Gas-Phase Collisions with Trimethylamine-N-Oxide Enable Activation-Controlled Protein Ion Charge Reduction.

Modulating protein ion charge is a useful tool for the study of protein folding and interactions by electrospray ionization mass spectrometry. Here, we investigate activation-dependent charge reduction of protein ions with the chemical chaperone trimethylamine-N-oxide (TMAO). Based on experiments carried out on proteins ranging from 4.

CherryPicker: An Algorithm for the Automated Parametrization of Large Biomolecules for Molecular Simulation.

Molecular simulations allow investigation of the structure, dynamics and thermodynamics of molecules at an atomic level of detail, and as such, are becoming increasingly important across many areas of science. As the range of applications increases, so does the variety of molecules. Simulation of a new type of molecule requires generation of parameters that result in accurate representation of the behavior of that molecule, and, in most cases, are compatible with existing parameter sets.

Changes in Milk Protein Interactions and Associated Molecular Modification Resulting from Thermal Treatments and Storage.

We investigated protein modifications that occur during short- and long-term storage of raw, pasteurized, and ultra-high-temperature processed (UHT) milks using RE-HPLC and redox proteomics. The RE-HPLC results show that casein dissociation and whey protein/κ-casein association occurred in both pasteurized and UHT milk. The extent of protein interactions was more pronounced in UHT milk after storage.

Multiscale Modeling and Simulation Approaches to Lipid-Protein Interactions.

Lipid membranes play a crucial role in living systems by compartmentalizing biological processes and forming a barrier between these processes and the environment. Naturally, a large apparatus of biomolecules is responsible for construction, maintenance, transport, and degradation of these lipid barriers. Additional classes of biomolecules are tasked with transport of specific substances or transduction of signals from the environment across lipid membranes.

Chemoenzymatic synthesis of glycoproteins.

The majority of the world's best-selling biotherapeutics are glycoproteins. However their production using cellular expression systems invariably produces inseparable mixtures of materials which differ in their attached carbohydrates. As in many cases correct carbohydrate structure is vital for in vivo efficacy, the development of methods for the production of glycoproteins in homogeneous form has become a significant scientific objective.

Improved Detection and Fragmentation of Disulphide-Linked Peptides.

Characterisation of peptides containing intact disulphide bonds (DSBs) via mass spectrometry is challenging. Our study demonstrates that the addition of aniline to alpha-cyano-4-hydroxycinnamic acid improves detection and fragmentation of complex DSB peptides by matrix-assisted laser desorption/ionization, tandem time-of-flight mass spectrometry (MALDI-TOF-TOF MS). This improved assignment will be a significant new tool when a simple screening to confirm the DSB existence is required.

HspB1 phosphorylation regulates its intramolecular dynamics and mechanosensitive molecular chaperone interaction with filamin C.

Mechanical force-induced conformational changes in proteins underpin a variety of physiological functions, typified in muscle contractile machinery. Mutations in the actin-binding protein filamin C (FLNC) are linked to musculoskeletal pathologies characterized by altered biomechanical properties and sometimes aggregates. HspB1, an abundant molecular chaperone, is prevalent in striated muscle where it is phosphorylated in response to cues including mechanical stress.

Prevalence of antibiotic-resistant Escherichia coli isolated from urban and agricultural streams in Canterbury, New Zealand.

Baseline studies are needed to identify environmental reservoirs of non-pathogenic but associating microbiota or pathogenic bacteria that are resistant to antibiotics and to inform safe use of freshwater ecosystems in urban and agricultural settings. Mesophilic bacteria and Escherichia coli were quantified and isolated from water and sediments of two rivers, one in an urban and one in an agricultural area near Christchurch, New Zealand. Resistance of E.

Oxidative cross-linking of calprotectin occurs in vivo, altering its structure and susceptibility to proteolysis.

Calprotectin, the major neutrophil protein, is a critical alarmin that modulates inflammation and plays a role in host immunity by strongly binding trace metals essential for bacterial growth. It has two cysteine residues favourably positioned to act as a redox switch. Whether their oxidation occurs in vivo and affects the function of calprotectin has received little attention.

Efficient synthesis and enzymatic extension of an N-GlcNAz asparagine building block.

N-Azidoacetyl-d-glucosamine (GlcNAz) is a particularly useful tool in chemical biology as the azide is a metabolically stable yet accessible handle within biological systems. Herein, we report a practical synthesis of FmocAsn(N-AcGlcNAz)OH, a building block for solid phase peptide synthesis (SPPS). Protecting group manipulations are minimised by taking advantage of the inherent chemoselectivity of phosphine-mediated azide reduction, and the resulting glycosyl amine is employed directly in the opening of Fmoc protected aspartic anhydride.

Differences between ultrastructure and protein composition in straight hair fibres.

Mammalian hairs are internally patterned from both a morphological and proteomic perspective to exhibit specific functional traits, including curvature, which is important for coat structure affecting thermo-insulation. Most functional traits in mammalian coats are complex emergent phenomena associated with single-fibre properties that are themselves multi-variate and poorly understood. Here we compare hair curvature, ultrastructure, microstructure, protein composition and felting (a functional attribute) between fibres from natural straight-wool mutants of domestic sheep (felting lustre-mutant sheep), their wild-type relatives and also with a straight-haired semi-lustrous breed, English Leicester.

Structure-function analyses of two plant -diaminopimelate decarboxylase isoforms reveal that active-site gating provides stereochemical control.

-Diaminopimelate decarboxylase catalyzes the decarboxylation of -diaminopimelate, the final reaction in the diaminopimelate l-lysine biosynthetic pathway. It is the only known pyridoxal-5-phosphate-dependent decarboxylase that catalyzes the removal of a carboxyl group from a d-stereocenter. Currently, only prokaryotic orthologs have been kinetically and structurally characterized.

Delivering "Chromatic Bacteria" Fluorescent Protein Tags to Proteobacteria Using Conjugation.

Recently, we published a large and versatile set of plasmids, the chromatic bacteria toolbox, to deliver eight different fluorescent protein genes and four combinations of antibiotic resistance genes to Gram-negative bacteria. Fluorescent tags are important tools for single-cell microbiology, synthetic community studies, biofilm, and host-microbe interaction studies. Using conjugation helper strain S17-1 as a donor, we show how plasmid conjugation can be used to deliver broad host range plasmids, Tn transposons delivery plasmids, and Tn transposon delivery plasmids into species belonging to the Proteobacteria.

Analysis of the Effect of Processing Conditions on Physical Properties of Thermally Set Cellulose Hydrogels.

Cellulose-based hydrogels were prepared by dissolving cellulose in aqueous sodium hydroxide (NaOH)/urea solutions and casting it into complex shapes by the use of sacrificial templates followed by thermal gelation of the solution. Both the gelling temperatures used (40⁻80 °C), as well as the method of heating by either induction in the form of a water bath and hot press or radiation by microwaves could be shown to have a significant effect on the compressive strength and modulus of the prepared hydrogels. Lower gelling temperatures and shorter heating times were found to result in stronger and stiffer gels.

Rapid synthesis of N-glycan oxazolines from locust bean gum via the Lafont rearrangement.

Enzymatic degradation of locust bean gum provides a Manβ(1 → 4)Man disaccharide, which may be converted into the core Manβ(1 → 4)GlcNAc disaccharide unit of all N-glycans via conversion to a 2-iodo-glycosyl azide, and Lafont rearrangement. The Manβ(1 → 4)GlcNAc disaccharide may be used as a key intermediate for elaboration into more complex N-glycan structures providing a route to N-glycan oxazolines as donor substrates for ENGase enzymes that is considerably shorter than those reported previously.

Utilisation of hydrocarbons and production of surfactants by bacteria isolated from plant leaf surfaces.

Leaves are covered by a cuticle composed of long (C11-C20) and very-long chain hydrocarbons (>C20), e.g. alkanes, fatty acids, alcohols, aldehydes, ketones and esters.

The First Purification of Functional Proteins from the Unculturable, Genome-Reduced, Bottlenecked α-Proteobacterium 's Liberibacter solanacearum'.

Liberibacter solanacearum' is an unculturable α-proteobacterium that is the causal agent of zebra chip disease of potato-a major problem in potato-growing areas, because it affects growth and yield. Developing effective treatments for ' L. solanacearum' has been hampered by the difficulty in functionally characterizing the proteins of this organism, largely because they are not easily expressed and purified in standard expression systems.

Engineering peroxiredoxin 3 to facilitate control over self-assembly.

Oligomeric proteins are abundant in nature and are useful for a range of nanotechnological applications; however, a key requirement in using these proteins is controlling when and how they form oligomeric assemblies. Often, protein oligomerisation is triggered by various cellular signals, allowing for controllable oligomerisation. An example of this is human peroxiredoxin 3 (Prx), a stable protein that natively forms dimers, dodecameric rings, stacks, and tubes in response to a range of environmental stimuli.

Effects of sub-lethal concentrations of copper ammonium acetate, pyrethrins and atrazine on the response of to antibiotics.

Antibiotic resistance in human and animal pathogens is mainly the outcome of human use of antibiotics. However, bacteria are also exposed to thousands of other antimicrobial agents. Increasingly those exposures are being investigated as co-selective agents behind the rapid rise and spread of resistance in bacterial pathogens of people and our domesticated animals.

A Multi-Bioassay Integrated Approach to Assess the Antifouling Potential of the Cyanobacterial Metabolites Portoamides.

The cyclic peptides portoamides produced by the cyanobacterium sp. LEGE 05292 were previously isolated and their ability to condition microcommunities by allelopathic effect was described. These interesting bioactive properties are, however, still underexplored as their biotechnological applications may be vast.

The Quest for Novel Antimicrobial Compounds: Emerging Trends in Research, Development, and Technologies.

Pathogenic antibiotic resistant bacteria pose one of the most important health challenges of the 21st century. The overuse and abuse of antibiotics coupled with the natural evolutionary processes of bacteria has led to this crisis. Only incremental advances in antibiotic development have occurred over the last 30 years.

Structural mass spectrometry comes of age: new insight into protein structure, function and interactions.

Mass spectrometry (MS) provides an impressive array of information about the structure, function and interactions of proteins. In recent years, many new developments have been in the field of native MS and these exemplify a new coming of age of this field. In this mini review, we connect the latest methodological and instrumental developments in native MS to the new insights these have enabled.

Chromatic Bacteria - A Broad Host-Range Plasmid and Chromosomal Insertion Toolbox for Fluorescent Protein Expression in Bacteria.

Differential fluorescent labeling of bacteria has become instrumental for many aspects of microbiological research, such as the study of biofilm formation, bacterial individuality, evolution, and bacterial behavior in complex environments. We designed a variety of plasmids, each bearing one of eight unique, constitutively expressed fluorescent protein genes in conjunction with one of four different antibiotic resistance combinations. The fluorophores mTagBFP2, mTurquoise2, sGFP2, mClover3, sYFP2, mOrange2, mScarlet-I, and mCardinal, encoding for blue, cyan, green, green-yellow, yellow, orange, red, and far-red fluorescent proteins, respectively, were combined with selectable markers conferring tetracycline, gentamicin, kanamycin, and/or chloramphenicol resistance.

Computational Prediction of Amino Acids Governing Protein-Membrane Interaction for the PIP Cell Signaling System.

Prediction and characterization of how transiently membrane-bound signaling proteins interact with the cell membrane is important for understanding and controlling cellular signal transduction networks. Existing computational methods rely on approximate descriptions of the components of the system or their interactions, and thus are unable to identify residue- or lipid-specific contributions. Our rotational interaction energy profiling method allows rapid evaluation of an electrostatically optimal orientation of a protein for membrane association, as well as the residues or lipid species responsible for its favorability.