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Biochemistry AND review

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https://www.readbyqxmd.com/read/28229928/an-expanded-genetic-code-for-probing-the-role-of-electrostatics-in-enzyme-catalysis-by-vibrational-stark-spectroscopy
#1
REVIEW
Jan-Stefan Völler, Hernan Biava, Peter Hildebrandt, Nediljko Budisa
BACKGROUND: To find experimental validation for electrostatic interactions essential for catalytic reactions represents a challenge due to practical limitations in assessing electric fields within protein structures. SCOPE OF REVIEW: This review examines the applications of non-canonical amino acids (ncAAs) as genetically encoded probes for studying the role of electrostatic interactions in enzyme catalysis. MAJOR CONCLUSIONS: ncAAs constitute sensitive spectroscopic probes to detect local electric fields by exploiting the vibrational Stark effect (VSE) and thus have the potential to map the protein electrostatics...
February 13, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28226215/multiple-functions-and-regulation-of-mammalian-peroxiredoxins
#2
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/28223859/histatin-peptides-pharmacological-functions-and-their-applications-in-dentistry
#3
REVIEW
Zohaib Khurshid, Shariq Najeeb, Maria Mali, Syed Faraz Moin, Syed Qasim Raza, Sana Zohaib, Farshid Sefat, Muhammad Sohail Zafar
There are many human oral antimicrobial peptides responsible for playing important roles including maintenance, repairing of oral tissues (hard or soft) and defense against oral microbes. In this review we have highlighted the biochemistry, physiology and proteomics of human oral histatin peptides, secreted from parotid and submandibular salivary glands in human. The significance of these peptides includes capability for ionic binding that can kill fungal Candida albicans. They have histidine rich amino acid sequences (7-12 family members; corresponding to residues 12-24, 13-24, 12-25, 13-25, 5-11, and 5-12, respectively) for Histatin-3...
January 2017: Saudi Pharmaceutical Journal: SPJ: the Official Publication of the Saudi Pharmaceutical Society
https://www.readbyqxmd.com/read/28211677/super-resolution-microscopy-shedding-light-on-the-cellular-plasma-membrane
#4
Matthew B Stone, Sarah A Shelby, Sarah L Veatch
Lipids and the membranes they form are fundamental building blocks of cellular life, and their geometry and chemical properties distinguish membranes from other cellular environments. Collective processes occurring within membranes strongly impact cellular behavior and biochemistry, and understanding these processes presents unique challenges due to the often complex and myriad interactions between membrane components. Super-resolution microscopy offers a significant gain in resolution over traditional optical microscopy, enabling the localization of individual molecules even in densely labeled samples and in cellular and tissue environments...
February 17, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28206852/british-journal-of-biomedical-science-in-2016-what-have-we-learned
#5
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/28202539/parps-and-adp-ribosylation-recent-advances-linking-molecular-functions-to-biological-outcomes
#6
REVIEW
Rebecca Gupte, Ziying Liu, W Lee Kraus
The discovery of poly(ADP-ribose) >50 years ago opened a new field, leading the way for the discovery of the poly(ADP-ribose) polymerase (PARP) family of enzymes and the ADP-ribosylation reactions that they catalyze. Although the field was initially focused primarily on the biochemistry and molecular biology of PARP-1 in DNA damage detection and repair, the mechanistic and functional understanding of the role of PARPs in different biological processes has grown considerably of late. This has been accompanied by a shift of focus from enzymology to a search for substrates as well as the first attempts to determine the functional consequences of site-specific ADP-ribosylation on those substrates...
January 15, 2017: Genes & Development
https://www.readbyqxmd.com/read/28194766/significance-of-ang-1-7-coupling-with-mas1-and-other-gpcrs-to-the-renin-angiotensin-system-iuphar-review-x
#7
REVIEW
Sadashiva S Karnik, Dhanachandra Khuraijam, Kalyan Tirupula, Hamiyet Unal
Angiotensins are a group of hormonal peptides including angiotensin II and angiotensin 1-7 produced by the renin angiotensin system. The biology, pharmacology and biochemistry of the receptors for angiotensins were extensively reviewed recently. In the review, the receptor nomenclature committee did not lay emphasis on designating MAS1 as the angiotensin 1-7 receptor on the basis of lack of classical G protein signaling and desensitization in response to angiotensin 1-7 as well as lack of consensus on confirmatory ligand pharmacological analyses...
February 14, 2017: British Journal of Pharmacology
https://www.readbyqxmd.com/read/28194570/genetic-and-biochemical-changes-of-the-serotonergic-system-in-migraine-pathobiology
#8
REVIEW
Claudia Francesca Gasparini, Robert Anthony Smith, Lyn Robyn Griffiths
Migraine is a brain disorder characterized by a piercing headache which affects one side of the head, located mainly at the temples and in the area around the eye. Migraine imparts substantial suffering to the family in addition to the sufferer, particularly as it affects three times more women than men and is most prevalent between the ages of 25 and 45, the years of child rearing. Migraine typically occurs in individuals with a genetic predisposition and is aggravated by specific environmental triggers. Attempts to study the biochemistry of migraine began as early as the 1960s and were primarily directed at serotonin metabolism after an increase of 5-hydroxyindoleacetic acid (5-HIAA), the main metabolite of serotonin was observed in urine of migraineurs...
December 2017: Journal of Headache and Pain
https://www.readbyqxmd.com/read/28187425/computational-lipidomics-and-lipid-bioinformatics-filling-in-the-blanks
#9
Josch Pauling, Edda Klipp
Lipids are highly diverse metabolites of pronounced importance in health and disease. While metabolomics is a broad field under the omics umbrella that may also relate to lipids, lipidomics is an emerging field which specializes in the identification, quantification and functional interpretation of complex lipidomes. Today, it is possible to identify and distinguish lipids in a high-resolution, high-throughput manner and simultaneously with a lot of structural detail. However, doing so may produce thousands of mass spectra in a single experiment which has created a high demand for specialized computational support to analyze these spectral libraries...
December 22, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28177894/one-carbon-metabolism-and-nucleotide-biosynthesis-as-attractive-targets-for-anticancer-therapy
#10
Oleg Shuvalov, Alexey Petukhov, Alexandra Daks, Olga Fedorova, Elena Vasileva, Nickolai A Barlev
Cancer-related metabolism has recently emerged as one of the "hallmarks of cancer". It has several important features, including altered metabolism of glucose and glutamine. Importantly, altered cancer metabolism connects different biochemical pathways into the one fine-tuned metabolic network, which stimulates high proliferation rates and plasticity to malignant cells. Among the keystones of cancer metabolism are one-carbon metabolism and nucleotide biosynthesis, which provide building blocks to anabolic reactions...
February 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28177242/nanodiscs-in-membrane-biochemistry-and-biophysics
#11
Ilia G Denisov, Stephen G Sligar
Membrane proteins play a most important part in metabolism, signaling, cell motility, transport, development, and many other biochemical and biophysical processes which constitute fundamentals of life on the molecular level. Detailed understanding of these processes is necessary for the progress of life sciences and biomedical applications. Nanodiscs provide a new and powerful tool for a broad spectrum of biochemical and biophysical studies of membrane proteins and are commonly acknowledged as an optimal membrane mimetic system that provides control over size, composition, and specific functional modifications on the nanometer scale...
February 8, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28162022/proteomic-analysis-of-red-blood-cells-and-the-potential-for-the-clinic-what-have-we-learned-so-far
#12
Angelo D'Alessandro, Lello Zolla
Red blood cells (RBC) are the most abundant host cells in the human body. Mature erythrocytes are devoid of nuclei and organelles and have always been regarded as circulating 'bags of hemoglobin'. The advent of proteomics has challenged this assumption, revealing unanticipated complexity and novel roles for RBCs not just in gas transport, but also in systemic metabolic homeostasis in health and disease. Areas covered: In this review we will summarize the main advancements in the field of discovery mode and redox/quantitative proteomics with respect to RBC biology...
March 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28153753/mistranslation-from-adaptations-to-applications
#13
REVIEW
Kyle S Hoffman, Patrick O'Donoghue, Christopher J Brandl
BACKGROUND: The conservation of the genetic code indicates that there was a single origin, but like all genetic material, the cell's interpretation of the code is subject to evolutionary pressure. Single nucleotide variations in tRNA sequences can modulate codon assignments by altering codon-anticodon pairing or tRNA charging. Either can increase translation errors and even change the code. The frozen accident hypothesis argued that changes to the code would destabilize the proteome and reduce fitness...
January 30, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28148393/analyses-of-alternative-polyadenylation-from-old-school-biochemistry-to-high-throughput-technologies
#14
Hsin-Sung Yeh, Wei Zhang, Jeongsik Yong
Alternations in usage of polyadenylation sites during transcription termination yield transcript isoforms from a gene. Recent findings of transcriptome-wide alternative polyadenylation (APA) as a molecular response to changes in biology position APA not only as a molecular event of early transcriptional termination but also as a cellular regulatory step affecting various biological pathways. With the development of high-throughput profiling technologies at a single nucleotide level and their applications targeted to the 3'-end of mRNAs, dynamics in the landscape of mRNA 3'-end is measureable at a global scale...
February 2, 2017: BMB Reports
https://www.readbyqxmd.com/read/28141967/telomerase-mechanism-of-telomere-synthesis
#15
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/28140328/impact-of-dietary-fibers-on-nutrient-management-and-detoxification-organs-gut-liver-and-kidneys
#16
REVIEW
Dorothy A Kieffer, Roy J Martin, Sean H Adams
Increased dietary fiber (DF) intake elicits a wide range of physiologic effects, not just locally in the gut, but systemically. DFs can greatly alter the gut milieu by affecting the gut microbiome, which in turn influences the gut barrier, gastrointestinal immune and endocrine responses, and nitrogen cycling and microbial metabolism. These gut-associated changes can then alter the physiology and biochemistry of the body's other main nutrient management and detoxification organs, the liver and kidneys. The molecular mechanisms by which DF alters the physiology of the gut, liver, and kidneys is likely through gut-localized events (i...
November 2016: Advances in Nutrition
https://www.readbyqxmd.com/read/28138099/polysaccharide-utilization-loci-fuelling-microbial-communities
#17
Julie M Grondin, Kazune Tamura, Guillaume Déjean, D Wade Abbott, Harry Brumer
The complex carbohydrates of terrestrial and marine biomass represent a rich nutrient source for free-living and mutualistic microbes alike. The enzymatic saccharification of these diverse substrates is of critical importance for fuelling a variety of complex microbial communities, including marine, soil, ruminant, and monogastric microbiota. Consequently, highly specific carbohydrate-active enzymes, recognition proteins, and transporters are enriched in the genomes of certain species, and are of critical importance in competitive environments...
January 30, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28130115/strategies-that-athletes-use-to-avoid-detection-of-androgenic-anabolic-steroid-doping-and-sanctions
#18
Hussain Alquraini, Richard J Auchus
Androgenic-anabolic steroids (AAS) are potent and widely used performance-enhancing substances (PES). Since the International Olympic Committee (IOC) began testing athletes for AAS in the 1970s, athletes and their teams have endeavored to beat the system to avoid doping violations and/or sanctions derived from positive test results. This review will discuss the strategies used to avoid detection based on the pharmacology, biochemistry, and genetics of AAS metabolism and testing principles. Another strategy used is to dope with testosterone under the guise that the athlete has a true medical condition that requires testosterone treatment, using the therapeutic use exemption (TUE) mechanism...
January 24, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28125290/molecular-characteristics-and-biological-functions-of-surface-active-and-surfactant-proteins
#19
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
#20
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
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