Differential effect of amino acid residues on the stability of double helices formed from polyribonucleotides and its possible relation to the evolution of the genetic code

1985 ◽  
Vol 21 (2) ◽  
pp. 192-198 ◽  
Author(s):  
Dietmar Porschke
Keyword(s):  
Amino Acid ◽  
Genetic Code ◽  
Differential Effect ◽  
Amino Acid Residues ◽  
Double Helices ◽  
The Stability

Structure of the genetic code suggested by the hydropathy correlation between anticodons and amino acid residues

2006 ◽  
Vol 37 (1) ◽  
pp. 83-103 ◽  
Author(s):  
Sávio Torres de Farias ◽  
Carlos Henrique Costa Moreira ◽  
Romeu Cardoso Guimarães
Keyword(s):  
Amino Acid ◽  
Genetic Code ◽  
Amino Acid Residues

scholarly journals Synthesis and Evaluation of Cyclic Acetals of Serine Hydroxylamine for Amide-Forming KAHA Ligations

Synthesis ◽  
2019 ◽  
Vol 51 (05) ◽  
pp. 1273-1283 ◽  
Author(s):  
Simon Baldauf ◽  
Jeffrey Bode
Keyword(s):  
Amino Acid ◽  
Amino Acid Residue ◽  
Amino Acid Residues ◽  
High Demand ◽  
Cyclic Acetals ◽  
Ligation Product ◽  
Canonical Amino Acid ◽  
The Stability ◽  
Peptide Segments ◽  
Derivatives Of

The α-ketoacid–hydroxylamine (KAHA) ligation allows the coupling of unprotected peptide segments. The most widely used variant employs a 5-membered cyclic hydroxylamine that forms a homoserine ester as the primary ligation product. While very effective, monomers that give canonical amino acid residues are in high demand. In order to preserve the stability and reactivity of cyclic hydroxylamines, but form a canonical amino acid residue upon ligation, we sought to prepare cyclic derivatives of serine hydroxylamine. An evaluation of several cyclization strategies led to cyclobutanone ketals as the leading structures. The preparation, stability, and amide-forming ligation of these serine-derived ketals are described.

scholarly journals Characterization and Incidence of the First Member of the Genus Mitovirus Identified in the Phytopathogenic Species Fusarium oxysporum

Viruses ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 279 ◽  
Author(s):  
Almudena Torres-Trenas ◽  
Encarnación Pérez-Artés
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Genetic Code ◽  
Fusarium Oxysporum ◽  
Amino Acid Residues ◽  
Fusarium Spp ◽  
Stem Loop ◽  
Universal Genetic Code ◽  
The Family ◽  
Amino Acid Tryptophan

A novel mycovirus named Fusarium oxysporum f. sp. dianthi mitovirus 1 (FodMV1) has been identified infecting a strain of Fusarium oxysporum f. sp. dianthi from Colombia. The genome of FodMV1 is 2313 nt long, and comprises a 172-nt 5’-UTR, a 2025-nt single ORF encoding an RdRp of 675 amino acid residues, and a 113-nt 3´-UTR. Homology BlastX searches identifies FodMV1 as a novel member of the genus Mitovirus in the family Narnaviridae. As the rest of mitoviruses, the genome of FodMV1 presents a high percentage of A+U (58.8%) and contains a number of UGA codons that encode the amino acid tryptophan rather than acting as stop codons as in the universal genetic code. Another common feature with other mitoviruses is that the 5′- and 3′-UTR regions of FodMV1 can be folded into potentially stable stem-loop structures. Result from phylogenetic analysis place FodMV1 in a different clade than the rest of mitoviruses described in other Fusarium spp. Incidence of FodMV1-infections in the collection of F. oxysporum f. sp. dianthi isolates analyzed is relatively high. Of particular interest is the fact that FodMV1 has been detected infecting isolates from two geographical areas as distant as Spain and Colombia.

Enhanced stability of Cu2+–ATCUN complexes under physiologically relevant conditions by insertion of structurally bulky and hydrophobic amino acid residues into the ATCUN motif

2016 ◽  
Vol 45 (23) ◽  
pp. 9436-9445 ◽  
Author(s):  
Takaaki Miyamoto ◽  
Yuta Fukino ◽  
Shinichiro Kamino ◽  
Masashi Ueda ◽  
Shuichi Enomoto
Keyword(s):  
Amino Acid ◽  
Amino Acid Residues ◽  
Hydrophobic Amino Acid ◽  
Hydrophobic Residues ◽  
The Stability ◽  
Enhanced Stability

The stability of Cu2+–ATCUN complexes under physiologically relevant conditions is enhanced by inserting bulky and hydrophobic residues at positions 1 and 2 of the ATCUN peptide.

Structure - function analysis of photosystem II subunit S (PsbS) in vivo

2002 ◽  
Vol 29 (10) ◽  
pp. 1131 ◽  
Author(s):  
Xiao-Ping Li ◽  
Alba Phippard ◽  
Jae Pasari ◽  
Krishna K. Niyogi
Keyword(s):  
Amino Acid ◽  
Photosystem Ii ◽  
Function Analysis ◽  
Amino Acid Sequences ◽  
Forward Genetics ◽  
Photochemical Quenching ◽  
Amino Acid Residues ◽  
The Stability ◽  
Psbs Gene

In land plants, photosystem II subunit S (PsbS) plays a key role in xanthophyll- and pH-dependent non-photochemical quenching (qE) of excess absorbed light energy. Arabidopsis thaliana (L.) Heynh. npq4 mutants are defective in the psbS gene and have impaired qE. Exactly how the PsbS protein is involved in qE is unclear, but it has been proposed that PsbS binds H+ and/or de-epoxidized xanthophylls in excess light as part of the qE mechanism. To identify amino acid residues that are important for PsbS function, we sequenced the psbS gene from eight npq4 point mutant alleles isolated by forward genetics screening, including two new alleles. In the four transmembrane helices of PsbS, several amino acid residues were found to affect the stability and/or function of the protein. By comparing the predicted amino acid sequences of PsbS from several plant species and studying the proposed topological structure of PsbS, eight possible H+-binding amino acid residues on the lumenal side of the protein were identified and then altered by site-directed mutagenesis in vitro. The mutant psbS genes were transformed into npq4-1, a psbS deletion mutant, to test the stability and function of the mutant PsbS proteins in�vivo. The results demonstrate that two conserved, protonatable amino acids, E122 and E226, are especially critical for the function of PsbS.

A comparative study of the effects of the Hofmeister series anions of the ionic salts and ionic liquids on the stability of α-chymotrypsin

2015 ◽  
Vol 39 (2) ◽  
pp. 938-952 ◽  
Author(s):  
Awanish Kumar ◽  
Anjeeta Rani ◽  
Pannuru Venkatesu
Keyword(s):  
Ionic Liquids ◽  
Amino Acid ◽  
Comparative Study ◽  
Hofmeister Series ◽  
Amino Acid Residues ◽  
Ionic Salts ◽  
The Stability ◽  
Catalytic Amino Acid

Direct interactions between the anion and the catalytic amino acid residues lead to denaturation of CT.

scholarly journals Extraction and purification of C-phycocyanin and genome analysis of an indigenous hypersaline cyanobacterium

2020 ◽  
Author(s):  
◽  
Trisha Mogany
Keyword(s):  
Molecular Weight ◽  
Amino Acid ◽  
16S Rrna ◽  
Genome Sequence ◽  
Extraction Method ◽  
Growth Conditions ◽  
Amino Acid Residues ◽  
Full Genome ◽  
Α And Β Subunits ◽  
The Stability

Cyanobacteria are photosynthetic microorganisms that inhabit diverse ecological habitats and are capable of producing wide range of natural products and bioactive metabolities including peptides, vitamins, enzymes and pigments such as phycobiliproteins. Amongst the group of phycobiliproteins, C-Phycocyanin (C-PC) is a light-harvesting accessory pigment known to possess excellent biotechnological applications due to their intense colour, fluorescent properties and health benefits. This study has focused on the characterisation and full genome analysis of a unique indigenous halophilic cyanobacterium capable of overproducing the pigment phycocyanin (C-PC). Further, development of a cost-effective extraction method for high purity C-PC and characterisation of the purified C-PC was accomplished. The strain was isolated from a hypersaline environment in KwaZulu-Natal, South Africa and was found to possess several unique traits such as its ability to accumulate high amount of phycocyanin, tolerance to high salinity (up to 180 g/L), ability to grow under varying growth conditions and high growth rate. The taxonomic identity of the isolate was revealed using a polyphasic approach including cell morphology, growth conditions, pigment composition, 16S rRNA analysis. The cells were oval to rod-shaped, 14-18 μm in size, and contained majority of C-PC, as well as some allophycocyanin and chlorophyll. The strain was moderately thermotolerant (35°C), alkalitolerant (pH 8.5) and was halophilic with an optimum NaCl of 120 g/L. Based on the 16S rRNA gene sequence phylogeny, the strain was found to be related to members of the ‘Euhalothece’ subcluster (99%). Further, the whole genome sequence was also determined, and the annotated genes have shown sequence similarity (90%) to the gas- vacuolate, spindle-shaped Dactylococcopsis salina PCC 8305. Based on the above results, the strain is considered to represent a novel species of Euhalothece. The size of the genome was determined to be 5,113,178 bp and contained 4332 protein-coding genes and 69 RNA genes with a GC content of 46.7%. The full genome sequence analysis also provided important information about the strain which facilitated the identification of key genes and proteins necessary for C-PC synthesis and salt acclimation. Genes encoding osmoregulation, oxidative stress, heat shock, persister cells, and UV-absorbing secondary metabolites, among others, were also identified. Further, single factor experiments were performed to optimise the factors (extraction buffers, freezing time, biomass:buffer ratio and lysozyme concentration) essential for C-PC extraction from cyanobacteria. A range of buffers viz., acetate, potassium phosphate (PPB), sodium phosphate (SPB), phosphate buffered saline (PPBS), Tris-chloride and double distilled water (control) with different pH and concentrations were investigated. Cell lysis was carried out by freezing the cells at different temperatures viz., at -196, and -80, and -20°C, and by thawing at 4 and 25°C. The freezing and thawing time varied from 0.5-24 h. Based on the results obtained, thawing temperature, enzyme concentration and biomass-buffer ratio were further selected for optimisation for maximum C-PC yield and purity using response surface methodology (RSM). Under optimised conditions, the yield of crude C-PC was increased to 78 mg/g (>90% percentage increase) with a purity index of 2.5 compared to extraction prior to optimisation. The crude C-PC was further purified using 6% w/v of activated charcoal combined with a two-step ammonium sulphate (NH4SO4) precipitation and ultrafiltration which resulted in high yield analytical grade C-PC with a purity index of 5. The purified C-PC showed a single absorption peak at 620 nm and emission at 640 nm. Based on the amino acid analysis the calculated molecular weight of α- and β-subunits were found to be 17.7 and 18.4 kDa respectively, which corresponded to the two bands seen on the SDS- PAGE. Additionally, the primary, secondary and tertiary structures of the C-PC was also evaluated based on the amino acid sequence obtained from the genome sequence. The C-PC physiochemical properties such as the molecular weight, isoelectric point, extinction coefficient, half-life, aliphatic index, amino acid property, instability index and Grand Average of Hydropathicity was predicted based on the in-silico analysis of the amino acid sequences. The physicochemical properties revealed that these proteins are non-polar and stable. Multiple sequence alignment analyses of the α- and β-subunits displayed significant differences amongst the amino acid residues of hypersaline/marine and freshwater cyanobacteria. These amino acids play a vital role in the stability of the C-PC. The secondary structure prediction of the α- and β -subunits consisted of > 50% of amino acid residues in α-helices, with 9-13% of amino acid residues in the extended strand. The stability of the purified C-PC under different conditions were investigated. The optimum pH range for purified C-PC was found to be 5.0–7.0 and was found to be stable up to 45oC. However, the relative concentration C-PC (CR%) and thermostability of the purified C-PC was observed to be pH dependent, a lower pH improved the stability at higher temperatures and vice-versa. An IC50 value of 0.540 ± 0.02 mg/mL was also observed using the DPPH assay indicating a higher antioxidant potential of the C-PC. C-phycocyanin exhibited a maximum absorbance of 1.37 ± 0.05 by ferric ion reducing assay. The presence of a high level of non-polar and aromatic residues such as Ala, Gly Glu, Leu, Arg, Ser, and Val could be regarded as an indication of higher antioxidant activity levels of the C-PC. Addition of preservatives sodium azide and sodium citrate (at 4°C) proved to be suitable for preservation of C-PC for up to 42 weeks. This research contributed to our understanding of molecular, cellular and biochemical mechanisms of the C-PC biosynthesis as well as newly identified metabolites in cyanobacteria. The study has also demonstrated an efficient extraction method for analytical grade C-PC from cyanobacterial strains for potential applications in biotechnological biomedical industries.

scholarly journals Pursuing Orally Bioavailable Hepcidin Analogues via Cyclic N-Methylated Mini-Hepcidins

Biomedicines ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 164
Author(s):  
Daniela Goncalves Monteiro ◽  
Johannes W. A. van Dijk ◽  
Randy Aliyanto ◽  
Eileen Fung ◽  
Elizabeta Nemeth ◽  
...  
Keyword(s):  
Amino Acid ◽  
Oral Bioavailability ◽  
Iron Absorption ◽  
Peptide Hormone ◽  
Proteolytic Degradation ◽  
Amino Acid Residues ◽  
Lysosomal Degradation ◽  
Tissue Iron ◽  
Orally Bioavailable ◽  
The Stability

The peptide hormone hepcidin is one of the key regulators of iron absorption, plasma iron levels, and tissue iron distribution. Hepcidin functions by binding to and inducing the internalisation and subsequent lysosomal degradation of ferroportin, which reduces both iron absorption in the gut and export of iron from storage to ultimately decrease systemic iron levels. The key interaction motif in hepcidin has been localised to the highly conserved N-terminal region, comprising the first nine amino acid residues, and has led to the development of mini-hepcidin analogs that induce ferroportin internalisation and have improved drug-like properties. In this work, we have investigated the use of head-to-tail cyclisation and N-methylation of mini-hepcidin as a strategy to increase oral bioavailability by reducing proteolytic degradation and enhancing membrane permeability. We found that backbone cyclisation and N-methylation was well-tolerated in the mini-hepcidin analogues, with the macrocylic analogues often surpassing their linear counterparts in potency. Both macrocyclisation and backbone N-methylation were found to improve the stability of the mini-hepcidins, however, there was no effect on membrane-permeabilizing activity.

scholarly journals Interactions of Aβ1-42 Peptide and Its Three Fragments (Aβ8-12, Aβ8-13, and Aβ5-16) with Selected Nonsteroidal Drugs and Compounds of Natural Origin

Symmetry ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 1579
Author(s):  
Krzysztof Żamojć ◽  
Karolina Streńska ◽  
Dariusz Wyrzykowski ◽  
Lech Chmurzyński ◽  
Joanna Makowska
Keyword(s):  
Molecular Dynamics ◽  
Steady State ◽  
Amino Acid ◽  
Complex Formation ◽  
Amino Acid Residues ◽  
Binding Properties ◽  
Natural Origin ◽  
Steady State Fluorescence ◽  
The Stability ◽  
Steady State Fluorescence Spectroscopy

In the following paper, we present the results of our studies on the interactions of the Aβ1-42 peptide and its three short fragments, namely Aβ5-16 (RHDSGYEVHHQK; HZ1), Aβ8-13 (SGYEVH; HZ2), and Aβ8-12 (SGYEV; HZ3) with selected painkillers (ibuprofen and aspirin) and compounds of natural origin (anabasine and epinephrine). Steady-state fluorescence spectroscopy was used to study the binding properties of the selected systems. Additionally, based on molecular dynamics (MD) calculations supported by NMR-derived restrains, we have proposed the most likely area of the interactions of Aβ1-42 and Aβ5-16 peptides with the investigated compounds. The influence of symmetrically oriented side chains of amino acid residues present in the first part of the Aβ1-42 sequence on the stability of the resulting complexes has been discussed. Finally, the changes in the peptide structures on account of complex formation were analyzed.

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