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Journal of Biochemistry

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https://www.readbyqxmd.com/read/28301769/reconstructing-ancient-proteins-to-understand-the-causes-of-structure-and-function
#1
Georg K A Hochberg, Joseph W Thornton
A central goal in biochemistry is to explain the causes of protein sequence, structure, and function. Mainstream approaches rationalize sequence and structure by how they determine function and compare related proteins to find mechanisms underlying their functional differences. Although productive, both strategies suffer from intrinsic limitations that have left important aspects of many proteins unexplained. These limits can be overcome by reconstructing ancient proteins, experimentally characterizing their properties, and retracing their evolution through time...
March 15, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28301754/bioanalytical-measurements-enabled-by-surface-enhanced-raman-scattering-sers-probes
#2
Lauren E Jamieson, Steven M Asiala, Kirsten Gracie, Karen Faulds, Duncan Graham
Since its discovery in 1974, surface-enhanced Raman scattering (SERS) has gained momentum as an important tool in analytical chemistry. SERS is used widely for analysis of biological samples, ranging from in vitro cell culture models, ex vivo tissue and blood samples, and direct in vivo application. New insights have been gained into biochemistry, with an emphasis on biomolecule detection, from small molecules such as glucose and amino acids to larger biomolecules such as DNA, proteins, and lipids. These measurements have increased our understanding of biological systems, and significantly, they have improved diagnostic capabilities...
February 23, 2017: Annual Review of Analytical Chemistry
https://www.readbyqxmd.com/read/28301747/single-cell-transcriptional-analysis
#3
Angela R Wu, Jianbin Wang, Aaron M Streets, Yanyi Huang
Despite being a relatively recent technological development, single-cell transcriptional analysis through high-throughput sequencing has already been used in hundreds of fruitful studies to make exciting new biological discoveries that would otherwise be challenging or even impossible. Consequently, this has fueled a virtuous cycle of even greater interest in the field and compelled development of further improved technical methodologies and approaches. Thanks to the combined efforts of the research community, including the fields of biochemistry and molecular biology, technology and instrumentation, data science, computational biology, and bioinformatics, the single-cell RNA-sequencing field is advancing at a pace that is both astounding and unprecedented...
March 16, 2017: Annual Review of Analytical Chemistry
https://www.readbyqxmd.com/read/28301744/endoplasmic-reticulum-plasma-membrane-contact-sites
#4
Yasunori Saheki, Pietro De Camilli
The endoplasmic reticulum (ER) has a broad localization throughout the cell and forms direct physical contacts with all other classes of membranous organelles, including the plasma membrane (PM). A number of protein tethers that mediate these contacts have been identified, and study of these protein tethers has revealed a multiplicity of roles in cell physiology, including regulation of intracellular Ca(2+) dynamics and signaling as well as control of lipid traffic and homeostasis. In this review, we discuss the cross talk between the ER and the PM mediated by direct contacts...
February 23, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28301743/eukaryotic-dna-replication-fork
#5
Peter M J Burgers, Thomas A Kunkel
This review focuses on the biogenesis and composition of the eukaryotic DNA replication fork, with an emphasis on the enzymes that synthesize DNA and repair discontinuities on the lagging strand of the replication fork. Physical and genetic methodologies aimed at understanding these processes are discussed. The preponderance of evidence supports a model in which DNA polymerase ε (Pol ε) carries out the bulk of leading strand DNA synthesis at an undisturbed replication fork. DNA polymerases α and δ carry out the initiation of Okazaki fragment synthesis and its elongation and maturation, respectively...
March 1, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28301742/microbial-rhodopsins-diversity-mechanisms-and-optogenetic-applications
#6
Elena G Govorunova, Oleg A Sineshchekov, Hai Li, John L Spudich
Microbial rhodopsins are a family of photoactive retinylidene proteins widespread throughout the microbial world. They are notable for their diversity of function, using variations of a shared seven-transmembrane helix design and similar photochemical reactions to carry out distinctly different light-driven energy and sensory transduction processes. Their study has contributed to our understanding of how evolution modifies protein scaffolds to create new protein chemistry, and their use as tools to control membrane potential with light is fundamental to optogenetics for research and clinical applications...
March 9, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28301741/mechanisms-of-autophagy-initiation
#7
James H Hurley, Lindsey N Young
Autophagy is the process of cellular self-eating by a double-membrane organelle, the autophagosome. A range of signaling processes converge on two protein complexes to initiate autophagy: the ULK1 (unc51-like autophagy activating kinase 1) protein kinase complex and the PI3KC3- C1 (class III phosphatidylinositol 3-kinase complex I) lipid kinase complex. Some 90% of the mass of these large protein complexes consists of noncatalytic domains and subunits, and the ULK1 complex has essential noncatalytic activities...
March 15, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28301740/mitochondrial-machineries-for-protein-import-and-assembly
#8
Nils Wiedemann, Nikolaus Pfanner
Mitochondria are essential organelles with numerous functions in cellular metabolism and homeostasis. Most of the >1,000 different mitochondrial proteins are synthesized as precursors in the cytosol and are imported into mitochondria by five transport pathways. The protein import machineries of the mitochondrial membranes and aqueous compartments reveal a remarkable variability of mechanisms for protein recognition, translocation, and sorting. The protein translocases do not operate as separate entities but are connected to each other and to machineries with functions in energetics, membrane organization, and quality control...
March 15, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28301739/systems-biology-of-metabolism
#9
Jens Nielsen
Metabolism is highly complex and involves thousands of different connected reactions; it is therefore necessary to use mathematical models for holistic studies. The use of mathematical models in biology is referred to as systems biology. In this review, the principles of systems biology are described, and two different types of mathematical models used for studying metabolism are discussed: kinetic models and genome-scale metabolic models. The use of different omics technologies, including transcriptomics, proteomics, metabolomics, and fluxomics, for studying metabolism is presented...
March 8, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28248237/comparative-skeletal-muscle-proteomics-using-two-dimensional-gel-electrophoresis
#10
REVIEW
Sandra Murphy, Paul Dowling, Kay Ohlendieck
The pioneering work by Patrick H. O'Farrell established two-dimensional gel electrophoresis as one of the most important high-resolution protein separation techniques of modern biochemistry (Journal of Biological Chemistry1975, 250, 4007-4021). The application of two-dimensional gel electrophoresis has played a key role in the systematic identification and detailed characterization of the protein constituents of skeletal muscles. Protein changes during myogenesis, muscle maturation, fibre type specification, physiological muscle adaptations and natural muscle aging were studied in depth by the original O'Farrell method or slightly modified gel electrophoretic techniques...
September 9, 2016: Proteomes
https://www.readbyqxmd.com/read/28226215/multiple-functions-and-regulation-of-mammalian-peroxiredoxins
#11
Sue Goo Rhee, In Sup Kil
Peroxiredoxins (Prxs) constitute a major family of peroxidases, with mammalian cells expressing six Prx isoforms (PrxI to PrxVI). Cells produce hydrogen peroxide (H2O2) at various intracellular locations where it can serve as a signaling molecule. Given that Prxs are abundant and possess a structure that renders the cysteine (Cys) residue at the active site highly sensitive to oxidation by H2O2, the signaling function of this oxidant requires extensive and highly localized regulation. Recent findings on the reversible regulation of PrxI through phosphorylation at the centrosome and on the hyperoxidation of the Cys at the active site of PrxIII in mitochondria are described in this review as examples of such local regulation of H2O2 signaling...
February 2, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28218647/diabetes-mellitus-and-younger-age-are-risk-factors-for-hyperphosphatemia-in-peritoneal-dialysis-patients
#12
Rameez Imtiaz, Steven Hawken, Brendan B McCormick, Simon Leung, Swapnil Hiremath, Deborah L Zimmerman
Hyperphosphatemia has been associated with adverse outcomes in patients with end stage kidney disease (ESKD). The purpose of this study was to determine risk factors for hyperphosphatemia in ESKD patients treated with peritoneal dialysis (PD). This information will be used to develop a patient specific phosphate binder application to facilitate patient self-management of serum phosphate. Adult PD patients documented their food, beverage, and phosphate binder intake for three days using a dietitian developed food journal...
February 17, 2017: Nutrients
https://www.readbyqxmd.com/read/28206852/british-journal-of-biomedical-science-in-2016-what-have-we-learned
#13
Andrew Blann
In 2016, the British Journal of Biomedical Science published 36 reports outlining specific advances in each of the various disciplines within biomedical science. These were one review, 25 original articles, 9 'In Brief' reports and one letter to the Editor. Of these, the majority were in blood science (5 in biochemistry, 7 in haematology and 2 in immunology) and infection science (8 in microbiology, 2 in virology) with a smaller number in cellular sciences (6 in cellular pathology and 2 in cytopathology). Three reports considered both biochemistry and immunology, while another reported an advance in the identification of chromosomal abnormalities...
January 2017: British Journal of Biomedical Science
https://www.readbyqxmd.com/read/28141967/telomerase-mechanism-of-telomere-synthesis
#14
R Alex Wu, Heather E Upton, Jacob M Vogan, Kathleen Collins
Telomerase is the essential reverse transcriptase required for linear chromosome maintenance in most eukaryotes. Telomerase supplements the tandem array of simple-sequence repeats at chromosome ends to compensate for the DNA erosion inherent in genome replication. The template for telomerase reverse transcriptase is within the RNA subunit of the ribonucleoprotein complex, which in cells contains additional telomerase holoenzyme proteins that assemble the active ribonucleoprotein and promote its function at telomeres...
January 30, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28125290/molecular-characteristics-and-biological-functions-of-surface-active-and-surfactant-proteins
#15
Margaret Sunde, Chi L L Pham, Ann H Kwan
Many critical biological processes take place at hydrophobic:hydrophilic interfaces, and a wide range of organisms produce surface-active proteins and peptides that reduce surface and interfacial tension and mediate growth and development at these boundaries. Microorganisms produce both small lipid-associated peptides and amphipathic proteins that allow growth across water:air boundaries, attachment to surfaces, predation, and improved bioavailability of hydrophobic substrates. Higher-order organisms produce surface-active proteins with a wide variety of functions, including the provision of protective foam environments for vulnerable reproductive stages, evaporative cooling, and gas exchange across airway membranes...
January 11, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28125289/structural-studies-of-amyloid-proteins-at-the-molecular-level
#16
David S Eisenberg, Michael R Sawaya
Dozens of proteins are known to convert to the aggregated amyloid state. These include fibrils associated with systemic and neurodegenerative diseases and cancer, functional amyloid fibrils in microorganisms and animals, and many denatured proteins. Amyloid fibrils can be much more stable than other protein assemblies. In contrast to globular proteins, a single protein sequence can aggregate into several distinctly different amyloid structures, termed polymorphs, and a given polymorph can reproduce itself by seeding...
January 3, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28125288/at-the-intersection-of-chemistry-biology-and-medicine
#17
Christopher T Walsh
After an undergraduate degree in biology at Harvard, I started graduate school at The Rockefeller Institute for Medical Research in New York City in July 1965. I was attracted to the chemical side of biochemistry and joined Fritz Lipmann's large, hierarchical laboratory to study enzyme mechanisms. That work led to postdoctoral research with Robert Abeles at Brandeis, then a center of what, 30 years later, would be called chemical biology. I spent 15 years on the Massachusetts Institute of Technology faculty, in both the Chemistry and Biology Departments, and then 26 years on the Harvard Medical School Faculty...
January 11, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28043964/interview-with-the-guest-editor-andrew-ewald
#18
(no author information available yet)
Andrew Ewald is an Associate Professor of Cell Biology, Oncology and Biomedical Engineering at the Johns Hopkins University School of Medicine, Baltimore, MD. He joined the Johns Hopkins faculty in 2008, after postdoctoral work with Zena Werb in mammary biology and cancer at the University of California, San Francisco. Andrew earned his PhD in 2003 in biochemistry and molecular biophysics from the California Institute of Technology, studying with Scott Fraser. Andrew studies how organs form and how breast cancer progresses to metastasis...
January 1, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/27981758/the-febs-journal-in-2017-quality-is-its-own-reward
#19
EDITORIAL
Seamus J Martin
Welcome to the first issue of 2017. I very much hope that the past year has been a productive one for all of you and that your research endeavors continue to be successful, despite the very challenging funding climate that many face. On a more positive note, the past year has been an excellent one for The FEBS Journal, with our new impact factor placing us within the top quartile of journals in Biochemistry and Molecular Biology and signs of this improving further in 2017. This article is protected by copyright...
December 15, 2016: FEBS Journal
https://www.readbyqxmd.com/read/27959639/physicochemical-property-variation-in-spider-silk-ecology-evolution-and-synthetic-production
#20
Sean J Blamires, Todd A Blackledge, I-Min Tso
The unique combination of great stiffness, strength, and extensibility makes spider major ampullate (MA) silk desirable for various biomimetic and synthetic applications. Intensive research on the genetics, biochemistry, and biomechanics of this material has facilitated a thorough understanding of its properties at various levels. Nevertheless, methods such as cloning, recombination, and electrospinning have not successfully produced materials with properties as impressive as those of spider silk. It is nevertheless becoming clear that silk properties are a consequence of whole-organism interactions with the environment in addition to genetic expression, gland biochemistry, and spinning processes...
January 31, 2017: Annual Review of Entomology
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