Multiple drug resistance (MDR) in Gram-negative bacteria represents one of the most intractable problems facing modern medicine. Not only is antibiotic resistance incrementally increasing during clinical treatment of infections, but also the evolution and acquisition of new mechanisms of antibiotic resistance lead to the sudden loss of the capacity to treat infections. The most recent superbug, MDR-Neisseria gonorrhoeae, causes the untreatable sexually transmitted infection gonorrhoeae. Chronic gonococcal infections have a high morbidity rate and, due to the explosion in cases worldwide, the community burden is enormous. N. gonorrhoeae colonizes the mucosal surfaces of the human body and has a number of virulence mechanisms that prevent clearance by the human immune system. The most important of these mechanisms is decoration of the lipooligosaccharide lipid A headgroups with phosphoethanolamine (PEA) by the enzyme, lipid A PEA transferase (LptA). Inactivation of the LptA results in the complete loss of PEA groups from lipid A, loss of bacterial colonisation of epithelial cells (Takahashi et al., 2008), increased sensitivity to cationic antimicrobial peptides (Tzeng et al., 2005) and reduced resistance to human complement mediated killing (Lewis et al., 2013). LptA knockouts of N. gonorrhoeae also result in the complete loss of virulence in models of human and mouse infections. Based on these findings we have undertaken a structure-guided approach to develop inhibitors of LptA that will assist in controlling infection and transmission by this important human pathogen. LptA is a membrane protein that interacts with two different lipid substrates. We have determined the crystal structure of the enzyme to 2.75Å resolution. The structure provides insights into the mechanism of substrate binding and catalysis and suggests that significant conformational changes occur through its catalytic cycle.

The decoration of the lipid A headgroups of the lipooligosaccharide (LOS) by the LOS phosphoethanolamine (PEA) transferase (LptA) in Neisseria spp. is central for resistance to polymyxin. The structure of the globular domain of LptA shows that the protein has five disulphide bonds, indicating that it is a potential substrate of the protein oxidation pathway in the bacterial periplasm. When neisserial LptA was expressed in Escherichia coli in the presence of the oxidoreductase, EcDsbA, polymyxin resistance increased 30-fold. LptA decorated one position of the E. coli lipid A headgroups with PEA. In the absence of the EcDsbA, LptA was degraded in E. coli. Neisseria spp. express three oxidoreductases, DsbA1, DsbA2 and DsbA3, each of which appear to donate disulphide bonds to different targets. Inactivation of each oxidoreductase in N. meningitidis enhanced sensitivity to polymyxin with combinatorial mutants displaying an additive increase in sensitivity to polymyxin, indicating that the oxidoreductases were required for multiple pathways leading to polymyxin resistance. Correlates were sought between polymyxin sensitivity, LptA stability or activity and the presence of each of the neisserial oxidoreductases. Only meningococcal mutants lacking DsbA3 had a measurable decrease in the amount of PEA decoration on lipid A headgroups implying that LptA stability was supported by the presence of DsbA3 but did not require DsbA1/2 even though these oxidoreductases could oxidise the protein. This is the first indication that DsbA3 acts as an oxidoreductase in vivo and that multiple oxidoreductases may be involved in oxidising the one target in N. meningitidis. In conclusion, LptA is stabilised by disulphide bonds within the protein. This effect was more pronounced when neisserial LptA was expressed in E. coli than in N. meningitidis and may reflect that other factors in the neisserial periplasm have a role in LptA stability.

Gram-negative bacteria possess an outer membrane envelope consisting of an outer leaflet of lipopolysaccharides, also called endotoxins, which protect the pathogen from antimicrobial peptides and have multifaceted roles in virulence. Lipopolysaccharide consists of a glycan moiety attached to lipid A, embedded in the outer membrane. Modification of the lipid A headgroups by phosphoethanolamine (PEA) or 4-amino-arabinose residues increases resistance to the cationic cyclic polypeptide antibiotic, polymyxin. Lipid A PEA transferases are members of the YhjW/YjdB/YijP superfamily and usually consist of a transmembrane domain anchoring the enzyme to the periplasmic face of the cytoplasmic membrane attached to a soluble catalytic domain. The crystal structure of the soluble domain of the protein of the lipid A PEA transferase from Neisseria meningitidis has been determined crystallographically and refined to 1.4 Å resolution. The structure reveals a core hydrolase fold similar to that of alkaline phosphatase. Loop regions in the structure differ, presumably to enable interaction with the membrane-localized substrates and to provide substrate specificity. A phosphorylated form of the putative nucleophile, Thr280, is observed. Metal ions present in the active site are coordinated to Thr280 and to residues conserved among the family of transferases. The structure reveals the protein components needed for the transferase chemistry; however, substrate-binding regions are not evident and are likely to reside in the transmembrane domain of the protein.

The enzyme phosphoethanolamine transferase A is involved in the addition of phosphoethanolamine moieties to lipid A in Neisseria meningitidis. The enzyme is composed of an N-terminal transmembrane domain and a C-terminal soluble domain that is present in the periplasm of the bacteria. A membrane-deletion construct of the enzyme was designed and expressed in Escherichia coli. Well ordered crystals that diffracted to 1.7 Å resolution were obtained by carrying out a limited trypsin digestion of the protein to remove a predicted N-terminal disordered portion. The crystals belonged to space group P2(1), with unit-cell parameters a=44.3, b=71.6, c=49.9 Å, β=109.2°, and contained one molecule in the asymmetric unit.

The Gram-negative bacterial cell envelope consists of an inner membrane (IM) that surrounds the cytoplasm and an asymmetrical outer-membrane (OM) that forms a protective barrier to the external environment. The OM consists of lipopolysaccahride (LPS), phospholipids, outer membrane proteins (OMPs), and lipoproteins. Oxidative protein folding mediated by periplasmic oxidoreductases is required for the biogenesis of the protein components, mainly constituents of virulence determinants such as pill, flagella, and toxins, of the Gram-negative OM. Recently, periplasmic oxidoreductases have been implicated in [PS biogenesis of Escherichia coli and Neisseria rneningitidis. Differences in OM biogenesis, in particular the transport pathways for endotoxin to the OM, the composition and role of the protein oxidation, and isomerization pathways and the regulatory networks that control them have been found in these two Gram-negative species suggesting that although form and function of the OM is conserved, the pathways required for the biosynthesis of the OM and the regulatory circuits that control them have evolved to suit the lifestyle of each organism.

MSIn addition, Fragment-Based approaches for drug discovery and even conventional SBDD protocols quite often encounter difficulties in introducing ligands either by soaking or co-crystallization of low affinity compounds.Often, this is because the active sites of the targets of interests are ocuppied by salts, additives or other chemicals that preclude the succesful crystallization/soaking of target:ligand complexes.We have explored the use of relative humidity control of protein crystals to overcome some of these issues.We have used crystals of PurE (EC.4.1.1.21),an enzyme from the purine biosynthesis pathway of B. anthracis as a test case.Our findings can be summarized as follows: i) using humidity control, it is possible to improve/optimize the diffraction quality of crystals soaked with ligands/inhibitors; ii) optimization of the relative humidity can compensate for the deterioration of the diffraction pattern that is observed upon desalting crystals grown in high salt; iii) combining de-salting protocols with PEG addition it is possible to achieve very high concentrations of weak ligands (5-10 mM range) in soaking solutions; and iv) fine control of the relative humidity of the crystals soaked in these solutions can compensate for the deterioration of crystal diffraction and restore 'high resolution' diffraction for SBDD and FBDD.

Oxidative protein folding in Gram-negative bacteria results in the formation of disulfide bonds between pairs of cysteine residues. This is a multistep process in which the dithiol-disulfide oxidoreductase enzyme, DsbA, plays a central role. The structure of DsbA comprises an all helical domain of unknown function and a thioredoxin domain, where active site cysteines shuttle between an oxidized, substrate-bound, reduced form and a DsbB-bound form, where DsbB is a membrane protein that reoxidizes DsbA. Most DsbA enzymes interact with a wide variety of reduced substrates and show little specificity. However, a number of DsbA enzymes have now been identified that have narrow substrate repertoires and appear to interact specifically with a smaller number of substrates. The transient nature of the DsbA-substrate complex has hampered our understanding of the factors that govern the interaction of DsbA enzymes with their substrates. Here we report the crystal structure of a complex between Escherichia coli DsbA and a peptide with a sequence derived from a substrate. The binding site identified in the DsbA-peptide complex was distinct from that observed for DsbB in the DsbA-DsbB complex. The structure revealed details of the DsbA-peptide interaction and suggested a mechanism by which DsbA can simultaneously show broad specificity for substrates yet exhibit specificity for DsbB. This mode of binding was supported by solution nuclear magnetic resonance data as well as functional data, which demonstrated that the substrate specificity of DsbA could be modified via changes at the binding interface identified in the structure of the complex.

DsbA is an enzyme found in the periplasm of Gram-negative bacteria that catalyzes the formation of disulfide bonds in a diverse array of protein substrates, many of which are involved in bacterial pathogenesis. Although most bacteria possess only a single essential DsbA, Neisseria meningitidis is unusual in that it possesses three DsbAs, although the reason for this additional redundancy is unclear. Two of these N. meningitidis enzymes (NmDsbA1 and NmDsbA2) play an important role in meningococcal attachment to human epithelial cells, whereas NmDsbA3 is considered to have a narrow substrate repertoire. To begin to address the role of DsbAs in the pathogenesis of N. meningitidis, we have determined the structure of NmDsbA3 to 2.3-Å resolution. Although the sequence identity between NmDsbA3 and other DsbAs is low, the NmDsbA3 structure adopted a DsbA-like fold. Consistent with this finding, we demonstrated that NmDsbA3 acts as a thiol-disulfide oxidoreductase in vitro and is reoxidized by Escherichia coli DsbB (EcDsbB). However, pronounced differences in the structures between DsbA3 and EcDsbA, which are clustered around the active site of the enzyme, suggested a structural basis for the unusual substrate specificity that is observed for NmDsbA3.