Proteome properties

Ebook "Proteomics and protein-protein interactions: Biology, chemistry, bioinformatics, and drug design" attempts to bridge the two extreme ends of protein science: on one end, systems proteomics, which describes, at a system level, the intricate connection network that proteins form in a cell, and on the other end, protein chemistry and biophysics, which describe the molecular properties of individual proteins and the structural and thermodynamic basis of their interactions within the network.

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Ebook "Genome instability: Methods and protocols" presents forty-two methods and protocols to analyze diverse aspects of genome instability. Chapters detail mutagenesis and repair, methods to quantify and analyze the properties of DNA double-strand breaks, profile replication, replication proteins strand-specifically, genome instability, fluorescence microscopic techniques, and genomic and proteomic approaches.

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Part 2 book "Farm animal proteomics 2014" includes content: Using shotgun proteomics to understand the effect of feed restriction on the Ovis aries wool proteome, comparative proteomic analysis of muscle tissue from pre-term and term calves, high frequencies of the αS1-casein zero variant and its relation to coagulation properties in milk from Swedish dairy goats,... and other contents.

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Post-translational modification is considered an important biological mechanism with critical impact on the diversification of the proteome. Although a long list of such modifications has been studied, succinylation of lysine residues has recently attracted the interest of the scientific community. The experimental detection of succinylation sites is an expensive process, which consumes a lot of time and resources. Therefore, computational predictors of this covalent modification have emerged as a last resort to tackling lysine succinylation.

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Scallops possess striated and catch adductor muscles, which have different structure and contractile properties. The striated muscle contracts very quickly for swimming, whereas the smooth catch muscle can keep the shells closed for long periods with little expenditure of energy. In this study, we performed proteomic and transcriptomic analyses of differences between the striated (fast) and catch (slow) adductor muscles in Yesso scallop Patinopecten yessoensis.

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Intrinsic structural disorder is a common property of many proteins, especially in eukaryotic and virus proteomes. The tendency of some proteins or protein regions to exist in a disordered state usually precludes their structural characterisation and renders them especially difficult for experimental handling after recombinant expression.

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Membrane proteins constitute up to 30% of the human proteome. These proteins have special properties because the transmembrane segments are embedded into lipid bilayer while extramembranous parts are in different environments. Membrane proteins have several functions and are involved in numerous diseases.

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Post-translational modification (PTM), which is a biological process, tends to modify proteome that leads to changes in normal cell biology and pathogenesis. In the recent times, there has been many reported PTMs. Out of the many modifications, phosphoglycerylation has become particularly the subject of interest.

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Stability is one of the most fundamental intrinsic characteristics of proteins and can be determined with various methods. Characterization of protein properties does not keep pace with increase in new sequence data and therefore even basic properties are not known for far majority of identified proteins.

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Mosquito eggshells show remarkable diversity in physical properties and structure consistent with adaptations to the wide variety of environments exploited by these insects. We applied proteomic, transcriptomic, and hybridization in situ techniques to identify gene products and pathways that participate in the assembly of the Aedes aegypti eggshell.

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Mass spectrometry analyses of complex protein samples yield large amounts of data and specific expertise is needed for data analysis, in addition to a dedicated computer infrastructure. Furthermore, the identification of proteins and their specific properties require the use of multiple independent bioinformatics tools and several database search algorithms to process the same datasets.

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Protein structures and their interaction with ligands have been in the focus of biochemistry and structural biology research for decades. The transportation of ligand into the protein active site is often complex process, driven by geometric and physico-chemical properties, which renders the ligand path full of jitter and impasses.

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Computational approaches in the identification of drug targets are expected to reduce time and effort in drug development. Advances in genomics and proteomics provide the opportunity to uncover properties of druggable genomes.

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The selection and prioritization of drug targets is a central problem in drug discovery. Computational approaches can leverage the growing number of large-scale human genomics and proteomics data to make insilico target identification, reducing the cost and the time needed.

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The reconstruction of metabolic networks and the three-dimensional coverage of protein structures have reached the genome-scale in the widely studied Escherichia coli K-12 MG1655 strain. The combination of the two leads to the formation of a structural systems biology framework, which we have used to analyze differences between the reactive oxygen species (ROS) sensitivity of the proteomes of sequenced strains of E. coli.

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Serine/arginine-rich splicing factors (SRSFs) and HNRNPA1 have oncogenic properties. However, their proteomic expressions and practical priority in gastric cancer (GC) and colorectal cancer (CRC) are mostly unknown. To apply SFs in clinics, effective marker selection and characterization of properties in the target organ are essential.

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As the strongest antagonist of the platelet activating factor, ginkgolide B (GB) possesses anti-ischemic, anti-oxidant and anti-convulsant properties, and it is used for the treatment of thrombosis in clinical practice.

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We will begin this chapter with an examination of functional genomics. Then we will consider a quest that is even more complex than genomics: proteomics, the study of an organism’s proteome—the properties and activities of all the proteins an organism makes in its lifetime. Finally, we will introduce bioinformatics, the discipline concerned with managing and using the vast stores of data that come from genomic, proteomic, and other massive biological studies.

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Chapter 24 introduce to genomics, proteomics, and bioinformatics. We will begin this chapter with an examination of functional genomics. Then we will consider a quest that is even more complex than genomics: proteomics, the study of an organism’s proteome-the properties and activities of all the proteins an organism makes in its lifetime. Finally, we will introduce bioinformatics, the discipline concerned with managing and using the vast stores of data that come from genomic, proteomic, and other massive biological studies.

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The retinoid-inducible serine carboxypeptidase 1 (Scpep1; formerly RISC) is a lysosomal matrix protein that was initially identified in a screen for genes induced by retinoic acid. Recently, it has been spotlighted by several proteome analyses of the lysosomal compartment, but its cellular function and properties remain unknown to date.

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