A tri-nucleotide mapping scheme based on residual volume of amino acids for short length exon prediction using sliding window DFT method

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Amit Kumar Singh ◽  
Vinay Kumar Srivastava
Keyword(s):  
Amino Acids ◽  
Sliding Window ◽  
Dft Method ◽  
Short Length ◽  
Residual Volume ◽  
Exon Prediction ◽  
Mapping Scheme

scholarly journals Theoretical Approach of the Adsorption of Herbicide Amitrole on the Soil using DFT Method

2018 ◽  
Vol 34 (3) ◽  
pp. 1240-1248
Author(s):  
Rabia Tazi ◽  
Hamza El Hadki ◽  
Mohammed Salah ◽  
Abdallah Zrineh ◽  
Mohammed El Azzouzi ◽  
...  
Keyword(s):  
Amino Acids ◽  
Organic Matter ◽  
Soil Organic Matter ◽  
Quantum Chemical ◽  
Dft Method ◽  
Aqueous Environment ◽  
Water As Solvent ◽  
Structural Configurations ◽  
Main Components ◽  
Global And Local

Quantum chemical calculations were performed on amitrole used as herbicide in agriculture to investigate its interaction with humic substances which are the main components of soil organic matter. They contain carboxylic, phenolic, amine and quinonic groups as well as specific structural configurations. Global and local reactivity have been studied to predict reactive centers and to determine the favorable site for interaction with surface. The results suggest us that hydrogen bonds are formed between this compound and the amino acids of soil organic matter. The effect of water as solvent is considered since adsorption of pesticide commonly occurs in aqueous environment.

Direct detection of inorganic ions and underivatized amino acids in seconds using high-speed capillary electrophoresis coupled with back-scatter interferometry

2021 ◽  
Author(s):  
Miyuru De Silva ◽  
Prabhavie M. Opallage ◽  
Robert C. Dunn
Keyword(s):  
Amino Acids ◽  
Capillary Electrophoresis ◽  
Amino Acid ◽  
High Speed ◽  
Direct Detection ◽  
Inorganic Ions ◽  
Short Length ◽  
Thin Wall ◽  
Underivatized Amino Acids

A short length, ultra-thin wall separation capillary combined with back-scatter interferometry enables amino acid separation and detection in seconds.

scholarly journals Improved activity of a synthetic indolicidin analog.

1997 ◽  
Vol 41 (4) ◽  
pp. 771-775 ◽  
Author(s):  
T J Falla ◽  
R E Hancock
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Candida Albicans ◽  
Short Length ◽  
Gram Negative Bacteria ◽  
Cationic Peptide ◽  
Gram Negative ◽  
Beta Galactosidase ◽  
Bovine Neutrophil ◽  
Positively Charged

A novel cationic peptide, CP-11, based on the structure of the bovine neutrophil peptide indolicidin, was designed to increase the number of positively charged residues, maintain the short length (13 amino acids), and enhance the amphipathicity relative to those of indolicidin. CP-11, and especially its carboxymethylated derivative, CP-11C, demonstrated improved activity against gram-negative bacteria and Candida albicans, while it maintained the activity of indolicidin against staphylococci and demonstrated a reduced ability to lyse erythrocytes. In Escherichia coli, CP-11 was better able than indolicidin to permeabilize both the outer membrane, as indicated by the enhancement of uptake of 1-N-phenylnaphthylamine, and the inner membrane, as determined by the unmasking of cytoplasmic beta-galactosidase, providing an explanation for its improved activity.

scholarly journals Small Toxic Proteins and the Antisense RNAs That Repress Them

2008 ◽  
Vol 72 (4) ◽  
pp. 579-589 ◽  
Author(s):  
Elizabeth M. Fozo ◽  
Matthew R. Hemm ◽  
Gisela Storz
Keyword(s):  
Amino Acids ◽  
Small Rna ◽  
Small Rnas ◽  
Short Length ◽  
Type I ◽  
Practical Applications ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas ◽  
Rna Genes ◽  
Toxic Proteins

SUMMARY There has been a great expansion in the number of small regulatory RNAs identified in bacteria. Some of these small RNAs repress the synthesis of potentially toxic proteins. Generally the toxin proteins are hydrophobic and less than 60 amino acids in length, and the corresponding antitoxin small RNA genes are antisense to the toxin genes or share long stretches of complementarity with the target mRNAs. Given their short length, only a limited number of these type I toxin-antitoxin loci have been identified, but it is predicted that many remain to be found. Already their characterization has given insights into regulation by small RNAs, has suggested functions for the small toxic proteins at the cell membrane, and has led to practical applications for some of the type I toxin-antitoxin loci.

scholarly journals Allowed N-glycosylation sites on the Kv1.2 potassium channel S1–S2 linker: implications for linker secondary structure and the glycosylation effect on channel function

2003 ◽  
Vol 375 (3) ◽  
pp. 769-775 ◽  
Author(s):  
Jing ZHU ◽  
Itaru WATANABE ◽  
Amanda POHOLEK ◽  
Matthew KOSS ◽  
Barbara GOMEZ ◽  
...  
Keyword(s):  
Amino Acids ◽  
Membrane Proteins ◽  
Glycosylation Site ◽  
Short Length ◽  
Loop Structure ◽  
Membrane Domains ◽  
Middle Section ◽  
Post Translational Modification ◽  
K Channels ◽  
Glycosylation Sites

N-glycosylation is a post-translational modification that plays a role in the trafficking and/or function of some membrane proteins. We have shown previously that N-glycosylation affected the function of some Kv1 voltage-gated potassium (K+) channels [Watanabe, Wang, Sutachan, Zhu, Recio-Pinto and Thornhill (2003) J. Physiol. (Cambridge, U.K.) 550, 51–66]. Kv1 channel S1–S2 linkers vary in length but their N-glycosylation sites are at similar relative positions from the S1 or S2 membrane domains. In the present study, by a scanning mutagenesis approach, we determined the allowed N-glycosylation sites on the Kv1.2 S1–S2 linker, which has 39 amino acids, by engineering N-glycosylation sites and assaying for glycosylation, using their sensitivity to glycosidases. The middle section of the linker (54% of linker) was glycosylated at every position, whereas both end sections (46% of linker) near the S1 or S2 membrane domains were not. These findings suggested that the middle section of the S1–S2 linker was accessible to the endoplasmic reticulum glycotransferase at every position and was in the extracellular aqueous phase, and presumably in a flexible conformation. We speculate that the S1–S2 linker is mostly a coiled-loop structure and that the strict relative position of native glycosylation sites on these linkers may be involved in the mechanism underlying the functional effects of glycosylation on some Kv1 K+ channels. The S3–S4 linker, with 16 amino acids and no N-glycosylation site, was not glycosylated when an N-glycosylation site was added. However, an extended linker, with an added N-linked site, was glycosylated, which suggested that the native linker was not glycosylated due to its short length. Thus other ion channels or membrane proteins may also have a high glycosylation potential on a linker but yet have similarly positioned native N-glycosylation sites among isoforms. This may imply that the native position of the N-glycosylation site may be important if the carbohydrate tree plays a role in the folding, stability, trafficking and/or function of the protein.

Synthesis, experimental and in silico studies of N-fluorenylmethoxycarbonyl-O-tert-butyl-N-methyltyrosine, coupled with CSD data: a survey of interactions in the crystal structures of Fmoc–amino acids

2020 ◽  
Vol 76 (4) ◽  
pp. 328-345 ◽  
Author(s):  
Joanna Bojarska ◽  
Milan Remko ◽  
Izabela D. Madura ◽  
Krzysztof Kaczmarek ◽  
Janusz Zabrocki ◽  
...  
Keyword(s):  
Amino Acids ◽  
Crystal Structures ◽  
In Silico ◽  
Density Functional ◽  
Crystal Packing ◽  
Noncovalent Interactions ◽  
Dft Method ◽  
Calculation Model ◽  
Hirshfeld Surface ◽  
In Silico Studies

Recently, fluorenylmethoxycarbonyl (Fmoc) amino acids (e.g. Fmoc–tyrosine or Fmoc–phenylalanine) have attracted growing interest in biomedical research and industry, with special emphasis directed towards the design and development of novel effective hydrogelators, biomaterials or therapeutics. With this in mind, a systematic knowledge of the structural and supramolecular features in recognition of those properties is essential. This work is the first comprehensive summary of noncovalent interactions combined with a library of supramolecular synthon patterns in all crystal structures of amino acids with the Fmoc moiety reported so far. Moreover, a new Fmoc-protected amino acid, namely, 2-{[(9H-fluoren-9-ylmethoxy)carbonyl](methyl)amino}-3-{4-[(2-hydroxypropan-2-yl)oxy]phenyl}propanoic acid or N-fluorenylmethoxycarbonyl-O-tert-butyl-N-methyltyrosine, Fmoc-N-Me-Tyr(t-Bu)-OH, C29H31NO5, was successfully synthesized and the structure of its unsolvated form was determined by single-crystal X-ray diffraction. The structural, conformational and energy landscape was investigated in detail by combined experimental and in silico approaches, and further compared to N-Fmoc-phenylalanine [Draper et al. (2015). CrystEngComm, 42, 8047–8057]. Geometries were optimized by the density functional theory (DFT) method either in vacuo or in solutio. The polarizable conductor calculation model was exploited for the evaluation of the hydration effect. Hirshfeld surface analysis revealed that H...H, C...H/H...C and O...H/H...O interactions constitute the major contributions to the total Hirshfeld surface area in all the investigated systems. The molecular electrostatic potentials mapped over the surfaces identified the electrostatic complementarities in the crystal packing. The prediction of weak hydrogen-bonded patterns via Full Interaction Maps was computed. Supramolecular motifs formed via C—H...O, C—H...π, (fluorenyl)C—H...Cl(I), C—Br...π(fluorenyl) and C—I...π(fluorenyl) interactions are observed. Basic synthons, in combination with the Long-Range Synthon Aufbau Modules, further supported by energy-framework calculations, are discussed. Furthermore, the relevance of Fmoc-based supramolecular hydrogen-bonding patterns in biocomplexes are emphasized, for the first time.

Sign in / Sign up

Export Citation Format

Share Document