Showing papers in "Journal of Molecular Biology in 2015"

TL;DR: The polyamines (PAs) spermidine, spermine, putrescine and cadaverine are an essential class of metabolites found throughout all kingdoms of life and their various intracellular functions are discussed.

TL;DR: Small heat shock proteins (sHsps) are virtually ubiquitous molecular chaperones that can prevent the irreversible aggregation of denaturing proteins and have evolved independently in metazoans, plants and fungi.

TL;DR: The number of antibody-antigen complexes has increased significantly, by 67% and 74% in the docking and affinity benchmarks, respectively, which now contain 230 and 179 entries.

TL;DR: The application to a single-domain antibody that targets the Alzheimer's Aβ peptide demonstrates that the CamSol method predicts with great accuracy solubility changes upon mutation, thus offering a cost-effective strategy to help the production of soluble proteins for academic and industrial purposes.

TL;DR: A theme of the review is the under-appreciated role of basic thermodynamic principles in MP folding and assembly, which not only dictates the final folded structure but also is the driving force for the evolution of the ribosome-translocon system of assembly.

TL;DR: It is found that circularization of exons is widespread and correlates with exon skipping, a feature that adds considerably to the regulatory complexity of the human transcriptome.

TL;DR: Current understanding of how Hsp70 molecular chaperones recognize and act on their substrates and the relationships between these fundamental processes and the functional roles played by these molecular machines are discussed.

TL;DR: Computational, structural, and functional studies now indicate that biological ion channels may also exploit hydrophobic gating to regulate ion flow within their pores.

TL;DR: New advanced in vitro models developed with knowledge about the chemical landscape at infectious sites are needed to address the need for novel anti-biofilm treatment strategies.

TL;DR: The development of reagents and methods used for BiFC-based screens in yeast, plants, and mammalian cells are described and novel protein interactions are uncovered, providing new insight into protein functions.

TL;DR: A systematic review of the most widely used in vitro biofilm systems is presented, and it is discussed why they are not always representative of the in vivo biofilms found in chronic infections.

TL;DR: Regulated protein aggregation serves cytoprotective functions vital for the maintenance of cell integrity and survival even under adverse stress conditions and during aging.

TL;DR: It is suggested that perinuclear actin and basolateral microtubule organization exerts mechanical control on nuclear morphology and chromatin dynamics.

TL;DR: The current understanding of the ATPase cycle of BiP in the unique environment of the ER is reviewed and how it is regulated by the nucleotide exchange factors, Grp170 (glucose-regulated protein of 170kDa) and Sil1, both of which perform unanticipated roles in various biological functions and disease states are reviewed.

TL;DR: This model of the TJ architecture provides a basis to discuss structural mechanisms underlying the selective ion permeability and barrier properties of TJs and proposes that extracellular variable regions are responsible for head-to-head interactions of TJ strands in adjoining cells, thus resulting in the formation of paracellular channels.

TL;DR: Key aspects of chaperonin function and how their unique properties underlie their contribution to maintaining cellular proteostasis are beginning to shed light.

TL;DR: Current knowledge on the structure of RyRs at high and low resolutions, their relationship to IP 3 Rs, an overview of the most commonly studied regulatory mechanisms, and models that relate disease-causing mutations to altered channel function are outlined.

TL;DR: This review examines the redox-regulated mechanisms by which cells maintain a functional proteome during oxidative stress and concludes with recent evidence showing that inorganic polyphosphate, whose accumulation significantly increases bacterial oxidative stress resistance, works by a protein-like chaperone mechanism.

TL;DR: The TOC receptor systems have diversified to recognize distinct sets of preproteins, thereby maximizing the efficiency of targeting in response to changes in gene expression during developmental and physiological events that impact organelle function.

TL;DR: This review will highlight fundamental insights into toxin-channel interactions and recently developed toxin screening methods and practical applications of engineered toxins.

TL;DR: It is proposed that the mitochondrial/cytosolic components of the ERMES complex establish a direct interaction between mitochondria and peroxisomes through Pex11, a role that is essential for efficient fatty acid β-oxidation.

TL;DR: The main three-dimensional features of each chromatin type are described and finally their relationships with TAD organization and epigenetic memory are described.

TL;DR: In this review, the available data on matrix and membrane protein import into peroxisomes is discussed and the role the various import pathways play inperoxisome maintenance is discussed.

TL;DR: In this article, the authors examined the localization of interactions between proteins of the Hippo pathway (YAP/TAZ) and TGFβ (Smad2/3) signaling pathway by using in situ proximity ligation assays.

TL;DR: The TMEM16 family might have diverged in two or three different subclasses, channels, scramblases and dual-function channel/scramblases, and the structural bases and functional implication of such a functional diversity within a single protein family remain to be elucidated.

TL;DR: It is shown that flagellum-based motility, chemotaxis and oxygen sensing are important for successful competition during B. subtilis pellicle formation and fitness in competition assays in the Gram-negative Pseudomonas aeruginosa.

TL;DR: This study demonstrated the different distribution and properties of disease-causing SAVs and polymorphisms within different structural regions and in relation to the energetic contribution of amino acid in protein–protein interfaces, thus highlighting the importance of a structural system biology approach for predicting the effect of S AVs.

TL;DR: Current major open questions and unresolved issues in the mitochondrial biogenesis and protein translocation field are identified and discussed in hope that it will stimulate and engage the pursuit of current efforts and expose new directions.

TL;DR: The structural basis of sign epistasis between G238S and R164S, two adaptive mutations in TEM-1 β-lactamase, an enzyme that endows antibiotics resistance is described, which underlines the reshaping potential of protein's structures and functions but also limits protein evolvability because of the fragility of the interactions networks that maintain protein structures.

TL;DR: It is shown that the amino acid composition and length of the IDL affects the ssDNA binding mode preferences of SSB protein, and surprisingly, the number of IDLs and the lengths of individualIDLs together with the acidic tip contribute to highly cooperative binding in the (SSB)35 binding mode.