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Showing 4 results for Tertiary
M. Mirzaie,
Volume 10, Issue 3 (9-2019)
Abstract
Aims: Prediction of three-dimensional structure from a sequence of amino acids is one of the important problems in structural bioinformatics. Proteins select a special structure among many possible conformations in order of seconds. Levinthal paradox expresses that random searches could not be an effective way to form a native structure and a principal mechanism should be available. Reduced alphabet fewer than 20 have been interested in protein structure because it could sufficiently simplify the protein folding problem. It is generally assumed that the native structure form in the lowest free energy among all conformational states. Therefore, it is needed to design a trustworthy potential function that could discriminate protein fold from incorrect ones.
Materials and Methods: Knowledge-based potential functions are one type of energy functions derived from a database of known protein structures. In this study, we introduce a knowledge-based potential and assess the power of five amino acids ALA, LEU, ILE, VAL, and PHE in discrimination of native structure using the reduced model. In the reduced model only the energy between the aforementioned amino acids are calculated.
Finding: The reduced model was evaluated using four criteria. The results indicate that there is no significant difference between the 20- amino acid model and the reduced model.
Conclusion: The presented model indicates that the power of discrimination of native structure is originally from the interaction between the aforementioned amino acids. Therefore, it needed a new strategy to capture the remaining interactions to improve the power of knowledge-based potential function.
Volume 12, Issue 1 (2-2023)
Abstract
Hibiscus chlorotic ringspot virus (HCRSV), genus Betacarmovirus, family Tombusviridae, is a common pathogen of hibiscus plants in tropical and subtropical regions. During 2020-2021, leaf samples of Chinese hibiscus Hibiscus rosa-sinensis L. with mottling and chlorotic ring spot symptoms were collected from Ahvaz and Molasani Khuzestan province, southwestern Iran. Total RNA extracted from symptomatic samples was subjected to RT-PCR analysis to amplify the sequence of the coat protein gene (CP) (p38) of HCRSV. Complete (1038 bp) and partial (932 bp) p38 sequences were determined and deposited in the GenBank database. The consensus sequences obtained from CP were compared with those of known isolates using the nBLAST program and phylogenetic analysis. The phylogenetic tree constructed based on the p38 sequences showed different ancestors for Iranian isolates of HCRSV. Additionally, the isolates studied were grouped into clades regardless of their geographic distribution, suggesting that there is no differentiation of population based on location and that populations are interconnected. Recombination analysis based on p38 sequences predicted at least two acceptable recombinant isolates, Ahvaz (Iran) and Israel. In silico prediction of CP structures of isolates involved in recombination events showed low sequence to structure identity between HCRSV isolates. In addition to reporting two new HCRSV isolates from Iran, our work demonstrated that HCRSV exhibits a high genetic variation through recombination and that the classification criterion could be changed from low nucleotide sequence identity to a higher value, along with the structural analysis of betacarmovirus proteins.
Volume 13, Issue 5 (12-2022)
Abstract
With its prevalence as a global language, universities in Vietnam have striven to enhance students’ proficiency in English. This endeavor responds to the language requirements set by Vietnamese Ministry of Education and Training (MoET), the prominence of English as a medium of instruction in higher education, and the necessity of preparing students for better employability. This study focuses on General English programs currently deployed in most universities in Vietnam in terms of expected learning outcomes, course design and assessment practices. Drawing on document analysis, it examines the General English program of a public university and a private one in Ho Chi Minh City in relation to these three components. Findings show that these universities conformed to MoET’s policy on language education but developed different approaches to language program design and assessment in order to achieve their respective learning outcomes and ensure the quality of language learning and teaching in their own contexts. This study provides course designers, coordinators and language teachers with in-depth understandings of the deployment of General English programs and the theoretical bases underpinning such processes. These insights will enable them to become more aware of the elements constituting such programs and the considerations to be taken in updating and innovating the language curricula.
Volume 17, Issue 108 (1-2021)
Abstract
In this study, a tertiary conjugate of flaxseed mucilage (FM)-gelatin–oxidized tannic acid (OTA) at two acidic and alkali pHs was fabricated. The total amount of biopolymers and added OTA was 2% (w/w solution) and 5 % (of total biopolymers), respectively. Fourier transforms infrared spectroscopy and solid state UV-visible spectroscopy were applied to confirm the complex formation and volume, solubility and phenolic content of the complexes were determined. Then, the effect of OTA concentration (0.5, 2.5, 5 and 10%) and reaction temperature (30, 40 and 50 °C) of gelatin with OTA were also evaluated through scanning electron microscopy analysis, yield complex and colorimetry. It was found that the addition of OTA to gelatin solution at alkali pH created strong bonds and a stable complex. The water solubility of acid complex (6.1%) was higher than that of alkali sample (3.6%). The optimal condition, regarding to high phenolic content and low solubility, was 5% OTA and the reaction temperature of 30 °C. This complex, may be suitable to apply for various applications such as protection of sensitive food ingredients from oxidative stresses and controlled release of bioactive components in delivery systems in food industry.
