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Annual Review of Biochemistry

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https://www.readbyqxmd.com/read/29394096/protein-quality-control-of-the-endoplasmic-reticulum-and-ubiquitin-proteasome-triggered-degradation-of-aberrant-proteins-yeast-pioneers-the-path
#1
Nicole Berner, Karl-Richard Reutter, Dieter H Wolf
Cells must constantly monitor the integrity of their macromolecular constituents. Proteins are the most versatile class of macromolecules but are sensitive to structural alterations. Misfolded or otherwise aberrant protein structures lead to dysfunction and finally aggregation. Their presence is linked to aging and a plethora of severe human diseases. Thus, misfolded proteins have to be rapidly eliminated. Secretory proteins constitute more than one-third of the eukaryotic proteome. They are imported into the endoplasmic reticulum (ER), where they are folded and modified...
February 2, 2018: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29401000/principles-of-protein-stability-and-their-application-in-computational-design
#2
Adi Goldenzweig, Sarel Fleishman
Proteins are increasingly used in basic and applied biomedical research.Many proteins, however, are only marginally stable and can be expressed in limited amounts, thus hampering research and applications. Research has revealed the thermodynamic, cellular, and evolutionary principles and mechanisms that underlie marginal stability. With this growing understanding, computational stability design methods have advanced over the past two decades starting from methods that selectively addressed only some aspects of marginal stability...
January 26, 2018: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29328784/dna-encoded-chemical-libraries-a-selection-system-based-on-endowing-organic-compounds-with-amplifiable-information
#3
Dario Neri, Richard A Lerner
The discovery of organic ligands that bind specifically to proteins is a central problem in chemistry, biology, and the biomedical sciences. The encoding of individual organic molecules with distinctive DNA tags, serving as amplifiable identification bar codes, allows the construction and screening of combinatorial libraries of unprecedented size, thus facilitating the discovery of ligands to many different protein targets. Fundamentally, one links powers of genetics and chemical synthesis. After the initial description of DNA-encoded chemical libraries in 1992, several experimental embodiments of the technology have been reduced to practice...
January 12, 2018: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29328783/signaling-to-and-from-the-rna-polymerase-iii-transcription-and-processing-machinery
#4
Ian M Willis, Robyn D Moir
RNA polymerase (Pol) III has a specialized role in transcribing the most abundant RNAs in eukaryotic cells, transfer RNAs (tRNAs), along with other ubiquitous small noncoding RNAs, many of which have functions related to the ribosome and protein synthesis. The high energetic cost of producing these RNAs and their central role in protein synthesis underlie the robust regulation of Pol III transcription in response to nutrients and stress by growth regulatory pathways. Downstream of Pol III, signaling impacts posttranscriptional processes affecting tRNA function in translation and tRNA cleavage into smaller fragments that are increasingly attributed with novel cellular activities...
January 12, 2018: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29298091/lesion-bypass-and-the-reactivation-of-stalled-replication-forks
#5
Kenneth J Marians
Accurate transmission of the genetic information requires complete duplication of the chromosomal DNA each cell division cycle. However, the idea that replication forks would form at origins of DNA replication and proceed without impairment to copy the chromosomes has proven naive. It is now clear that replication forks stall frequently as a result of encounters between the replication machinery and template damage, slow-moving or paused transcription complexes, unrelieved positive superhelical tension, covalent protein-DNA complexes, and as a result of cellular stress responses...
January 3, 2018: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29272143/biological-insight-from-super-resolution-microscopy-what-we-can-learn-from-localization-based-images
#6
David Baddeley, Joerg Bewersdorf
Super-resolution optical imaging based on the switching and localization of individual fluorescent molecules [photoactivated localization microscopy (PALM), stochastic optical reconstruction microscopy (STORM), etc.] has evolved remarkably over the last decade. Originally driven by pushing technological limits, it has become a tool of biological discovery. The initial demand for impressive pictures showing well-studied biological structures has been replaced by a need for quantitative, reliable data providing dependable evidence for specific unresolved biological hypotheses...
December 22, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29195049/a-solid-state-conceptualization-of-information-transfer-from-gene-to-message-to-protein
#7
Masato Kato, Steven L McKnight
In this review, we describe speculative ideas and early stage research concerning the flow of genetic information from the nuclear residence of genes to the disparate, cytoplasmic sites of protein synthesis. We propose that this process of information transfer is meticulously guided by transient structures formed from protein segments of low sequence complexity/intrinsic disorder. These low complexity domains are ubiquitously associated with regulatory proteins that control gene expression and RNA biogenesis, but they are also found in the central channel of nuclear pores, the nexus points of intermediate filament assembly, and the locations of action of other well-studied cellular proteins and pathways...
December 1, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28841344/retrospective-on-cholesterol-homeostasis-the-central-role-of-scap
#8
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
#9
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-b-12-gene-regulation-by-cobalamin-based-photoreceptors
#10
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 B12that 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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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