Protein secondary structure

Ebook "Biophysical chemistry of proteins: An introduction to laboratory methods" is structured in nine sections, each containing several chapters. The volume starts with an overview of analytical techniques and progresses through purification of proteins; protein modification and inactivation; protein size, shape, and structure; enzyme kinetics; protein-ligand interactions; industrial enzymology; and laboratory quality control. The book is targeted at all scientists interested in protein research.

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Fourier-transform infrared spectroscopy (FTIR)is a well-established spectroscopic method in the analysis of small molecules and protein secondary structure. However, FTIR is not commonly applied for inline monitoring of protein chromatography.

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Adenosine-to-inosine (A-to-I) RNA editing, mediated by ADAR1 and ADAR2, occurs at tens of thousands to millions of sites across mammalian transcriptomes. A-to-I editing can change the protein coding potential of a transcript and alter RNA splicing, miRNA biology, RNA secondary structure and formation of other RNA species

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mRNA can form local secondary structure within the protein-coding sequence, and the strength of this structure is thought to influence gene expression regulation. Previous studies suggest that secondary structure strength may be maintained under selection, but the details of this phenomenon are not well understood.

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Lecture Bioinformatics I present the content: introduction to bioinformatics, sequence analysis, molecular evolution, RNA secondary structure prediction, protein sequences, protein structures, storage of biological sequence information, similarities & differences in sequences, introduction to alignment approaches, introduction to dynamic programming, dynamic programming methodology, moving from global to local alignment,...

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Saintpaulia ionantha H. Wendl (synonym Streptocarpus ionanthus) has been considered an ornamental plant. The PHANTASTICA (PHAN) gene has a significant role in the formation of plant organs adaxial–abaxial polarity. In the present study the PHAN gene was identified in Saintpaulia for the first time using PCR. To determine the expression pattern of the PHAN gene, gene expression was compared at 3 developmental stages using real time PCR.

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Filamentous fungi produce a vast amount of bioactive secondary metabolites (SMs) synthesized by e.g. hybrid polyketide synthase-nonribosomal peptide synthetase enzymes (PKS-NRPS; NRPS-PKS). While their domain structure suggests a common ancestor with other SM proteins, their evolutionary origin and dynamics in fungi are still unclear.

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Marine endophytic fungi (MEF) are good sources of structurally unique and biologically active secondary metabolites. Due to the increase in antimicrobial resistance, the secondary metabolites from MEF ought to be fully explored to identify candidates which could serve as lead compounds for novel drug development.

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With more than 300 million potentially infected people every year, and with the expanded habitat of mosquitoes due to climate change, Dengue virus (DENV) cannot be considered anymore only a tropical disease.

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As genome sequencing is becoming routine in biomedical research, the total number of protein sequences is increasing exponentially, recently reaching over 108 million. However, only a tiny portion of these proteins (i.e. ~75,000 or < 0.07%) have solved tertiary structures determined by experimental techniques.

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In recent years, the important functional roles of RNAs in biological processes have been repeatedly demonstrated. Computing the similarity between two RNAs contributes to better understanding the functional relationship between them. But due to the long-range correlations of RNA, many efficient methods of detecting protein similarity do not work well.

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The structures of biological macromolecules provide a framework for studying their biological functions. Three-dimensional structures of proteins, nucleic acids, or their complexes, are difficult to visualize in detail on flat surfaces, and algorithms for their spatial superposition and comparison are computationally costly.

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Many content-based statistical features of secondary structural elements (CBF-PSSEs) have been proposed and achieved promising results in protein structural class prediction, but until now position distribution of the successive occurrences of an element in predicted secondary structure sequences hasn’t been used.

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Traditional approaches to elucidation of protein structures by Nuclear Magnetic Resonance spectroscopy (NMR) rely on distance restraints also known as Nuclear Overhauser effects (NOEs).

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In this study a novel protein isolated from Trichosanthes dioica of Cucurbitaceae family which upon testing exhibited ribosome inactivating property was tested for anticancer properties. This may pave the way for exploration of these proteins for potential use as anti-cancer agents in future.

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Protein structures are flexible and often show conformational changes upon binding to other molecules to exert biological functions. As protein structures correlate with characteristic functions, structure comparison allows classification and prediction of proteins of undefined functions.

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RNA-binding proteins interact with specific RNA molecules to regulate important cellular processes. It is therefore necessary to identify the RNA interaction partners in order to understand the precise functions of such proteins.

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The high demanding computational requirements necessary to carry out protein motion simulations make it difficult to obtain information related to protein motion. On the one hand, molecular dynamics simulation requires huge computational resources to achieve satisfactory motion simulations.

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Protein sequence alignment is essential for a variety of tasks such as homology modeling and active site prediction. Alignment errors remain the main cause of low-quality structure models. A bioinformatics tool to refine alignments is needed to make protein alignments more accurate.

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Alignment of large and diverse sequence sets is a common task in biological investigations, yet there remains considerable room for improvement in alignment quality. Multiple sequence alignment programs tend to reach maximal accuracy when aligning only a few sequences, and then diminish steadily as more sequences are added.

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