Showing papers in "Journal of Molecular Biology in 2006"

TL;DR: The development of a database of MoRFs derived from the RCSB Protein Data Bank is described and preliminary results of bioinformatics analyses of these sequences are presented, suggesting that functionally significant residual structure can exist in MoRF regions prior to the actual binding event.

TL;DR: The species barrier, as defined by the receptor specificity preferences of 1918 human viruses compared to likely avian virus progenitors, can be circumvented by changes at only two positions in the HA receptor binding site.

TL;DR: This approach could be used to engineer bacteria to sense the microenvironment of a tumor and respond by invading cancerous cells and releasing a cytotoxic agent.

TL;DR: It is demonstrated that L1 expression leads to a high level of double-strand break (DSB) formation in DNA using immunolocalization of gamma-H2AX foci and the COMET assay, the first characterization of a DNA repair response from expression of a non-long terminal repeat (non-LTR) retrotransposon in mammalian cells and the first demonstration that a host DNA repair gene is required for successful integration.

TL;DR: It is proposed that the loss of mature cardiolipin species in Barth Syndrome results in unstable respiratory chain supercomplexes, thereby affecting Complex I biogenesis, respiratory activities and subsequent pathology.

TL;DR: Aquaporin-4 contains a short 3(10) helix in an extracellular loop, which mediates weak but specific interactions between AQP4 molecules in adjoining membranes, which suggests a previously unexpected role for AQP 4 in cell adhesion.

TL;DR: A comprehensive analysis of the HAD superfamily is presented that identifies their unique structural features and provides a detailed classification of the entire superfamily and suggests that at the highest level the HADS is unified with several other superfamilies, namely the DHH, receiver, von Willebrand A, TOPRIM, classical histone deacetylases and PIN/FLAP nuclease domains.

TL;DR: Additional factors, including the interhelical contacts, the length, structure and flexibility of the linker connecting the EF-hand motifs, and the overall energy balance provide the fine-tuning of the Ca2+-induced conformational change in theEF-hand proteins.

TL;DR: A series of vectors for easy construction of N- terminal and C-terminal fusions of the target protein to the yellow spectral variant of the green fluorescent protein fragments are designed, demonstrating the utility of these vectors for the analysis of specific protein-protein interactions in various cellular compartments, including the nucleus, plasmodesmata, and chloroplasts of different plant species and cell types.

TL;DR: Observations confirm the suggestion that DJ-1 may act as an oxidative-stress-induced chaperone to prevent α-synuclein fibrillation and indicates that excess oxidative stress could also lead to enhanced α- synuclein aggregation and hence PD.

TL;DR: A comparison of the biochemical, structural and regulatory characteristics of the two mammalian AC families reveals the mechanisms underlying their different properties but also illustrates many unifying themes for these evolutionary related signaling enzymes.

TL;DR: It is shown that FA sites 2, 4 and 5 bind FA with high affinity, while sites 1, 3, 6 and 7 exhibit low affinity for FA, thus providing the first complete determination of relative affinities of all seven long-chain FA sites on HSA.

TL;DR: The geometry of the polypeptide exit tunnel has been determined using the crystal structure of the large ribosomal subunit from Haloarcula marismortui to determine the only passage in the solvent channel system that is both large enough to accommodate nascent peptides, and that traverses the particle.

TL;DR: In this article, the authors used the Galactose (gal) system of Escherichia coli to study the dynamics of the incoherent type-1 feed-forward loop (I1-FFL).

TL;DR: It is shown that a semi-rational approach can be used to derive hundreds of novel proteins from I-CreI, a homing endonuclease from the LAGLIDADG family, and rules for protein/DNA interaction can be inferred from statistical analysis.

TL;DR: It is shown that prokaryotic transcriptional regulatory networks have evolved principally through widespread tinkering of transcriptional interactions at the local level by embedding orthologous genes in different types of regulatory motifs, suggesting that organisms with similar lifestyles across a wide phylogenetic range tend to conserve equivalent interactions and network motifs.

TL;DR: The 2,6-diaminopurine-bound structure of a C74U mutant of the xpt-pbuX guanine riboswitch, along with a detailed thermodynamic and kinetic analysis of nucleobase recognition by both the native and mutant riboswitches, demonstrate clearly that the pyrimidine at position 74 is the sole determinant of purine Riboswitch specificity.

TL;DR: An integrated overview of the entire program of sporulation gene expression is presented, which is governed by the RNA polymerase sigma factors sigma(F) andSigma(G) and the DNA-binding proteins RsfA and SpoVT and the ykoV gene product, a homolog of the non-homologous end-joining protein Ku, is shown to associate with the nucleoid during germination.

TL;DR: Improved accuracy of the models clarifies the disagreement between NMR and X-ray studies of oxyHb, and reveals a hydrogen bond in both subunit types, but with subtly different geometry which may explain the very different behaviour when this residue is mutated to glycine in alpha or beta globin.

TL;DR: This work explored the transcriptional control of three major regulatory systems to understand specific aspects of their upstream control, and observed that ubiquitin E3 ligases are regulated primarily by unique transcription factors, whereas E1 and E2 enzymes share common transcription factors to a much greater extent.

TL;DR: Two methods of identifying which non-synonomous single base changes have a deleterious effect on protein function in vivo are developed, providing a set of possible contributors to human complex disease traits.

TL;DR: The accumulation of spheroidal oligomers of increasing size but unchanged vibrational spectra during the fibrilization process suggests that a cooperative conformational change may contribute to the kinetic control of fibrillization.

TL;DR: It is shown here that introduction of a P10 sequence C-terminal to polyGln in synthetic peptides decreases both the rate of formation and the apparent stability of the amyloid-like aggregates associated with Huntington's disease.

TL;DR: A rational case is presented for including mesophase-swelling additives in screens for in meso crystallogenesis, which will contribute to broadening the range of membrane proteins that yield to structure determination.

TL;DR: This work analyses the aggregation propensities of 28 complete proteomes using TANGO, a statistical mechanics algorithm to predict protein aggregation, and shows that chaperones achieve these requirements by preferentially binding hydrophobic sequences that are capped by positively charged gatekeeper residues.

TL;DR: The structure, equilibria, and folding kinetics of an engineered 35-residue subdomain of the chicken villin headpiece, an ultrafast-folding protein, are investigated and it is suggested that the increased stability is electrostatic in origin.

TL;DR: Surprisingly, optimal SPs in cutinase secretion were inefficient in esterase secretion and vice versa, indicating the importance of an optimal fit between the SP and the respective mature part of the desired secretion target proteins.

TL;DR: Findings add the sigmaE regulon to the growing list of stress induced regulatory circuits that include small regulatory RNAs and provide insight in a homeostatic loop that prevent a build-up of unassembled outer membrane proteins in the envelope.

TL;DR: Simulation results suggest that by simply increasing the relative stability of the beta-prone state of the polypeptide, disordered aggregation changes into fibrillogenesis with the presence of oligomeric on-pathway intermediates, and finally without intermediates in the case of a very stable beta- prone state.

TL;DR: It is concluded that integration systems derived from phiC31 integrase have great potential utility and an analysis of the safety of integration sites in terms of proximity to cancer genes suggested minimal cancer risk.