Amino Acid Residues
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2021 ◽  
Author(s):  
Ravindra S Kale ◽  
Jacob Seep ◽  
Larry Sallans ◽  
Laurie K Frankel ◽  
Terry M. Bricker

Under aerobic conditions the production of Reactive Oxygen Species (ROS) by electron transport chains is unavoidable, and occurs in both autotrophic and heterotrophic organisms. In photosynthetic organisms both Photosystem II (PS II) and Photosystem I (PS I), in addition to the cytochrome b6/f complex, are demonstrated sources of ROS. All of these membrane protein complexes exhibit oxidative damage when isolated from field-grown plant material. An additional possible source of ROS in PS I and PS II is the distal, chlorophyll-containing light-harvesting array LHC II, which is present in both photosystems. These serve as possible sources of 1O2 produced by the interaction of 3O2 with 3chl* produced by intersystem crossing. We have hypothesized that amino acid residues close to the sites of ROS generation will be more susceptible to oxidative modification than distant residues. In this study, we have identified oxidized amino acid residues in a subset of the spinach LHC II proteins (Lhcb1 and Lhcb2) that were associated with either PS II membranes (i.e. BBYs) or PS I-LHC I-LHC II membranes, both of which were isolated from field-grown spinach. We identified oxidatively modified residues by high-resolution tandem mass spectrometry. Interestingly, two different patterns of oxidative modification were evident for the Lhcb1 and Lhcb2 proteins from these different sources. In the LHC II associated with PS II membranes, oxidized residues were identified to be located on the stromal surface of Lhcb1 and, to a much lesser extent, Lhcb2. Relatively few oxidized residues were identified as buried in the hydrophobic core of these proteins. The LHC II associated with PS I-LHC I-LHC II membranes, however, exhibited fewer surface-oxidized residues but, rather a large number of oxidative modifications buried in the hydrophobic core regions of both Lhcb1 and Lhcb2, adjacent to the chlorophyll prosthetic groups. These results appear to indicate that ROS, specifically 1O2, can modify the Lhcb proteins associated with both photosystems and that the LHC II associated with PS II membranes represent a different population from the LHC II associated with PS I-LHC I-LHC II membranes.


Antibiotics ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1465
Author(s):  
Xiaoou Zhao ◽  
Mengna Zhang ◽  
Inam Muhammad ◽  
Qi Cui ◽  
Haipeng Zhang ◽  
...  

The poor stability of antibacterial peptide to protease limits its clinical application. Among these limitations, trypsin mainly exists in digestive tract, which is an insurmountable obstacle to orally delivered peptides. OM19R is a random curly polyproline cationic antimicrobial peptide, which has high antibacterial activity against some gram-negative bacteria, but its stability against pancreatin is poor. According to the structure-activity relationship of OM19R, all cationic amino acid residues (l-arginine and l-lysine) at the trypsin cleavage sites were replaced with corresponding d-amino acid residues to obtain the designed peptide OM19D, which not only maintained its antibacterial activity but also enhanced the stability of trypsin. Proceeding high concentrations of trypsin and long-time (such as 10 mg/mL, 8 h) treatment, it still had high antibacterial activity (MIC = 16–32 µg/mL). In addition, OM19D also showed high stability to serum, plasma and other environmental factors. It is similar to its parent peptide in secondary structure and mechanism of action. Therefore, this strategy is beneficial to improve the protease stability of antibacterial peptides.


Membranes ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 939
Author(s):  
Daria N. Melnikova ◽  
Ekaterina I. Finkina ◽  
Ivan V. Bogdanov ◽  
Anastasia A. Ignatova ◽  
Natalia S. Matveevskaya ◽  
...  

Plant lipid transfer proteins (LTPs) are known to be clinically significant allergens capable of binding various lipid ligands. Recent data showed that lipid ligands affected the allergenic properties of plant LTPs. In this work, we checked the assumption that specific amino acid residues in the Len c 3 structure can play a key role both in the interaction with lipid ligands and IgE-binding capacity of the allergen. The recombinant analogues of Len c 3 with the single or double substitutions of Thr41, Arg45 and/or Tyr80 were obtained by site-directed mutagenesis. All these amino acid residues are located near the “bottom” entrance to the hydrophobic cavity of Len c 3 and are likely included in the IgE-binding epitope of the allergen. Using a bioinformatic approach, circular dichroism and fluorescence spectroscopies, ELISA, and experiments mimicking the allergen Len c 3 gastroduodenal digestion we showed that the substitution of all the three amino acid residues significantly affected structural organization of this region and led both to a change of the ligand-binding capacity and the allergenic potential of Len c 3.


2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Alexander A. Zamyatnin ◽  
Tatiana A. Belozerskaya ◽  
Andrey A. Zamyatnin

Prior to this study, we discovered a protein characterized by many different amino acid sequences with the same number of amino acid residues. This turned out to be a unique cytochrome b, in which 1048 molecules out of 1689 contain 379 amino acid residues. A detailed study of the occurrence of this protein in living organisms at different taxonomic levels (from biological domains to biological orders of animals) has been carried out in the work presented here. We found that the main part of all b cytochromes is present in eukaryotes (99.2%), in biological kingdoms (95.9% in animals), in biological phylums (97.5% in chordates), and in biological classes (79.7% in mammals). Withal, this protein, containing 379 amino acid residues and characterized by many different amino acid sequences, is found only in eukaryotes (100%), only in animals (100%) and mainly in mammals (81.1%). Thus, a representative that has cytochrome b with a corresponding number of amino acid residues has not yet been identified among archaea and prokaryotes, while it is common in representatives of different biological types, classes, and orders of animals. It is believed that the structural diversity of a given protein within the same length and its one function of participation in the process of electron transfer relate to the physicochemical features of the extra- and intramembrane fragments of the polypeptide chain of this protein.


Author(s):  
T. V. Ryabtseva ◽  
D. A. Makarevich ◽  
A. D. Taganovich

The aim of the study was the design, characteristics and analysis of the TNFα interaction with oligopeptideanalogs of the interaction site of TNFα with TNFα-R2. Here are the results of the analysis contact zone of TNFα with TNFα-R2, determination of the potentially most effective oligopeptides, study of the binding free energy of oligopeptides and its changes depending on the number of amino acid residues in the peptide chain, as well as the TNFα form (monomer or trimer). Here are described the most typical loci of oligopeptides interaction with cytokine. To confirm the calculations, the effectiveness of the selected oligopeptides was evaluated in experiments in vitro.For visualization of the molecular complex and work with the pdb file we are used Chimera 1.14 software with AutoDocVina utility. For in vitro studies, were used indirect enzyme immunoassay reagent kits. The initial concentration of oligopeptides is 10 µM, the initial concentration of TNFα (×10–8): 0; 0.0287; 0.0862; 0.2300; 0.5750; 1.4370 µM. When oligopeptides interact with mTNFα, the binding efficiency increase was observed with an increase in the number of amino acid residues in the chain. With tTNFα, such dependence was not observed. A statistically significant difference was  observed in the binding energy of di-, tri-, and tetra peptides with mTNFα, with tTNFα, the differences found were not statistically significant.Thus, the data were obtained, which allowed us to come to the following conclusions: 1) the energy of interaction of oligopeptides with tTNFα does not depend on the number of amino acid residues in the oligopeptide; 2) the trimerized form of TNFα interacts most effectively with oligopeptides in comparison with mTNFα; 3) oligopeptides containing the -Trp- and being a spatial analogue of the TNFα-R2 fragment (-Trp65-Asn66-Trp67-Val68-Pro69-) interact most effectively; 4) it was selected three oligopeptides are the most promising for the binding of TNFα. The experiments in vitro confirmed the effectiveness only one oligopeptide


Viruses ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2257
Author(s):  
Chengqian Liu ◽  
Jun Gao ◽  
Hong Li ◽  
Fengping Sun ◽  
Hongyu Liang ◽  
...  

Canine parvovirus type 2 (CPV-2) has spread and mutated globally over the past 40 years. In the present study, 206 samples from dogs suspected of CPV-2 infection were collected from five veterinary clinics in Shanghai city, China. The average positive rate for CPV-2 was detected to be 40.78% using the PCR method. Using an F81 cell (feline kidney cell) culture, the isolates of three CPV-2c strains were obtained. The near full-length genome sequences of the isolates were determined and submitted to GenBank: CPV-SH2001 (MW650830), CPV-SH2002 (MW811188), and CPV-SH2003 (MW811189). By comparing the amino acid sequences of 12 CPV strains with those of 48 related strains retrieved from GenBank, all of the CPV strains from Shanghai were typed as belonging to a relatively new CPV-2c variant spreading in Asia, with typical amino acid residues (5Gly, 267Tyr, 324Ile, and 370Arg) in the VP2 protein. The divergence time of this new CPV-2c clade was estimated by the phylogenetic tree using the maximum likelihood and RelTime with Dated Tips (RTDT) approaches. Our results indicate that the 426 and 324 VP2 amino acid residues are under strong selection pressure with a posterior probability of 0.966 and 0.943, respectively. Therefore, this study provides insight into the phylogenetic characteristics of the current CPV-2c variant in Shanghai city, China.


2021 ◽  
Vol 17 (11) ◽  
pp. e1010057
Author(s):  
Hui Liu ◽  
Junjun Cheng ◽  
Usha Viswanathan ◽  
Jinhong Chang ◽  
Fengmin Lu ◽  
...  

The core protein (Cp) of hepatitis B virus (HBV) assembles pregenomic RNA (pgRNA) and viral DNA polymerase to form nucleocapsids where the reverse transcriptional viral DNA replication takes place. Core protein allosteric modulators (CpAMs) inhibit HBV replication by binding to a hydrophobic “HAP” pocket at Cp dimer-dimer interfaces to misdirect the assembly of Cp dimers into aberrant or morphologically “normal” capsids devoid of pgRNA. We report herein that a panel of CpAM-resistant Cp with single amino acid substitution of residues at the dimer-dimer interface not only disrupted pgRNA packaging, but also compromised nucleocapsid envelopment, virion infectivity and covalently closed circular (ccc) DNA biosynthesis. Interestingly, these mutations also significantly reduced the secretion of HBeAg. Biochemical analysis revealed that the CpAM-resistant mutations in the context of precore protein (p25) did not affect the levels of p22 produced by signal peptidase removal of N-terminal 19 amino acid residues, but significantly reduced p17, which is produced by furin cleavage of C-terminal arginine-rich domain of p22 and secreted as HBeAg. Interestingly, p22 existed as both unphosphorylated and phosphorylated forms. While the unphosphorylated p22 is in the membranous secretary organelles and the precursor of HBeAg, p22 in the cytosol and nuclei is hyperphosphorylated at the C-terminal arginine-rich domain and interacts with Cp to disrupt capsid assembly and viral DNA replication. The results thus indicate that in addition to nucleocapsid assembly, interaction of Cp at dimer-dimer interface also plays important roles in the production and infectivity of progeny virions through modulation of nucleocapsid envelopment and uncoating. Similar interaction at reduced p17 dimer-dimer interface appears to be important for its metabolic stability and sensitivity to CpAM suppression of HBeAg secretion.


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