Self-assembly of a hydrophobic polypeptide containing a short hydrophilic middle segment: Vesicles to large compound micelles

This report describes a facile route to prepare the vesicles and large compound micelles (LCMs) from a series of poly(epsilon-benzyloxycarbonyl L-lysine)-block-poly[diethylene glycol bis(3-amino propyl) ether]-block-poly(epsilon-benzyloxycarbonyl L-lySine) (PZLL-DGBE-PZLL) in their water solution, depending on molecular weight of the polypeptides. A pyrene probe is used to demonstrate the aggregate formation of PZLL-DGBE-PZLL in solution, and also to measure their critical micelle concentration as a function of molecular weight of the polymer.

Novel hydrophilic-hydrophobic multiblock copolyimides as proton exchange membranes: Enhancing the proton conductivity

A series of novel multiblock copolymers based on sulfonated copolyimides were developed and evaluated for use as proton exchange membranes (PEMs). In these multiblock copolyimides, the hydrophilic blocks were composed of the sulfonated dianhydride and the sulfonated diamine, with sulfonic acid groups on every aromatic ring (i.e., fully sulfonated). This molecular design was implemented to effectively enhance the proton conductivity. The properties of the multiblock copolyimides with varying IEC values or block lengths were investigated to obtain a better understanding of the relationship between molecular structure and properties of proton exchange membranes. The water uptake and proton conductivity were found to be highly dependent upon their structure. The block copolymers displayed significantly higher proton conductivities, especially at low relative humidity than the random copolymers with a similar IEC.

Daunomycin binding to detergent micelles: A model system for evaluating the hydrophobic contribution to drug-DNA interactions

The interaction of daunomycin with sodium dodecyl sulfate and Triton X-100 micelles was investigated as a model for the hydrophobic contribution to the free energy of DNA intercalation reactions. Measurements of visible absorbance, fluorescence lifetime, steady-state fluorescence emission intensity, and fluorescence anisotropy indicate that the anthraquinone ring partitions into the hydrophobic micelle interior. Fluorescence quenching experiments using both steady-state and lifetime measurements demonstrate reduced accessibility of daunomycin in sodium dodecyl sulfate micelles to the anionic quencher iodide and to the neutral quencher acrylamide. Quenching of daunomycin fluorescence by iodide in Triton X-100 micelles was similar to that seen with free daunomycin. Studies of the energetics of the interaction of daunomycin with micelles by fluorescence and absorbance titration methods and by isothermal titration calorimetry in the presence of excess micelles revealed that association with sodium dodecyl sulfate and Triton X-100 micelles is driven by a large negative enthalpy. Association of the drug with both types of micelles also has a favorable entropic contribution, which is larger in magnitude for Triton X-100 micelles than for sodium dodecyl sulfate micelles.

Self-assembled monolayer growth of phospholipids on hydrophobic surface toward mimetic biomembranes: Scanning probe microscopy study

Atomic force microscopy (AFM) and lateral force microscopy (LFM) were used simultaneously to analyze a model membrane bilayer structure consisting of a phospholipid outer monolayer deposited onto organosilane-derivatized mica surfaces, which were constructed by using painting and self-assembly methods. The phospholipid used as outer monolayer was dimyristoylphosphatidylcholine (DMPC). The hydrocarbon-covered substrate that formed the inner half bilayer was composed of a self-assembly monolayer (SAM) of octadecyltrichloroorganosilane (OTS) on mica. SAMs of DMPC were formed by exposing hydrophobic mica to a solution of DMPC in decane/isobutanol and subsequently immersing into pure water. AFM images of samples immersed in solution for varying exposure times showed that before forming a complete monolayer the molecules aggregated into dense islands (2.2-2.6 nm high) on the surface. The islands had a compact and rounded morphology. LFM, coupled with topographic data obtained with the atomic force mode, had made possible the distinction between DMPC and OTS. The rate constant of DMPC growth was calculated. This is the first systematic study of the SAM formation of DMPC by AFM and LFM imaging. It reveals more direct information about the film morphology than previous studies with conventional surface analytical techniques such as infrared spectroscopy, X-ray, or fluorescence microscopy.

Hydrophobic pocket modification and humanized catalytic antibodies with glutathione peroxidase activity (I) - Preparation and characterization of haptenes and conjugates

The thiol group of glutathione (GSH) was protected by 2,4-dinitrochlorobenzene (DNCB), the product S-substituted dinitrophenyl GSH(GSH-S-DNP) was alcoholized to obtain haptenes 4 and 5 respectively. As haptenes, the two GSH derivatives were characterized by means of H-1 NMR, MALDI-TOF-MS and IR, followed by individually coupling with bovine serum albumin (BSA) via glutaraldehyde. BSB-Hp4 and BSA-Hp5 were purified by Sephadex G-25 gel filtration chromatography. For each conjugate, the average haptene-BSA ratio was 12 : 1. The electrophoresis analysis showed that the average molecular weight of each conjugate was 76 500. The CD spectrum indicated that the conjugates had more a-helix content than BSA did.

Docking and molecular dynamics study on the inhibitory activity of coumarins on aldose reductase

In order to explore the inhibitory mechanism of coumarins toward aldose reductase (ALR2), AutoDock and Gromacs software were used for docking and molecular dynamics studies on 14 coumarins (CM) and ALR2 protease. The docking results indicate that residues TYR48, HIS110, and TRP111 construct the active pocket of ALR2 and, besides van der Waals and hydrophobic interaction, CM mainly interact with ALR2 by forming hydrogen bonds to cause inhibitory behavior. Except for CM1, all the other coumarins take the lactone part as acceptor to build up the hydrogen bond network with active-pocket residues. Unlike CM3, which has two comparable binding modes with ALR2, most coumarins only have one dominant orientation in their binding sites. The molecular dynamics calculation, based on the docking results, implies that the orientations of CM in the active pocket show different stabilities. Orientation of CM1 and CM3a take an unstable binding mode with ALR2; their conformations and RMSDs relative to ALR2 change a lot with the dynamic process. While the remaining CM are always hydrogen-bonded with residues TYR48 and HIS110 through the carbonyl O atom of the lactone group during the whole process, they retain the original binding mode and gradually reach dynamic equilibrium.

Diagnóstico Molecular na era da sequenciação de 3ª geração e da PCR digital

Projeto de Pós-Graduação/Dissertação apresentado à Universidade Fernando Pessoa como parte dos requisitos para obtenção do grau de Mestre em Ciências Farmacêuticas

Thermodynamic analysis of a molecular chaperone binding to unfolded protein substrates.

Molecular chaperones are a highly diverse group of proteins that recognize and bind unfolded proteins to facilitate protein folding and prevent nonspecific protein aggregation. The mechanisms by which chaperones bind their protein substrates have been studied for decades. However, there are few reports about the affinity of molecular chaperones for their unfolded protein substrates. Thus, little is known about the relative binding affinities of different chaperones and about the relative binding affinities of chaperones for different unfolded protein substrates. Here we describe the application of SUPREX (stability of unpurified proteins from rates of H-D exchange), an H-D exchange and MALDI-based technique, in studying the binding interaction between the molecular chaperone Hsp33 and four different unfolded protein substrates, including citrate synthase, lactate dehydrogenase, malate dehydrogenase, and aldolase. The results of our studies suggest that the cooperativity of the Hsp33 folding-unfolding reaction increases upon binding with denatured protein substrates. This is consistent with the burial of significant hydrophobic surface area in Hsp33 when it interacts with its substrate proteins. The SUPREX-derived K(d) values for Hsp33 complexes with four different substrates were all found to be within the range of 3-300 nM.

Plasmon-induced electrical conduction in molecular devices.

Metal nanoparticles (NPs) respond to electromagnetic waves by creating surface plasmons (SPs), which are localized, collective oscillations of conduction electrons on the NP surface. When interparticle distances are small, SPs generated in neighboring NPs can couple to one another, creating intense fields. The coupled particles can then act as optical antennae capturing and refocusing light between them. Furthermore, a molecule linking such NPs can be affected by these interactions as well. Here, we show that by using an appropriate, highly conjugated multiporphyrin chromophoric wire to couple gold NP arrays, plasmons can be used to control electrical properties. In particular, we demonstrate that the magnitude of the observed photoconductivity of covalently interconnected plasmon-coupled NPs can be tuned independently of the optical characteristics of the molecule-a result that has significant implications for future nanoscale optoelectronic devices.

Cysteine proteinase-1 and cut protein isoform control dendritic innervation of two distinct sensory fields by a single neuron.

Dendrites often exhibit structural changes in response to local inputs. Although mechanisms that pattern and maintain dendritic arbors are becoming clearer, processes regulating regrowth, during context-dependent plasticity or after injury, remain poorly understood. We found that a class of Drosophila sensory neurons, through complete pruning and regeneration, can elaborate two distinct dendritic trees, innervating independent sensory fields. An expression screen identified Cysteine proteinase-1 (Cp1) as a critical regulator of this process. Unlike known ecdysone effectors, Cp1-mutant ddaC neurons pruned larval dendrites normally but failed to regrow adult dendrites. Cp1 expression was upregulated/concentrated in the nucleus during metamorphosis, controlling production of a truncated Cut homeodomain transcription factor. This truncated Cut, but not the full-length protein, allowed Cp1-mutant ddaC neurons to regenerate higher-order adult dendrites. These results identify a molecular pathway needed for dendrite regrowth after pruning, which allows the same neuron to innervate distinct sensory fields.

Surface physics at the nano-scale via scanning probe microscopy and molecular dynamics simulations

Probe-based scanning microscopes, such as the STM and the AFM, are used to obtain the topographical and electronic structure maps of material surfaces, and to modify their morphologies on nanoscopic scales. They have generated new areas of research in condensed matter physics and materials science. We will review some examples from the fields of experimental nano-mechanics, nano-electronics and nano-magnetism. These now form the basis of the emerging field of Nano-technology. A parallel development has been brought about in the field of Computational Nano-science, using quantum-mechanical techniques and computer-based numerical modelling, such as the Molecular Dynamics (MD) simulation method. We will report on the simulation of nucleation and growth of nano-phase films on supporting substrates. Furthermore, a theoretical modelling of the formation of STM images of metallic clusters on metallic substrates will also be discussed within the non-equilibrium Keldysh Green function method to study the effects of coherent tunnelling through different atomic orbitals in a tip-sample geometry.

Ab initio molecular dynamics simulation of a room temperature ionic liquid

Ab initio molecular dynamics simulations have been performed for the first time on the room-temperature organic ionic liquid dimethyl imidazolium chloride [DMIM][Cl] using density functional theory. The aim is to compare the local liquid structure with both that obtained from two different classical force fields and from neutron scattering experiments. The local structure around the cation shows significant differences compared to both the classical calculations and the neutron results. In particular, and unlike in the gas-phase ion pair, chloride ions tend to be located near a ring C-H proton in a position suggesting hydrogen bonding. The results are used to suggest ways in which the classical potentials may be improved.