Study on the interaction between baicalein and the amyloid β peptide by molecular spectroscopy

The amyloid β peptide (Aβ) is the major protein constituent of neuritic plaques in Alzheimer's disease (AD).And Aβ(1-42) is the major component in amyloid plaque core deposits.     

Investigation of the interaction between HⅣ-1 DNA and cyclic peptides by electrospray ionization mass spectrometry

The interaction between HⅣ-1 DNA and five cyclic peptides (CP1-CP5) was investigated using electrospray ionization mass spectrometry (ESI-MS). It revealed that CP1 [c(Ala-Tyr-Leu-Ala-Gly)] and CP4 [c(Pro-D-Tyr-Leu-D-Ala-Gly)] have the higher binding affinity with the duplex DNA among the five cyclic peptides.     

Investigation of noncovalent complexes between β-cyclodextrin and polyamide acids containing N-methylpyrrole and N-methylimidazole by electrospray ionization mass spectrometry

Electrospray ionization (ESI) mass spectrometry was utilized to investigate noncovalent complexes between beta-cyclodextrin (beta-CD) and five novel polyamide acids containing N-methylpyrrole and N-methylimidazole. The 1:1 binding mode was specified by examining the binding stoichiometry from ESI mass spectra. It found that polyamide acids with beta-CD have binding affinities in the order: ImImImbetaCOOH > ImPyImbetaCOOH > ImPyPybetaCOOH > PyPyPybetaCOOH > NO(2)PyPyPybetaCOOH. The method gives, simultaneously, the binding constants between beta-CD and polyamide acids based on a novel linear equation.     

Dynamics of noncovalent interactions in all-α and all-β class proteins: implications for the stability of amyloid aggregates

A fully folded functional protein is stabilized by several noncovalent interactions. When a protein undergoes conformational motions, the existing noncovalent interactions may be maintained. They may also break or new interactions may be formed. Knowledge of the dynamical nature of the different types of noncovalent interactions is extremely important to understand the structural stability, function, and folding of a protein. There are experimental limitations to investigate the dynamics of different noncovalent interactions simultaneously in a biomolecule. We have carried out molecular dynamics simulations on four different proteins, two belonging to all-α class proteins and the other two are representatives of all-β class proteins. The dynamical nature of eight different noncovalent interactions was studied by monitoring the maximum residence time (MRT) and lifetime (LT). The conventional hydrogen bonds are the dominant interactions in all four proteins, and the majority of those formed between the main-chain atoms were maintained during most of the simulation time with MRT greater than 10 ns. Such interactions with more than 1 ns lifetime provide stability to the secondary structures, and hence they are responsible for the overall stability of the protein. The weak C-H···O hydrogen bond is the next major type of interactions. However, a large number of such interactions are observed between the main-chain atoms only in all-β proteins as interstrand interactions, and, surprisingly, they are observed during most part of the simulation although their average lifetime is only about 20 to 30 ps. The strong cation···π and salt-bridge interactions are present few in number. However, in many cases they are almost uninterrupted indicating the higher strength of these interactions. Four other interactions involving the π-electron cloud of aromatic rings are very small in number, and, in many cases, their presence is not maintained throughout the simulation. Our results clearly indicate that the weak C-H···O interactions between the main-chain atoms are the distinguishing factor between the all-α and all-β class of proteins, and these interstrand interactions can provide additional stability to all-β protein structures. Based on these results, we hypothesize that such weak C-H···O interstrand interactions could play a major role in providing stability to amyloid type of aggregates that are responsible for the pathological state of many proteins.     

Investigation of the Interaction between Isoflavonoids and Bovine Serum Albumin by Fluorescence Spectroscopy

The interactions of bovine serum albumin （BSA） with three structurally related isoflavonoids, genistein, puerarin and daidzein, were studied under physiological conditions by fluorescence spectroscopic technique. The quenching mechanism of these compounds with BSA was suggested as static quenching and the binding constants were determined at different temperatures based on the fluorescence quenching results. The transfer efficiency of energy and distance between the acceptor and BSA were investigated on the basis of the mechanism of the Forster energy transference. According to the thermodynamic parameters it has been suggested that the acting force be mainly hydrophobic force. The comparison of binding potency of the three isoflavonoids to BSA showed that the substitution by 5-OH and 8-Glc could enhance the binding affinity. All these obtained in the work can make us better understand the mode of the action and pharmacological activities of the isoflavonoids.     

Investigation of the Interaction between Nafion and Several Trisbipyridyl Complexes by Spectroscopic Method

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Synthesis of mutual azo prodrugs of anti-inflammatory agents and peptides facilitated by α-aminoisobutyric acid

Reported is the synthesis of azo mutual prodrugs of the nonsteroidal anti-inflammatory agents (NSAIDs) 4-aminophenylacetic acid (4-APAA) or 5-aminosalicylic acid (5-ASA) with peptides, including an antibiotic peptide temporin analogue modified at the amino terminal by an α-aminoisobutyric acid (Aib) residue. These prodrugs are designed for colonic delivery of two agents to treat infection and inflammation by the bacterial pathogen Clostridium difficile .     

Exploring the “intensity fading” phenomenon in the study of noncovalent interactions by MALDI-TOF mass spectrometry

The difficulties to detect intact noncovalent complexes involving proteins and peptides by MALDI-TOF mass spectrometry have hindered a widespread use of this approach. Recently, "intensity fading MS" has been presented as an alternative strategy to detect noncovalent interactions in solution, in which a reduction in the relative signal intensity of low molecular mass binding partners (i.e., protease inhibitors) can be observed when their target protein (i.e., protease) is added to the sample. Here we have performed a systematic study to explore how various experimental conditions affect the intensity fading phenomenon, as well as a comparison with the strategy based on the direct detection of intact complexes by MALDI MS. For this purpose, the study is focused on two different protease-inhibitor complexes naturally occurring in solution, together with a heterogeneous mixture of nonbinding molecules derived from a biological extract, to examine the specificity of the approach, i.e., those of carboxypeptidase A (CPA) bound to potato carboxypeptidase inhibitor (PCI) and of trypsin bound to bovine pancreatic trypsin inhibitor (BPTI). Our results show that the intensity fading phenomenon occurs when the binding assay is carried out in the sub-muM range and the interacting partners are present in complex mixtures of nonbinding compounds. Thus, at these experimental conditions, the specific inhibitor-protease interaction causes a selective reduction in the relative abundance of the inhibitor. Interestingly, we could not detect any gaseous noncovalent inhibitor-protease ions at these conditions, presumably due to the lower high-mass sensitivity of MCP detectors.     

Protein-metal interactions of calmodulin and α-synuclein monitored by selective noncovalent adduct protein probing mass spectrometry

The metal binding properties of proteins are biologically significant, particularly in relationship to the molecular origins of disease and the discovery of therapeutic pharmaceutical treatments. Herein, we demonstrate that selective noncovalent adduct protein probing mass spectrometry (SNAPP-MS) is a sensitive technique to investigate the structural effects of protein-metal interactions. We utilize specific, noncovalent interactions between 18-crown-6 ether (18C6) and lysine to probe protein structure in the presence and absence of metal ions. Application of SNAPP-MS to the calmodulin-Ca²⁺ system demonstrates that changes in protein structure are reflected in a substantial change in the number and intensity of 18C6s, which bind to the protein as observed by MS. In this manner, SNAPP is demonstrated to be a sensitive technique for monitoring ligand-induced conformational rearrangements in proteins. In addition, SNAPP is well-suited to examine the properties of natively unfolded proteins, where structural changes are more difficult to detect by other methods. For example, α-synuclein is a protein associated in the pathology of Parkinson’s disease, which is known to aggregate more rapidly in the presence of Al³⁺ and Cu²⁺. The 18C6 SNAPP distributions for α-synuclein change dramatically in the presence of 3 μM Al³⁺, revealing that Al³⁺ binding causes a significant change in the conformational dynamics of the monomeric form of this disordered protein. In contrast, binding of Cu²⁺ does not induce a significant shift in 18C6 binding, suggesting that noteworthy structural reorganizations at the monomeric level are minimal. These results are consistent with the idea that the metal-induced aggregation caused by Al³⁺ and Cu²⁺ proceed by independent pathways.     

Evaluation of the β value of the phenylene unit by probing exchange interaction between two nitroxides

Oligophenylene molecular rods with bicyclo[2.2.2]octane having two nitronyl nitroxide radicals were synthesized to investigate the decay constant of p-phenylene. By the measurement and simulation of the ESR spectra of the biradicals with different rod length, it was found that the exchange interaction was decreased with the decay constant β of 0.51 ± 0.01 ?(-1). This result indicates that the spin-spin exchange interaction between neutral radicals has a decay constant similar to the molecular conductance.     

A dispersion-corrected density functional theory study of the noncovalent interactions between nucleobases and carbon nanotube models containing stone–wales defects

The noncovalent bonding between nucleobases (NBs) and Stone–Wales (SW) defect-containing closed-end single-walled carbon nanotubes (SWNTs) was theoretically studied in the framework of density function theory using a dispersion-corrected functional PBE-G06/DNP. The models employed in this study were armchair nanotube (ANT) (5,5) and zigzag nanotube (ZNT) (10,0), which incorporated SW defects in different orientations. In one of them, the (7,7) junction is tilted with respect to SWNT axis (ANT-t and ZNT-t), whereas in ANT-p and ZNT-p models the (7,7) junction is parallel and perpendicular to the axis, respectively. The binding energies for uracil, thymine, cytosine, 5-methylcytosine, adenine, and guanine interacting with the defect-containing nanotube models were compared to the values previously obtained with the same calculation technique for the case of defect-free SWNTs, both in the gas phase (vacuum) and in aqueous medium. For most models, the interaction strength tends to be higher for purine than for pyrimidine complexes, with a clear exception of the systems including ZNT-p, both in vacuum and in aqueous medium. As it could be expected, the binding strength in the latter case is lower as compared to that in vacuum, roughly by 2–4 kcal/mol, due to the implicit inclusion of a medium (i.e., water) via the conductor-like screening model model. The closest contacts between NBs and SWNT models, frontier orbital distribution, and highest-occupied molecular orbital–lowest-unoccupied molecular orbital gap energies are analyzed as well. © 2019 Wiley Periodicals, Inc.     

Role of saturability of noncovalent interactions in the analysis of the three-dimensional structure—opioid activity relationship

The effect of the saturability of noncovalent interactions on the character of opioid activity of opioid receptor ligands belonging to different structural classes was investigated. A three-dimensional model for an opiate pharmacophore was used to show that the involvement of pharmacophore elements, which are responsible for the agonist ligand binding to opioid receptors, in intramolecular interactions gives rise to antagonistic properties.     

Investigation of topology of intermolecular interactions in the benzene–acetylene co-crystal by different theoretical methods

Crystal structure of benzene–acetylene co-crystal was analysed based on calculated energies of intermolecular interactions between basic molecules located in asymmetric part of unit cell and their neighbours belonging to their first coordination sphere. It is demonstrated that the basic structural motif of the crystal is represented by infinite chains formed by the hydrogen-bonded benzene and acetylene molecules. Energy of interaction of the basic pair of molecules to neighbours within the chain is 2.2 times higher than the energy of interactions with molecules of any neighbouring chain. This ratio almost does not depend on method of calculation of interaction energy. Also, results of calculations were compared with analysis of topology of electron density distribution in crystal. The possibility to find the basic structural motif of the crystal based on properties of intermolecular bond critical points is demonstrated.     

The interactions between doxorubicin and amphiphilic and acidic β-sheet peptides towards drug delivery hydrogels

Amphiphilic β-sheet peptides decorated by acidic amino acids may spontaneously assemble into ordered monolayers at interfaces as well as form hydrogels at near physiological pH values. Here we monitored interactions between the peptide Pro-Asp-(Phe-Asp)(5)-Pro and the mildly amphiphilic chemotherapeutic drug doxorubicin (Dox). The peptide in the form of monolayers at the air water interface was found to enhance Dox adsorption, pointing to favorable interactions between the amphiphilic peptide and Dox. In solutions the fluorescence emission of Dox which was fitted to the Stern-Volmer quenching models suggested the formation of Dox associated forms >25 μM and larger forms at >100 μM. In presence of the peptide these larger associated forms appeared already at Dox concentrations >50 μM, indicating enhanced interactions between Dox and the peptide in the β-sheet conformation. Peptide hydrogels loaded with the drug showed sustained release profiles over several days. Smaller fractions of the drug were released with increase in either peptide or initially loaded drug concentrations. The released Dox was found to retain its cytotoxic activity in vitro. This study provides insights on the interactions between the amphiphilic and acidic peptide and Dox that are useful for the bottom up development of Dox-loaded peptide hydrogels for local drug delivery applications.     

Investigation of the interaction of DNA and neutral red by fluorescence spectroscopic analysis

The binding characteristics of neutral red (NR) with DNA were investigated by fluorescence spectrometry. Chemometrics approach as singular value decomposition (SVD) was used to evaluate the number of spectral species in the drug-DNA binding process, and then the intrinsic binding constant of 1.6 × 104 in base pairs and the binding site number of 0.97 were obtained from the Scatchard plot.     

Investigation of protein–protein interactions in living cells by chemical crosslinking and mass spectrometry

The identification of protein–protein interactions within their physiological environment is the key to understanding biological processes at the molecular level. However, the artificial nature of in vitro experiments, with their lack of other cellular components, may obstruct observations of specific cellular processes. In vivo analyses can provide information on the processes within a cell that might not be observed in vitro. Chemical crosslinking combined with mass spectrometric analysis of the covalently connected binding partners allows us to identify interacting proteins and to map their interface regions directly in the cell. In this paper, different in vivo crosslinking strategies for deriving information on protein–protein interactions in their physiological environment are described.