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Annual Review of Biochemistry

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https://www.readbyqxmd.com/read/29925267/protein-serine-threonine-phosphatases-keys-to-unlocking-regulators-and-substrates
#1
David L Brautigan, Shirish Shenolikar
Protein serine/threonine phosphatases (PPPs) are ancient enzymes, with distinct types conserved across eukaryotic evolution. PPPs are segregated into types primarily on the basis of the unique interactions of PPP catalytic subunits with regulatory proteins. The resulting holoenzymes dock substrates distal to the active site to enhance specificity. This review focuses on the subunit and substrate interactions for PPP that depend on short linear motifs. Insights about these motifs from structures of holoenzymes open new opportunities for computational biology approaches to elucidate PPP networks...
June 20, 2018: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29925266/protein-evolution-and-design
#2
Gunnar von Heijne
This article introduces the Protein Evolution and Design theme of the Annual Review of Biochemistry Volume 87.
June 20, 2018: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29925265/the-structural-enzymology-of-iterative-aromatic-polyketide-synthases-a-critical-comparison-with-fatty-acid-synthases
#3
Shiou-Chuan (Sheryl) Tsai
Polyketides are a large family of structurally complex natural products including compounds with important bioactivities. Polyketides are biosynthesized by polyketide synthases (PKSs), multienzyme complexes derived evolutionarily from fatty acid synthases (FASs). The focus of this review is to critically compare the properties of FASs with iterative aromatic PKSs, including type II PKSs and fungal type I nonreducing PKSs whose chemical logic is distinct from that of modular PKSs. This review focuses on structural and enzymological studies that reveal both similarities and striking differences between FASs and aromatic PKSs...
June 20, 2018: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29925264/how-messenger-rna-and-nascent-chain-sequences-regulate-translation-elongation
#4
Junhong Choi, Rosslyn Grosely, Arjun Prabhakar, Christopher P Lapointe, Jinfan Wang, Joseph D Puglisi
Translation elongation is a highly coordinated, multistep, multifactor process that ensures accurate and efficient addition of amino acids to a growing nascent-peptide chain encoded in the sequence of translated messenger RNA (mRNA). Although translation elongation is heavily regulated by external factors, there is clear evidence that mRNA and nascent-peptide sequences control elongation dynamics, determining both the sequence and structure of synthesized proteins. Advances in methods have driven experiments that revealed the basic mechanisms of elongation as well as the mechanisms of regulation by mRNA and nascent-peptide sequences...
June 20, 2018: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29925263/chromatin-and-metabolism
#5
Tamaki Suganuma, Jerry L Workman
Chromatin is a mighty consumer of cellular energy generated by metabolism. Metabolic status is efficiently coordinated with transcription and translation, which also feed back to regulate metabolism. Conversely, suppression of energy utilization by chromatin processes may serve to preserve energy resources for cell survival. Most of the reactions involved in chromatin modification require metabolites as their cofactors or coenzymes. Therefore, the metabolic status of the cell can influence the spectra of posttranslational histone modifications and the structure, density and location of nucleosomes, impacting epigenetic processes...
June 20, 2018: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29925262/nuclear-genomic-instability-and-aging
#6
Laura J Niedernhofer, Aditi U Gurkar, Yinsheng Wang, Jan Vijg, Jan H J Hoeijmakers, Paul D Robbins
The nuclear genome decays as organisms age. Numerous studies demonstrate that the burden of several classes of DNA lesions is greater in older mammals than in young mammals. More challenging is proving this is a cause rather than a consequence of aging. The DNA damage theory of aging, which argues that genomic instability plays a causal role in aging, has recently gained momentum. Support for this theory stems partly from progeroid syndromes in which inherited defects in DNA repair increase the burden of DNA damage leading to accelerated aging of one or more organs...
June 20, 2018: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29925261/protein-quality-control-degradation-in-the-nucleus
#7
Charisma Enam, Yifat Geffen, Tommer Ravid, Richard G Gardner
Nuclear proteins participate in diverse cellular processes, many of which are essential for cell survival and viability. To maintain optimal nuclear physiology, the cell employs the ubiquitin-proteasome system to eliminate damaged and misfolded proteins in the nucleus that could otherwise harm the cell. In this review, we highlight the current knowledge about the major ubiquitin-protein ligases involved in protein quality control degradation (PQCD) in the nucleus and how they orchestrate their functions to eliminate misfolded proteins in different nuclear subcompartments...
June 20, 2018: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29925260/transition-metal-sequestration-by-the-host-defense-protein-calprotectin
#8
Emily M Zygiel, Elizabeth M Nolan
In response to microbial infection, the human host deploys metal-sequestering host-defense proteins, which reduce nutrient availability and thereby inhibit microbial growth and virulence. Calprotectin (CP) is an abundant antimicrobial protein released from neutrophils and epithelial cells at sites of infection. CP sequesters divalent first-row transition metal ions to limit the availability of essential metal nutrients in the extracellular space. While functional and clinical studies of CP have been pursued for decades, advances in our understanding of its biological coordination chemistry, which is central to its role in the host-microbe interaction, have been made in more recent years...
June 20, 2018: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29925259/metabolite-enzyme-coevolution-from-single-enzymes-to-metabolic-pathways-and-networks
#9
Lianet Noda-Garcia, Wolfram Liebermeister, Dan S Tawfik
How individual enzymes evolved is relatively well understood. However, individual enzymes rarely confer a physiological advantage on their own. Judging by its current state, the emergence of metabolism seemingly demanded the simultaneous emergence of many enzymes. Indeed, how multicomponent interlocked systems, like metabolic pathways, evolved is largely an open question. This complexity can be unlocked if we assume that survival of the fittest applies not only to genes and enzymes but also to the metabolites they produce...
June 20, 2018: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29925258/the-molecular-basis-of-g-protein-coupled-receptor-activation
#10
William I Weis, Brian K Kobilka
G protein-coupled receptors (GPCRs) mediate the majority of cellular responses to external stimuli. Upon activation by a ligand, the receptor binds to a partner heterotrimeric G protein and promotes exchange of GTP for GDP, leading to dissociation of the G protein into α and βγ subunits that mediate downstream signals. GPCRs can also activate distinct signaling pathways through arrestins. Active states of GPCRs form by small rearrangements of the ligand-binding, or orthosteric, site that are amplified into larger conformational changes...
June 20, 2018: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29925257/reductionist-approach-in-peptide-based-nanotechnology
#11
Ehud Gazit
The formation of ordered nanostructures by molecular self-assembly of proteins and peptides represents one of the principal directions in nanotechnology. Indeed, polyamides provide superior features as materials with diverse physical properties. A reductionist approach allowed the identification of extremely short peptide sequences, as short as dipeptides, which could form well-ordered amyloid-like β-sheet-rich assemblies comparable to supramolecular structures made of much larger proteins. Some of the peptide assemblies show remarkable mechanical, optical, and electrical characteristics...
June 20, 2018: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29925256/a-lifetime-of-adventures-in-glycobiology
#12
Stuart Kornfeld
My initial research experience involved studying how bacteria synthesize nucleotide sugars, the donors for the formation of cell wall polysaccharides. During this time, I became aware that mammalian cells also have a surface coat of sugars and was intrigued as to whether these sugars might be arranged in specific sequences that function as information molecules in biologic processes. Thus began a long journey that has taken me from glycan structural analysis and determination of plant lectin-binding preferences to the biosynthesis of Asn-linked oligosaccharides and the mannose 6-phosphate (Man-6-P) lysosomal enzyme targeting pathway...
June 20, 2018: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29925255/a-rich-man-poor-man-story-of-s-adenosylmethionine-and-cobalamin-revisited
#13
Jennifer Bridwell-Rabb, Tsehai A J Grell, Catherine L Drennan
S-adenosylmethionine (AdoMet) has been referred to as both "a poor man's adenosylcobalamin (AdoCbl)" and "a rich man's AdoCbl," but today, with the ever-increasing number of functions attributed to each cofactor, both appear equally rich and surprising. The recent characterization of an organometallic species in an AdoMet radical enzyme suggests that the line that differentiates them in nature will be constantly challenged. Here, we compare and contrast AdoMet and cobalamin (Cbl) and consider why Cbl-dependent AdoMet radical enzymes require two cofactors that are so similar in their reactivity...
June 20, 2018: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29925254/metabolic-regulation-of-transcription-and-chromatin
#14
Ronald C Conaway
Although cell metabolism has been established as a major regulator of eukaryotic gene expression, the mechanisms underlying this regulation are still being uncovered. Recent years have seen great advances in our understanding of biochemical mechanisms of metabolic regulation of transcription and chromatin. Prime examples include insights into how nutrients and cellular energy status regulate synthesis of ribosomal RNAs by RNA polymerases I and III during ribosome biogenesis and how a variety of enzymes that catalyze modifications of histones in chromatin are regulated by the levels of certain metabolites...
June 20, 2018: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29727582/along-the-central-dogma-controlling-gene-expression-with-small-molecules
#15
Tilman Schneider-Poetsch, Minoru Yoshida
The central dogma of molecular biology, that DNA is transcribed into RNA and RNA translated into protein, was coined in the early days of modern biology. Back in the 1950s and 1960s, bacterial genetics first opened the way toward understanding life as the genetically encoded interaction of macromolecules. As molecular biology progressed and our knowledge of gene control deepened, it became increasingly clear that expression relied on many more levels of regulation. In the process of dissecting mechanisms of gene expression, specific small-molecule inhibitors played an important role and became valuable tools of investigation...
June 20, 2018: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29709199/the-mre11-rad50-nbs1-complex-conducts-the-orchestration-of-damage-signaling-and-outcomes-to-stress-in-dna-replication-and-repair
#16
Aleem Syed, John A Tainer
Genomic instability in disease and its fidelity in health depend on the DNA damage response (DDR), regulated in part from the complex of meiotic recombination 11 homolog 1 (MRE11), ATP-binding cassette-ATPase (RAD50), and phosphopeptide-binding Nijmegen breakage syndrome protein 1 (NBS1). The MRE11-RAD50-NBS1 (MRN) complex forms a multifunctional DDR machine. Within its network assemblies, MRN is the core conductor for the initial and sustained responses to DNA double-strand breaks, stalled replication forks, dysfunctional telomeres, and viral DNA infection...
June 20, 2018: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29668306/dosage-compensation-of-the-x-chromosome-a-complex-epigenetic-assignment-involving-chromatin-regulators-and-long-noncoding-rnas
#17
Maria Samata, Asifa Akhtar
X chromosome regulation represents a prime example of an epigenetic phenomenon where coordinated regulation of a whole chromosome is required. In flies, this is achieved by transcriptional upregulation of X chromosomal genes in males to equalize the gene dosage differences in females. Chromatin-bound proteins and long noncoding RNAs (lncRNAs) constituting a ribonucleoprotein complex known as the male-specific lethal (MSL) complex or the dosage compensation complex mediate this process. MSL complex members decorate the male X chromosome, and their absence leads to male lethality...
June 20, 2018: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29668305/chalkophores
#18
Grace E Kenney, Amy C Rosenzweig
Copper-binding metallophores, or chalkophores, play a role in microbial copper homeostasis that is analogous to that of siderophores in iron homeostasis. The best-studied chalkophores are members of the methanobactin (Mbn) family-ribosomally produced, posttranslationally modified natural products first identified as copper chelators responsible for copper uptake in methane-oxidizing bacteria. To date, Mbns have been characterized exclusively in those species, but there is genomic evidence for their production in a much wider range of bacteria...
June 20, 2018: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29661000/regulation-of-clathrin-mediated-endocytosis
#19
Marcel Mettlen, Ping-Hung Chen, Saipraveen Srinivasan, Gaudenz Danuser, Sandra L Schmid
Clathrin-mediated endocytosis (CME) is the major endocytic pathway in mammalian cells. It is responsible for the uptake of transmembrane receptors and transporters, for remodeling plasma membrane composition in response to environmental changes, and for regulating cell surface signaling. CME occurs via the assembly and maturation of clathrin-coated pits that concentrate cargo as they invaginate and pinch off to form clathrin-coated vesicles. In addition to the major coat proteins, clathrin triskelia and adaptor protein complexes, CME requires a myriad of endocytic accessory proteins and phosphatidylinositol lipids...
June 20, 2018: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29652515/structure-and-function-of-the-26s-proteasome
#20
Jared A M Bard, Ellen A Goodall, Eric R Greene, Erik Jonsson, Ken C Dong, Andreas Martin
As the endpoint for the ubiquitin-proteasome system, the 26S proteasome is the principal proteolytic machine responsible for regulated protein degradation in eukaryotic cells. The proteasome's cellular functions range from general protein homeostasis and stress response to the control of vital processes such as cell division and signal transduction. To reliably process all the proteins presented to it in the complex cellular environment, the proteasome must combine high promiscuity with exceptional substrate selectivity...
June 20, 2018: Annual Review of Biochemistry
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