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Trends in Biochemical Sciences

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https://www.readbyqxmd.com/read/28096055/an-ancient-family-of-rna-binding-proteins-still-important
#1
REVIEW
Melissa L Wells, Lalith Perera, Perry J Blackshear
RNA-binding proteins are important modulators of mRNA stability, a crucial process that determines the ultimate cellular levels of mRNAs and their encoded proteins. The tristetraprolin (TTP) family of RNA-binding proteins appeared early in the evolution of eukaryotes, and has persisted in modern eukaryotes. The domain structures and biochemical functions of family members from widely divergent lineages are remarkably similar, but their mRNA 'targets' can be very different, even in closely related species. Recent gene knockout studies in species as distantly related as plants, flies, yeasts, and mice have demonstrated crucial roles for these proteins in a wide variety of physiological processes...
January 14, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28089412/whaddaya-know-a-guide-to-uncertainty-and-subjectivity-in-structural-biology
#2
REVIEW
Joel P Mackay, Michael J Landsberg, Andrew E Whitten, Charles S Bond
The methods of structural biology, while powerful, are technically complex. Although the Protein Data Bank (PDB) provides a repository that allows anyone to download any structure, many users would not appreciate the caveats that should be considered when examining a structure. Here, we describe several key uncertainties associated with the application of X-ray crystallography, NMR spectroscopy, single-particle electron microscopy (SPEM), and small-angle scattering (SAS) to biological macromolecules. The take-home message is that structures are not absolute truths - they are models that fit the experimental data and therefore have uncertainty and subjectivity associated with them...
January 11, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28063638/functional-dissection-of-the-m6a-rna-modification
#3
Brooke Huisman, Gabriel Manske, Stephen Carney, Sundeep Kalantry
No abstract text is available yet for this article.
January 4, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/27986367/translating-the-sugar-code-into-immune-and-vascular-signaling-programs
#4
REVIEW
Juan P Cerliani, Ada G Blidner, Marta A Toscano, Diego O Croci, Gabriel A Rabinovich
The vast range and complexity of glycan structures and their dynamic variations in health and disease have presented formidable challenges toward understanding the biological significance of these molecules. Despite these limitations, compelling evidence highlights a major role for galectins, a family of soluble glycan-binding proteins, as endogenous decoders that translate glycan-containing information into a broad spectrum of cellular responses by modulating receptor clustering, reorganization, endocytosis, and signaling...
December 13, 2016: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/27956059/speed-limits-for-nonvesicular-intracellular-sterol-transport
#5
REVIEW
Jeremy S Dittman, Anant K Menon
Sterol transport between the endoplasmic reticulum (ER) and plasma membrane (PM) occurs by nonvesicular mechanisms requiring sterol transport proteins (STPs). Here we examine the idea that transport is enhanced at membrane contact sites where the ER is closely apposed to the PM. We conclude that sterol desorption from the membrane, rather than STP-mediated diffusion, is rate limiting in the cellular context, so there is no apparent kinetic benefit to having STP-mediated sterol transfer occur at contact sites...
December 9, 2016: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/27932073/pyroptosis-gasdermin-mediated-programmed-necrotic-cell-death
#6
REVIEW
Jianjin Shi, Wenqing Gao, Feng Shao
Pyroptosis was long regarded as caspase-1-mediated monocyte death in response to certain bacterial insults. Caspase-1 is activated upon various infectious and immunological challenges through different inflammasomes. The discovery of caspase-11/4/5 function in sensing intracellular lipopolysaccharide expands the spectrum of pyroptosis mediators and also reveals that pyroptosis is not cell type specific. Recent studies identified the pyroptosis executioner, gasdermin D (GSDMD), a substrate of both caspase-1 and caspase-11/4/5...
December 5, 2016: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/27932072/a-case-for-sec61-channel-involvement-in-erad
#7
REVIEW
Karin Römisch
Proteins that misfold in the endoplasmic reticulum (ER) need to be transported back to the cytosol for degradation by proteasomes, a process known as ER-associated degradation (ERAD). The first candidate discussed as a retrograde protein transport conduit was the Sec61 channel which is responsible for secretory protein transport into the ER during biogenesis. The Sec61 channel binds the proteasome 19S regulatory particle which can extract an ERAD substrate from the ER. Nevertheless its role as a general export channel has been dismissed, and Hrd1 and Der1 have been proposed as alternatives...
December 5, 2016: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/27884598/coiled-coils-a-model-system-for-the-21st-century
#8
REVIEW
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
https://www.readbyqxmd.com/read/27876551/stressed-and-inflamed-can-gsk3-be-blamed
#9
REVIEW
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
https://www.readbyqxmd.com/read/27876550/eukaryotic-phosphate-homeostasis-the-inositol-pyrophosphate-perspective
#10
REVIEW
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
https://www.readbyqxmd.com/read/27856135/a-fresh-look-at-aging-proteins
#11
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
https://www.readbyqxmd.com/read/27839654/envelope-stress-responses-an-interconnected-safety-net
#12
REVIEW
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
https://www.readbyqxmd.com/read/27825513/visualizing-gpcr-megaplexes-which-enable-sustained-intracellular-signaling
#13
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
https://www.readbyqxmd.com/read/27816326/regulation-of-dna-alkylation-damage-repair-lessons-and-therapeutic-opportunities
#14
REVIEW
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
https://www.readbyqxmd.com/read/27814948/the-growing-and-glowing-toolbox-of-fluorescent-and-photoactive-proteins
#15
REVIEW
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
https://www.readbyqxmd.com/read/28029518/a-new-view-into-the-regulation-of-purine-metabolism-the-purinosome
#16
REVIEW
Anthony M Pedley, Stephen J Benkovic
Other than serving as building blocks for DNA and RNA, purine metabolites provide a cell with the necessary energy and cofactors to promote cell survival and proliferation. A renewed interest in how purine metabolism may fuel cancer progression has uncovered a new perspective into how a cell regulates purine need. Under cellular conditions of high purine demand, the de novo purine biosynthetic enzymes cluster near mitochondria and microtubules to form dynamic multienzyme complexes referred to as 'purinosomes'...
October 28, 2016: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/27955862/liquid-phase-transition-in-the-postsynaptic-density
#17
Mary B Kennedy, Tara L Mastro
No abstract text is available yet for this article.
January 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/27916448/getting-in-touch-with-j%C3%A3-rg-grandl
#18
(no author information available yet)
No abstract text is available yet for this article.
January 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/27825771/riches-in-rags-revealing-the-v-d-j-recombinase-through-high-resolution-structures
#19
REVIEW
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...
January 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/27765496/emerging-mechanisms-in-initiating-and-terminating-autophagy
#20
REVIEW
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...
January 2017: Trends in Biochemical Sciences
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