Structure and thermodynamics of Diol inclusion compounds

Includes bibliographical references.This work is predominantly concerned with the structural analysis of the coordinatoclathrates formed by the host compound trans-9,10-dihydroxy-9,10-diphenyl- 9,10-dihydroanthracene (1) with compounds containing neutral nitrogen atoms (Lewis bases). The structures of inclusion compounds with two nitriles (acetonitrile and 3- hydroxypropionitrile), with pyridine and with three substituted pyridines (3- methylpyridine, 2,4-dimethylpyridine and 2,6-dimethylpyridine) have been solved by single crystal X-ray diffraction methods. The crystal packing modes and hydrogen bonding schemes have been elucidated, while the guest cavities have been investigated. The thermal stability of the complexes was analysed by thermogravimetric analyses and differential scanning calorimetry. These techniques were employed in determining the guest content, in investigating the thermal properties of the compounds and in establishing the activation energies for the desorption processes. Desorption studies, utilising X-ray powder diffraction, were used to investigate the structures resulting from the desorption of guest from the complexes. The selectivity of the host for either of the isomers 2,4- and 2,6-dimethylpyridine was investigated

Seeing is believing

Have you ever wondered how something small like a virus or a bacterium can infect a person and cause anything from minor irritations such as a sore throat, to more severe symptoms like fever and measles, or even kill? Or have you marvelled at the elegant yet intricate double helix structure of DNA? How do we know that these things really exist or how they work? And how do we know what medicines to take to treat a particular disease? Thinking about or answering such questions was way beyond our reach until a few decades ago. Then came the discovery and refinement of crystallography in the first half of the 20th century and its application to biology from the 1950s onward. Slowly this opened our eyes to the wonders of the microcosm, showing us how biology works at the cellular, molecular and even atomic level. We live in a physical, three-dimensional world. We are born with two eyes and two ears set slightly apart. This allows us to perceive the world around us. We not only see the height and the width of any object but its depth too. This in turn allows us to understand how one thing relates to another – is it smaller, thicker, broader, behind or in front of another? Are boxes neatly stacked one on top of the other or are they randomly thrown onto a big heap?http://www.questinteractive.co.zaam201

Resistance related metabolic pathways for drug target identification in Mycobacterium tuberculosis

Criteria used to filter high priority M.tuberculosis drug targets. The genes highlighted in bold satisfied all the selection criteria. The hyphen (−) indicates exclusion from further analysis. Abbreviations used: NUI- Not under investigation, PDB- Protein Data Bank, TBSGC- TB Structural Genome Consortium. References 12-Sassetti et al., 2003; 34-Lamichhane et al., 2003. Data can be viewed in Microsoft excel. (XLS 12 kb

Structural and biophysical characterization of the multidomain xylanase Xyl

The depletion of fossil fuels, associated pollution, and resulting health hazards are of concern worldwide. Woody biomass constitutes an alternative source of cleaner and renewable energy. The efficient use of woody biomass depends on xylan depolymerisation as the endo-β-1,4-xylopyranosyl homopolymer is the main component of hemicellulose, the second most abundant component of wood. Xylan depolymerisation is achieved by hemicellulolytic xylanases of glycoside hydrolase (GH) families 5, 8, 10, 11, 30 and 43 of the CAZY database. We analysed a multidomain xylanase (Xyl) from the hindgut metagenome of the snouted harvester termite Trinervitermes trinervoides that releases xylobiose and xylotriose from beech and birch xylan and wheat arabinoxylan. The four domains of Xyl include an Nterminal GH11 xylanase domain, two family 36-like carbohydrate-binding domains CBM36- 1 and 2, and a C-terminal CE4 esterase domain. Previous analyses indicated that CBM36-1 deletion slightly increased GH11 catalysis at low pH whereas removal of both CBMs decreased xylanase activity at 60˚C from 90 to 56%. Possible cooperativity between the domains suggested by these observations was explored. A crystal structure of the twodomain construct, GH11-CBM36-1, confirmed the structure of the GH11 domain whereas the CBM36-1 domain lacked electron density, possibly indicating a random orientation of the CBM36-1 domain around the GH11 domain. Isothermal titration calorimetry (ITC) experiments similarly did not indicate specific interactions between the individual domains of Xyl supporting a “beads-on-a-string” model for Xyl domains.DATA AVAILABILITY STATEMENT : All PDB files are available from the https://www.rcsb.org/ database (accession numbers 7AX7, 7AY3, 7AYP, 7ZSZ).U.K. Global Challenge Research Fund Grant: START - Synchrotron Techniques for African Research and Technology (Science and Technology Facilities Council) and South African NRF grant.http://www.plosone.orgdm2022BiochemistryGeneticsMicrobiology and Plant Patholog

Extending the host range of Listeria monocytogenes by rational protein design

SummaryIn causing disease, pathogens outmaneuver host defenses through a dedicated arsenal of virulence determinants that specifically bind or modify individual host molecules. This dedication limits the intruder to a defined range of hosts. Newly emerging diseases mostly involve existing pathogens whose arsenal has been altered to allow them to infect previously inaccessible hosts. We have emulated this chance occurrence by extending the host range accessible to the human pathogen Listeria monocytogenes by the intestinal route to include the mouse. Analyzing the recognition complex of the listerial invasion protein InlA and its human receptor E-cadherin, we postulated and verified amino acid substitutions in InlA to increase its affinity for E-cadherin. Two single substitutions increase binding affinity by four orders of magnitude and extend binding specificity to include formerly incompatible murine E-cadherin. By rationally adapting a single protein, we thus create a versatile murine model of human listeriosis

Crystallization of Intact and Subunit L-Deficient Monomers from Synechocystis PCC 6803 Photosystem I

Photosystem I monomers from wildtype cells of Synechocystis PCC 6803 and from a mu­tant deficient in the psaL gene were crystallized. PsaL encodes for the hydrophobic subunit L, which has been proposed to constitute the trimerization domain in the PS I trimer. The absence of subunit L facilitated crystallization of the PS I monomer. The unit cell dimensions and the space group for the crystals from this preparation could be determined to be a = b = 132 Å , c -525 Å, α = β = 90°, y = 120°, the space group is P61 or P65. The results show the potential of using specifically designed deletion mutants of an integral membrane protein for the systematic improvement of crystal structure data

Molecular mechanism of protrusion formation during cell-to-cell spread of Listeria

The bacterial pathogen Listeria monocytogenes spreads within human tissues using a motility process dependent on the host actin cytoskeleton. Cell-to-cell spread involves the ability of motile bacteria to remodel the host plasma membrane into protrusions, which are internalized by neighboring cells. Recent results indicate that formation of Listeria protrusions in polarized human cells involves bacterial antagonism of a host signaling pathway comprised of the scaffolding protein Tuba and its effectors N-WASP and Cdc42. These three human proteins form a complex that generates tension at apical cell junctions. Listeria relieves this tension and facilitates protrusion formation by secreting a protein called InlC. InlC interacts with a Src Homology 3 (SH3) domain in Tuba, thereby displacing N-WASP from this domain. Interaction of InlC with Tuba is needed for efficient Listeria spread in cultured human cells and infected animals. Recent structural data has elucidated the mechanistic details of InlC/Tuba interaction, revealing that InlC and N-WASP compete for partly overlapping binding surfaces in the Tuba SH3 domain. InlC binds this domain with higher affinity than N-WASP, explaining how InlC is able to disrupt Tuba/N-WASP complexes.Grants from the National Institutes of Health (R01AI085072) and the Marsden Fund of the Royal Society of New Zealand (UOO1003), Medical Research Council of South Africa, the National Research Foundation of South Africa and previously by the Helmholtz Centre for Infection Research, Braunschweig, Germany.http://www.frontiersin.org/Cellular_and_Infection_Microbiologyhb201

Structural details of human tuba recruitment by InlC of Listeria monocytogenes elucidate bacterial cell-cell spreading

The human pathogen Listeria monocytogenes is able to directly spread to neighboring cells of host tissues, a process recently linked to the virulence factor InlC. InlC targets the sixth SH3 domain (SH3-6) of human Tuba, disrupting its physiological interaction with the cytoskeletal protein N-WASP. The resulting loss of cortical actin tension may slacken the junctional membrane, allowing protrusion formation by motile Listeria. Complexes of Tuba SH3-6 with physiological partners N-WASP and Mena reveal equivalent binding modes but distinct affinities. The interaction surface of the infection complex InlC/Tuba SH3-6 is centered on phenylalanine 146 of InlC stacking upon asparagine 1569 of Tuba. Replacing Phe146 by alanine largely abrogates molecular affinity and in vivo mimics deletion of inlC. Collectively, our findings indicate that InlC hijacks Tuba through its LRR domain, blocking the peptide binding groove to prevent recruitment of its physiological partners.Medical Research Council and the National Research Foundation of South Africa. National Institutes of Health (grant R01AI085072)http://www.journals.elsevier.com/structurehb201

Elucidation of repeat motifs R1- and R2-related TRIOBP variants in autosomal recessive nonsyndromic hearing loss DFNB28 among indigenous South African individuals

DATA AVAILABILITY STATEMENT : The data that support the findings of this study are available from the corresponding author upon reasonable request.BACKGROUND : DFNB28, a recessively inherited nonsyndromic form of deafness in humans, is caused by mutations in the TRIOBP gene (MIM #609761) on chromosome 22q13. Its protein TRIOBP helps to tightly bundle F-actin filaments, forming a rootlet that penetrates through the cuticular plate into the cochlear hair cell body. Repeat motifs R1 and R2, located in exon 7 of the TRIOBP-5 isoform, are the actin-binding domains. Deletion of both repeat motifs R1 and R2 results in complete disruption of both actin-binding and bundling activities, whereas deletion of the R2 motif alone retains F-actin bundling ability in stereocilia rootlets. METHODS : Target sequencing, using a custom capture panel of 180 known and candidate genes associated with sensorineural hearing loss, bioinformatics processing, and data analysis were performed. Genesis 2.0 was used for variant filtering based on quality/score read depth and minor allele frequency (MAF) thresholds of 0.005 for recessive NSHL, as reported in population-based sequencing databases. All variants were reclassified based on the American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) guidelines together with other variant interpretation guidelines for genetic hearing loss . Candidate variants were confirmed via Sanger sequencing according to standard protocols, using the ABIPRISM 3730 DNA Analyzer. DNA sequence analysis was performed with DNASTAR Lasergene software. RESULTS : Candidate TRIOBP variants identified among 94 indigenous sub-Saharan African individuals were characterized through segregation analysis. Family TS005 carrying variants c.572delC, p.Pro191Argfs*50, and c.3510_3513dupTGCA, p.Pro1172Cysfs*13, demonstrated perfect cosegregation with the deafness phenotype. On the other hand, variants c.505C > A p.Asp168Glu and c.3636 T > A p.Leu1212Gln in the same family did not segregate with deafness and we have classified these variants as benign. A control family, TS067, carrying variants c.2532G > T p.Leu844Arg, c.2590C > A p.Asn867Lys, c.3484C > T p.Pro1161Leu, and c.3621 T > C p.Phe1187Leu demonstrated no cosegregation allowing us to classify these variants as benign. Together with published TRIOBP variants, the results showed that genotypes combining two truncating TRIOBP variants affecting repeat motifs R1 and R2 or R2 alone lead to a deafness phenotype, while a truncating variant affecting repeat motifs R1 and R2 or R2 alone combined with a missense variant does not. Homozygous truncating variants affecting repeat motif R2 cosegregate with the deafness phenotype. CONCLUSION : While a single intact R1 motif may be adequate for actin-binding and bundling in the stereocilia of cochlear hair cells, our findings indicate that a truncated R2 motif in cis seems to be incompatible with normal hearing, either by interfering with the function of an intact R1 motif or through another as yet unknown mechanism. Our study also suggests that most heterozygous missense variants involving exon 7 are likely to be tolerated.Fulbright Senior Research Scholar Award; R01 DC05575 and R01 DC012115 National institutes of Health/ National Institute on Deafness and other Communication Disorders; South African Medical Research Council; University of Pretoria RDP Fund.http://www.wileyonlinelibrary.com/journal/mgg3hj2023BiochemistryGeneticsImmunologyMicrobiology and Plant PathologyOtorhinolaryngolog