Synthesis of an immobilized Bombyx mori pheromone-binding protein liquid chromatography stationary phase

The pheromone-binding protein from the silkworm moth, Bombyx mori (BmorPBP) has been covalently bonded to a liquid chromatographic stationary phase. The resulting column was evaluated using radiolabeled bombykol and the immobilized protein retained its ability to bind this ligand. The data also demonstrate that the BmorPBP column was able to distinguish between four compounds, and rank them in their relative order of affinity for the protein from highest to lowest: bombykol > bombykal > 1-hexadecanol > (Z,E)-5,7-dodecadien-1-ol, and that the immobilized BmorPBP retained its pH-dependent conformational mobility.The results of this study demonstrate that pheromone-binding protein from the silkworm moth, Bombyx mori and an odorant binding protein (OBP) obtained from the female mosquito Culex quinquefasciatoes have been immobilized on a silica support with retention of ligand-binding activity. The data indicate that proteins from non-mammalian organisms can be used to create liquid chromatography affinity columns.     

Ab initio fragment molecular orbital (FMO) method applied to analysis of the ligand-protein interaction in a pheromone-binding protein

Full quantum computation of the electronic state of proteins has recently become possible by the advent of the ab initio fragment molecular orbital (FMO) method. We applied this method to the analysis of the interaction between the Bombyx mori pheromone-binding protein and its ligand, bombykol. The protein–ligand interaction of this molecular complex was minutely analyzed by the FMO method, and the analysis revealed several important interactions between the ligand and amino acid residues.     

Deciphering the Selectivity of Bombyx mori Pheromone Binding Protein for Bombykol over Bombykal: A Theoretical Approach

In this article we report calculations dedicated to estimate the selectivity of the Bombyx mori pheromone binding protein towards the two closely related pheromonal components Bombykol and Bombykal. The selectivity is quantified by the binding free‐energy difference, obtained either by the thermodynamic integration or by the MM‐GBSA approach. In the latter, the selectivity is decomposed on a per‐residue basis, which identifies the residues considered crucial for the selectivity of the protein for Bombykol over Bombykal. A discussion on the role of Bombyx mori pheromone binding protein is provided on the basis of these results.     

A unique urinary constituent, 6-hydroxy-6-methyl-3-heptanone, is a pheromone that accelerates puberty in female mice.

BACKGROUND: Olfactorily mediated puberty acceleration in female mice (measured by an increase in uterine weight) has been observed since the 1960s without the active chemosignal being structurally identified. There are many controversies in the literature as to whether this male-originated pheromone is a volatile substance. We investigated the chemical nature of the urinary fractions that are responsible for the characteristic uterine weight increases. RESULTS: The active pheromone was identified as 5,5-dimethyl-2-ethyltetrahydrofuran-2-ol and/or its open-chain tautomer (6-hydroxy-6-methyl-3-heptanone). A series of cyclic vinyl ethers were isolated from chromatographically active fractions of the urine. Because these compounds did not accelerate puberty, we postulated that these ethers were degradation products of a lactol (5,5-dimethyl-2-ethyltetrahydrofuran-2-ol). The lactol was then detected directly in the mouse urine extract using a silylation agent. Synthetic 6-hydroxy-6-methyl-3-heptanone had strong biological activity, whereas its close structural analogs did not. CONCLUSIONS: The male house mouse excretes into its urine a large quantity of a volatile substance that has a unique lactol/hydroxyketone structure. This substance is capable of binding to the less volatile urinary constituents, such as proteins or peptides, and is active in puberty-acceleration bioassays. The controversies regarding the volatility of the puberty-accelerating pheromones can now be explained by considering a complex of volatile lactol/hydroxyketone and urinary proteins.     

Sexual attraction in the silkworm moth. Nature of binding of bombykol in pheromone binding protein--an ab initio study

An analysis of the crystal structure of [BmPBP...bombykol] complex identified nine amino acid residues involved in a variety of intermolecular interactions binding the ligand. Using simple model fragments as the representatives of the residues, the interaction energies of their complexes with bombykol were calculated using high-level ab initio methods. The results were discussed in terms of the method and basis set dependence and were further corrected to account for their pair nonadditivities. This enabled us to describe quantitatively the nature and origin of the binding forces in terms of contribution of the individual amino acids and individual types of interaction to the overall stability. All of these interactions are well defined and cannot be considered as nonspecific hydrophobic interactions, one of the major conclusions of this work.     

Properties of mouse vomeronasal receptor and assessment of its role in pheromone signalling

Vomeronasal type 2 receptor (V2Rx) from Swiss mouse (Mus musculus (L.)) was analyzed by high-resolution ion-exchange chromatography, reversed-phase high-performance liquid chromatography (RP-HPLC), matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), Ion Spray tandem mass spectrometry (MS/MS), 10% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and 1-aminoanthracene (1-AMA) fluorometric assay. Vomeronasal sensory neuronal cell bound proteins were resolved into major protein peaks. Several proteins were identified and subsequently purified as the V2Rx receptor on 10% SDS-PAGE with trace amounts of other protein bands. The molecular weight of the identified V2Rx was 109 kDa. MALDI-TOF and micro-sequencing experiments demonstrated that the identified V2Rx receptor shared considerable sequence similarity with vomeronasal receptor type 2 (NCBI Accession Number AB267725), which is a seven transmembrane peptide with 912 amino acid residues. The molecular characterization revealed that the N-terminus of the V2Rx receptor contained the 11GAEAAE16 domain involved in pheromone signalling. The biometric assay (octanamine-V2Rx binding) showed the identified V2Rx receptor and mouse sex pheromone to 2-octanamine (methyl heptyl) in a 1:1 ratio. Uptake of odourants determined in physiological condition showed enhanced V2Rx receptors as volatile hydrophobic pheromone receptors in the vomeronasal neuron of the Swiss mouse.     

Investigation of the binding of Salvianolic acid B to human serum albumin and the effect of metal ions on the binding

The studies on the interaction between HSA and drugs have been an interesting research field in life science, chemistry and clinical medicine. There are also many metal ions present in blood plasma, thus the research about the effect of metal ions on the interaction between drugs and plasma proteins is crucial. In this study, the interaction of Salvianolic acid B (Sal B) with human serum albumin (HSA) was investigated by the steady-state, synchronous fluorescence and circular dichroism (CD) spectroscopies. The results showed that Sal B had a strong ability to quench the intrinsic fluorescence of HSA through a static quenching mechanism. Binding parameters calculated showed that Sal B was bound to HSA with the binding affinities of 10(5) L mol(-1). The thermodynamic parameters studies revealed that the binding was characterized by positive enthalpy and positive entropy changes, and hydrophobic interactions were the predominant intermolecular forces to stabilize the complex. The specific binding distance r (2.93 nm) between donor (HSA) and acceptor (Sal B) was obtained according to F?rster non-radiative resonance energy transfer theory. The synchronous fluorescence experiment revealed that Sal B cannot lead to the microenvironmental changes around the Tyr and Trp residues of HSA, and the binding site of Sal B on HSA is located in hydrophobic cavity of subdomain IIA. The CD spectroscopy indicated the secondary structure of HSA is not changed in the presence of Sal B. Furthermore, The effect of metal ions (e.g. Zn(2+), Cu(2+), Co(2+), Ni(2+), Fe(3+)) on the binding constant of Sal B-HSA complex was also discussed.     

Common and divergent structural features of a series of corticotropin releasing factor-related peptides

Members of the corticoliberin family include the corticotropin releasing factors (CRFs), sauvagine, the urotensins, and urocortin 1 (Ucn1), which bind to both the CRF receptors CRF-R1 and CRF-R2, and the urocortins 2 (Ucn2) and 3 (Ucn3), which are selective agonists of CRF-R2. Structure activity relationship studies led to several potent and long-acting analogues with selective binding to either one of the receptors. NMR structures of six ligands of this family (the antagonists astressin B and astressin2-B, the agonists stressin1, and the natural ligands human Ucn1, Ucn2, and Ucn3) were determined in DMSO. These six peptides show differences in binding affinities, receptor-selectivity, and NMR structure. Overall, their backbones are alpha-helical, with a small kink or a turn around residues 25-27, resulting in a helix-loop-helix motif. The C-terminal helices are of amphipathic nature, whereas the N-terminal helices vary in their amphipathicity. The C-terminal helices thereby assume a conformation very similar to that of astressin bound to the ECD1 of CRF-R2 recently reported by our group.1 On the basis of an analysis of the observed 3D structures and relative potencies of [Ala]-substituted analogues, it is proposed that both helices could play a crucial role in receptor binding and selectivity. In conclusion, the C-terminal helices may interact along their hydrophobic faces with the ECD1, whereas the entire N-terminal helical surface may be involved in receptor activation. On the basis of the common and divergent features observed in the 3D structures of these ligands, multiple binding models are proposed that may explain their plurality of actions.     

Redesign of protein domains using one-bead-one-compound combinatorial chemistry

A novel combinatorial strategy for the redesign of proteins based on the strength and specificity of intra- and interprotein interactions is described. The strategy has been used to redesign the hydrophobic core of the B domain of protein A. Using one-bead-one-compound combinatorial chemistry, 300 analogues of the C-terminal alpha-helix of the B domain, H3x, have been synthesized using a biocompatible resin and the HMFS linker, allowing the screening to occur while the peptides were bound to the resin. The screening was based on the ability of the H3x analogues to interact with the N-terminal helices of the B domain, H1-H2, and retain the native B domain activity, that is binding to IgG. Eight different analogues containing some nonconservative mutations were obtained from the library, the two most frequent of which, H3P1 and H3P2, were studied in detail. CD analysis revealed that the active analogues interact with H1-H2. To validate the redesign strategy the covalent modified domains H1-H2-H3P1 and H1-H2-H3P2 were synthesized and characterized. CD and NMR analysis revealed that they had a unique, stable, and well-defined three-dimensional structure similar to that for the wild-type B domain. This combinatorial strategy allows us to select for redesigned proteins with the desired activity or the desired physicochemical properties provided the right screening test is used. Furthermore, it is rich in potential for the chemical modification of proteins overcoming the drawbacks associated with the total synthesis of large protein domains.     

全硫取代三苯甲基自由基酯基衍生物与牛血清白蛋白的相互作用

采用荧光光谱、电子顺磁共振（EPR）波谱、紫外-可见吸收光谱和分子对接等技术研究了全硫取代三苯甲基（TAM）自由基酯基衍生物ET-03与牛血清白蛋白（BSA）的相互作用,发现ET--03与BSA能自发发生结合作用;主要以疏水作用力结合在BSA亚结构域ⅡA（位点Ⅰ）和亚结构域ⅢA（位点Ⅱ）上;ET-03对BSA的荧光猝灭效应为动态、静态混合猝灭机制,且可能存在非辐射能量转移.研究结果表明,酯基衍生化TAM自由基与白蛋白能自发结合,有望用于蛋白构效关系研究;同时也提示将TAM自由基酯基衍生物用于活体成像或自旋标记物时应考虑其与蛋白相互作用的影响.     

Dynamics of xenon binding inside the hydrophobic cavity of pseudo-wild-type bacteriophage T4 lysozyme explored through xenon-based NMR spectroscopy

Wild-type bacteriophage T4 lysozyme contains a hydrophobic cavity with binding properties that have been extensively studied by X-ray crystallography and NMR. In the present study, the monitoring of 1H chemical shift variations under xenon pressure enables the determination of the noble gas binding constant (K = 60.2 M(-1)). Although the interaction site is highly localized, dipolar cross-relaxation effects between laser-polarized xenon and nearby protons (SPINOE) are rather poor. This is explained by the high value of the xenon-proton dipolar correlation time (0.8 ns), much longer than the previously reported values for xenon in medium-size proteins. This indicates that xenon is highly localized within the protein cavity, as confirmed by the large chemical shift difference between free and bound xenon. The exploitation of the xenon line width variation vs xenon pressure and protein concentration allows the extraction of the exchange correlation time between free and bound xenon. Comparison to the exchange experienced by protein protons indicates that the exchange between the open and closed conformations of T4 lysozyme is not required for xenon binding.     

Synthetic ligands for apo-neocarzinostatin

Neocarzinostatin (NCS) is a 1:1 complex of an enediyne chromophore (NCSChrom), non-covalently bound to an 11 kDa protein (apoNCS). We are exploring apoNCS as a generic protein system for sequestering small molecules for therapeutic applications. Here, we disclose a new flavone ligand 1 for apoNCS and present a high-resolution NMR structure of this ligand bound to apoNCS. This is the first high-resolution structure of a completely non-cognate ligand bound to the apoNCS protein. This work provides unambiguous evidence that a completely new class of ligand can bind specifically to apoNCS. Furthermore, the mode of binding is different than that of the naphthoate-based ligands, and for such a simple hydrophobic compound, the new ligand surprisingly binds specifically. This work indicates that apo-Neocarzinostatin has multiple selective and distinct binding modes for small-molecule cargo.     

Organic Ligand Binding by a Hydrophobic Cavity in a Designed Tetrameric Coiled‐Coil Protein

The design and characterization of a hydrophobic cavity in de novo designed proteins provides a wide range of information about the functions of de novo proteins. We designed a de novo tetrameric coiled‐coil protein with a hydrophobic pocketlike cavity. Tetrameric coiled coils with hydrophobic cavities have previously been reported. By replacing one Leu residue at the a position with Ala, hydrophobic cavities that did not flatten out due to loose peptide chains were reliably created. To perform a detailed examination of the ligand‐binding characteristics of the cavities, we originally designed two other coiled‐coil proteins: AM2, with eight Ala substitutions at the adjacent a and d positions at the center of a bundled structure, and AM2W, with one Trp and seven Ala substitutions at the same positions. To increase the association of the helical peptides, each helical peptide was connected with flexible linkers, which resulted in a single peptide chain. These proteins exhibited CD spectra corresponding to superhelical structures, despite weakened hydrophobic packing. AM2W exhibited binding affinity for size‐complementary organic compounds. The dissociation constants, K_d, of AM2W were 220 nM for adamantane, 81 μM for 1‐adamantanol, and 294 μM for 1‐adamantaneacetic acid, as measured by fluorescence titration analyses. Although it was contrary to expectations, AM2 did not exhibit any binding affinity, probably due to structural defects around the designed hydrophobic cavity. Interestingly, AM2W exhibited incremental structure stability through ligand binding. Plugging of structural defects with organic ligands would be expected to facilitate protein folding.     

An Unusual Protein–Protein Interaction through Coupled Unfolding and Binding

Aptides, a novel class of high‐affinity peptides, recognize diverse molecular targets with high affinity and specificity. The solution structure of the aptide APT specifically bound to fibronectin extradomain B (EDB), which represents an unusual protein–protein interaction that involves coupled unfolding and binding, is reported. APT binding is accompanied by unfolding of the C‐terminal β strand of EDB, thereby permitting APT to interact with the freshly exposed hydrophobic interior surfaces of EDB. The β‐hairpin scaffold of APT drives the interaction by a β‐strand displacement mechanism, such that an intramolecular β sheet is replaced by an intermolecular β sheet. The unfolding of EDB perturbs the tight domain association between EDB and FN8 of fibronectin, thus highlighting its potential use as a scaffold that switches between stretched and bent conformations.     

De novo design and characterization of copper centers in synthetic four-helix-bundle proteins.

The design and chemical synthesis of de novo metalloproteins on cellulose membranes with the structure of an antiparallel four-helix bundle is described. All possible combinations of three different sets of amphiphilic helices were assembled on cyclic peptide templates which were bound by a cleavable linker to the cellulose. In the hydrophobic interior, the four-helix bundle proteins carry a cysteine and several histidines at various positions for copper ligation. This approach was used successfully to synthesize, for the first time, copper proteins based on a four-helix bundle. UV-vis spectra monitored on the solid support showed ligation of copper(II) by about one-third out of the 96 synthesized proteins and tetrahedral complexes of cobalt(II) by most of these proteins. Three of the most stable copper-binding proteins were synthesized in solution and their structural properties analyzed by spectroscopic methods. Circular dichroism, one-dimensional NMR, and size-exclusion chromatography indicate a folding into a compact state containing a high degree of secondary structure with a reasonably ordered hydrophobic core. They displayed UV-vis absorption, resonance Raman, and EPR spectra intermediate between those of type 1 and type 2 copper centers. The present approach provides a sound basis for further optimizing the copper binding and its functional properties by using combinatorial protein chemistry guided by rational principles.     

Homology modeling of the receptor binding domain of human thrombopoietin

Platelet production in blood is regulated by a lineage specific humoral factor, thrombopoietin (TPO). The amino terminal domain of TPO (TPO-N) is responsible for the signal transduction mediated by the TPO receptor, c-mpl. From the predicted length of helices we found that TPO-N belongs to the long-chain subfamily of the four-helix bundle cytokine family. We built a three dimensional model of TPO-N by a comparative homology modeling procedure. The four helices of TPO-N with an up-up-down-down topology are stabilized by a tightly packed central hydrophobic core and the extended loop AB makes an additional hydrophobic core with helices B and D outside of the four helix bundle scaffold. An interpretation of the previous site directed mutageneses results in light of the model enabled us to identify two isolated receptor binding sites. The surface made of Lys 136, Lys 138 and Lys 140 in helix D, and Pro 42 and Glu 50 in loop AB forms the first receptor binding site, while the surface of Asp 8, Arg 10 and Lys14 in helix A represents the second binding site for the sequential receptor oligomerization.     

Design of a functional protein for molecular recognition: specificity of ligand binding in a metal-assembled protein cavity probed by 19f NMR

A metal-assembled homotrimeric coiled coil based on the GCN4-p1 sequence has been designed that noncovalently binds hexafluorobenzene and other similar ligands in a hydrophobic cavity, created by making the core substitution Asn16Ala ([Fe(bpyGCN4-N16A)3]2+). The KD of binding of hexafluorobenzene with [Fe(bpyGCN4-N16A)3]2+ was observed to be 1.1(9) x 10(-4) M by diffusion NMR experiments. A control coiled coil with the core substitution Asn16Val ([Fe(bpyGCN4-N16V)3]2+) exhibited a significantly weaker association with hexafluorobenzene, providing evidence that even in the absence of structural data, benzene-like ligands bind in the cavity created by the Asn16Ala substitution. 19F NMR was employed to observe hexafluorobenzene binding and to monitor titrations with competing hydrophobic and polar ligands similar in size and shape to hexafluorobenzene. All hydrophobic ligands bound with greater affinity than the polar ligands in the hydrophobic core, although the cavity seems to be somewhat flexible in terms of the sizes of molecules it can accommodate. Thus 19F NMR has proved to be a useful spectral tool to probe molecular recognition in a hydrophobic cavity of a metal-assembled coiled coil.     

Spectral deciphering of the interaction between an intramolecular hydrogen bonded ESIPT drug, 3,5-dichlorosalicylic acid, and a model transport protein

The present work demonstrates a detailed characterization of the interaction of a bio-active drug molecule 3,5-dichlorosalicyclic acid (3,5DCSA) with a model transport protein Bovine Serum Albumin (BSA). The drug molecule is a potential candidate exhibiting Excited-State Intramolecular Proton Transfer (ESIPT) reaction and the modulation of ESIPT photophysics within the bio-environment of the protein has been exploited spectroscopically to monitor the drug-protein binding interaction. Apart from evaluating the binding constant (K (±10%) = 394 M(-1)) the probable location of the neutral drug molecule within the protein cavity (hydrophobic subdomain IIA) is explored by AutoDock-based blind docking simulation. The rotational relaxation dynamics of the drug within the protein has been interpreted on the lexicon of the two-step and wobbling-in-cone model. Circular dichroism (CD) spectroscopy delineates the effect of drug binding on the protein secondary structure in terms of decrease of α-helical content of BSA with increasing drug concentration. Also the esterase activity of the drug:protein conjugate system is found to be reduced in comparison to the native protein.     

人血清白蛋白与季铵盐双子表面活性剂的相互作用

在298.15 K下, 应用等温滴定量热法研究了人血清白蛋白(HSA)与两种季铵盐双子表面活性剂[(C_nN)₂Cl₂, n＝12, 14]在缓冲溶液(pH＝7.0)中相互作用的热力学性质. 实验结果表明, HSA对这两种表面活性剂有两类结合位点, 分别为结合时需要吸收热量的强结合位点和可放出热量的弱结合位点. 两种表面活性剂对应的第一类结合——强结合为熵驱动过程, 且该结合位点对应的结合位点数、结合常数和热力学参数差别不大. 至于第二类结合——弱结合位点, 由于 (C₁₄N)₂Cl₂ 疏水链过长, 只有部分进入HSA的疏水空腔内, 因此相应的的结合位点数和放热量减小, 而熵变增加, 为焓和熵共同驱动的反应. 圆二色研究表明(C_nN)₂Cl₂的加入使HSA的二级结构发生变化, 这说明(C_nN)₂Cl₂与HSA的相互作用既包含结合反应也包含(C_nN)₂Cl₂诱导该蛋白部分结构改变的过程.