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Nanostructured Cellular Biomolecules and Their Transformation in Context of Bionanotechnology
Published in Anil Kumar Anal, Bionanotechnology, 2018
Protein synthesis initiates with the assembly of the translation complex. Ribosome identifies the initiation codon, which is usually AUG (codes for methionine), but GUG, UUG, or AUU may also be used. Among the two methionyl-tRNAMet molecule that translates AUG codons, initiator tRNA is used at the initiation codon. At the end of the initiation step, mRNA is positioned in such a way that the next codon can be translated during the elongation step, the initiator tRNA is attached to P site and A site of ribosome is ready to receive incoming aminoacyl-tRNA. During chain elongation process, tRNA with the correct aminoacyl-tRNA attach into the A site. The peptidyl transferase catalyzes a transfer of the amino acid from the P site to the amino acid at the A site with the formation of peptide bond such that the growing polypeptide chain is covalently attached to the tRNA in the A site, forming a peptidyl-tRNA. The first amino acid on the polypeptide has a free amino group, so it is called the N-terminal and the last amino acid has a free carboxylic group, so it is called the C-terminal. The mRNA shifts by one codon such that two tRNAs at the P and A site translocate. Following this, deaminoacylated tRNA is displaced from P to exit, E site and peptidyl-tRNA is displaced from A to P site. When one of the three stop codons (UAA, UAG, UGA) on the mRNA is reached, tRNA does not recognize these termination codons and release factor causing the hydrolysis of the peptidyl-tRNA releasing polypeptide chain (Moran et al. 2012).
Biomolecular Processing and Molecular Electronics
Published in Sergey Edward Lyshevski, Molecular Electronics, Circuits, and Processing Platforms, 2018
The transcription and translation processes are illustrated in Figure 3.18. Transcription results in nucleotide-to-nucleotide transfer of coded information from DNA to RNA. RNA synthesis on a DNA template is catalyzed by RNA polymerase. Promoters (specific nucleotides sequences flanking the start of a gene) signal the initiation of mRNA synthesis. Transcription factors (proteins) help RNA polymerase recognize promoter sequences and bind to the RNA. Transcription continues until the RNA polymerase reaches the termination (stop) sequence of nucleotides on the DNA template. As the mRNA peels away, the DNA double helix re-forms. Translation results in the code transfer from RNA nucleotides to polypeptide amino acids (transfer RNA interprets the genetic code during translation, and each kind of tRNA brings a specific amino acid to the ribosome). Transfer RNA molecules pick up specific amino acids and line up by means of their anticodon triplets at complementary codon sites on the mRNA molecule. The ATP process is catalyzed by aminoacryl-tRNA synthetase enzymes. The ribosome controls the coupling of tRNA to mRNA codons. They provide a site for the binding of mRNA, as well as P and A sites (peptidyl-tRNA and aminoacyl-tRNA sites) for holding adjacent tRNA as amino acids are linked in the growing polypeptide chain. There are three major stages—initiation (integrates mRNA with tRNA with the attached first amino acid), elongation (polypeptide chain is completed adding amino acids attached to its tRNA by binding and translocation tRNA and mRNA along the ribosome), and termination (termination codonds cause the protein release freeing the polypeptide chain and dislocation of the ribosome subunits). Several ribosomes can read a single mRNA, forming polyribosome clusters. Complex proteins usually undertake one or several changes during and after translation that affect their 3D structures. This leads to the cell transitional dynamics.
Devising and Synthesis of NEMS and MEMS
Published in Sergey Edward Lyshevski, Nano- and Micro-Electromechanical Systems, 2018
In biosystems, information processing, verification, assembling, and other processes are completed within so-called transcription and translation (see Figure 5.20). Transcription results in nucleotide-to-nucleotide transfer of information from DNA to RNA. RNA synthesis on a DNA template is catalyzed by RNA polymerase. Promoters (specific nucleotides sequences flanking the start of a gene) signal the initiation of mRNA synthesis. Transcription factors (proteins) help RNA polymerase recognize promoter sequences and bind to the RNA. Transcription continues until the RNA polymerase reaches the termination (stop) sequence of nucleotides on the DNA template. As the mRNA peels away, the DNA double helix reforms. Translation results in the informational transfer from RNA nucleotides to polypeptide amino acids (transfer RNA interprets the genetic code during translation, and each kind of tRNA brings a specific amino acid to ribosomes). Transfer RNA molecules pick up specific amino acids and line up by means of their anticodon triplets at complementary codon sites on the mRNA molecule. The binding of a specific amino acid to its particular tRNA is a precise ATP process catalyzed by aminoacryl-tRNA synthetase enzymes. Ribosomes control the coupling of tRNA to mRNA codons. They provide a site for the binding of mRNA, as well as P and A sites for holding adjacent tRNA as amino acids are linked in the growing polypeptide chain. There are three major stages: initiation (integrates mRNA with tRNA with the attached first amino acid), elongation (polypeptide chain is completed, adding amino acids attached to its tRNA by binding and translocation tRNA and mRNA along the ribosome), and termination (termination codons cause the protein release freeing the polypeptide chain and dislocation of the ribosome subunits). Several ribosomes can read a single mRNA, forming polyribosome clusters. Complex proteins usually undertake one or several changes during and after translation that affect their three-dimensional structures influencing cells. This leads to the cell transitional dynamics.
Tryptophan capped gold-aryl nanoparticles for energy transfer study with SARS-CoV-2 spike proteins
Published in Soft Materials, 2022
Javad B. M. Parambath, Sofian M. Kanan, Ahmed A. Mohamed
The plot of log (F0-F)/F versus log [Trp-AuNPs] presented a straight line, Figure 5(b), where the slope is the binding site (n) and the intercept is log Ka.[33] The binding constant Ka and (n) values for S-protein/Trp-AuNPs bioconjugate are also summarized in Table 1. The calculated binding site parameter (n) is approximately one indicating a single binding site in the emission quenching experiment. Several quenching mechanisms are proposed for nanomaterials including non-radiative recombination, energy and electron transfer, and surface adsorption. Various factors control the rate of energy transfer such as the degree of spectral overlap, the comparative orientation of the transition dipoles, and donor-acceptor distance.[34]
Blocking a chemical communication between Trichoplax organisms leads to their disorderly movement
Published in International Journal of Parallel, Emergent and Distributed Systems, 2020
A. V. Kuznetsov, A. V. Halaimova, M. A. Ufimtseva, E. S. Chelebieva
BSA in high concentrations (1 and 10%) prevented the adhesion of trichoplaxes to a substrate and caused to the dissociation of animals into separate cells, which may correlate with the blockage of active sites and the binding of Ca2+ ions by BSA protein molecules [33,34]. It should be noted the interaction of BSA with numerous ligands and biologically active substances that affect the cell growth in culture. These include hormones, growth factors, amino acids, lipids, metal ions and many others [35,36]. BSA is a universal blocker of nonspecific interaction with polypeptides [37]. It was shown in [38] that the peptide binding site is in the pocket of BCA, previously defined as a fatty acid binding site. BSA is known to adsorb small compounds, such as sulpiride, which is an antipsychotic drug used in the treatment of mental disorders [39]. It has recently been shown that the interaction of BSA with low molecular weight compounds is provided by hydrophobic and electrostatic forces. The binding process is spontaneous and leads to a change in Gibbs free energy [40–43].
Screening and identification of novel inhibitors against human 4-aminobutyrate-aminotransferase: A computational approach
Published in Egyptian Journal of Basic and Applied Sciences, 2018
S. Vijayakumar, G. Kasthuri, S. Prabhu, P. Manogar, N. Parameswari
In this study, the site analysis has produced five active drugable binding sites from the target. The site map shown their binding cavity residues were Gln267, Hip162, Glh231, Asp264, Val138, Tyr161, Arg164, Gly163, Gly134, Lys293, Ser133, Val75, Gly298, Pro300, Ala296, Asn132, Leu299, Ser302, Ile295, Gly235, Leu301 and Gln267 (Fig. 3). Similarly, Iftikhar et al., [37] have analyzed the ligand binding sites in 4-aminobutyrate aminotransferase for docking with known analogues. Recently, many computational studies have been carried out this binding site analysis method in many kinds of target molecules [38,39] . Moreover, Vijayakumar et al., [40] has described that the potentiality of the binding site analysis in Maestro v 10.2, Schrodinger suite. As a result of this analysis, the qualified binding site was taken for grid generation, which is help to fix the possible binding site in target [41].