Synthesis of a hemifluorinated amphiphile designed for self-assembly and two-dimensional crystallization of membrane protein

The work reported herein deals with the synthesis and the preliminary physical-chemical analysis of new hemifluorinated surfactant made up of one fluorinated chain linked to a tricarboxylic acid polar head which is able to complex a Ni atom and should favor the two-dimensional crystallization of membrane proteins. Such a compound forms a Langmuir film which is a fluid at 20 °C and not perturbed by the presence of hydrocarbon detergent in aqueous solution.     

Peptide photocaging: A brief account of the chemistry and biological applications

In this mini-review, we summarized the state-of-the-art development of photo-protecting groups for peptide photocaging including the un-caging mechanism of different PPGs, the synthesis of photo-caged peptides, and the recent applications of peptide photocaging in chemical biology.     

In search of new lead compounds for trypanosomiasis drug design: A protein structure-based linked-fragment approach

Summary A modular method for pursuing structure-based inhibitor design in the framework of a design cycle is presented. The approach entails four stages: (1) a design pathway is defined in the three-dimensional structure of a target protein; (2) this pathway is divided into subregions; (3) complementary building blocks, also called fragments, are designed in each subregion; complementarity is defined in terms of shape, hydrophobicity, hydrogen bond properties and electrostatics; and (4) fragments from different subregions are linked into potential lead compounds. Stages (3) and (4) are qualitatively guided by force-field calculations. In addition, the designed fragments serve as entries for retrieving existing compounds from chemical databases. This linked-fragment approach has been applied in the design of potentially selective inhibitors of triosephosphate isomerase from Trypanosoma brucei, the causative agent of sleeping sickness.     

Coupling of CE‐MS for protein and peptide analysis

The review is focused on the latest developments in the analysis of proteins and peptides by capillary electrophoresis techniques coupled to mass spectrometry. First, the methodology and instrumentation are overviewed. In this section, recent progress in capillary electrophoresis with mass spectrometry interfaces and capillary electrophoresis with matrix‐assisted laser desorption/ionization is mentioned, as well as separation tasks. The second part is devoted to applications—mainly bottom‐up and top‐down proteomics. It is obvious that capillary electrophoresis with mass spectrometry methods are well suited for peptide and protein analysis (proteomic research) and it is described how these techniques are complementary and not competitive with the often used liquid chromatography with mass spectrometry methods.     

Peptide/protein hybrid materials: enhanced control of structure and improved performance through conjugation of biological and synthetic polymers

The conjugation of peptides/proteins and synthetic polymers is a useful strategy to overcome some of the limitations related to the use of the individual components. This review will highlight two aspects: enhanced structural control at the nanometer level and improved performance, in particular with respect to biomedical applications. In the former case, peptide sequences are mainly used to mediate self-assembly of synthetic polymers. In the latter case, conjugation of an appropriate synthetic polymer to a pharmaceutically active peptide/protein can, for example, prevent premature enzymatic degradation and enhance blood circulation times, which is therapeutically advantageous.     

Cell specific peptide-conjugated polysaccharide nanogels for protein delivery

A cell specific peptide (Arg‐Gly‐Asp; RGD)‐modified nanogel was prepared and evaluated for its potential to act as a protein delivery carrier. A bovine serum albumin (BSA)/RGD‐modified nanogel complex was efficiently internalized into cells through integrin‐mediated endocytosis. Endosomal escape of the RGD‐modified nanogel was observed after 24 h incubation. The nanogel proved useful for targeted protein delivery.

     

Emerging Methods and Design Principles for Cell‐Penetrant Peptides

Biomolecules such as antibodies, proteins, and peptides are important tools for chemical biology and leads for drug development. They have been used to inhibit a variety of extracellular proteins, but accessing intracellular proteins has been much more challenging. In this review, we discuss diverse chemical approaches that have yielded cell‐penetrant peptides and identify three distinct strategies: masking backbone amides, guanidinium group patterning, and amphipathic patterning. We summarize a growing number of large data sets, which are starting to reveal more specific design guidelines for each strategy. We also discuss advantages and disadvantages of current methods for quantifying cell penetration. Finally, we provide an overview of best‐odds approaches for applying these new methods and design principles to optimize cytosolic penetration for a given bioactive peptide.     

A perspective on general direction and challenges facing antimicrobial peptides

The emergence of drug resistant bacterium threatens the global public healthcare systems.The urgent need to obtain new antimicrobials has driven antimicrobial peptides(AMPs)research into spotlight.Here we give a brief introduction of the recent progress of AMPs regarding their structures,properties, production and modification,and antimicrobial mechanism.Thereby,this review will give an insight into the trends and challenges facing on this particular kind of antimicrobial materials.     

Fluorescence study of peptide and protein containing interpolyelectrolyte complexes

Four polyelectrolyte (PE)-protein and PE-peptide systems were selected for fluorescence experiments. The mode of binding of proteins to PE and structure of forming polycomplexes depends upon the ratio of components and chemical composition of polymer macromolecules. Complex formation of proteins with oppositely charged polycations is realized by the self-assembly of non-stoichiometric polycomplex particles with characteristic composition. These polycomplex particles have a rigid rod-like carcass structures in which protein molecules are practically exposed to the solvent. Two types of ternary polyanion-Cu²⁺-protein polycomplex particles are formed depending on the monomer composition of the copolymer. At higher content of hydrophobic N-isopropylacrylamide monomer unites, the protein globules in the structure of ternary polycomplex particles are densely covered by the shell of a polymer coil and practically “fenced of” from the water environment. At higher content of acrylic acid unites, polycomplex particles have more friable structures in which protein molecules are practically exposed to the solution. The PE-peptide conjugate species can be represented rather as a macromolecule of a segmented (block) copolymer in which the hydrophobic blocks, i.e. the sequences of copolymer and peptide unit pairs, which have formed the covalent and salt bonds alternate with hydrophilic ones, i.e. the sequences of the copolymer chain not participating in the formation of double strand blocks.     

The influence of densely organized maltose shells on the biological properties of poly(propylene imine) dendrimers: new effects dependent on hydrogen bonding

Maltose-modified poly(propylene imine) (PPI) dendrimers were synthesized by reductive amination of unmodified second- to fifth-generation PPI dendrimers in the presence of excess maltose. The dendrimers were characterized by using (1)H NMR, (13)C NMR, and IR spectroscopies; laser-induced liquid beam ionization/desorption mass spectrometry; dynamic light scattering analyses; and polyelectrolyte titration. Their scaffolds have enhanced molecular rigidity and their outer spheres, at which two maltose units are bonded to the former primary amino groups on the surface, have hydrogen-bond-forming properties. Furthermore, the structural features reveal the presence of a dense shell. Experiments involving encapsulation (1-anilinonaphthalene-8-sulfonic acid) and biological properties (hemolysis and interactions with human serum albumin (HSA) and prion peptide 185-208) were performed to compare the modified with the unmodified dendrimers. These experiments gave the following results: 1) The modified dendrimers entrapped a low-molecular-weight fluorescent dye by means of a dendritic box effect, in contrast to the interfacial uptake characteristic of the unmodified PPI dendrimers. 2) Both low- and high-generation dendrimers containing maltose units showed markedly reduced toxicity. 3) The desirable features of bio-interactions depended on the generation of the dendrimer; they were retained after maltose substitution, but were now mainly governed by nonspecific hydrogen-bonding interactions involving the maltose units. The modified dendrimers interacted with HSA as strongly as the parent compounds and appeared to have potential use as antiprion agents. These improvements will initiate the development of the next platform of glycodendrimers in which apparently contrary properties can be combined, and this will enable, for example, therapeutic products such as more efficient and less toxic antiamyloid agents to be synthesized.     

A new azobenzene-based design strategy for detergents in membrane protein research

Mass spectrometry enables the in-depth structural elucidation of membrane protein complexes, which is of great interest in structural biology and drug discovery. Recent breakthroughs in this field revealed the need for design rules that allow fine-tuning the properties of detergents in solution and gas phase. Desirable features include protein charge reduction, because it helps to preserve native features of protein complexes during transfer from solution into the vacuum of a mass spectrometer. Addressing this challenge, we here present the first systematic gas-phase study of azobenzene detergents. The utility of gas-phase techniques for monitoring light-driven changes of isomer ratios and molecular properties are investigated in detail. This leads to the first azobenzene detergent that enables the native mass spectrometry analysis of membrane proteins and whose charge-reducing properties can be tuned by irradiation with light. More broadly, the presented work outlines new avenues for the high-throughput characterization of supramolecular systems and opens a new design strategy for detergents in membrane protein research.

Here, L. H. Urner and co-workers identify a new detergent design strategy for the non-denaturing structural analysis of membrane proteins by studying the gas-phase properties of azobenzene-based oligoglycerol detergents.     

Membrane protein and peptide sample handling for MS analysis using a structured MALDI target

Different sample handling methods for hydrophobic proteins and peptides were evaluated in association with the utilization of a structured matrix-assisted laser/desorption ionization (MALDI) target for increased sensitivity. The fluorinated organic solvent hexafluoroisopropanol (HFIP) was used for the solubilization of both the full-length protein bacteriorhodopsin (BR) and a cyanogen bromide digest thereof, and compared to the performance of the non-ionic detergents octyl--d-glucopyranoside (OG), dodecyl--d-maltoside (DM), and Triton X-100. A concentrating effect was seen when using the structured MALDI plate for BR dissolved in all the different detergents, of which OG generated the best-quality spectra for the full-length integral membrane protein as well as for the hydrophobic peptides. However, the uneven analyte distribution obtained with the detergent preparations required selective and thus time-consuming acquisition of spectra. When instead HFIP was used as sample solvent, a tenfold increase in sensitivity was achieved for full-length BR. Addition of acids to the HFIP-solubilized sample, or to the MALDI matrix solution, improved the signals for a few of the peptides, while degrading the spectra of others. Consequently, the addition of acid could be used as a complementary sample preparation method for hydrophobic peptides. On-target washing to remove contaminants (e.g., salt) was performed, and a recrystallization protocol for signal improvement specifically suited for hydrophobic peptides is described. Results from digestion and solubilization in different micro centrifuge tubes were examined to determine the influence of different materials on the possible sample loss due to wall adhesion. Studies of sample solution storage times suggest immediate analysis after solubilization to obtain best results.