Showing papers in "Journal of Molecular Biology in 2014"

TL;DR: The current knowledge of the roles TLRs play in antiviral innate immune responses is reviewed, examples of TLR-mediated viral recognition are discussed, and strategies used by viruses to antagonize the host antiviral inherent immune responses are described.

TL;DR: A global framework needs to be developed to better understand how dietary fibers can be used to obtain predicted changes in microbiota composition for improved health and this will require a multi-disciplinary effort that includes biological scientists, clinicians, and carbohydrate specialists.

TL;DR: Recent findings on TRIM antiviral functions, current limitations and an outlook for future research are reviewed.

TL;DR: The crystal structure of the reconstituted covalent complex of SpyTag and SpyCatcher is determined and insight into split protein β-strand complementation is given and a distinct approach to ultrastable molecular interaction is enhanced.

TL;DR: Comparisons of the effects of BAL27862 and colchicine on the microtubule mitotic spindle and in tubulin protease-protection experiments suggest different outcomes of tubulin binding.

TL;DR: The current understanding of APOBEC3 structure, editing and non-editing mechanisms of AP OBEC3-mediated restriction, Vif-APOBec3 interactions that trigger APOB EC3 degradation, and the contribution of APobEC3 proteins to restriction and control of HIV-1 replication in infected patients are reviewed.

TL;DR: This work has developed a method, SuSPect (Disease-Susceptibility-based SAV Phenotype Prediction), for predicting how likely SAVs are to be associated with disease, which performs significantly better than other available batch methods on the VariBench benchmarking dataset.

TL;DR: Despite the rapid expansion of knowledge regarding the functions of this highly conserved and ancient antiviral protein, there still remains large gaps in understanding of the precise mechanisms at play for viperin to exert such a wide variety of roles within the cell.

TL;DR: The host innate immune response to DENV and the mechanisms of immune evasion that DENV has developed to manipulate cellular antiviral responses are discussed.

TL;DR: A slow, rate-limiting step is revealed along the unfolding pathway of unimolecular quadruplex formation in sequence analogs of human telomeric DNA.

TL;DR: It is posited that numerous, subtle variations in polysaccharides diversify the spectrum of available nutrient niches, each of which may be best filled by a subset of microorganisms that possess the corresponding proteins to recognize and degrade different carbohydrates.

TL;DR: This work focuses on the new areas of metabolic pathway construction and optimization, biocomputing, heterologous expression and multiplexed assembly techniques, and the advantages and disadvantages of each type as they are applied in genome engineering and synthetic biology.

TL;DR: Comparison of the structures of asialylated Fc, sialylation Fc and F241A Fc suggests that increased conformational flexibility of the CH2 domain is associated with the switch from pro-inflammatory to anti-inflammatory activity of the Fc.

TL;DR: Understanding how environmental factors recruit the epigenetic machinery in animal models reveals new insight into disease mechanisms in humans.

TL;DR: These findings underscore commonalities between BacNaVs and eukaryotic voltage-gated channels and provide a framework for understanding gating and ion permeation in this superfamily.

TL;DR: A biochemical analysis identifies key residues in the active site, an inhibitory role for the CTR, and distinct structural features of the CTR that mediate binding and inhibition of the SIRT1 catalytic domain.

TL;DR: The presence of viruses in blood suggests that virome members can traverse mucosal barriers, as indeed these communities are substantially altered when mucosal defenses are weakened, and the extent to which they can carry gene functions involved in the pathogenesis of their hosts, particularly antibiotic resistance is shown.

TL;DR: To probe the dynamics of RPA-DNA interactions, ensemble and single-molecule fluorescence approaches are combined to examine human RPA (hRPA) diffusion along ssDNA and find that an hRPA heterotrimer can diffuse rapidly along ss DNA.

TL;DR: A simple binary but atomic-level hydrophobicity scale that allows for the classification of polar and non-polar moieties within single residues, including backbone atoms, is introduced.

TL;DR: The data indicate that the inhibitory effects of O-GlcNAc on tau aggregation may result from enhanced monomer solubility or the destabilization of fibrils or soluble aggregates, rather than by altering the conformational properties of the monomeric protein.

TL;DR: A protocol for the efficient in vitro assembly of CCMV VLPs is established and potential strategies that the virus may employ in vivo are suggested.

TL;DR: It is demonstrated that EZH2 is transcriptionally regulated by estradiol in vitro and in vivo, and its expression is potentially dysregulated upon exposure to estrogenic EDCs.

TL;DR: Strategies to exploit miRNAs therapeutically for curbing HIV-1 infectivity, replication and latency are suggested since they hold an untapped potential that deserves further investigation.

TL;DR: Four p97 inhibitors have differential responses to Walker A and B mutations, to disease-causing IBMPFD mutations, and to the presence of the N domain binding cofactor protein p47, providing the first evidence that p97 cofactors and disease mutations can alter p97 inhibitor potency.

TL;DR: Advances in another field, engineering of microbial communities for wastewater treatment bioreactors, could inspire development of mechanistic mathematical models of the gut microbiota, and how the integration of microbiome shotgun sequencing and metabolic modeling approaches may fulfill the promise of a mechanistic model.

TL;DR: It is demonstrated that, next to direct contributions from the interface, the non-interacting surface (NIS) also plays an important role in binding affinity, especially polar and charged residues, indicating an evolutionary selection pressure.

TL;DR: The results show that new enzymatic functions could evolve rapidly from the current diversity of enzymes and range of promiscuous activities, and support the idea that the highly distinct reactions in the MBL superfamily could have evolved from a common ancestor traversing a continuous network via promiscuously enzymes.

TL;DR: The results demonstrate the value of selecting from the diversity of BMC shell building blocks found in genomic sequence data for the construction of novel compartments and the use of these remarkably homogeneous shells for applications such as three-dimensional scaffolding and the construction

TL;DR: High-resolution crystal structures of human recombinant and serum-derived IgG4-Fc reveal conformational variability at the CH3–CH3 interface that may promote Fab-arm exchange, and a unique conformation for the FG loop in the CH2 domain that would explain the poor FcγRII, F cγRIII and C1q binding properties of IgG 4 compared with IgG1 and -3.

TL;DR: A key challenge for future research is to identify the molecular interaction between specific bacterial effectors and animal receptors, as well as to determine how these interactions translate into microbiota-dependent signaling, metabolism, and immune function in the host.