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Journal of Molecular Biology

Ananda Ayyappan Jaguva Vasudevan, Henning Hofmann, Dieter Willbold, Dieter Häussinger, Bernd W Koenig, Carsten Münk
The retroviral restriction factors of the APOBEC3 (A3) cytidine deaminase family catalyze the deamination of cytidines in single-stranded viral DNA. APOBEC3C (A3C) is a strong antiviral factor against viral infectivity factor (vif)-deficient simian immunodeficiency (SIV) Δvif, however, a weak inhibitor against human immunodeficiency virus (HIV)-1 for reasons unknown. The precise link between the antiretroviral effect of A3C and its catalytic activity is incompletely understood. Here we show that the S61P mutation in human A3C (A3C...
March 15, 2017: Journal of Molecular Biology
Andreas Postlmayr, Anton Wutz
Animal development entails the sequential and coordinated specialisation of cells. During cell differentiation transcription factors, cell signalling pathways and chromatin associated protein complexes cooperate in regulating the expression of a large number of genes. Here we review the present understanding of the establishment of chromatin states by focusing on X chromosome inactivation (XCI) as a model for facultative heterochromatin formation in female embryonic cells. The inactive X chromosome (Xi) is large enough to be investigated by biochenical and microscopy techniques...
March 15, 2017: Journal of Molecular Biology
Heike Rampelt, Maria Bohnert, Ralf M Zerbes, Susanne E Horvath, Bettina Warscheid, Nikolaus Pfanner, Martin van der Laan
The mitochondrial contact site and cristae organizing system (MICOS) is crucial for maintaining the architecture of the mitochondrial inner membrane. MICOS is enriched at crista junctions that connect the two inner membrane domains: inner boundary membrane and cristae membrane. MICOS promotes the formation of crista junctions, whereas the oligomeric F1Fo-ATP synthase is crucial for shaping cristae rims, indicating antagonistic functions of these machineries in organizing inner membrane architecture. We report that the MICOS core subunit Mic10, but not Mic60, binds to the F1Fo-ATP synthase...
March 14, 2017: Journal of Molecular Biology
Michael G Rossmann
No abstract text is available yet for this article.
March 14, 2017: Journal of Molecular Biology
Christiane S Heilingloh, Stefan Klingl, Claudia Egerer-Sieber, Benedikt Schmid, Sigrid Weiler, Petra Mühl-Zürbes, Jörg Hofmann, Joachim D Stump, Heinrich Sticht, Mirko Kummer, Alexander Steinkasserer, Yves A Muller
CD83 is a type-I membrane protein and an efficient marker for identifying mature dendritic cells. Whereas membrane-bound full-length CD83 co-stimulates the immune system, a soluble variant (sCD83), consisting of the extracellular domain, only, displays strong immune-suppressive activities. Besides a prediction that sCD83 adopts a V-set Ig-like fold, however, little is known about the molecular architecture of CD83 and the mechanism by which CD83 exerts is function on dendritic cells and additional immune cells...
March 14, 2017: Journal of Molecular Biology
Greg M Findlay, Laurent David, Tobias A Beyer
No abstract text is available yet for this article.
March 13, 2017: Journal of Molecular Biology
Anna K Lee, Patrick Ryan Potts
Melanoma antigen (MAGE) genes are conserved in all eukaryotes and encode for proteins sharing a common MAGE homology domain. Although only a single MAGE gene exists in lower eukaryotes, the MAGE family rapidly expanded in eutherians and consists of more than 50 highly conserved genes in humans. A subset of MAGEs initially garnered interest as cancer biomarkers and immunotherapeutic targets due to their antigenic properties and unique expression pattern that is primary restricted to germ cells and aberrantly re-activated in various cancers...
March 11, 2017: Journal of Molecular Biology
Dan Zhao, Yuanyuan Li, Xiaozhe Xiong, Zhonglei Chen, Haitao Li
Histone post-translational modifications (PTMs) carry an epigenetic layer of message to regulate diverse cellular processes at the chromatin level. Many of these PTMs are selectively recognized by dedicated effector proteins for normal cell growth and development, while dysregulation of these recognition events is often implicated in human diseases, notably cancer. Thus, it is fundamentally important to elucidate the regulatory mechanism(s) underlying readout of PTMs on histones. The YEATS domain is an emerging reader module that selectively recognizes histone lysine acylation with a preference for crotonylation over acetylation...
March 11, 2017: Journal of Molecular Biology
Edurne Rujas, Sara Insausti, Miguel García-Porras, Rubén Sánchez-Eugenia, Kouhei Tsumoto, José L Nieva, Jose M M Caaveiro
The exceptional breadth of broadly neutralizing antibodies (bNAbs) against the membrane-proximal external region (MPER) of the transmembrane protein gp41 makes this class of antibodies an ideal model to design HIV vaccines. From a practical point of view, however, the preparation of vaccines eliciting bNAbs is still a major roadblock that limits their clinical application. Fresh mechanistic insights are necessary to develop more effective strategies. In particular, the function of the unusually long complementary determining region three of the heavy chain (CDRH3) of 4E10, an anti-MPER bNAb, is an open question that fascinates researchers in the field...
March 11, 2017: Journal of Molecular Biology
Marie D Harton, Eric Batchelor
Stochastic fluctuations, termed "noise," in the level of biological molecules can greatly impact cellular functions. While biological noise can sometimes be detrimental, recent studies have provided an increasing number of examples in which biological noise can be functionally beneficial. Rather than provide an exhaustive review of the growing literature in this field, in this review we focus on single cell studies based on quantitative microscopy that have generated a deeper understanding of the sources, characteristics, limitations, and benefits of biological noise...
March 10, 2017: Journal of Molecular Biology
David J E Callaway, Tsutomu Matsui, Thomas Weiss, Laura R Stingaciu, Christopher B Stanley, William T Heller, Zimei Bu
The phosphorylation of specific residues in a flexible disordered activation loop yields precise control of signal transduction. One paradigm is the phosphorylation of S339/S340 in the intrinsically disordered tail of the multi-domain scaffolding protein NHERF1, which affects the intracellular localization and trafficking of NHERF1 assembled signaling complexes. Using neutron spin echo spectroscopy (NSE), we show salt-concentration-dependent excitation of nanoscale motion at the tip of the C-terminal tail in the phosphomimic S339D/S340D mutant...
March 8, 2017: Journal of Molecular Biology
Martina Rangl, Luca Rima, Jessica Klement, Atsushi Miyagi, Sandro Keller, Simon Scheuring
Phospholipases are abundant in various types of cells and compartments, where they play key roles in physiological processes as diverse as digestion, cell proliferation, and neural activation. In Gram-negative bacteria, outer membrane phospholipase A (OmpLA) is involved in outer-membrane lipid homeostasis and bacterial virulence. Although the enzymatic activity of OmpLA can be probed with an assay relying on an artificial monoacyl thioester substrate, only little is known about its activity on diacyl phospholipids...
March 7, 2017: Journal of Molecular Biology
Thomas Steinbrecher, Robert Abel, Anthony Clark, Richard Friesner
Protein side-chain mutation is fundamental both to natural evolutionary processes and to the engineering of protein therapeutics, which constitute an increasing fraction of important medications. Molecular simulation enables the prediction of the effects of mutation on properties such as binding affinity, secondary and tertiary structure, conformational dynamics, and thermal stability. A number of widely differing approaches have been applied to these predictions, including sequence-based algorithms, knowledge-based potential functions, and all-atom molecular mechanics calculations...
March 6, 2017: Journal of Molecular Biology
Samantha S Stadmiller, Annelise H Gorensek-Benitez, Alex J Guseman, Gary J Pielak
Many organisms can adapt to changes in the solute content of their surroundings (i.e., the osmolarity). Hyperosmotic shock causes water efflux and a concomitant reduction in cell volume, which is countered by the accumulation of osmolytes. This volume reduction increases the crowded nature of the cytoplasm, which is expected to affect protein stability. In contrast to traditional theory, which predicts that more crowded conditions can only increase protein stability, recent work shows that crowding can destabilize proteins through transient attractive interactions...
March 2, 2017: Journal of Molecular Biology
Eun A Kim, Joseph Panushka, Trevor Meyer, Ryan Carlisle, Samantha Baker, Nicholas Ide, Michael Lynch, Brian R Crane, David F Blair
Structural models of the complex that regulates the direction of flagellar rotation assume either ~34 or ~25 copies of the protein FliG. Support for ~34 came from cross-linking experiments identifying an inter-subunit contact most consistent with that number; support for ~25 came from the observation that flagella can assemble and rotate when FliG is genetically fused to FliF, for which the accepted number is ~25. Here, we have undertaken cross-linking and other experiments to address more fully the question of FliG number...
March 1, 2017: Journal of Molecular Biology
Kristen M Ramsey, Holly E Dembinski, Wei Chen, Clarisse G Ricci, Elizabeth A Komives
We recently discovered that IκBα enhances the rate of release of nuclear factor kappa B (NFκB) from DNA target sites in a process we have termed molecular stripping. Coarse-grained molecular dynamics simulations of the stripping pathway revealed two mechanisms for the enhanced release rate: the negatively charged PEST region of IκBα electrostatically repels the DNA, and the binding of IκBα appears to twist the NFκB heterodimer so that the DNA can no longer bind. Here, we report amide hydrogen/deuterium exchange data that reveal long-range allosteric changes in the NFκB (RelA-p50) heterodimer induced by DNA or IκBα binding...
February 27, 2017: Journal of Molecular Biology
Jordan Blondelle, Paige Shapiro, Andrea A Domenighetti, Stephan Lange
The role of cullin E3-ubiquitin ligases for muscle homeostasis is best known during muscle atrophy, as the cullin-1 substrate adaptor atrogin-1 is among the most well-characterized muscle atrogins. We investigated whether cullin activity was also crucial during terminal myoblast differentiation and aggregation of acetylcholine receptors for the establishment of neuromuscular junctions in vitro. The activity of cullin E3-ligases is modulated through post-translational modification with the small ubiquitin-like modifier nedd8...
February 24, 2017: Journal of Molecular Biology
Binyuan Zhai, Kevin DuPrez, Tzanko I Doukov, Huan Li, Mengting Huang, Guijun Shang, Jinfeng Ni, Lichuan Gu, Yulong Shen, Li Fan
Holliday junction (HJ) is a hallmark intermediate in DNA recombination and must be processed by dissolution (for double HJ) or resolution to ensure genome stability. Although HJ resolvases have been identified in all domains of life, there is a long-standing effort to search in prokaryotes and eukarya for proteins promoting HJ migration. Here, we report the structural and functional characterization of a novel ATPase, Sulfolobus islandicusPilT N-terminal-domain-containing ATPase (SisPINA), encoded by the gene adjacent to the resolvase Hjc coding gene...
February 24, 2017: Journal of Molecular Biology
Silva Lilleorg, Kaspar Reier, Jaanus Remme, Aivar Liiv
In bacteria, ribosomal subunits are connected via 12 intersubunit bridges involving RNA-RNA, RNA-protein and protein-protein interactions. The only protein-protein bridge in the ribosome is B1b, which is mainly formed by the bacterial protein L31 (bL31) and connects the head domain of 30S subunit and the central protuberance of the 50S subunit. It is known to be the most dynamic intersubunit bridge. Here, we have evaluated the role of bL31 and thereby the bridge B1b in the working cycle of the ribosome. First, bL31 deficient ribosomes are severely compromised in their ability to ensure translational fidelity in particular reading frame maintenance in vivo...
February 23, 2017: Journal of Molecular Biology
Jiawen Chen, Yinghao Wu
Intercellular contacts in multicellular organisms are maintained by membrane receptors called cell adhesion molecules (CAMs), which are expressed on cell surfaces. One interesting feature of CAMs is that almost all of their extracellular regions contain repeating copies of structural domains. It is not clear why so many extracellular domains need to be evolved through natural selection. We tackled this problem by computational modeling. A generic model of CAMs was constructed based on the domain organization of neuronal CAM, which is engaged in maintaining neuron-neuron adhesion in central nervous system...
February 22, 2017: Journal of Molecular Biology
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