Search

The interaction between borate-ion-stabilized silver (Ag) nanoparticles and (−)-epigallocatechin gallate (EGCG) has been investigated. The added EGCG molecules chelate with the borate ions to form a borate ester. This complex provides a better stability to the metal particles by formation of a cap around them. The spectral line profile of the surface plasmon resonance band of the metal particles has been used to probe the metal-molecule interactions. The withdrawal of electron density from the surface of the Ag particle by the phenolic group of EGCG molecule results in a red-shift of the surface plasmon resonance band of the particles in the sol. In this study we show that both borate-ester-capped Ag nanoparticles and the borate ester itself can be transported by blood plasma serum albumin. [ABSTRACT FROM AUTHOR]

Six 5′-deoxy-5′-morpholine, piperidine, and pyrrolidine of pyrimidine nucleosides have been synthesized and characterized. Their inhibitory action to ribonuclease A has been studied by biochemical analysis and X-ray crystallography. These compounds are moderate inhibitors of RNase A with mid-to-upper micromolar inhibition constants (Ki). The high resolution X-ray crystal structures of the RNase A−inhibitor complexes have shown that all inhibitors bind at the enzyme catalytic cleft with the pyrimidine nucleobase at the B1R2subsites while the 5′ group binds away from the main subsite P1, where P−O5′bond cleavage occurs, toward the solvent close to subsite P0. Structure−activity relationship analysis has demonstrated that the compounds with the larger group in the 5′ position are more potent. Comparative structural analysis of these RNase A complexes with other similar RNase A−ligand complexes provides a structural explanation of their potency and suggests ways to improve their efficiency and selectivity. These inhibitors can be the starting point for the development of compounds that can be used as pharmaceuticals against pathologies associated with RNase A homologues such as human angiogenin, which is implicated in tumor induced neovascularization. [ABSTRACT FROM AUTHOR]

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 Förster 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, c( 50 ns), observed for Trp residue/residues in the complexes of HSA and BSA compared with that in the free proteins. [ABSTRACT FROM AUTHOR]

Human placental ribonuclease inhibitor (hRI) containing six tryptophan (Trp) residues located at positions 19, 261, 263, 318, 375, and 438 and its complex with RNase A have been studied using steady-state and time-resolved fluorescence (298 K) as well as low-temperature phosphorescence (77 K). Two Trp residues in wild-type hRI and also in the protein−protein complex with RNase A are resolved optically. The accessible surface area values of Trp residues in the wild-type hRI and its complex and consideration of inter-Trp energy transfer in the wild-type hRI reveal that one of the Trp residues is Trp19, which is located in a hydrophobic buried region. The other Trp residue is tentatively assigned as Trp375 based on experimental results on wild-type hRI and its complex. This residue in the wild-type hRI is more or less solvent exposed. Both the Trp residues are perturbed slightly on complex formation. Trp19 moves slightly toward a more hydrophobic region, and the environment of Trp375 becomes less solvent exposed. The complex formation also results in a more heterogeneous environment for both the optically resolved Trp residues. [ABSTRACT FROM AUTHOR]

Motivation: Throughout evolution, homologous proteins have common regions that stay semi-rigid relative to each other and other parts that vary in a more noticeable way. In order to compare the increasing number of structures in the PDB, flexible geometrical alignments are needed, that are reliable and easy to use. Results: We present a protein structure alignment method whose main feature is the ability to consider different rigid transformations at different sites, allowing for deformations beyond a global rigid transformation. The performance of the method is comparable with that of the best ones from 10 aligners tested, regarding both the quality of the alignments with respect to hand curated ones, and the classification ability. An analysis of some structure pairs from the literature that need to be matched in a flexible fashion are shown. The use of a series of local transformations can be exported to other classifiers, and a future golden protein similarity measure could benefit from it. Availability: A public server for the program is available at http://dmi.uib.es/ProtDeform/. Contact: jairo@uib.es Supplementary information: All data used, results and examples are available at http://dmi.uib.es/people/jairo/bio/ProtDeform.Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Issues relating to sustenance of the usefulness of genetically modified first generation Bt crop plants in the farmer’s field are of great concern for crop scientists. Additional biotechnological strategies need to be in place to safeguard the possibility for yield loss of Bt crop by other lepidopteran insects that are insensitive to the Cry1A toxin, and also against the possibility for emergence of resistant insects. In this respect, Cry2A toxin has figured as a prospective candidate to be the second toxin to offer the required protection along with Cry1A. In the present study, the entomocidal potency of Cry2A toxin was enhanced through knowledge-based protein engineering of the toxin molecule. Deletion of 42 amino acid residues from the N-terminal end of the peptide followed by the replacement of Lys residues by nonpolar amino acids in the putative transmembrane region including the introduction of Pro resulted in a 4.1–6.6-fold increase in the toxicity of the peptide against three major lepidopteran insect pests of crop plants. [ABSTRACT FROM AUTHOR]