Gerald Audette

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Verified

Gerald verified their affiliation via an institutional email.

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• Ph.D.
• Professor at York University

Following the “Would You Publish This” session of the 2023 American Crystallographic Association conference where issues in solving the phase problem of the P1 pilin from Pseudomonas aeruginosa were presented and discussed, advice was taken in using an AlphaFold model to perform molecular replacement (MR). Diffraction data collection occurred in 20...

One of the most important means by which we can share our enthusiasm for structural science is through our trainees. Our students, both undergraduate and graduate, and postdoctoral researchers in our groups gain more than just technical skills through our interactions, they gain their own appreciation and excitement for science that they then can s...

For many projects involving the structural solution of a protein, a high-resolution crystal structure is a desirable goal for completing the project. However, protein crystallisation is a bottleneck to success; what do you do if a protein never crystallizes, and you don't have access to cryo-EM? TraG is a desirable structural target; it is a protei...

The process of bacterial conjugation, often referred to as lateral gene transfer, is a crucial process in the evolution of bacteria for growth in unique environments and is a main route for the development of multi-drug resistant bacteria in health care settings. Bacterial conjugation is a contact dependent mechanism of transferring genetic materia...

One of the most important means by which we can share our enthusiasm for structural science is our mentorship of trainees. Our trainees at all levels gain more than just technical skills from the time we spend with them; they develop their own appreciation and excitement for structural science that they then can spread through their connections and...

The type IV pilus is a diverse molecular machine capable of conferring a variety of functions and is produced by a wide range of bacterial species. The ability of the pilus to perform host-cell adherence makes it a viable target for the development of vaccines against infection by human pathogens such as Pseudomonas aeruginosa . Here, the 1.3 Å res...

Bacteria have evolved elaborate mechanisms to thrive in stressful environments. F-like plasmids in gram-negative bacteria encode for a multi-protein Type IV Secretion System (T4SSF) that is functional for bacterial proliferation and adaptation through the process of conjugation. The periplasmic protein TrbB is believed to have a stabilizing chapero...

We propose that through the emergence of advanced nanomedical technologies over the next few decades, the intrinsic human immune system might be significantly augmented through the incorporation of what we refer to as a conceptual “sentinel” nanomedical platform. It might be possible that these sentinels, which would be exceptionally “trained,”...

The R100 plasmid and the secretion system it encodes are representative of F-like conjugative type IV secretion systems for the transmission of mobile DNA elements in gram-negative bacteria, serving as a major contributor to the spread of antibiotic resistance in bacterial pathogens. The TraG protein of F-like systems consists of a membrane-bound N...

Wastewater treatment plants and other remediation facilities serve important roles, both in public health, but also as dynamic research platforms for acquiring useful resources and biomolecules for various applications. An example of this is methanotrophic bacteria within anaerobic digestion processes in wastewater treatment plants. These bacteria...

Conjugative type IV secretion systems (T4SS) transmit mobile DNA elements in bacteria and are a significant contributor to the evolution of antibiotic resistance. Of the proteins produced from the F and R100 plasmids of Escherichia coli; the representative conjugative plasmids of gram-negative bacteria, TraG is among the largest and consists of a m...

With the adverse environmental ramifications of the use of petroleum-based plastic outweighing the challenges facing the industrialization of bioplastics, polyhydroxyalkanoate (PHA) biopolymer has gained broad interest in recent years. Thus, an efficient approach for maximizing polyhydroxybutyrate (PHB) polymer production in methanotrophic bacteria...

Efficient in silico development of novel antibiotics requires high-resolution, dynamic models of drug targets. As conjugation is considered the prominent contributor to the spread of antibiotic resistance genes, targeted drug design to disrupt vital components of conjugative systems has been proposed to lessen the proliferation of bacterial antibio...

We previously demonstrated that genome reorganization, through chromosome territory repositioning, occurs concurrently with significant changes in gene expression in normal primary human fibroblasts treated with the drug rapamycin, or stimulated into quiescence. Although these events occurred concomitantly, it is unclear how specific changes in gen...

Nanobiotechnology involves the study of structures found in nature to construct nanodevices for biological and medical applications with the ultimate goal of commercialization. Within a cell most biochemical processes are driven by proteins and associated macromolecular complexes. Evolution has optimized these protein-based nanosystems within livin...

Hyper-activated STAT5B variants are high value oncology targets for pharmacologic intervention. STAT5BN642H, a frequently-occurring oncogenic driver mutation, promotes aggressive T-cell leukemia/lymphoma in patient carriers, although the molecular origins remain unclear. Herein, we emphasize the aggressive nature of STAT5BN642H in driving T-cell ne...

The crystal structures of an inter­mediate, C10H9ClN4O, 3-[(6-chloro-7H-purin-7-yl)meth­yl]cyclo­butan-1-one (I), and two N-7 and N-9 regioisomeric oxetanocin nucleoside analogs, C10H13ClN4O, 3-[(6-chloro-8,9-di­hydro-7H-purin-7-yl)meth­yl]cyclo­butan-1-ol (II) and C10H11ClN4O, 3-[(6-chloro-9H-purin-9-yl)meth­yl]cyclo­butan-1-ol (IV), are reported....

A synthesis of cyclobutene nucleoside analogs in which the nucleobase is tethered by a methylene group is described. The coupling of 6-chloropurine with 3-hydroxymethyl-cyclobutanone proceeds via its triflate to give both N-7 and N-9 regioisomers with relative yields corresponding to the calculated charge distribution of the 6-chloropurinyl anion....

Helicobacter pylori infects the gastric epithelium of half the global population, where infections can persist into adenocarcinomas and peptic ulcers. H. pylori secretes several proteins that lend to its pathogenesis and survival including VacA, CagA, γ-glutamyltransferase and HP0175. HP0175, also known as HpCBF2, classified as a peptidyl-prolyl ci...

Bacterial conjugation, such as that mediated by the E. coli F plasmid, is a main mechanism driving bacterial evolution. Two important proteins required for F-pilus assembly and DNA transfer proficiency are TraW and TrbC. As members of a larger complex, these proteins assemble into a type IV secretion system and are essential components of pore form...

The transfer of genetic material by bacterial conjugation is a process that takes place via complexes formed by specific transfer proteins. In Escherichia coli, these transfer proteins make up a DNA transfer machinery known as the mating pair formation, or DNA transfer complex, which facilitates conjugative plasmid transfer. The objective of this p...

This handbook examines the entire "product life cycle," from the creation of nanomedical products to their final market introduction. While focusing on critical issues relevant to nanoproduct development and translational activities, it tackles topics such as regulatory science, patent law, FDA law, ethics, personalized medicine, risk analysis, tox...

This handbook provides a comprehensive roadmap of basic research in nanomedicine as well as clinical applications. However, unlike other texts in nanomedicine, it not only highlights current advances in diagnostics and therapeutics but also explores related issues like nomenclature, historical developments, regulatory aspects, nanosimilars and 3D n...

Conjugative DNA transfer by the F-plasmid is achieved through a type IV secretion system (T4SS) encoded within the plasmid's transfer region; TraF is one of several F-T4SS proteins essential for F-pilus assembly. In order to identify regions of the protein important for TraF function, a series of deletion mutants were assessed for their ability to...

Truncated pilin monomers from Pseudomonas aeruginosa strain K122-4 (ΔK122) have been shown to enter a monomer-dimer equilibrium in solution prior to oligomerization into protein nanotubes. Here, we examine the structural changes occurring between the monomeric and dimeric states of ΔK122 using time-resolved hydrogen-deuterium exchange mass spectrom...

Tau is an intrinsically disordered protein (IDP) whose primary physiological role is to stabilize microtubules in neuronal axons at all stages of development. In Alzheimer's and other tauopathies, tau forms intracellular insoluble amyloid aggregates known as neurofibrillary tangles, a process that appears in many cases to be preceded by hyperphosph...

The transfer of genetic material within a bacterial population through the process of conjugation distributes novel genetic elements for survival in unique environments. Bacterial conjugation is important to public health as the spread antibiotic resistance genes among bacteria results in multi-drug resistance. Indeed, approximately 70% of bacteria...

This review describes the evolution of time-resolved electrospray ionization mass spectrometry (TRESI-MS), a technology that was developed in large part at Western University. TRESI-MS was initially designed to characterize rapid chemical and biochemical reactions occurring on the millisecond time scale without need for a chromophore. Early TRESI-M...

The response-regulatory protein LytR belongs to a family of transcription factors involved in the regulation of important virulence factors in pathogenic bacteria. The protein consists of a receiver domain and an effector domain, which play an important role in controlled cell death and lysis. The LytR receiver domain (LytRN) has been overexpressed...

The efficient localization of increased levels of active enzymes onto conducting scaffolds is important for the development of enzyme-based biofuel cells. Cross-linked enzyme clusters (CEC) of glucose oxidase (GOx) constrained to functionalized carbon nanotubes (CEC-CNTs) were generated in order to evaluate the potential of using CECs for developin...

Self-assembling protein nanotubes (PNTs) are an intriguing alternative to carbon nanotubes for applications in bionanotechnology, in part due to greater inherent biocompatibility. The type IV pilus of the gram negative bacteria Pseudomonas aeruginosa is a protein-based fibre composed of a single subunit, the type IV pilin. Engineered pilin monomers...

The development of biologically relevant nanosystems such as biomolecular probes and sensors requires systems that effectively interface specific biochemical environments with abiotic architectures. The most widely studied nanomaterial, carbon nanotubes, has proven challenging in their adaptation for biomedical applications despite their numerous a...

The steroid binding mechanism of a DNA aptamer was studied using isothermal titration calorimetry (ITC), NMR spectroscopy, quasi-elastic light scattering (QELS), and small-angle X-ray spectroscopy (SAXS). Binding affinity determination of a series of steroid-binding aptamers derived from a parent cocaine-binding aptamer demonstrates that substituti...

Nanotechnology has influenced the direction of research across the sciences, medicine, and engineering. Carbon nanotubes (CNTs) and, more recently, protein nanotubes (PNTs) and protein-inorganic nanocomposites have received considerable attention due to their unique nanostructures that can be utilized as a scaffold to house proteins or create nanow...

The type IV pilus of Pseudomonas aeruginosa is a nanofibre composed of multiple copies of a single protein subunit, the type IV pilin. In the presence of a hydrophobic surface or solution, engineered pilin monomers oligomerize into soluble, high molecular weight structures-protein nanotubes (PNTs). P. aeruginosa pilins, pili and pilin-derived PNTs...

Bio-fuel cells are alternative energy devises based on bio-electrocatalysis of natural substrates by enzymes or microorganisms. Here we review bio-fuel cells and bio-batteries based on the recent literature. In general, the bio-fuel cells are classified based on the type of electron transfer; mediated electron transfer and direct electron transfer...

The type IV pili of Pseudomonas aeruginosa are essentially protein nanofibres composed of multiple copies of a single pilin subunit. Type IV pili extend from the bacterial surface, and mediate specific adherence to biotic and abiotic surfaces. While deletion of the N-terminal region of the pilin's *-helix allows for the ready expression of a highly...

One approach to develop nanosystems that incorporate biological concepts involves the addition of biotic moieties (carbohydrates, DNA, protein) to abiotic scaffolds such as carbon nanotubes. These hybrids have interesting properties but incorporation of specific, site-directed functionalization is challenging and the resulting material is best desc...

The mating pair stabilization (Mps) protein of the F plasmid, TraG, is unique to F-like type IV secretion systems. TraG is a polytopic inner-membrane protein with a large C-terminal periplasmic domain that is required for piliation and Mps, whereas the N-terminal region is sufficient for pilus synthesis. The C-terminal region of TraG is thought to...

Pseudomonas aeruginosa readily binds to stainless steel and other abiotic surfaces, causing major problems in both the medical and food industries. In this study, we show that P. aeruginosa binds to abiotic surfaces in a concentration-dependent, saturable manner during the initial stages of biofilm formation. P. aeruginosa type IV pili mediate bind...

The minimal catalytic domain of α-(1,3/1,4)-fucosyltransferases (FucTs) from Helicobacter pylori strains NCTC11639 and UA948 was mapped by N- and C-terminal truncations. Only the C terminus could be truncated without significant loss of activity. 11639FucT and UA948FucT contain 10 and 8 heptad repeats, respectively, which connect the catalytic doma...

Pseudomonas aeruginosa readily binds to stainless steel and other abiotic surfaces, causing major problems in both the medical and food industries. In this study, we show that P. aeruginosa binds to abiotic surfaces in a concentration-dependent, saturable manner during the initial stages of biofilm formation. P. aeruginosa type IV pili mediate bind...

Ectromelia, vaccinia, smallpox and other closely related viruses of the orthopoxvirus genus encode a glutaredoxin gene that is not present in poxviruses outside of this genus. The vaccinia glutaredoxin O2L has been implicated as the reducing agent for ribonucleotide reductase and may thus play an important role in viral deoxyribonucleotide synthesi...

Ly-49 receptors regulate mouse natural killer cell functions. Members of the polymorphic Ly-49 multigene family recognize specific alleles of major histocompatibility complex class I (MHC I) or MHC I-like proteins. Previous studies have provided insight into the nature of Ly-49A and -C interaction with their high-affinity MHC I ligands, H-2Dd and K...

The opportunistic pathogen Pseudomonas aeruginosa produces multifunctional, polar, filamentous appendages termed type IV pili. Type IV pili are involved in colonization during infection, twitching motility, biofilm formation, bacteriophage infection, and natural transformation. Electrostatic surface analysis of modeled pilus fibers generated from P...

TraF, a component of the Escherichia coli type IV secretory system, has been crystallized and preliminary X-ray diffraction data have been collected. TraF is a 26 kDa protein encoded by the E. coli F plasmid and is required for conjugative plasmid transfer and the formation of sex pili. The N-terminal domain of TraF has no recognizable sequence fea...

Adherence of pathogens to host cells is critical for the initiation of infection and is thus an attractive target for anti-infective therapeutics and vaccines. In the opportunistic human pathogen Pseudomonas aeruginosa, host-cell adherence is achieved predominantly by type IV pili. Analysis of several clinical strains of P. aeruginosa reveals poor...

Bacterial pili are nanofibers made of protein subunits. Here we report the controlled assembly of protein nanotubes from an engineered Pseudomonas aeruginosa type IV pilin monomer. The nanotubes are up to 100 μm long with an outer diameter of 6 nm and a predicted inner diameter of 2 nm. Protein nanotube formation appears to proceed through a hydrop...

The monomeric pilin from Pseudomonas aeruginosa strain K122-4 has been crystallized and preliminary X-ray diffraction data have been collected. Pilin is the monomeric subunit of the type IV pilus, the dominant adhesin of the opportunistic pathogen P. aeruginosa. The K122-4 pilin crystallizes as a dimer in space group P1, with unit-cell parameters a...

Many biologically important interactions occur between proteins and carbohydrates. The examination of these interactions at the atomic level is critical not only in understanding the nature of these interactions and their biological role, but also in the design of effective modulators of these interactions. While experimentally obtained structural...

The structural basis for carbohydrate,specificity of the first lectin from,Ulex europaeus,(UE-I) is reported. UE-I is a dimeric metalloglycoprotein that binds the H-type 2 human,blood group determinant,(-L-Fuc(12)--D- Gal(1 4)--D-GlcNAc-), the blood group determinant present on the surface of O-type erythrocytes. The structural characteristics of U...

The tertiary and quaternary structure of the lectin I from Ulex europaeus (UE-I) has been determined to 2.2 A resolution. UE-I is a dimeric metalloglycoprotein that binds the H-type 2 human blood group determinant [alpha-L-Fucalpha(1-->2)-beta-D-Galbeta(1-->4)-beta-D-Glc NAcalpha-]. Nine changes from the published amino acid sequence were necessary...

A monomeric isocitrate dehydrogenase has been crystallized for the first time. This enzyme catalyzes the conversion of isocitrate to oxalosuccinate and subsequently to α-ketoglutarate and CO2; the coenzyme NADP+ is reduced to NADPH during the reaction. Polyethylene glycol 2000 monomethyl ether was used to crystallize the enzyme in space group C2 wi...

The histidine-containing phosphocarrier protein HPr is a central component of the phosphoenolpyruvate:sugar phosphotransferase system (PTS), which transfers metabolic carbohydrates across the cell membrane in many bacterial species. In Gram-positive bacteria, phosphorylation of HPr at conserved serine 46 (P-Ser-HPr) plays several regulatory roles w...

Various 2-arylideneindanones 1, 2-arylidenetetralones 2, and 2-arylidenebenzosuberones 3 were synthesized with the aim of determining the relative orientations of the two aryl rings which favored cytotoxicity. Molecular modeling of the unsubstituted compound in each series revealed differences in the spatial arrangements of the two aryl rings, and...

In the title compound, C13H21N3O5, the pyrimidine ring adopts the antiperiplanar (-ap) conformation [chi = 193.54 (19) degrees]. The deoxyribose sugar ring has the C2'-exo-C3'-endo (2T3) twist conformation. The pseudo-rotational parameters of the deoxyribose sugar ring are P = 6.83 (2) degrees and Tm = 38.27 (2) degrees. The exocyclic side chain at...

In the title molecule (C11H17N3O4) the pyrimidine ring adopts the anticlinal (-ac) conformation [chi = 245.10 (18)degrees]. The deoxyribose sugar ring has the C2'-endo (E-2) envelope conformation. The pseudorotational parameters of the deoxyribose sugar ring are P = 168.92 (2)degrees and tau(m) = 33.86 (2)degrees. The exocyclic side chain at C5' ha...

Ca2+ binding to the N-domain of skeletal muscle troponin C (sNTnC) induces an "opening" of the structure [Gagné, S. M., et al. (1995) Nat. Struct. Biol. 2, 784-789], which is typical of Ca2+-regulatory proteins. However, the recent structures of the E41A mutant of skeletal troponin C (E41A sNTnC) [Gagné, S. M., et al. (1997) Biochemistry 36, 4386-4...

In the title compound, C13H17N3O5, the deoxyribose sugar ring adopts a C2'-exo-C3'-endo symmetrical half-chair conformation (T-3(2)), with pseudorotational parameters of P = 2.54 (1)degrees and tau(m) = 27.82 (7)degrees. The deoxyribose sugar ring is in the anticlinal (-ac) conformation with respect to the base [chi = -93.2 (4)degrees]. The exocycl...