Euclidean distance geometry and applications

Euclidean distance geometry is the study of Euclidean geometry based on the concept of distance. This is useful in several applications where the input data consists of an incomplete set of distances, and the output is a set of points in Euclidean space that realizes the given distances. We survey some of the theory of Euclidean distance geometry and some of the most important applications: molecular conformation, localization of sensor networks and statics.Comment: 64 pages, 21 figure

Distance geometry and related methods for protein structure determination from NMR data

The method of choice to reveal the conformation of protein molecules in atomic detail has been X-ray single-crystal analysis. Since the first structural analysis of diffraction patterns, computer calculations have been an important tool in these studies (Blundell & Johnson, 1976). As is described by Sheldrick (1985), it has been taken for granted that a necessary first step in the determination of a protein structure would be writing computer programs to fit structure factors. In contrast the combined use of the structural analysis of NMR data and computer calculations has been quite limited. An early attempt of such structural calculations was the quantitative determination of mononucleotide conformations in solution using lanthanide ion shifts (Barry et al. 1971

Elucidating the Energetics of Bacterial Signal Transduction: Insights From Phoq

Bacteria transduce signals across the membrane using two-component systems, consisting of a membrane-spanning sensor histidine kinase and a cytoplasmic response regulator. The histidine kinase, PhoQ, serves as a master regulator of virulence response in S. typhimurium and E. coli. It also is inhibited by divalent cations, particularly Mg2+. While the periplasmic sensor domain of this protein has a unique function, the cytoplasmic portion of this modular protein is made of structurally conserved domains found in many other bacterial sensor kinases. Signal transduction through these conserved domains is thought to be universal; however, the structural and energetic rearrangements that occur during signaling have generated numerous models. Through Bayesian inference we constructed a two-state model based on cysteine crosslinking data and homologous crystal structures. These two signaling states differ in membrane depth of the periplasmic acidic patch as well as the reciprocal displacement of diagonal helices along the dimer interface. Comparative studies of multiple histidine kinases suggest that diagonal displacement of helices is a common mode of signal transduction. A similar scissor-like model was previously ruled out in CheA-linked chemoreceptors; therefore, this new evidence suggests that sensor His-kinase and CheA-linked receptors possess different signaling mechanisms. To unify the various signaling mechanisms that exist for the different protein domains, we built a thermodynamic model based on Linked Equilibrating Domains (LED). We used this model to quantitatively interpret functional data of single-point Ala, Phe and Cys mutants throughout the signal transducing regions of PhoQ. Data from 35 mutants, including both activating and deactivating phenotypes, were globally fit using LED, and gross features such as Vmax and Kd were related to more nuanced population distributions and thermodynamic coupling. LED analysis highlights the principles by which individual signaling domains can be connected to create a functional signal transducer. These principles allow us to quantitatively explain signaling in histidine kinases and are likely to be broadly applicable to many other signal transduction proteins

Structure and dynamics of Pseudomonas aeruginosa ICP

Pseudomonas aeruginosa inhibitor of cysteine peptidases (PA-ICP) is a potent protein inhibitor of papain-like cysteine peptidases (CPs) identified in Pseudomonas aeruginosa, an opportunistic pathogenic bacteria that can cause severe infections in human. It belongs to the newly characterized natural CP inhibitors of the I42 family, designated the ICP family. The members of this family are present in some protozoa and bacterial pathogens. They can inhibit both parasite and mammalian CPs with high affinity and specificity. Whether the main biological function of the proteins in the pathogens is to regulate the hydrolytic activity of the organisms’ endogenous CPs or exogenous CPs so as to facilitate the pathogens’ invasion or survival is still under investigation. Although Pseudomonas aeruginosa contains a CP inhibitor, no CP genes are found in its genome, suggesting that the targets of PA-ICP may be exogenous. This hypothesis is supported by the presence of a putative secretion signal peptide at the N-terminus of PA-ICP which may be involved in exporting the protein to target exogenous CPs. In order to shed light on the biological function and inhibitory specificity of PA-ICP, the structure and backbone dynamics of this protein were characterised using NMR spectroscopy. In this project, the inhibitory activity of PA-ICP to a range of mammalian model CPs was also studied. Like its previously studied homologs, PA-ICP adopts an immunoglobulin fold comprised of seven β-strands. Three highly conserved sequence motifs located in mobile loop regions form the CP binding site. The inhibitor exhibits higher affinity toward the mammalian CP cathepsin L than cathepsins H and B. Homology modelling of the PA-ICP-cathspin L interaction based on the crystal structure of the chgasin-cathpsin L complex shows that PA-ICP may inhibit the peptidases by blocking the enzyme’s active site and that the interactions between chagasin and CPs may be conserved in PA-ICP-peptidase complexes. The specificity of the inhibitors may be determined by the relative flexibility of the loops bearing the binding site motifs and the electrostatic properties of certain residues near the binding sites