dichroism data revealed alpha-helix formation in the peptides in interaction with heparin, SDS micelles or the co-solvent TFE. The process is dependent on electrostatic and hydrogen bond interactions and the end-to-end distances obtained are smaller than expected for the peptides in linear α-helix conformation, indicating the occurrence of structural arrangements leading to additional decrease in the distances.     

Study on the relationship between structure and taste activity of the umami peptide of Stropharia rugosoannulata prepared by ultrasound

Through virtual screening, electronic tongue verification, and molecular docking technology, the structure-taste activity relationship of 47 kinds of umami peptides (octapeptide - undecapeptide) from Stropharia rugosoannulata prepared by simultaneous ultrasonic-assisted directional enzymatic hydrolysis was analyzed. The umami peptides of S.rugosoannulata can form hydrogen bond interaction and electrostatic interaction with umami receptors T1R1/T1R3. The amino acid residues at the peptides' N-terminal and C-terminal play a vital role in binding with the receptors to form a stable complex. D, E, and R are the primary amino acids in the peptides that easily bind to T1R1/T1R3. The basic amino acid in the peptides is more easily bound to T1R1, and the acidic amino acid is more easily bound to T1R3. The active amino acid sites of the receptors to which the peptides bind account for 42%−65% of the total active amino acid residues in the receptors. ASP147 and ASP219 are the critical amino acid residues for T1R1 to recognize the umami peptides, and ARG64, GLU45, and GLU48 are the critical amino acid residues for T1R3 to recognize the umami peptides. The increase in the variety and quantity of umami peptides is the main reason for improving the umami taste of the substrate prepared by synchronous ultrasound-assisted directional enzymatic hydrolysis. This study provides a theoretical basis for understanding simultaneous ultrasound-assisted directional enzymatic hydrolysis for preparing umami peptides from S.rugosoannulata, enhancing the flavor of umami, and the relationship between peptide structure and taste activity.     

蜂毒肽与多组分生物膜作用：电性与相态的影响

蜂毒肽非特异性地靶向杀伤细菌具有重要的生物医学应用前景. 利用荧光光谱与荧光显微考察了蜂毒肽与单组分、多组分磷脂膜的作用机制. 发现对于不同电性与相态的磷脂膜, 肽-膜作用呈现为稳定桶板型孔、非稳U型孔及变薄裂解等多种机制, 具有显著不同的内含物泄露效率. 多组分磷脂囊泡的泄露实验表明, 泄露由肽亲和性较强的磷脂组分决定. 相较于凝胶相磷脂, 蜂毒肽与液相磷脂的亲和性强, 凝胶-液相混合囊泡与纯液相磷脂囊泡的泄露性质相近; 相较于双电性磷脂, 蜂毒肽与负电性磷脂的亲和性强, 双电-负电混合囊泡与纯负电磷脂囊泡的泄露性质相近. 研究深化了多肽与多组分生物膜作用机制的理解.     

Interactions of lactoferricin B derivatives with model cell membrane studied by Raman spectroscopy

In this work, we employed Raman spectroscopy to study the effect of the antimicrobial peptide lactoferricin B (LfB) on model cell membranes. We used two derivatives of LfB (RRWQWRMKKLG and RRWQWR) with broad‐spectrum activity against gram‐positive and gram‐negative bacteria, fungus, viruses and tumors. Raman spectra of the peptides showed no conformational change in the temperature range 4–60 °C. The positions of the amide I and amide III bands suggest that in an aqueous solution these peptides preferentially adopt a random coil‐like conformation. We also investigated the effect the peptides had on the melting behavior of model cell membranes composed of zwitterionic lipid dipalmitoylglycero‐phosphocholine (DPPC) and anionic lipid dipalmitoylglycero‐phosphoglycerol (DPPG). Raman CH stretching bands were used to follow the melting of the lipid vesicles. We found that the melting of DPPC lipid vesicles is not affected by the presence of the peptides, while the presence of the peptides reduced cooperativity of the phase transition for anionic DPPG vesicle, suggesting that both peptides interact strongly and specifically with this model cell membrane composed of anionic lipid. Copyright © 2006 John Wiley & Sons, Ltd.     

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.     

Structural aspects of antibody-antigen interaction revealed through small random peptide libraries

Summary Two small random peptide libraries, one composed of 4550 dodecapeptides and one of 8000 tripeptides, were synthesized in newly developed credit-card format miniPEPSCAN cards (miniPEPSCAN libraries). Each peptide was synthesized in a discrete well (455 peptides/card). The two miniPEPSCAN libraries were screened with three different monoclonal antibodies (Mabs). Two other random peptide libraries, expressed on the wall of bacteria (recombinant libraries) and composed of 10⁷ hexa- and octapeptides, were screened with the same three Mabs. The aim of this study was to compare the amino acid sequence of peptides selected from small and large pools of random peptides and, in this way, investigate the potential of small random peptide libraries. The screening of the two miniPEPSCAN libraries resulted in the identification of a surprisingly large number of antibody-binding peptides, while the screening of the large recombinant libraries, using the same Mabs, resulted in the identification of only a small number of peptides. The large number of peptides derived from the small random peptide libraries allowed the determination of consensus sequences. These consensus sequences could be related to small linear and nonlinear parts of the respective epitopes. The small number of peptides derived from the large random peptide libraries could only be related to linear epitopes that were previously mapped using small libraries of overlapping peptides covering the antigenic protein. Thus, with respect to the cost and speed of identifying peptides that resemble linear and nonlinear parts of epitopes, small diversity libraries based on synthetic peptides appear to be superior to large diversity libraries based on expression systems.Abbreviations ABTS 2,2-azino-di-3-ethylbenzthiazoline sulfonate - EGF epidermal growth factor - Mab monoclonal antibody - OD_ccd optical density obtained using CCD camera - RAMPO rabbit-antimouse peroxidase - SDS sodium dodecylsulfate - TGEV transmissible gastroenteritis virus     

Microspectroscopic Study of Liposome-to-cell Interaction Revealed by Förster Resonance Energy Transfer

We report the Förster resonance energy transfer (FRET)-labeling of liposomal vesicles as an effective approach to study in dynamics the interaction of liposomes with living cells of different types (rat hepatocytes, rat bone marrow, mouse fibroblast-like cells and human breast cancer cells) and cell organelles (hepatocyte nuclei). The in vitro experiments were performed using fluorescent microspectroscopic technique. Two fluorescent dyes (DiO as the energy donor and DiI as an acceptor) were preloaded in lipid bilayers of phosphatidylcholine liposomes that ensures the necessary distance between the dyes for effective FRET. The change in time of the donor and acceptor relative fluorescence intensities was used to visualize and trace the liposome-to-cell interaction. We show that FRET-labeling of liposome vesicles allows one to reveal the differences in efficiency and dynamics of these interactions, which are associated with composition, fluidity, and metabolic activity of cell plasma membranes.     

蛋白质与表面活性剂相互作用的导数紫外光谱

利用四阶导数紫外光谱法研究了在pH=7.40,离子强度I=0.0131mol·L-1的磷酸盐缓冲溶液中,浓度为1.0g·L-1的牛血清白蛋白（BSA）与十二烷基硫酸钠（SDS）相互作用的过程中,芳香族氨基酸残基微环境极性的变化.通过研究发现,随着SDS浓度的不断增大,三种芳香族氨基酸残基微环境极性的变化趋势不同,从而可以判断BSA与SDS相互作用过程中BSA构象的变化.     

Fluorescence studies on the conformation of litorin in solution and in the presence of model membranes

The conformation of the nonapeptide hormone litorin has been studied in buffer and in the presence of lipids, using static and dynamic fluorescence. The results obtained show that, in buffer, the hormone probably exists in a collection of flexible conformers, slowly interconverting between them. The marked changes observed in fluorescence spectra and lifetimes upon addition of dimyristoylphosphatidylserine vesicles clearly show that the peptide interacts with lipids assuming lipid specific conformations. Interestingly, no significative spectroscopic changes are produced by exposure to dimirystoylphosphatidylcholine vesicles both in the gel and liquid-christalline phases, suggesting a requirement for negatively charged lipids during the process of hormone-membrane interaction.     

Membrane-peptide interaction studied by PELDOR and CW ESR: Peptide conformations and cholesterol effect on the spatial peptide distribution in the membrane

Pulsed electron-electron double resonance (PELDOR) combined with continuous-wave electron paramagnetic resonance was used to study inter- and intramolecular dipole-dipole interactions between spin labels for spin-labeled analogs of trichogin GA IV bound to multilamellar membranes of egg L-α-phosphatidylcholine (ePC) and in ePC membranes containing cholesterol. All samples were frozen to 77 K. For mono-labeled peptide concentrations in lipid over the range between 0.5 to 2.2 mol%, it is shown that in these membranes trichogin molecules are distributed homogeneously and are likely to be located on or near the inner and outer membrane surfaces. Addition of cholesterol to a final concentration of 16.5 mol% leads to an increase of the local concentration of trichogin molecules in the membranes. For the double-labeled trichogin, a distribution of the intramolecular distance between the two spin labels was observed. The distribution function is characterized by two main maxima located at distances of 1.3 and 1.8 nm. The distance of 1.3 nm is close to that expected for the α-helix structure of the peptide chain. The distance of 1.8 nm corresponds to a mixed structure in which a 3₁₀-helix is combined with a set of even more elongated conformations.     

荧光光谱对自组装多肽作为药物载体的初步研究

为解决疏水性药物普遍存在的因水中溶解度低而给药困难、生物利用度低的问题,采用了新型两亲性自组装多肽RGA16(Ac-RADAGAGARADAGAGS-NH₂)作为载体包裹和释放疏水性模型药物。以芘为模型疏水性药物,以鸡蛋卵磷脂脂质体模拟细胞膜,通过稳态荧光光谱表征和测定芘的存在形式和浓度。两亲性自组装多肽RGA16能够在水溶液中稳定模型疏水性药物芘的晶体。扫描电镜图像显示多肽RGA16与芘晶体相互吸引,两者形成10 μm以上大小的复合体。在机械搅拌下多肽RGA16与水溶液中的芘相互作用5 d左右形成稳定的胶体混悬液(多肽-芘复合体)。被多肽包裹时,芘以晶体的形式存在。而当与EPC脂质体溶液混合时,芘可从多肽的包裹中以分子形式释放到EPC的双层膜中。芘从自组装多肽所稳定的胶态晶体向EPC脂质体释放的过程采用连续时间扫描稳态荧光光谱加以观察。通过将释放过程中芘单体的荧光强度与标准曲线相比较,确定了特定时间点EPC脂质体中芘的转移量。以上结果表明：该两亲性自组装多肽RGA16具有作为小分子量疏水性药物载体的潜力。     

Interactions between oligopeptides and oxidised titanium surfaces detected by vibrational spectroscopy

Five alternating polar/hydrophobic oligopeptides derived from EAK 16 (AEAEAKAKAEAEAKAK) were examined in comparison with EAK 16 (peptide 1) both after solubilisation/lyophilisation and deposition on oxidised titanium surfaces. The peptides were synthesised for their possible use as biomimetic materials due to their self‐assembling properties and the presence, in one of them, of the arginine‐glycine‐aspartic (RGD) sequence, an active modulator of cell adhesion. Infrared (IR) and Raman spectroscopies were used to investigate the influence of the amino acid substitution on the self‐assembling properties of the peptides under both experimental conditions. In the lyophilised peptides, β‐sheet was the prevailing conformation (65–69%) as in EAK 16, irrespective of acid substitution (E→D, peptide 2), basic substitution (K→O, peptide 3), hydrophobic spacer substitution (A→Abu, peptide 4 and A→Y, peptide 5) and RGD insertion (peptide 6). After deposition on oxidised titanium, the main conformation remained β‐sheet. The side‐chain shortening of the acidic amino acid residue (peptide 2) or the insertion of a rigid and bulky residue such as Y (peptide 5) decreased the self‐assembling ability more than the side‐chain shortening of the basic amino acid residue (peptide 3) or the insertion of the RGD head (peptide 6). The interaction with the oxidised titanium surface was mainly due to carboxylate groups with a bidentate bridging coordination and C  O peptidic groups. Copyright © 2010 John Wiley & Sons, Ltd.     

New planar substrates for the in situ synthesis of peptide arrays

The performance of new cellulose membranes, aminofunctionalized via a PEG spacer, as a solid support in the synthesis of peptide arrays is described. The new membranes are stable to trifluoroacetic acid (TFA) and strong aqueous base for days. These properties extend the scope of synthesis considerably, e.g., more efficient side chain cleavage protocols can be applied which yielded peptides of improved purity. For the first time, cellulose membranes with a loading as high as 5 micromol/cm2 were accessible. Additionally, newly developed polypropylene membranes with hydroxy- or amino functionalities were successfully employed for the SPOT synthesis of peptides and phosphopeptides. The membranes are compatible with antibody binding as well as enzymatic phosphorylation assays.     

内禀无序蛋白构象与带电氨基酸残基排布关系——以精氨酸和天冬氨酸组成的随机多肽为例

内禀无序蛋白的结构特征与其氨基酸序列有着密切的联系.其中一个核心问题是正负带电氨基酸残基的排列如何影响无序蛋白或者多肽的构象?为了回答这一问题,本研究以天冬氨酸和精氨酸两种带电残基组成的随机多肽为研究对象,利用全原子蒙特卡罗模拟和温度副本交换采样方法,研究了随机多肽的电荷排布与结构之间的定性关系.结果表明:正负带电残基在序列上混合均匀时,由于肽链内部的静电吸引和排斥相互抵消,肽链倾向于形成无规卷曲的构象;正负带电残基分离时,由于长程静电相互吸引,多肽倾向于形成类β-发卡的形状.     

Solvent effects on conformational stability of peptides: RISM analyses

We describe features of our methodology for predicting tertiary structures (i.e., conformations) of proteins in solvent just from the amino-acid sequences and molecular models for the solvent. The methodology, which is a combination of the Monte Carlo simulated annealing technique and the reference interaction site model theory, is illustrated for the small peptides, Met-enkephalin and C-peptide. Important roles played by water are discussed, and the alcohol effects on peptide conformations are newly analyzed.     

Orientation of the antimicrobial peptide PGLa in lipid membranes determined from 19F-NMR dipolar couplings of 4-CF3-phenylglycine labels

A highly sensitive solid state (19)F-NMR strategy is described to determine the orientation and dynamics of membrane-associated peptides from specific fluorine labels. Several analogues of the antimicrobial peptide PGLa were synthesized with the non-natural amino acid 4-trifluoromethyl-phenylglycine (CF(3)-Phg) at different positions throughout the alpha-helical peptide chain. A simple 1-pulse (19)F experiment allows the simultaneous measurement of both the anisotropic chemical shift and the homonuclear dipolar coupling within the rotating CF(3)-group in a macroscopically oriented membrane sample. The value and sign of the dipolar splitting determines the tilt of the CF(3)-rotational axis, which is rigidly attached to the peptide backbone, with respect to the external magnetic field direction. Using four CF(3)-labeled peptide analogues (with L-CF(3)-Phg at Ile9, Ala10, Ile13, and Ala14) we confirmed that PGLa is aligned at the surface of lipid membranes with its helix axis perpendicular to the bilayer normal at a peptide:lipid ratio of 1:200. We also determined the azimuthal rotation angle of the helix, which agrees well with the orientation expected from its amphiphilic character. Peptide analogues with a D-CF(3)-Phg label resulting from racemization of the amino acid during synthesis were separately collected by HPLC. Their spectra provide additional information about the PGLa structure and orientation but allow only to discriminate qualitatively between multiple solutions. The structural and functional characterization of the individual CF(3)-labeled peptides by circular dichroism and antimicrobial assays showed only small effects for our four substitutions on the hydrophobic face of the helix, but a significant disturbance was observed in a fifth analogue where Ala8 on the hydrophilic face had been replaced. Even though the hydrophobic CF(3)-Phg side chain cannot be utilized in all positions, it allows highly sensitive NMR measurements over a wide range of experimental conditions and dynamic regimes of the peptide.     

Peptaibols类抗菌肽—Trichokonin Ⅵ在不同溶剂中构象变化的圆二色谱研究

Trichoder Ⅵ是拟康氏木霉SMF2(Trichoderma pseudokoningii SMF2)产生的一种含有20个氨基酸的peptaibol类抗菌肽。采用圆二色谱法研究了不同极性溶剂体系和膜拟态环境对Trichokonin Ⅵ的二级结构的影响,Trichokonin Ⅵ在不同有机溶剂体系中具有典型的螺旋结构特征,而在水溶液体系中螺旋明显减少,不超过30%的三氟乙醇可以随浓度增加而诱导螺旋结构的增加。Trichokonin Ⅵ在磷酸缓冲液中峰的强度随浓度增加而增强,具有浓度依赖性。SDS浓度的增加可以诱导螺旋含量的增加。与非拟态环境相比,膜拟态环境可以明显增加Trichokonin Ⅵ的螺旋含量,表明Trichokonin Ⅵ可以和脂膜相互作用。     

Potential energy surface of alanine polypeptide chains

The multidimensional potential energy surfaces of the peptide chains consisting of three and six alanine (Ala) residues have been studied with respect to the degrees of freedom related to the twist of these molecules relative to the peptide backbone (these degrees of freedom are responsible for the folding of such peptide molecules and proteins). The potential energy surfaces have been calculated ab initio within the framework of the density functional theory taking into account all electrons in the system. The probabilities of transitions between various stable conformations of polypeptide molecules are evaluated. The results are compared to the data obtained by molecular dynamics simulations and to the available experimental data. The influence of the secondary structure of the polypeptide chain on its conformational properties with respect to rotations has been studied. It is shown that, in a chain of six amino acid (Ala) residues, the secondary structure type (helix or sheet conformation) influences the stable isomer states of the polypeptide.     

Polarity dependence of EPR parameters for TOAC and MTSSL spin labels: correlation with DOXYL spin labels for membrane studies

TOAC (2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid) is a nitroxyl amino acid that can be incorporated in the backbone of peptides. DOXYL (4,4-dimethyl-oxazolidine-1-oxyl) is a nitroxyl ring that can be attached rigidly at specific C-atom positions in the acyl chains of phospholipids. Spin-labelled phosphatidylcholines of the DOXYL type have been used previously to establish the transmembrane polarity profile in biological lipid bilayers [D. Marsh, Polarity and permeation profiles in lipid membranes, Proc. Natl. Acad. Sci. USA 87 (2001) 7777-7782]. Here, we determine the polarity dependence of the isotropic (14)N-hyperfine couplings, a(o)(N), and g-values, g(o), in a wide range of protic and aprotic media, for a TOAC-containing dipeptide (Fmoc-TOAC-Aib-OMe) and for a DOXYL-containing fatty acid (12-DOXYL-stearic acid). The correlation between datasets for TOAC and DOXYL nitroxides in the various solvents is used to establish the polarity profile for isotropic hyperfine couplings of TOAC in a transmembrane peptide. This calibration can be used to determine the location of TOAC at selected residue positions in a transmembrane or surface-active peptide. A similar calibration procedure is also applied to a(o)(N) and g(o) for the pyrroline methanethiosulphonate nitroxide (MTSSL) that is used in site-directed spin-labelling studies of membrane proteins.     

A simple coarse-grained model for interacting protein complex

ABSTRACT

We present a simple coarse-grained model in which each amino acid residue is represented by one coarse-grained particle for interacting protein complex. In order to determine the coarse-grained potential function of the interaction between amino acid residues, free energy profile as a function of the distance between amino acid side chains is investigated by using all-atom molecular dynamics simulations with thermodynamic integration method. The Langevin dynamics simulation with Gō-like model and our coarse-grained model reproduces homotetramer complex structure of GCN4-pLI and shows that interaction between hydrophobic amino acid residues promote the association of GCN4-pLI monomers.