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Trends in Biochemical Sciences

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https://www.readbyqxmd.com/read/29132948/extending-the-structural-view-of-class-b-gpcrs
#1
REVIEW
Chris de Graaf, Gaojie Song, Can Cao, Qiang Zhao, Ming-Wei Wang, Beili Wu, Raymond C Stevens
The secretin-like class B family of G protein-coupled receptors (GPCRs) are key players in hormonal homeostasis. Recent structures of various receptors in complex with a variety of orthosteric and allosteric ligands provide fundamental new insights into the function and mechanism of class B GPCRs, including: (i) ligand-induced changes in the relative orientation of the extracellular and transmembrane receptor domains; (ii) intramolecular interaction networks that stabilize conformational changes to accommodate intracellular G protein binding; and (iii) allosteric modulation of receptor activation...
November 10, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/29126750/hidden-secrets-of-sigma54-promoters-revealed
#2
Nan Hao, Keith E Shearwin
Bacterial sigma54 (σ(54)) promoters are the DNA-binding motif for σ(54)-containing RNA polymerase (RNAP) holoenzymes. A recent study using a combination of synthetic oligonucleotide library screening, biochemical characterization, and bioinformatics has uncovered a new and unexpected role for σ(54) promoters, encoding a form of bacterial 'insulator sequence' to dampen unwanted translation.
November 7, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/29122461/histone-marks-in-the-driver-s-seat-functional-roles-in-steering-the-transcription-cycle
#3
REVIEW
Leah A Gates, Charles E Foulds, Bert W O'Malley
Particular chromatin modifications are associated with different states of gene transcription, yet our understanding of which modifications are causal 'drivers' in promoting transcription is incomplete. Here, we discuss new developments describing the ordered, mechanistic role of select histone marks occurring during distinct steps in the RNA polymerase II (Pol II) transcription cycle. In particular, we highlight the interplay between histone marks in specifying the 'next step' of transcription. While many studies have described correlative relationships between histone marks and their occupancy at distinct gene regions, we focus on studies that elucidate clear functional consequences of specific histone marks during different stages of transcription...
November 6, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/29089160/the-unsolved-problem-of-how-cells-sense-micron-scale-curvature
#4
REVIEW
Kevin S Cannon, Benjamin L Woods, Amy S Gladfelter
Membrane curvature is a fundamental feature of cells and their organelles. Much of what we know about how cells sense curved surfaces comes from studies examining nanometer-sized molecules on nanometer-scale curvatures. We are only just beginning to understand how cells recognize curved topologies at the micron scale. In this review, we provide the reader with an overview of our current understanding of how cells sense and respond to micron-scale membrane curvature.
October 28, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/29102083/cracking-the-chaperone-code-cellular-roles-for-hsp70-phosphorylation
#5
Nitika, Andrew W Truman
Heat shock protein 70 (Hsp70) is a molecular chaperone required for protein folding, cell viability, and cancer cell proliferation. Recent studies suggest that Hsp70 phosphorylation regulates important cellular processes, such as cell cycle progression, apoptosis, protein degradation, and resistance to anticancer therapeutics.
October 25, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/29037863/outer-membrane-protein-ompb-methylation-may-mediate-bacterial-virulence
#6
REVIEW
David C H Yang, Amila H Abeykoon, Bok-Eum Choi, Wei-Mei Ching, P Boon Chock
Methylation of outer membrane proteins (OMPs) has been implicated in bacterial virulence. Lysine methylation in rickettsial OmpB is correlated with rickettsial virulence, and N- and O-methylations are also observed in virulence-relevant OMPs from several pathogenic bacteria that cause typhus, leptospirosis, tuberculosis, and anaplasmosis. We summarize recent findings on the structure of methylated OmpB, biochemical characterization, and crystal structures of OmpB methyltransferases. Native rickettsial OmpB purified from highly virulent strains contains multiple clusters of trimethyllysine, in contrast with mostly monomethyllysine, and no trimethyllysine is found in an avirulent strain...
October 13, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28965669/visualizing-nuclear-rna-editing
#7
Hodaya Hochberg, Yaron Shav-Tal
RNA editing results in the site-specific conversion of adenosine to inosine in mRNAs. Genomics has revealed millions of editing sites in metazoans, but examining the spatial aspects of editing in cells has been challenging. A new method, inosineFISH (inoFISH), provides the ability to detect edited and unedited mRNAs within intact cells.
November 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28964625/regulation-of-the-hippo-pathway-transcription-factor-tead
#8
REVIEW
Kimberly C Lin, Hyun Woo Park, Kun-Liang Guan
The TEAD transcription factor family is best known for transcriptional output of the Hippo signaling pathway and has been implicated in processes such as development, cell growth and proliferation, tissue homeostasis, and regeneration. Our understanding of the functional importance of TEADs has increased dramatically since its initial discovery three decades ago. The majority of our knowledge of TEADs is in the context of Hippo signaling as nuclear DNA-binding proteins passively activated by Yes-associated protein (YAP) and transcriptional activator with PDZ-binding domain (TAZ), transcription coactivators downstream of the Hippo pathway...
November 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28964624/sharing-the-saga
#9
REVIEW
Dominique Helmlinger, László Tora
Transcription initiation is a major regulatory step in eukaryotic gene expression. Co-activators establish transcriptionally competent promoter architectures and chromatin signatures to allow the formation of the pre-initiation complex (PIC), comprising RNA polymerase II (Pol II) and general transcription factors (GTFs). Many GTFs and co-activators are multisubunit complexes, in which individual components are organized into functional modules carrying specific activities. Recent advances in affinity purification and mass spectrometry analyses have revealed that these complexes often share functional modules, rather than containing unique components...
November 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28947091/the-ubiquitin-code-in-the-ubiquitin-proteasome-system-and-autophagy
#10
REVIEW
Yong Tae Kwon, Aaron Ciechanover
The conjugation of the 76 amino acid protein ubiquitin to other proteins can alter the metabolic stability or non-proteolytic functions of the substrate. Once attached to a substrate (monoubiquitination), ubiquitin can itself be ubiquitinated on any of its seven lysine (Lys) residues or its N-terminal methionine (Met1). A single ubiquitin polymer may contain mixed linkages and/or two or more branches. In addition, ubiquitin can be conjugated with ubiquitin-like modifiers such as SUMO or small molecules such as phosphate...
November 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28927699/biochemical-mechanisms-of-pathogen-restriction-by-intestinal-bacteria
#11
REVIEW
Kavita J Rangan, Howard C Hang
The intestine is a highly complex ecosystem where many bacterial species interact with each other and host cells to influence animal physiology and susceptibility to pathogens. Genomic methods have provided a broad framework for understanding how alterations in microbial communities are associated with host physiology and infection, but the biochemical mechanisms of specific intestinal bacterial species are only emerging. In this review, we focus on recent studies that have characterized the biochemical mechanisms by which intestinal bacteria interact with other bacteria and host pathways to restrict pathogen infection...
November 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28917971/how-fast-is-protein-ligand-association
#12
Stefano Gianni, Per Jemth
There is increasing interest in studying protein interactions and their role in cell biology using kinetics. However, there is confusion about the proper terminology in terms of the distinction between rates and rate constants. We recommend a more stringent use of the words speed, fast, slow, rate, and rate constant.
November 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28917970/how-do-enzymes-meet-nanoparticles-and-nanomaterials
#13
REVIEW
Ming Chen, Guangming Zeng, Piao Xu, Cui Lai, Lin Tang
Enzymes are fundamental biological catalysts responsible for biological regulation and metabolism. The opportunity for enzymes to 'meet' nanoparticles and nanomaterials is rapidly increasing due to growing demands for applications in nanomaterial design, environmental monitoring, biochemical engineering, and biomedicine. Therefore, understanding the nature of nanomaterial-enzyme interactions is becoming important. Since 2014, enzymes have been used to modify, degrade, or make nanoparticles/nanomaterials, while numerous nanoparticles/nanomaterials have been used as materials for enzymatic immobilization and biosensors and as enzyme mimicry...
November 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28893460/stress-activated-chaperones-a-first-line-of-defense
#14
REVIEW
Wilhelm Voth, Ursula Jakob
Proteins are constantly challenged by environmental stress conditions that threaten their structure and function. Especially problematic are oxidative, acid, and severe heat stress which induce very rapid and widespread protein unfolding and generate conditions that make canonical chaperones and/or transcriptional responses inadequate to protect the proteome. We review here recent advances in identifying and characterizing stress-activated chaperones which are inactive under non-stress conditions but become potent chaperones under specific protein-unfolding stress conditions...
November 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28927698/biochemistry-of-mitochondrial-coenzyme-q-biosynthesis
#15
REVIEW
Jonathan A Stefely, David J Pagliarini
Coenzyme Q (CoQ, ubiquinone) is a redox-active lipid produced across all domains of life that functions in electron transport and oxidative phosphorylation and whose deficiency causes human diseases. Yet, CoQ biosynthesis has not been fully defined in any organism. Several proteins with unclear molecular functions facilitate CoQ biosynthesis through unknown means, and multiple steps in the pathway are catalyzed by currently unidentified enzymes. Here we highlight recent progress toward filling these knowledge gaps through both traditional biochemistry and cutting-edge 'omics' approaches...
October 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28916413/emerging-structural-understanding-of-amyloid-fibrils-by-solid-state-nmr
#16
REVIEW
Beat H Meier, Roland Riek, Anja Böckmann
Amyloid structures at atomic resolution have remained elusive mainly because of their extensive polymorphism and because their polymeric properties have hampered structural studies by classical approaches. Progress in sample preparation, as well as solid-state NMR methods, recently enabled the determination of high-resolution 3D structures of fibrils such as the amyloid-β fibril, which is involved in Alzheimer's disease. Notably, the simultaneous but independent structure determination of Aβ1-42, a peptide that forms fibrillar deposits in the brain of Alzheimer patients, by two independent laboratories, which yielded virtually identical results, has highlighted how structures can be obtained that allow further functional investigation...
October 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28870425/emerging-insights-into-the-roles-of-the-paf1-complex-in-gene-regulation
#17
REVIEW
S Branden Van Oss, Christine E Cucinotta, Karen M Arndt
The conserved, multifunctional Polymerase-Associated Factor 1 complex (Paf1C) regulates all stages of the RNA polymerase (Pol) II transcription cycle. In this review, we examine a diverse set of recent studies from various organisms that build on foundational studies in budding yeast. These studies identify new roles for Paf1C in the control of gene expression and the regulation of chromatin structure. In exploring these advances, we find that various functions of Paf1C, such as the regulation of promoter-proximal pausing and development in higher eukaryotes, are complex and context dependent...
October 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28869131/in-the-hunger-games-the-winner-takes-everything
#18
Franziska Püschel, Cristina Muñoz-Pinedo
Entosis is an atypical form of cell death that occurs when a cell engulfs and kills another cell. A recent article by Overholtzer and colleagues indicates that glucose deprivation promotes entosis. AMP-activated protein kinase (AMPK) activation in the loser cells triggers their engulfment and elimination by winner cells, which endure starvation.
October 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28864230/there-is-an-inclusion-for-that-material-properties-of-protein-granules-provide-a-platform-for-building-diverse-cellular-functions
#19
REVIEW
Daniel Kaganovich
Proteins perform a staggering variety of functions in the cell. Traditionally, protein function was thought to be hard-wired into the folded structure and conformational dynamics of each protein molecule. Recent work describes a new mode of protein functionality driven by the collective behavior of many different proteins; most of which lack a defined structure. These proteins form clusters or granules in which unstructured polypeptides interact transiently. Nonspecific multivalent interactions drive the formation of phase-separated structures resembling aggregates...
October 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28802547/good-ol-fat-links-between-lipid-signaling-and-longevity
#20
REVIEW
Victor Bustos, Linda Partridge
Aging is the single greatest risk factor for the development of disease. Understanding the biological molecules and mechanisms that modulate aging is therefore critical for the development of health-maximizing interventions for older people. The effect of fats on longevity has traditionally been disregarded as purely detrimental. However, new studies are starting to uncover the possible beneficial effects of lipids working as signaling molecules on health and longevity. These studies highlight the complex links between aging and lipid signaling...
October 2017: Trends in Biochemical Sciences
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