Studies on tryptophan residues of Abrus agglutinin Stopped-flow kinetics of modification and fluorescence-quenching studies

The presence of two essential tryptophan residues/molecule was implicated in the binding site of Abrus agglutinin [Patanjali, Swamy, Anantharam, Khan & Surolia (1984) Biochem. J. 217, 773-781]. A detailed study of the stopped-flow kinetics of the oxidation of tryptophan residues revealed three classes of tryptophan residues in the native protein. A discrete reorganization of tryptophan residues into two phases was observed upon ligand binding. The heterogeneity of tryptophan exposure was substantiated by quenching studies with acrylamide, succinimide and Cs+. Our study revealed the microenvironment of tryptophan residues to be hydrophobic, and also the presence of acidic amino acid residues in the vicinity of surface-localized tryptophan residues.

Chemical modification studies on Abrus agglutinin Involvement of tryptophan residues in sugar binding

The galactose-binding lectin from the seeds of the jequirity plant (Abrus precatorius) was subjected to various chemical modifications in order to detect the amino acid residues involved in its binding activity. Modification of lysine, tyrosine, arginine, histidine, glutamic acid and aspartic acid residues did not affect the carbohydratebinding activity of the agglutinin. However, modification of tryptophan residues carried out in native and denaturing conditions with N-bromosuccinimide and 2- hydroxy-5-nitrobenzyl bromide led to a complete loss of its carbohydrate-binding activity. Under denaturing conditions 30 tryptophan residues/molecule were modified by both reagents, whereas only 16 and 18 residues/molecule were available for modification by N-bromosuccinimide and 2-hydroxy-5-nitrobenzyl bromide respectively under native conditions. The relative loss in haemagglutinating activity after the modification of tryptophan residues indicates that two residues/molecule are required for the carbohydrate-binding activity of the agglutinin. A partial protection was observed in the presence of saturating concentrations of lactose (0.15 M). The decrease in fluorescence intensity of Abrus agglutinin on modification of tryptophan residues is linear in the absence of lactose and shows a biphasic pattern in the presence of lactose, indicating that tryptophan residues go from a similar to a different molecular environment on saccharide binding. The secondary structure of the protein remains practically unchanged upon modification of tryptophan residues, as indicated by c.d. and immunodiffusion studies, confirming that the loss in activity is due to modification only.

Interaction of EcoP1 modification methylase with S-adenosyl-L-methionine: a UV-crosslinking study

EcoP1 modification methylase was radioactively labeled when incubated with S-adenosyl-L-[methyl-3H]methionine in the presence of ultraviolet light. Crosslinking of the enzyme as detected by electrophoresis on sodium dodecyl sulfate-polyacrylamide gel followed by fluorography and autoradiography, was shown to be specific by a number of criteria. More importantly, EcoP1 modification methylase was also radioactively labeled with S-adenosyl-L-[carboxyl-14C]methionine demonstrating that labeling involved binding of the entire AdoMet molecule rather than methylation of the protein. Further, c2 EcoP1 mutant DNA modification methylases which show negligible or very little methylation activity, correspondingly formed a weak or no adduct upon crosslinking. These results suggest that photolabeling of EcoP1 DNA modification methylase occurs at the AdoMet binding site.

DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins

Depth measures the extent of atom/residue burial within a protein. It correlates with properties such as protein stability, hydrogen exchange rate, protein-protein interaction hot spots, post-translational modification sites and sequence variability. Our server, DEPTH, accurately computes depth and solvent-accessible surface area (SASA) values. We show that depth can be used to predict small molecule ligand binding cavities in proteins. Often, some of the residues lining a ligand binding cavity are both deep and solvent exposed. Using the depth-SASA pair values for a residue, its likelihood to form part of a small molecule binding cavity is estimated. The parameters of the method were calibrated over a training set of 900 high-resolution X-ray crystal structures of single-domain proteins bound to small molecules (molecular weight < 1.5 KDa). The prediction accuracy of DEPTH is comparable to that of other geometry-based prediction methods including LIGSITE, SURFNET and Pocket-Finder (all with Matthew's correlation coefficient of similar to 0.4) over a testing set of 225 single and multi-chain protein structures. Users have the option of tuning several parameters to detect cavities of different sizes, for example, geometrically flat binding sites. The input to the server is a protein 3D structure in PDB format. The users have the option of tuning the values of four parameters associated with the computation of residue depth and the prediction of binding cavities. The computed depths, SASA and binding cavity predictions are displayed in 2D plots and mapped onto 3D representations of the protein structure using Jmol. Links are provided to download the outputs. Our server is useful for all structural analysis based on residue depth and SASA, such as guiding site-directed mutagenesis experiments and small molecule docking exercises, in the context of protein functional annotation and drug discovery.

Stable and Potent Analogues Derived from the Modification of the Dicarbonyl Moiety of Curcumin

Curcumin has shown promising therapeutic utilities for many diseases, including cancer; however, its clinical application is severely limited because of its poor stability under physiological conditions. Here we find that curcumin also loses its activity instantaneously in a reducing environment. Curcumin can exist in solution as a tautomeric mixture of keto and enol forms, and the enol form was found to be responsible for the rapid degradation of the compound. To increase the stability of curcumin, several analogues were synthesized in which the diketone moiety of curcumin was replaced by isoxazole (compound 2) and pyrazole (compound 3) groups. Isoxazole and pyrazole curcumins were found to be extremely stable at physiological pH, in addition to reducing atmosphere, and they can kill cancer cells under serum-depleted condition. Using molecular modeling, we found that both compounds 2 and 3 could dock to the same site of tubulin as the parent molecule, curcumin. Interestingly, compounds 2 and 3 also show better free radical scavenging activity than curcumin. Altogether, these results strongly suggest that compounds 2 and 3 could be good replacements for curcumin in future drug development.

Measurement of forces during the modification of C60 islands

A UHV atomic force microscope with a conducting tip is used to measure the tip-sample conductance as a function of the applied force on well-ordered, monolayer islands of C60 on Cu(111). By imaging the sample before and after each force-distance experiment, it was possible to investigate the forces required for the removal of individual C60 molecules from the islands. The removal of C60 occurs near defects or edges of the C60 islands and requires an applied force of 5-20 nN, which corresponds to applied pressures of order 1 GPa. In addition, it was possible to investigate the strength of the C60 film on the molecular scale. It was found that the mechanical stiffness of a C60 molecule is of order 6 N/m and the islands appear to undergo a reversible yield process at an applied pressure of around 1.2 GPa.

The modification of self-assembled monolayer on indium tin oxide as cathode in inverted bottom-emitting organic light-emitting diodes

Self-assembled monolayers (SAMs) of a series of p-substituted benzoyl chlorides were formed on indium tin oxide as the cathode for the fabrication of inverted bottom-emitting organic light-emitting diodes (IBOLEDs). The studies on the efficiency of electron injection and device performances showed that the direct tunneling of electron and the formation of dipole associated with the monolayer-forming molecule lead to significant enhancement in electron injection. Consequently, the device efficiency is greatly improved.

CNT Templated Regioselective Enzymatic Polymerization of Phenol in Water and Modification of Surface of MWNT Thereby

Carbon nanotubes (CNTs) are used as templates to synthesize regioselective polymers from enzymatic polymerization of phenol in water. About 90% of total polymeric units in the obtained polymers are the highly thermally stable oxyphenylene units. The polymer-yields are dependent on the quantities of CNTs used. On the basis of MWNT-templated enzymatic polymerization of phenol, covalent attachment of polyphenol chains to the surface of MWNT by way of a linking molecule, hydroquinone, is achieved. This approach supplies a novel way for producing high-performance polymers and for functionalization of the surface of CNT.

Recent development of tip modification techniques in chemical force microscope

A review is given on the recent development of scanning probe microscope (SPM) tip modification techniques for chemical force microscope, including the preparation and application of SPM tip modified by self-assembled monolayer, atomic force microscope (AFM) tip modified by biological molecule, scanning tunneling microscope tip modified by electrochemical method, AFM tip modified by carbon nanotube.

A new crystal modification of gutta percha

Single chain and pauci chain single crystals of gutta percha in nanometer size were prepared by a dilute solution spraying method. A new crystal modification of gutta percha was found. The unit cell of the new modification of gutta percha was determined by electron diffraction crystal structure analysis to be a hexagonal form with cell dimensions: a = b = 0.695 nm, c = 0.661 nm, alpha = beta = 90 degrees, gamma =120 degrees; the space group is P6. The molecular packing in the unit cell was determined by computer modelling with Cerius(2) 2.0 software. (C) 1998 Elsevier Science Ltd. All rights reserved.

New tools for chemical modification of proteins

Tese de doutoramento, Farmácia (Química Farmacêutica e Terapêutica), Universidade de Lisboa, Faculdade de Farmácia, 2014

Programmable Logic-Based Delivery of Small-Molecule Therapeutics from Gels

Thesis (Master's)--University of Washington, 2015

Hypusine Modification of the Ribosome-binding Protein eIF5A, a Target for New Anti-Inflammatory Drugs: Understanding the Action of the Inhibitor GC7 on a Murine Macrophage Cell Line

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)