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Trends in Biochemical Sciences

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December 1, 2016: Trends in Biochemical Sciences
Andrei N Lupas, Jens Bassler
α-Helical coiled coils were described more than 60 years ago as simple, repetitive structures mediating oligomerization and mechanical stability. Over the past 20 years, however, they have emerged as one of the most diverse protein folds in nature, enabling many biological functions beyond mechanical rigidity, such as membrane fusion, signal transduction, and solute transport. Despite this great diversity, their structures can be described by parametric equations, making them uniquely suited for rational protein design...
November 21, 2016: Trends in Biochemical Sciences
Richard S Jope, Yuyan Cheng, Jeffrey A Lowell, Ryan J Worthen, Yoel H Sitbon, Eleonore Beurel
Psychological stress has a pervasive influence on our lives. In many cases adapting to stress strengthens organisms, but chronic or severe stress is usually harmful. One surprising outcome of psychological stress is the activation of an inflammatory response that resembles inflammation caused by infection or trauma. Excessive psychological stress and the consequential inflammation in the brain can increase susceptibility to psychiatric diseases, such as depression, and impair learning and memory, including in some patients with cognitive deficits...
November 19, 2016: Trends in Biochemical Sciences
Cristina Azevedo, Adolfo Saiardi
Phosphate, as a cellular energy currency, essentially drives most biochemical reactions defining living organisms, and thus its homeostasis must be tightly regulated. Investigation into the role of inositol pyrophosphates (PP-IPs) has provided a novel perspective on the regulation of phosphate homeostasis. Recent data suggest that metabolic and signaling interplay between PP-IPs, ATP, and inorganic polyphosphate (polyP) influences and is influenced by cellular phosphate homeostasis. Different studies have demonstrated that the SPX protein domain is a key component of proteins involved in phosphate metabolism...
November 19, 2016: Trends in Biochemical Sciences
Reiner A Veitia
Recent analyses of the degradation profiles of thousands of proteins by McShane et al. have shown that many proteins are less stable during the hours following their synthesis. Many of such nonexponentially degraded (NED) proteins are components of macromolecular complexes. This may explain why, in cases of trisomy, the effect of overexpression can be attenuated.
November 14, 2016: Trends in Biochemical Sciences
Marcin Grabowicz, Thomas J Silhavy
The Escherichia coli cell envelope is a protective barrier at the frontline of interaction with the environment. Fidelity of envelope biogenesis must be monitored to establish and maintain a contiguous barrier. Indeed, the envelope must also be repaired and modified in response to environmental assaults. Envelope stress responses (ESRs) sense envelope damage or defects and alter the transcriptome to mitigate stress. Here, we review recent insights into the stress-sensing mechanisms of the σ(E) and Cpx systems and the interaction of these ESRs...
November 7, 2016: Trends in Biochemical Sciences
Karla K Rodgers
Development of the adaptive immune system is dependent on V(D)J recombination, which forms functional antigen receptor genes through rearrangement of component gene segments. The V(D)J recombinase, comprising recombination-activating proteins RAG1 and RAG2, guides the initial DNA cleavage events to the recombination signal sequence (RSS), which flanks each gene segment. Although the enzymatic steps for RAG-mediated endonucleolytic activity were established over two decades ago, only recently have high-resolution structural studies of the catalytically active core regions of the RAG proteins shed light on conformational requirements for the reaction...
November 5, 2016: Trends in Biochemical Sciences
Fiona H Marshall
A range of cutting-edge techniques have been employed to visualize 'megaplexes' consisting of a G protein-coupled receptor (GPCR) bound to β-arrestin in intracellular endosomes following agonist-induced internalization. Surprisingly, the complex includes simultaneous binding of the heterotrimeric G protein, which retains full functional activity and supports sustained signaling from within the cell.
November 4, 2016: Trends in Biochemical Sciences
Jennifer M Soll, Robert W Sobol, Nima Mosammaparast
Alkylation chemotherapy is one of the most widely used systemic therapies for cancer. While somewhat effective, clinical responses and toxicities of these agents are highly variable. A major contributing factor for this variability is the numerous distinct lesions that are created upon alkylation damage. These adducts activate multiple repair pathways. There is mounting evidence that the individual pathways function cooperatively, suggesting that coordinated regulation of alkylation repair is critical to prevent toxicity...
November 2, 2016: Trends in Biochemical Sciences
Erik A Rodriguez, Robert E Campbell, John Y Lin, Michael Z Lin, Atsushi Miyawaki, Amy E Palmer, Xiaokun Shu, Jin Zhang, Roger Y Tsien
Over the past 20 years, protein engineering has been extensively used to improve and modify the fundamental properties of fluorescent proteins (FPs) with the goal of adapting them for a fantastic range of applications. FPs have been modified by a combination of rational design, structure-based mutagenesis, and countless cycles of directed evolution (gene diversification followed by selection of clones with desired properties) that have collectively pushed the properties to photophysical and biochemical extremes...
November 1, 2016: Trends in Biochemical Sciences
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No abstract text is available yet for this article.
October 20, 2016: Trends in Biochemical Sciences
Manuela Antonioli, Martina Di Rienzo, Mauro Piacentini, Gian Maria Fimia
Autophagy is a major degradative process activated in a rapid and transient manner to cope with stress conditions. Whether autophagy is beneficial or detrimental depends upon the rate of induction and the appropriateness of the duration. Alterations in both autophagy initiation and termination predispose the cell to death, and affect the execution of other inducible processes such as inflammation. In this review we discuss how stress signaling pathways dynamically control the activity of the autophagy machinery by mediating post-translational modifications and regulatory protein interactions...
October 17, 2016: Trends in Biochemical Sciences
Toshifumi Inada
Accurate gene expression is a prerequisite for all cellular processes. Quality control machineries respond to errors during protein synthesis by refolding polypeptides or targeting them for degradation. As another layer of gene expression control, aberrant mRNAs can also be detected and eliminated by mRNA quality control systems while engaging the ribosome. In this review, I focus on recent studies on the cotranslational quality control mechanisms induced by abnormal translational elongation and termination, which result in the rapid degradation of aberrant polypeptides and mRNAs...
October 13, 2016: Trends in Biochemical Sciences
Jason Wu, Amanda H Lewis, Jörg Grandl
In 2010, two proteins, Piezo1 and Piezo2, were identified as the long-sought molecular carriers of an excitatory mechanically activated current found in many cells. This discovery has opened the floodgates for studying a vast number of mechanotransduction processes. Over the past 6 years, groundbreaking research has identified Piezos as ion channels that sense light touch, proprioception, and vascular blood flow, ruled out roles for Piezos in several other mechanotransduction processes, and revealed the basic structural and functional properties of the channel...
October 12, 2016: Trends in Biochemical Sciences
Germán Rivas, Allen P Minton
Biochemical processes take place in heterogeneous and highly volume-occupied or crowded environments that can considerably influence the reactivity and distribution of participating macromolecules. We summarize here the thermodynamic consequences of excluded-volume and long-range nonspecific intermolecular interactions for macromolecular reactions in volume-occupied media. In addition, we summarize and compare the information content of studies of crowding in vitro and in vivo. We emphasize the importance of characterizing the behavior not only of labeled tracer macromolecules but also the composition and behavior of unlabeled macromolecules in the immediate vicinity of the tracer...
September 23, 2016: Trends in Biochemical Sciences
Liliane Christ, Camilla Raiborg, Eva M Wenzel, Coen Campsteijn, Harald Stenmark
The endosomal sorting complex required for transport (ESCRT) machinery is an assembly of protein subcomplexes (ESCRT I-III) that cooperate with the ATPase VPS4 to mediate scission of membrane necks from the inside. The ESCRT machinery has evolved as a multipurpose toolbox for mediating receptor sorting, membrane remodeling, and membrane scission, with ESCRT-III as the major membrane-remodeling component. Cellular membrane scission processes mediated by ESCRT-III include biogenesis of multivesicular endosomes, budding of enveloped viruses, cytokinetic abscission, neuron pruning, plasma membrane wound repair, nuclear pore quality control, nuclear envelope reformation, and nuclear envelope repair...
September 23, 2016: Trends in Biochemical Sciences
Boran Kartal, Jan T Keltjens
Anaerobic ammonium-oxidizing (anammox) bacteria are one of the latest scientific discoveries in the biogeochemical nitrogen cycle. These microorganisms are able to oxidize ammonium (NH4(+)) with nitrite (NO2(-)) as the oxidant instead of oxygen and form dinitrogen (N2) as the end product. Recent research has shed a light on the biochemistry underlying anammox metabolism with two key intermediates, nitric oxide (NO) and hydrazine (N2H4). Substrates and intermediates are converted exploiting the catalytic and electron-transfer potentials of c-type heme proteins known from numerous biochemical reactions and that have acquired new functionality in anammox biochemistry...
September 23, 2016: Trends in Biochemical Sciences
Oleg Laptenko, David R Tong, James Manfredi, Carol Prives
The p53 tumor suppressor is a transcription factor (TF) that exerts antitumor functions through its ability to regulate the expression of multiple genes. Within the p53 protein resides a relatively short unstructured C-terminal domain (CTD) that remarkably participates in virtually every aspect of p53 performance as a TF. Because these aspects are often interdependent and it is not always possible to dissect them experimentally, there has been a great deal of controversy about the CTD. In this review we evaluate the significance and key features of this interesting region of p53 and its impact on the many aspects of p53 function in light of previous and more recent findings...
September 23, 2016: Trends in Biochemical Sciences
Shu-Ou Shan
The GTPase superfamily of proteins provides molecular switches to regulate numerous cellular processes. The 'GTPase switch' paradigm, in which external regulatory factors control the switch of a GTPase between 'on' and 'off' states, has been used to interpret the regulatory mechanism of many GTPases. However, recent work unveiled a class of nucleotide hydrolases that do not adhere to this classical paradigm. Instead, they use nucleotide-dependent dimerization cycles to regulate key cellular processes. In this review article, recent studies of dimeric GTPases and ATPases involved in intracellular protein targeting are summarized...
September 19, 2016: Trends in Biochemical Sciences
Michael L Tress, Federico Abascal, Alfonso Valencia
Alternative splicing is commonly believed to be a major source of cellular protein diversity. However, although many thousands of alternatively spliced transcripts are routinely detected in RNA-seq studies, reliable large-scale mass spectrometry-based proteomics analyses identify only a small fraction of annotated alternative isoforms. The clearest finding from proteomics experiments is that most human genes have a single main protein isoform, while those alternative isoforms that are identified tend to be the most biologically plausible: those with the most cross-species conservation and those that do not compromise functional domains...
September 16, 2016: Trends in Biochemical Sciences
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