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In the present work we demonstrate that linker amino acids promote engagement with DNA.
If control of DNA function is exerted through firmly bound amino-acids and peptides, then DNA from bacteria grown under these two sets of conditions should contain different amounts of amino-acids.
Our findings suggest that some of the conserved amino acids may be involved in DNA recognition and binding.
These data describe a probable cellular-DNA binding platform that involves at least 5 amino acids, in the following order of importance: 124>128>(98, 125)>123.
The amino acids found complexed to DNA in intact cells by chromate were thought to originate from reactions of free amino acids or small peptides with the DNA rather than being proteolytic products derived from larger proteins that were cross-linked to the DNA.
Thus, we predict that appropriate amino acids at these positions may form contacts with DNA.
Amino acids likely provide building blocks for nucleic acids, peptidoglycan, and protein synthesis.
In conclusion, the majority of amino acid-base interactions observed follow general principles that apply across all protein-DNA complexes, although there are individual exceptions.
Our data suggest that the occurrence of additional amino acids that are widely distributed and genetically encoded is unlikely.

Related Questions

Amino acid fish gene expression5 answersAmino acid gene expression in fish has been studied in several species including common carp (Zhang et al., 2020), rainbow trout (Brezas et al., 2020), turbot (Xu et al., 2017), grass carp (Chen, 2012), and rainbow trout (Calo et al., 2018). These studies have identified various genes involved in amino acid metabolism and transport. In common carp, genome-wide association analysis identified 62 genes associated with amino acid content (Zhang et al., 2020). Transcriptome analysis in rainbow trout showed that expression levels of intestinal amino acid transporters were affected by diet and strain (Brezas et al., 2020). Turbot exhibited distinct expression patterns of peptide and amino acid transporter genes along the digestive tract (Xu et al., 2017). Grass carp showed tissue-specific expression of the y+LAT2 gene, which is involved in amino acid transport (Chen, 2012). Rainbow trout expressed mRNA encoding amino acid receptors in the gastrointestinal tract (Calo et al., 2018). These studies provide insights into the genetic mechanisms and physiological adaptations related to amino acid metabolism in fish.
Are there any known amino acid sequences?5 answersThere are several known amino acid sequences mentioned in the abstracts. One sequence is represented by SEQ ID No.1 and is used for determining the clinic boundary of the quantity of protective CMV specific CD8+T cells in peripheral blood of a patient. Another sequence is an N-terminal amino acid sequence of 13 special thermophilic Fe/Mn-SOD from Geobacillus category, which improves heat-resistance temperature and heat stability of SOD. There is also an amino acid sequence shown in SEQ ID No.8 that is used in identification of an odor compound, specifically n-heptaldehyde. Additionally, there are amino acid sequences of mitochondrial and cytosolic aspartate aminotransferases that have been studied and compared in various species, including pig, horse, rat, human, chicken, and Escherichia coli. Lastly, there is an amino acid sequence used for detecting blood plasma POU5F1 natural antibodies, which has applications in tumor risk prediction and clinical tumor prevention.
Is there amino acid in milk?5 answersYes, milk contains amino acids. Amino acids are the building blocks of proteins, and milk is a good source of high-quality proteins that contain all essential amino acids. Additionally, milk-containing beverages can have a relatively high content of amino acids, providing nutritional value and excellent taste and flavor. Human milk, in particular, has been found to contain various free amino acids, which can have an important role in infants' growth and development. Furthermore, amino acid milk coatings and amino acid cleansing milk have been developed, providing convenient and easily available options for home use. Therefore, milk and milk-containing products can be considered as a source of amino acids.
Does fish oil contain amino acids?9 answers
How many amino acids are there in human?10 answers
Which is best amino acid?10 answers

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What are the ideal temperature ranges for storing E. coli samples in culture for laboratory tests?
5 answers
The ideal temperature ranges for storing E. coli samples in culture for laboratory tests vary based on the specific conditions. E. coli strains stored at 4 °C for over 40–50 years retained viability and characteristic features. Additionally, storing E. coli cells at 2 to 8°C in 0.9% NaCl for 30 days maintained viability. However, the viability of E. coli cells decreased when stored at higher temperatures such as 15, 20, and 25 °C, especially in hyperosmotic conditions. Freezing E. coli samples at -24 and -80 °C before subjecting them to high hydrostatic pressure (HHP) led to significant reductions in bacterial counts, indicating enhanced microbial inactivation. Therefore, for optimal preservation and viability of E. coli samples in laboratory settings, storing them at lower temperatures around 4 °C or freezing them at ultra-low temperatures like -80 °C could be beneficial.
How do oomycetes absorb nutrients oomycetes OR absorb OR nutrients site:.edu, site:.org, site:.gov?
5 answers
Oomycetes absorb nutrients through various mechanisms depending on their lifestyle and interactions with hosts. They utilize extracellular digestion by secreting enzymes to break down organic material, reabsorbing the digested nutrients. In pathogen-host symbiosis, oomycetes adapt their metabolism to facilitate interactions with hosts, with plant pathogenic oomycetes showing variations in metabolic networks linked to lifestyle differences. During infection, oomycetes like Phytophthora infestans and Pythium ultimum exhibit distinct metabolic gene expression patterns, with Ph. infestans relying more on host nutrients during its biotrophic stage and transitioning to necrotrophy later on. Additionally, oomycete phytopathogens have evolved to colonize plants by using effectors to interfere with host processes, including fundamental metabolisms that indirectly affect defenses.
What are molar extinction coefficients?
4 answers
Molar extinction coefficients refer to the measure of how strongly a substance absorbs light at a particular wavelength. These coefficients have been extensively studied across various organic compounds, proteins, amino acids, and other biomolecules. The values of molar extinction coefficients are influenced by factors such as energy, effective atomic number, and the nature of atoms present in the molecules. For instance, different amino acids exhibit varying molar extinction coefficients, with tryptophan having a significantly higher value compared to others. Experimental and theoretical studies have shown good agreement in determining these coefficients, highlighting their importance in understanding the light absorption properties of different substances across a wide range of photon energies.
How have mass spectrometry instruments evolved over time in the analysis of triple-negative breast cancer (TNBC)?
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Mass spectrometry (MS) instruments have evolved significantly in the analysis of triple-negative breast cancer (TNBC). High-resolution MS instruments like time-of-flight (TOF) and Orbitrap MS have become prominent due to their sensitivity and selectivity. Novel approaches, such as colloidosomes-coupled matrix-assisted laser desorption/ionization time-of-flight MS, have been developed for TNBC diagnosis, offering high sensitivity and accuracy with minimal sample consumption. Liquid chromatography-tandem MS assays have enabled the detection of specific lipid biomarkers for TNBC, distinguishing TNBC from controls with high sensitivity and specificity. Additionally, conductive spray polymer ionization MS combined with machine learning has facilitated rapid metabolic fingerprinting for TNBC diagnosis and serum screening with high sensitivity and specificity. These advancements showcase the continuous progress in MS technology for TNBC analysis.
Can hypochlorous acid spray effectively treat folliculitis in humans?
5 answers
Hypochlorous acid (HOCl) has shown promise in treating various skin conditions, including folliculitis, due to its antimicrobial and wound healing properties. Studies have highlighted the effectiveness of HOCl in treating skin wounds, pruritus, diabetic ulcers, and inflammatory skin disorders. HOCl is known for its potent antimicrobial activity against a wide range of microorganisms, making it a potential alternative to conventional antibiotics. The use of stable HOCl formulations has made it viable for routine treatment of skin infections, with reports of improved healing of ulcers and significant antimicrobial activity against common bacteria. Additionally, HOCl has been investigated for its wound healing properties in hair transplant procedures, showcasing its potential as a post-operative wound healing aid. Therefore, HOCl spray may effectively treat folliculitis in humans by targeting the underlying microbial infection and promoting wound healing.
What are the different sources and uses of hyaluronidase?
5 answers
Hyaluronidase, an enzyme that degrades hyaluronic acid, is sourced from various organisms like bacteria, insects, snakes, fish, and mammals, with six identified types in humans. Its uses span across different medical fields, including dermatology, plastic surgery, and ophthalmology. In dermatology, hyaluronidase aids in drug delivery, treats mucin-related disorders, and assists in surgeries like dermatofibrosarcoma protuberans. Plastic surgery benefits from hyaluronidase in managing filler complications, skin graft harvesting, and scar treatment. Additionally, it is utilized in cancer therapy, drug dispersion, and reducing tissue edema. The enzyme's applications continue to expand, making it a valuable tool in various clinical scenarios.
Is any enzyme capable for decarboxylate 3,5-dihydrohybenzoate?
5 answers
Yes, enzymes capable of decarboxylating 3,5-dihydroxybenzoate have been identified. A 3,4-dihydroxybenzoate decarboxylase from Clostridium hydroxybenzoicum JW/Z-1T was found to catalyze the decarboxylation of 3,4-dihydroxybenzoate. Additionally, a new oxidative decarboxylation pathway for 3,5-dibromo-4-hydroxybenzoate (DBHB) catabolism was discovered in Pigmentiphaga sp. strain H8, involving the enzyme OdcA that mediates the oxidative decarboxylation of DBHB to 2,6-dibromohydroquinone. These findings highlight the enzymatic capability for decarboxylating hydroxybenzoate compounds, shedding light on the diverse enzymatic pathways involved in the catabolism of such aromatic compounds.
Can acly be biotinylated?
5 answers
Yes, acyl can be biotinylated. Biotinylation is the process of attaching biotin to a molecule, and it is commonly used in various research applications. While biotinylation is often associated with proteins, it can also be applied to other molecules, including acyl compounds. Biotinylation can occur through in vitro chemical synthesis, where biotin is covalently linked to reactive functional groups on the molecule. Additionally, biotinylation techniques, such as amide bond formation, [3+2] cycloadditions, Staudinger ligation, and thioether formation, can be utilized to attach biotin to small molecules like acyl compounds. Therefore, acyl compounds can indeed undergo biotinylation, expanding the scope of molecules that can be labeled and studied using this versatile technique.
Amino-acid- and peptide-directed synthesis of chiral plasmonic gold nanoparticles
4 answers
Amino acids and peptides have been utilized to direct the synthesis of chiral plasmonic gold nanoparticles with exceptional optical properties. These nanoparticles exhibit high chiroptic responses and unique morphologies, such as cube-like outlines with chiral wings or rhombic dodecahedron-like shapes with curved edges and elliptical cavities. Strategies have been developed to enhance the uniformity and optical activity of these chiral nanoparticles, resulting in improved dissymmetry factors and precise control over their properties. By systematically varying peptide sequences, particularly in the β-sheet region, it is possible to tailor the assembly and optical properties of gold nanoparticle superstructures, leading to the formation of helical structures with tunable metrics and chiroptical characteristics.
Are there examples of uncouplers that lower body temperature?
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Various uncouplers have been identified that can lower body temperature by dissipating energy as heat instead of producing ATP. For instance, the mitochondrial uncoupling protein 1 (UCP1) found in brown adipose tissue is crucial for generating heat during cold exposure to defend body temperature. Additionally, studies have explored the use of chemical uncouplers like dinitrophenol (DNP) to increase mitochondrial uncoupling, leading to a decrease in metabolic efficiency and potentially lowering body temperature. Moreover, recent research has introduced a novel mitochondrial uncoupler named BAM15, which selectively uncouples mitochondria without affecting the plasma membrane potential, showing promise in protecting against ischemia-reperfusion injury in kidneys and potentially influencing body temperature regulation. These examples highlight the role of uncouplers in modulating body temperature through mitochondrial uncoupling mechanisms.
Is ABCG2 a knotted homodimer?
4 answers
Yes, ABCG2 is a homodimeric ATP-binding cassette (ABC) transporter that plays a crucial role in multidrug resistance in cancer cells. Structural studies have revealed that ABCG2 forms a symmetric homodimer configuration, with a key amino acid residue, F439, being essential for both transport and binding of various substrates and inhibitors. Molecular dynamics simulations and docking studies have provided insights into the structural stability and drug-binding sites of the ABCG2 homodimer. Additionally, investigations using bimolecular fluorescence complementation have confirmed the formation of specific ABCG2 dimers, supporting the concept of ABCG2 functioning as a homodimer. These findings collectively highlight the homodimeric nature of ABCG2 and its significance in mediating drug resistance mechanisms in cancer cells.