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Trends in Biochemical Sciences

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https://www.readbyqxmd.com/read/28202332/cdc20-at-the-crossroads-between-chromosome-segregation-and-mitotic-exit
#1
REVIEW
Maria Kapanidou, Natalie L Curtis, Victor M Bolanos-Garcia
Cell-division cycle protein 20 homologue (Cdc20) has important functions in chromosome segregation and mitotic exit. Cdc20 is the target of the spindle assembly checkpoint (SAC) and a key cofactor of the anaphase-promoting complex or cyclosome (APC/C) E3 ubiquitin ligase, thus regulating APC/C ubiquitin activity on specific substrates for their subsequent degradation by the proteasome. Here we discuss the roles of Cdc20 in SAC signalling and mitotic exit, describe how the integration of traditional approaches with emerging technologies has revealed new details of Cdc20 functions, comment about the potential of Cdc20 as a therapeutic target for the treatment of human malignancies, and discuss recent advances and controversies in the mechanistic understanding of the control of chromosome segregation during cell division...
February 12, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28196646/metabolomics-a-primer
#2
REVIEW
Xiaojing Liu, Jason W Locasale
Metabolomics generates a profile of small molecules that are derived from cellular metabolism and can directly reflect the outcome of complex networks of biochemical reactions, thus providing insights into multiple aspects of cellular physiology. Technological advances have enabled rapid and increasingly expansive data acquisition with samples as small as single cells; however, substantial challenges in the field remain. In this primer we provide an overview of metabolomics, especially mass spectrometry (MS)-based metabolomics, which uses liquid chromatography (LC) for separation, and discuss its utilities and limitations...
February 11, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28185716/mitochondrial-complex-ii-at-the-crossroads
#3
REVIEW
Ayenachew Bezawork-Geleta, Jakub Rohlena, Lanfeng Dong, Karel Pacak, Jiri Neuzil
Mitochondrial complex II (CII), also called succinate dehydrogenase (SDH), is a central purveyor of the reprogramming of metabolic and respiratory adaptation in response to various intrinsic and extrinsic stimuli and abnormalities. In this review we discuss recent findings regarding SDH biogenesis, which requires four known assembly factors, and modulation of its enzymatic activity by acetylation, succinylation, phosphorylation, and proteolysis. We further focus on the emerging role of both genetic and epigenetic aberrations leading to SDH dysfunction associated with various clinical manifestations...
February 6, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28118949/a-golden-age-for-working-with-public-proteomics-data
#4
REVIEW
Lennart Martens, Juan Antonio Vizcaíno
Data sharing in mass spectrometry (MS)-based proteomics is becoming a common scientific practice, as is now common in the case of other, more mature 'omics' disciplines like genomics and transcriptomics. We want to highlight that this situation, unprecedented in the field, opens a plethora of opportunities for data scientists. First, we explain in some detail some of the work already achieved, such as systematic reanalysis efforts. We also explain existing applications of public proteomics data, such as proteogenomics and the creation of spectral libraries and spectral archives...
January 21, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28118948/trim-family-proteins-roles-in-autophagy-immunity-and-carcinogenesis
#5
REVIEW
Shigetsugu Hatakeyama
Tripartite motif (TRIM) family proteins, most of which have E3 ubiquitin ligase activities, have various functions in cellular processes including intracellular signaling, development, apoptosis, protein quality control, innate immunity, autophagy, and carcinogenesis. The ubiquitin system is one of the systems for post-translational modifications, which play crucial roles not only as markers for degradation of target proteins by the proteasome but also as regulators of protein-protein interactions and of the activation of enzymes...
January 21, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28096055/an-ancient-family-of-rna-binding-proteins-still-important
#6
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/27986367/translating-the-sugar-code-into-immune-and-vascular-signaling-programs
#7
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/27932073/pyroptosis-gasdermin-mediated-programmed-necrotic-cell-death
#8
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
#9
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/28089412/whaddaya-know-a-guide-to-uncertainty-and-subjectivity-in-structural-biology
#10
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...
February 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28063638/functional-dissection-of-the-m6a-rna-modification
#11
Brooke Huisman, Gabriel Manske, Stephen Carney, Sundeep Kalantry
No abstract text is available yet for this article.
February 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28029518/a-new-view-into-the-regulation-of-purine-metabolism-the-purinosome
#12
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'...
February 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/27956059/speed-limits-for-nonvesicular-intracellular-sterol-transport
#13
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...
February 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/27884598/coiled-coils-a-model-system-for-the-21st-century
#14
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...
February 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/27856135/a-fresh-look-at-aging-proteins
#15
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.
February 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/27814948/the-growing-and-glowing-toolbox-of-fluorescent-and-photoactive-proteins
#16
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...
February 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/27712956/alternative-splicing-may-not-be-the-key-to-proteome-complexity
#17
REVIEW
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...
February 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/27955862/liquid-phase-transition-in-the-postsynaptic-density
#18
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
#19
(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
#20
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
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