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Critical Reviews in Biochemistry and Molecular Biology

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https://www.readbyqxmd.com/read/29999430/the-molecular-era-of-protein-s-acylation-spotlight-on-structure-mechanisms-and-dynamics
#1
María-Eugenia Zaballa, F Gisou van der Goot
S-Acylation (commonly referred to as S-palmitoylation) is a post-translational modification consisting in the covalent attachment of an acyl chain to a cysteine residue of the target protein. The lability of the resulting thioester bond gives S-acylation an essential characteristic: its reversibility. S-acylation dynamically regulates different aspects in the life of a protein (including stability, localization, interactome, and function) and, thus, plays critical roles in cellular physiology. For long, the reversibility of S-acylation has been neglected and thereby its potential as a regulatory mechanism for protein function undervalued...
July 12, 2018: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29972306/ribonucleotide-discrimination-by-translesion-synthesis-dna-polymerases
#2
Alexandra Vaisman, Roger Woodgate
The well-being of all living organisms relies on the accurate duplication of their genomes. This is usually achieved by highly elaborate replicase complexes which ensure that this task is accomplished timely and efficiently. However, cells often must resort to the help of various additional "specialized" DNA polymerases that gain access to genomic DNA when replication fork progression is hindered. One such specialized polymerase family consists of the so-called "translesion synthesis" (TLS) polymerases; enzymes that have evolved to replicate damaged DNA...
July 4, 2018: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29863423/ironing-out-siderophore-biosynthesis-a-review-of-non-ribosomal-peptide-synthetase-nrps-independent-siderophore-synthetases
#3
Cassandra S Carroll, Margo M Moore
Iron is required for microbial growth and proliferation. To survive in low-iron environments, some microorganisms secrete ferric iron chelators called siderophores. Siderophore biosynthesis occurs via two pathways: the non-ribosomal peptide synthetase (NRPS) pathway and the NRPS-independent siderophore (NIS) synthetase pathway. NIS enzymes function by adenylating a carboxylic acid substrate, typically citrate, or a derivative, followed by nucleophilic capture of an amine or alcohol and displacement of a citryl intermediate...
June 4, 2018: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29793351/bacterial-regulatory-rnas-complexity-function-and-putative-drug-targeting
#4
Hong-Leong Cheah, Carsten A Raabe, Li-Pin Lee, Timofey S Rozhdestvensky, Marimuthu Citartan, Siti Aminah Ahmed, Thean-Hock Tang
Over the past decade, RNA-deep sequencing has uncovered copious non-protein coding RNAs (npcRNAs) in bacteria. Many of them are key players in the regulation of gene expression, taking part in various regulatory circuits, such as metabolic responses to different environmental stresses, virulence, antibiotic resistance, and host-pathogen interactions. This has contributed to the high adaptability of bacteria to changing or even hostile environments. Their mechanisms include the regulation of transcriptional termination, modulation of translation, and alteration of messenger RNA (mRNA) stability, as well as protein sequestration...
May 24, 2018: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29718780/isoprenoids-and-protein-prenylation-implications-in-the-pathogenesis-and-therapeutic-intervention-of-alzheimer-s-disease
#5
Angela Jeong, Kiall Francis Suazo, W Gibson Wood, Mark D Distefano, Ling Li
The mevalonate-isoprenoid-cholesterol biosynthesis pathway plays a key role in human health and disease. The importance of this pathway is underscored by the discovery that two major isoprenoids, farnesyl and geranylgeranyl pyrophosphate, are required to modify an array of proteins through a process known as protein prenylation, catalyzed by prenyltransferases. The lipophilic prenyl group facilitates the anchoring of proteins in cell membranes, mediating protein-protein interactions and signal transduction...
June 2018: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29637793/functions-of-the-sirtuin-deacylase-sirt5-in-normal-physiology-and-pathobiology
#6
Surinder Kumar, David B Lombard
Sirtuins are NAD+ -dependent protein deacylases/ADP-ribosyltransferases that have emerged as candidate targets for new therapeutics to treat metabolic disorders and other diseases, including cancer. The sirtuin SIRT5 resides primarily in the mitochondrial matrix and catalyzes the removal of negatively charged lysine acyl modifications; succinyl, malonyl, and glutaryl groups. Evidence has now accumulated to document the roles of SIRT5 as a significant regulator of cellular homeostasis, in a context- and cell-type specific manner, as has been observed previously for other sirtuin family members...
June 2018: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29569941/complexities-of-post-transcriptional-regulation-and-the-modeling-of-cerna-crosstalk
#7
Claire L Smillie, Tamara Sirey, Chris P Ponting
Control of gene and protein expression is required for cellular homeostasis and is disrupted in disease. Following transcription, mRNA turnover and translation is modulated, most notably by microRNAs (miRNAs). This modulation is controlled by transcriptional and post-transcriptional events that alter the availability of miRNAs for target binding. Recent studies have proposed that some transcripts - termed competitive endogenous RNAs (ceRNAs) - sequester a miRNA and diminish its repressive effects on other transcripts...
June 2018: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29564928/cryptides-latent-peptides-everywhere
#8
Federica Iavarone, Claudia Desiderio, Alberto Vitali, Irene Messana, Claudia Martelli, Massimo Castagnola, Tiziana Cabras
Proteomic surveys with top-down platforms are today revealing thousands of naturally occurring fragments of bigger proteins. Some of them have not functional meaning because they derive from pathways responsible for protein degradation, but many have specific functions, often completely different from that one of the parent proteins. These peptides encrypted in the protein sequence are nowadays called cryptides. They are frequent in the animal and plant kingdoms and represent a new interesting -omic field of investigation...
June 2018: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29557675/the-hedgehog-pathway-in-nonalcoholic-fatty-liver-disease
#9
Mariana Verdelho Machado, Anna Mae Diehl
Nonalcoholic fatty liver disease (NAFLD) encompasses a spectrum of obesity-associated liver diseases and it has become the major cause of cirrhosis in the Western world. The high prevalence of NAFLD-associated advanced liver disease reflects both the high prevalence of obesity-related fatty liver (hepatic steatosis) and the lack of specific treatments to prevent hepatic steatosis from progressing to more serious forms of liver damage, including nonalcoholic steatohepatitis (NASH), cirrhosis, and primary liver cancer...
June 2018: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29513138/protein-kinase-c-perfectly-balanced
#10
Alexandra C Newton
Protein kinase C (PKC) isozymes belong to a family of Ser/Thr kinases whose activity is governed by reversible release of an autoinhibitory pseudosubstrate. For conventional and novel isozymes, this is effected by binding the lipid second messenger, diacylglycerol, but for atypical PKC isozymes, this is effected by binding protein scaffolds. PKC shot into the limelight following the discovery in the 1980s that the diacylglycerol-sensitive isozymes are "receptors" for the potent tumor-promoting phorbol esters...
April 2018: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29457927/structural-fingerprints-interactions-and-signaling-networks-of-ras-family-proteins-beyond-ras-isoforms
#11
Saeideh Nakhaei-Rad, Fereshteh Haghighi, Parivash Nouri, Soheila Rezaei Adariani, Jana Lissy, Neda S Kazemein Jasemi, Radovan Dvorsky, Mohammad Reza Ahmadian
No abstract text is available yet for this article.
April 2018: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29457544/mesoscale-organization-of-domains-in-the-plasma-membrane-beyond-the-lipid-raft
#12
Stella M Lu, Gregory D Fairn
The plasma membrane is compartmentalized into several distinct regions or domains, which show a broad diversity in both size and lifetime. The segregation of lipids and membrane proteins is thought to be driven by the lipid composition itself, lipid-protein interactions and diffusional barriers. With regards to the lipid composition, the immiscibility of certain classes of lipids underlies the "lipid raft" concept of plasmalemmal compartmentalization. Historically, lipid rafts have been described as cholesterol and (glyco)sphingolipid-rich regions of the plasma membrane that exist as a liquid-ordered phase that are resistant to extraction with non-ionic detergents...
April 2018: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29424242/rce1-mechanism-and-inhibition
#13
Shahienaz E Hampton, Timothy M Dore, Walter K Schmidt
Ras converting enzyme 1 (Rce1) is an integral membrane endoprotease localized to the endoplasmic reticulum that mediates the cleavage of the carboxyl-terminal three amino acids from CaaX proteins, whose members play important roles in cell signaling processes. Examples include the Ras family of small GTPases, the γ-subunit of heterotrimeric GTPases, nuclear lamins, and protein kinases and phosphatases. CaaX proteins, especially Ras, have been implicated in cancer, and understanding the post-translational modifications of CaaX proteins would provide insight into their biological function and regulation...
April 2018: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29424237/greasing-the-wheels-or-a-spanner-in-the-works-regulation-of-the-cardiac-sodium-pump-by-palmitoylation
#14
Jacqueline Howie, Krzysztof J Wypijewski, Fiona Plain, Lindsay B Tulloch, Niall J Fraser, William Fuller
The ubiquitous sodium/potassium ATPase (Na pump) is the most abundant primary active transporter at the cell surface of multiple cell types, including ventricular myocytes in the heart. The activity of the Na pump establishes transmembrane ion gradients that control numerous events at the cell surface, positioning it as a key regulator of the contractile and metabolic state of the myocardium. Defects in Na pump activity and regulation elevate intracellular Na in cardiac muscle, playing a causal role in the development of cardiac hypertrophy, diastolic dysfunction, arrhythmias and heart failure...
April 2018: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29411648/expanding-the-boundary-of-biocatalysis-design-and-optimization-of-in-vitro-tandem-catalytic-reactions-for-biochemical-production
#15
Yajie Wang, Hengqian Ren, Huimin Zhao
Biocatalysts have been increasingly used in the synthesis of fine chemicals and medicinal compounds due to significant advances in enzyme discovery and engineering. To mimic the synergistic effects of cascade reactions catalyzed by multiple enzymes in nature, researchers have been developing artificial tandem enzymatic reactions in vivo by harnessing synthetic biology and metabolic engineering tools. There is also growing interest in the development of one-pot tandem enzymatic or chemo-enzymatic processes in vitro due to their neat and concise catalytic systems and product purification procedures...
April 2018: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29250983/the-impact-of-non-genetic-heterogeneity-on-cancer-cell-death
#16
Zintis Inde, Scott J Dixon
The goal of cancer chemotherapy is to induce homogeneous cell death within the population of targeted cancer cells. However, no two cells are exactly alike at the molecular level, and sensitivity to drug-induced cell death, therefore, varies within a population. Genetic alterations can contribute to this variability and lead to selection for drug resistant clones. However, there is a growing appreciation for the role of non-genetic variation in producing drug-tolerant cellular states that exhibit reduced sensitivity to cell death for extended periods of time, from hours to weeks...
February 2018: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29239216/protein-depalmitoylases
#17
Sang Joon Won, Melanie Cheung See Kit, Brent R Martin
Protein depalmitoylation describes the removal of thioester-linked long chain fatty acids from cysteine residues in proteins. For many S-palmitoylated proteins, this process is promoted by acyl protein thioesterase enzymes, which catalyze thioester hydrolysis to solubilize and displace substrate proteins from membranes. The closely related enzymes acyl protein thioesterase 1 (APT1; LYPLA1) and acyl protein thioesterase 2 (APT2; LYPLA2) were initially identified from biochemical assays as G protein depalmitoylases, yet later were shown to accept a number of S-palmitoylated protein and phospholipid substrates...
February 2018: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29108429/sources-of-spontaneous-mutagenesis-in-bacteria
#18
Jeremy W Schroeder, Ponlkrit Yeesin, Lyle A Simmons, Jue D Wang
Mutations in an organism's genome can arise spontaneously, that is, in the absence of exogenous stress and prior to selection. Mutations are often neutral or deleterious to individual fitness but can also provide genetic diversity driving evolution. Mutagenesis in bacteria contributes to the already serious and growing problem of antibiotic resistance. However, the negative impacts of spontaneous mutagenesis on human health are not limited to bacterial antibiotic resistance. Spontaneous mutations also underlie tumorigenesis and evolution of drug resistance...
February 2018: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29108427/what-is-all-this-fuss-about-tus-comparison-of-recent-findings-from-biophysical-and-biochemical-experiments
#19
Bojk A Berghuis, Vlad-Stefan Raducanu, Mohamed M Elshenawy, Slobodan Jergic, Martin Depken, Nicholas E Dixon, Samir M Hamdan, Nynke H Dekker
Synchronizing the convergence of the two-oppositely moving DNA replication machineries at specific termination sites is a tightly coordinated process in bacteria. In Escherichia coli, a "replication fork trap" - found within a chromosomal region where forks are allowed to enter but not leave - is set by the protein-DNA roadblock Tus-Ter. The exact sequence of events by which Tus-Ter blocks replisomes approaching from one direction but not the other has been the subject of controversy for many decades...
February 2018: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29098880/specificity-of-reversible-adp-ribosylation-and-regulation-of-cellular-processes
#20
Kerryanne Crawford, Juan José Bonfiglio, Andreja Mikoč, Ivan Matic, Ivan Ahel
Proper and timely regulation of cellular processes is fundamental to the overall health and viability of organisms across all kingdoms of life. Thus, organisms have evolved multiple highly dynamic and complex biochemical signaling cascades in order to adapt and survive diverse challenges. One such method of conferring rapid adaptation is the addition or removal of reversible modifications of different chemical groups onto macromolecules which in turn induce the appropriate downstream outcome. ADP-ribosylation, the addition of ADP-ribose (ADPr) groups, represents one of these highly conserved signaling chemicals...
February 2018: Critical Reviews in Biochemistry and Molecular Biology
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