journal
MENU ▼
Read by QxMD icon Read
search

Annual Review of Biochemistry

journal
https://www.readbyqxmd.com/read/28841344/retrospective-on-cholesterol-homeostasis-the-central-role-of-scap
#1
Michael S Brown, Arun Radhakrishnan, Joseph L Goldstein
Scap is a polytopic membrane protein that functions as a molecular machine to control the cholesterol content of membranes in mammalian cells. In the 21 years since our laboratory discovered Scap, we have learned how it binds sterol regulatory element-binding proteins (SREBPs) and transports them from the endoplasmic reticulum (ER) to the Golgi for proteolytic processing. Proteolysis releases the SREBP transcription factor domains, which enter the nucleus to promote cholesterol synthesis and uptake. When cholesterol in ER membranes exceeds a threshold, the sterol binds to Scap, triggering several conformational changes that prevent the Scap-SREBP complex from leaving the ER...
August 25, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28654328/biochemistry-of-catabolic-reductive-dehalogenation
#2
REVIEW
Maeva Fincker, Alfred M Spormann
A wide range of phylogenetically diverse microorganisms couple the reductive dehalogenation of organohalides to energy conservation. Key enzymes of such anaerobic catabolic pathways are corrinoid and Fe-S cluster-containing, membrane-associated reductive dehalogenases. These enzymes catalyze the reductive elimination of a halide and constitute the terminal reductases of a short electron transfer chain. Enzymatic and physiological studies revealed the existence of quinone-dependent and quinone-independent reductive dehalogenases that are distinguishable at the amino acid sequence level, implying different modes of energy conservation in the respective microorganisms...
June 20, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28654327/a-new-facet-of-vitamin-b12-gene-regulation-by-cobalamin-based-photoreceptors
#3
REVIEW
S Padmanabhan, Marco Jost, Catherine L Drennan, Montserrat Elías-Arnanz
Living organisms sense and respond to light, a crucial environmental factor, using photoreceptors, which rely on bound chromophores such as retinal, flavins, or linear tetrapyrroles for light sensing. The discovery of photoreceptors that sense light using 5'-deoxyadenosylcobalamin, a form of vitamin B12 that is best known as an enzyme cofactor, has expanded the number of known photoreceptor families and unveiled a new biological role of this vitamin. The prototype of these B12-dependent photoreceptors, the transcriptional repressor CarH, is widespread in bacteria and mediates light-dependent gene regulation in a photoprotective cellular response...
June 20, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28654326/the-ubiquitin-system-autophagy-and-regulated-protein-degradation
#4
REVIEW
Alexander Varshavsky
This brief disquisition about the early history of studies on regulated protein degradation introduces several detailed reviews about the ubiquitin system and autophagy.
June 20, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28654325/a-bright-future-for-antibiotics
#5
REVIEW
Donna Matzov, Anat Bashan, Ada Yonath
Multidrug resistance is a global threat as the clinically available potent antibiotic drugs are becoming exceedingly scarce. For example, increasing drug resistance among gram-positive bacteria is responsible for approximately one-third of nosocomial infections. As ribosomes are a major target for these drugs, they may serve as suitable objects for novel development of next-generation antibiotics. Three-dimensional structures of ribosomal particles from Staphylococcus aureus obtained by X-ray crystallography have shed light on fine details of drug binding sites and have revealed unique structural motifs specific for this pathogenic strain, which may be used for the design of novel degradable pathogen-specific, and hence, environmentally friendly drugs...
June 20, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28654324/conceptual-and-experimental-tools-to-understand-spatial-effects-and-transport-phenomena-in-nonlinear-biochemical-networks-illustrated-with-patchy-switching
#6
REVIEW
Rebecca R Pompano, Andrew H Chiang, Christian J Kastrup, Rustem F Ismagilov
Many biochemical systems are spatially heterogeneous and exhibit nonlinear behaviors, such as state switching in response to small changes in the local concentration of diffusible molecules. Systems as varied as blood clotting, intracellular calcium signaling, and tissue inflammation are all heavily influenced by the balance of rates of reaction and mass transport phenomena including flow and diffusion. Transport of signaling molecules is also affected by geometry and chemoselective confinement via matrix binding...
June 20, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28654323/metabolite-measurement-pitfalls-to-avoid-and-practices-to-follow
#7
REVIEW
Wenyun Lu, Xiaoyang Su, Matthias S Klein, Ian A Lewis, Oliver Fiehn, Joshua D Rabinowitz
Metabolites are the small biological molecules involved in energy conversion and biosynthesis. Studying metabolism is inherently challenging due to metabolites' reactivity, structural diversity, and broad concentration range. Herein, we review the common pitfalls encountered in metabolomics and provide concrete guidelines for obtaining accurate metabolite measurements, focusing on water-soluble primary metabolites. We show how seemingly straightforward sample preparation methods can introduce systematic errors (e...
June 20, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28654322/site-specific-self-catalyzed-dna-depurination-a-biological-mechanism-that-leads-to-mutations-and-creates-sequence-diversity
#8
REVIEW
Jacques R Fresco, Olga Amosova
Self-catalyzed DNA depurination is a sequence-specific physiological mechanism mediated by spontaneous extrusion of a stem-loop catalytic intermediate. Hydrolysis of the 5'G residue of the 5'GA/TGG loop and of the first 5'A residue of the 5'GAGA loop, together with particular first stem base pairs, specifies their hydrolysis without involving protein, cofactor, or cation. As such, this mechanism is the only known DNA catalytic activity exploited by nature. The consensus sequences for self-depurination of such G- and A-loop residues occur in all genomes examined across the phyla, averaging one site every 2,000-4,000 base pairs...
June 20, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28654321/redox-based-regulation-of-bacterial-development-and-behavior
#9
REVIEW
Abigail J Sporer, Lisa J Kahl, Alexa Price-Whelan, Lars E P Dietrich
Severe changes in the environmental redox potential, and resulting alterations in the oxidation states of intracellular metabolites and enzymes, have historically been considered negative stressors, requiring responses that are strictly defensive. However, recent work in diverse organisms has revealed that more subtle changes in the intracellular redox state can act as signals, eliciting responses with benefits beyond defense and detoxification. Changes in redox state have been shown to influence or trigger chromosome segregation, sporulation, aerotaxis, and social behaviors, including luminescence as well as biofilm establishment and dispersal...
June 20, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28498721/mechanisms-of-deubiquitinase-specificity-and-regulation
#10
REVIEW
Tycho E T Mevissen, David Komander
Protein ubiquitination is one of the most powerful posttranslational modifications of proteins, as it regulates a plethora of cellular processes in distinct manners. Simple monoubiquitination events coexist with more complex forms of polyubiquitination, the latter featuring many different chain architectures. Ubiquitin can be subjected to further posttranslational modifications (e.g., phosphorylation and acetylation) and can also be part of mixed polymers with ubiquitin-like modifiers such as SUMO (small ubiquitin-related modifier) or NEDD8 (neural precursor cell expressed, developmentally downregulated 8)...
June 20, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28498720/protein-misfolding-amyloid-formation-and-human-disease-a-summary-of-progress-over-the-last-decade
#11
REVIEW
Fabrizio Chiti, Christopher M Dobson
Peptides and proteins have been found to possess an inherent tendency to convert from their native functional states into intractable amyloid aggregates. This phenomenon is associated with a range of increasingly common human disorders, including Alzheimer and Parkinson diseases, type II diabetes, and a number of systemic amyloidoses. In this review, we describe this field of science with particular reference to the advances that have been made over the last decade in our understanding of its fundamental nature and consequences...
June 20, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28489421/mechanisms-and-functions-of-spatial-protein-quality-control
#12
REVIEW
Emily Mitchell Sontag, Rahul S Samant, Judith Frydman
A healthy proteome is essential for cell survival. Protein misfolding is linked to a rapidly expanding list of human diseases, ranging from neurodegenerative diseases to aging and cancer. Many of these diseases are characterized by the accumulation of misfolded proteins in intra- and extracellular inclusions, such as amyloid plaques. The clear link between protein misfolding and disease highlights the need to better understand the elaborate machinery that manages proteome homeostasis, or proteostasis, in the cell...
June 20, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28471691/the-evolution-of-organellar-coat-complexes-and-organization-of-the-eukaryotic-cell
#13
REVIEW
Michael P Rout, Mark C Field
Eukaryotic cells possess a remarkably diverse range of organelles that provide compartmentalization for distinct cellular functions and are likely responsible for the remarkable success of these organisms. The origins and subsequent elaboration of these compartments represent a key aspect in the transition between prokaryotic and eukaryotic cellular forms. The protein machinery required to build, maintain, and define many membrane-bound compartments is encoded by several paralog families, including small GTPases, coiled-bundle proteins, and proteins with β-propeller and α-solenoid secondary structures...
June 20, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28460188/proteasomal-and-autophagic-degradation-systems
#14
REVIEW
Ivan Dikic
Autophagy and the ubiquitin-proteasome system are the two major quality control pathways responsible for cellular homeostasis. As such, they provide protection against age-associated changes and a plethora of human diseases. Ubiquitination is utilized as a degradation signal by both systems, albeit in different ways, to mark cargoes for proteasomal and lysosomal degradation. Both systems intersect and communicate at multiple points to coordinate their actions in proteostasis and organelle homeostasis. This review summarizes molecular details of how proteasome and autophagy pathways are functionally interconnected in cells and indicates common principles and nodes of communication that can be therapeutically exploited...
June 20, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28441058/protein-misfolding-diseases
#15
F Ulrich Hartl
The majority of protein molecules must fold into defined three-dimensional structures to acquire functional activity. However, protein chains can adopt a multitude of conformational states, and their biologically active conformation is often only marginally stable. Metastable proteins tend to populate misfolded species that are prone to forming toxic aggregates, including soluble oligomers and fibrillar amyloid deposits, which are linked with neurodegeneration in Alzheimer and Parkinson disease, and many other pathologies...
June 20, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28441057/oxidative-stress
#16
REVIEW
Helmut Sies, Carsten Berndt, Dean P Jones
Oxidative stress is two sided: Whereas excessive oxidant challenge causes damage to biomolecules, maintenance of a physiological level of oxidant challenge, termed oxidative eustress, is essential for governing life processes through redox signaling. Recent interest has focused on the intricate ways by which redox signaling integrates these converse properties. Redox balance is maintained by prevention, interception, and repair, and concomitantly the regulatory potential of molecular thiol-driven master switches such as Nrf2/Keap1 or NF-κB/IκB is used for system-wide oxidative stress response...
June 20, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28426242/cellular-electron-cryotomography-toward-structural-biology-in-situ
#17
REVIEW
Catherine M Oikonomou, Grant J Jensen
Electron cryotomography (ECT) provides three-dimensional views of macromolecular complexes inside cells in a native frozen-hydrated state. Over the last two decades, ECT has revealed the ultrastructure of cells in unprecedented detail. It has also allowed us to visualize the structures of macromolecular machines in their native context inside intact cells. In many cases, such machines cannot be purified intact for in vitro study. In other cases, the function of a structure is lost outside the cell, so that the mechanism can be understood only by observation in situ...
June 20, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28426241/extracellular-heme-uptake-and-the-challenge-of-bacterial-cell-membranes
#18
REVIEW
Weiliang Huang, Angela Wilks
Iron is essential for the survival of most bacteria but presents a significant challenge given its limited bioavailability. Furthermore, the toxicity of iron combined with the need to maintain physiological iron levels within a narrow concentration range requires sophisticated systems to sense, regulate, and transport iron. Most bacteria have evolved mechanisms to chelate and transport ferric iron (Fe(3+)) via siderophore receptor systems, and pathogenic bacteria have further lowered this barrier by employing mechanisms to utilize the host's hemoproteins...
June 20, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28399656/teaching-old-dyes-new-tricks-biological-probes-built-from-fluoresceins-and-rhodamines
#19
REVIEW
Luke D Lavis
Small-molecule fluorophores, such as fluorescein and rhodamine derivatives, are critical tools in modern biochemical and biological research. The field of chemical dyes is old; colored molecules were first discovered in the 1800s, and the fluorescein and rhodamine scaffolds have been known for over a century. Nevertheless, there has been a renaissance in using these dyes to create tools for biochemistry and biology. The application of modern chemistry, biochemistry, molecular genetics, and optical physics to these old structures enables and drives the development of novel, sophisticated fluorescent dyes...
June 20, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28399655/cyclic-gmp-amp-as-an-endogenous-second-messenger-in-innate-immune-signaling-by-cytosolic-dna
#20
REVIEW
Kazuki Kato, Hiroki Omura, Ryuichiro Ishitani, Osamu Nureki
The innate immune system functions as the first line of defense against invading bacteria and viruses. In this context, the cGAS/STING [cyclic guanosine monophosphate (GMP)-adenosine monophosphate (AMP) synthase/STING] signaling axis perceives the nonself DNA associated with bacterial and viral infections, as well as the leakage of self DNA by cellular dysfunction and stresses, to elicit the host's immune responses. In this pathway, the noncanonical cyclic dinucleotide 2',3'-cyclic GMP-AMP (2',3'-cGAMP) functions as a second messenger for signal transduction: 2',3'-cGAMP is produced by the enzyme cGAS upon its recognition of double-stranded DNA, and then the 2',3'-cGAMP is recognized by the receptor STING to induce the phosphorylation of downstream factors, including TBK1 (TANK binding kinase 1) and IRF3 (interferon regulatory factor 3)...
June 20, 2017: Annual Review of Biochemistry
journal
journal
25554
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"