Charles A. Haynes

Globular proteins at solid/liquid interfaces

Abstract Seven years have passed since one of us (W.N.) published the last comprehensive review on the mechanism of globular protein adsorption to solid/water interfaces. Since that time, annual contributions to the field have steadily increased and substantial progress has been made in a number of important areas. This review takes a fresh look at the driving force for protein adsorption by combining recent advances with key results from the past. The analysis indicates that four effects, namely structural rearrangements in the protein molecule, dehydration of (parts of) the sorbent surface, redistribution of charged groups in the interfacial layer, and protein surface polarity usually make the primary contributions to the overall adsorption behavior.

Crystal structure of enteropathogenic Escherichia coli intimin-receptor complex.

Intimin and its translocated intimin receptor (Tir) are bacterial proteins that mediate adhesion between mammalian cells and attaching and effacing (A/E) pathogens. Enteropathogenic Escherichia coli (EPEC) causes significant paediatric morbidity and mortality world-wide. A related A/E pathogen, enterohaemorrhagic E. coli (EHEC; O157:H7) is one of the most important food-borne pathogens in North America, Europe and Japan. A unique and essential feature of A/E bacterial pathogens is the formation of actin-rich pedestals beneath the intimately adherent bacteria and localized destruction of the intestinal brush border. The bacterial outer membrane adhesin, intimin, is necessary for the production of the A/E lesion and diarrhoea. The A/E bacteria translocate their own receptor for intimin, Tir, into the membrane of mammalian cells using the type III secretion system. The translocated Tir triggers additional host signalling events and actin nucleation, which are essential for lesion formation. Here we describe the the crystal structures of an EPEC intimin carboxy-terminal fragment alone and in complex with the EPEC Tir intimin-binding domain, giving insight into the molecular mechanisms of adhesion of A/E pathogens.

Characterization and affinity applications of cellulose-binding domains

Cellulose-binding domains (CBDs) are discrete protein modules found in a large number of carbohydrolases and a few nonhydrolytic proteins. To date, almost 200 sequences can be classified in 13 different families with distinctly different properties. CBDs vary in size from 4 to 20 kDa and occur at different positions within the polypeptides; N-terminal, C-terminal and internal. They have a moderately high and specific affinity for insoluble or soluble cellulosics with dissociation constants in the low micromolar range. Some CBDs bind irreversibly to cellulose and can be used for applications involving immobilization, others bind reversibly and are more useful for separations and purifications. Dependent on the CBD used, desorption from the matrix can be promoted under various different conditions including denaturants (urea, high pH), water, or specific competitive ligands (e.g. cellobiose). Family I and IV CBDs bind reversibly to cellulose in contrast to family II and III CBDs which are in general, irreversibly bound. The binding of family II CBDs (CBD(Cex)) to crystalline cellulose is characterized by a large favourable increase in entropy indicating that dehydration of the sorbent and the protein are the major driving forces for binding. In contrast, binding of family IV CBDs (CBD(N1)) to amorphous or soluble cellulosics is driven by a favourable change in enthalpy which is partially offset by an unfavourable entropy change. Hydrogen bond formation and van der Waals interactions are the main driving forces for binding. CBDs with affinity for crystalline cellulose are useful tags for classical column affinity chromatography. The affinity of CBD(N1) for soluble cellulosics makes it suitable for use in large-scale aqueous two-phase affinity partitioning systems.

A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes

A well-balanced human diet includes a significant intake of non-starch polysaccharides, collectively termed ‘dietary fibre’, from the cell walls of diverse fruits and vegetables. Owing to the paucity of alimentary enzymes encoded by the human genome, our ability to derive energy from dietary fibre depends on the saccharification and fermentation of complex carbohydrates by the massive microbial community residing in our distal gut. The xyloglucans (XyGs) are a ubiquitous family of highly branched plant cell wall polysaccharides whose mechanism(s) of degradation in the human gut and consequent importance in nutrition have been unclear. Here we demonstrate that a single, complex gene locus in Bacteroides ovatus confers XyG catabolism in this common colonic symbiont. Through targeted gene disruption, biochemical analysis of all predicted glycoside hydrolases and carbohydrate-binding proteins, and three-dimensional structural determination of the vanguard endo-xyloglucanase, we reveal the molecular mechanisms through which XyGs are hydrolysed to component monosaccharides for further metabolism. We also observe that orthologous XyG utilization loci (XyGULs) serve as genetic markers of XyG catabolism in Bacteroidetes, that XyGULs are restricted to a limited number of phylogenetically diverse strains, and that XyGULs are ubiquitous in surveyed human metagenomes. Our findings reveal that the metabolism of even highly abundant components of dietary fibre may be mediated by niche species, which has immediate fundamental and practical implications for gut symbiont population ecology in the context of human diet, nutrition and health.

Driving forces for phase separation and partitioning in aqueous two-phase systems

A set of simple analytical equations, derived from the Flory-Huggins theory, are used to identify the dominant driving forces for phase separation and solute (e.g., protein) partitioning, in the absence and presence of added electrolyte, in every general class of aqueous two-phase systems. The resulting model appears to capture the basic nature of two-phase systems and all trends observed experimentally. Case studies are used to identify fundamental differences in and the magnitudes of enthalpic and entropic contributions to partitioning in polymer-polymer (e.g., PEG-dextran), polymer-salt, and thermoseparating polymer-water (e.g., UCON-water) two-phase systems. The model therefore provides practitioners with a better understanding of partition systems, and industry with a simple, fundamental tool for selecting an appropriate two-phase system for a particular separation.

Structural and biochemical characterization of the type III secretion chaperones CesT and SigE.

Several Gram-negative bacterial pathogens have evolved a type III secretion system to deliver virulence effector proteins directly into eukaryotic cells, a process essential for disease. This specialized secretion process requires customized chaperones specific for particular effector proteins. The crystal structures of the enterohemorrhagic Escherichia coli O157:H7 Tir-specific chaperone CesT and the Salmonella enterica SigD-specific chaperone SigE reveal a common overall fold and formation of homodimers. Site-directed mutagenesis suggests that variable, delocalized hydrophobic surfaces observed on the chaperone homodimers are responsible for specific binding to a particular effector protein. Isothermal titration calorimetry studies of Tir–CesT and enzymatic activity profiles of SigD–SigE indicate that the effector proteins are not globally unfolded in the presence of their cognate chaperones.

Modelling multiple chemical equilbria in chiral partition systems

Ligand-exchange chiral extraction (LEXCEX) is an emerging technology for large-scale continuous resolution of enantiomers of amino acids and a wide range of chiral therapeutics and drug precursors. LEXCEX is based on the ability of a chiral ligand (Li), solubilized in the non-aqueous phase of a water/alcohol two-phase system through complexation with a transition metal ion (i.e., Cu), to preferentially extract one enantiomer (En) into the organic phase through formation of a ternary electroneutral complex. Here we show that the efficiency of the extraction depends, often strongly, on a number of process variables, including the selectivity of the ligand, the solubility of the enantiomers and complexes containing them in the organic phase, pH and transition-metal ion (Cu) concentration. Phase-equilibria in LEXCEX systems is governed by the complex chemical equilibria in both the aqueous and organic phases. To better understand this extraction process, we develop a model for ligand-exchange chiral extraction which couples a complete description of chemical equilibria in each phase with the overall phase equilibria of the system. The model requires the complete set of protonation constants and binary and ternary formation constants for each species present in either the aqueous or organic phase. When coupled with phase equilibrium constraints, the model quantitatively predicts extraction performance as a function of key operating parameters, thereby providing a simple computational approach to process optimization. Measured equilibrium formation constants for ternary complexes containing the N-decyl-l-hydropxy-proline ligand are found to depend strongly on solvent environment, with complex stabilities in general decreasing when the complex is transferred from water to n-octanol. The role of solvent in ternary complex stability is explored through a series of molecular mechanics simulations.

Structure and biochemical analysis of a secretin pilot protein

The ability to translocate virulence proteins into host cells through a type III secretion apparatus (TTSS) is a hallmark of several Gram‐negative pathogens including Shigella, Salmonella, Yersinia, Pseudomonas, and enteropathogenic Escherichia coli. In common with other types of bacterial secretion apparatus, the assembly of the TTSS complex requires the preceding formation of its integral outer membrane secretin ring component. We have determined at 1.5 Å the structure of MxiM28–142, the Shigella pilot protein that is essential for the assembly and membrane association of the Shigella secretin, MxiD. This represents the first atomic structure of a secretin pilot protein from the several bacterial secretion systems containing an orthologous secretin component. A deep hydrophobic cavity is observed in the novel ‘cracked barrel’ structure of MxiM, providing a specific binding domain for the acyl chains of bacterial lipids, a proposal that is supported by our various lipid/MxiM complex structures. Isothermal titration analysis shows that the C‐terminal domain of the secretin, MxiD525–570, hinders lipid binding to MxiM.

The crystal structure of MexR from Pseudomonas aeruginosa in complex with its antirepressor ArmR

The intrinsic antimicrobial resistance of the opportunistic human pathogen Pseudomonas aeruginosa is compounded in mutant strains that overexpress multidrug efflux pumps such as the prominent drug-proton antiporter, MexAB-OprM. The primary regulator of the mexAB-oprM operon is the MarR family repressor, MexR. An additional repressor, NalC, also regulates mexAB-oprM by controlling expression of ArmR, an antirepressor peptide that is hypothesized to prevent the binding of MexR to its cognate DNA operator via an allosteric protein–peptide interaction. To better understand how ArmR modulates MexR, we determined the MexR-binding region of ArmR as its C-terminal 25 residues and solved the crystal structure of MexR in a 2:1 complex with this ArmR fragment at 1.8 Å resolution. This structure reveals that the C-terminal residues of ArmR form a kinked α-helix, which occupies a pseudosymmetrical and largely hydrophobic binding cavity located at the centre of the MexR dimer. Although the ArmR-binding cavity partially overlaps with the small molecule effector-binding sites of other MarR family members, it possesses a larger and more complex binding surface to accommodate the greater size and specific physicochemical properties of a peptide effector. Comparison with the structure of apo-MexR reveals that ArmR stabilizes a dramatic conformational change that is incompatible with DNA-binding. Thus, this work defines the structural mechanism by which ArmR allosterically derepresses MexR-controlled gene expression in P. aeruginosa and reveals important insights into the regulation of multidrug resistance.

Structural Characterization of the Type-III Pilot-Secretin Complex from Shigella flexneri

Assembly of the type-III secretion apparatus, which translocates proteins through both membranes of Gram-negative bacterial pathogens into host cells, requires the formation of an integral outer-membrane secretin ring. Typically, a small lipidated pilot protein is necessary for the stabilization and localization of this ring. Using NMR spectroscopy, we demonstrate that the C-terminal residues 553-570 of the Shigella flexneri secretin MxiD encompass the minimal binding domain for its cognate pilot MxiM. Although unstructured in isolation, upon complex formation with MxiM, these residues fold into an amphipathic turn-helix motif that caps the elongated hydrophobic cavity of the cracked beta-barrel pilot. Along with a rearrangement of core aromatic residues, this prevents the binding of lipids within the cavity. The mutually exclusive association of lipids and MxiD with MxiM establishes a framework for understanding the role of a pilot in the outer-membrane insertion and multimerization of the secretin ring.