Large protein complex

Ebook "DNA helicases and DNA motor proteins" is to provide the first systematic overview of structure, function and regulation of DNA helicases and related molecular motors. By integrating the knowledge obtained through the diverse technical approaches ranging from single-molecule biophysics to cellular and molecular biological studies the editors aim to provide a unified view on how helicases function in the cell, are regulated in response to different cellular stresses and are integrated into large macromolecular assemblies to form a complex and adaptive living system.

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Human proteins are widely used as drug targets. Integration of large-scale protein-level genome-wide association studies (GWAS) and disease-related GWAS has thus connected genetic variation to disease mechanisms via protein. Previous proteome-by-phenome-wide Mendelian randomization (MR) studies have been mainly focused on plasma proteomes.

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SMARCB1, also known as INI1, is a member of a large protein complex involved in chromatin remodeling and thus the regulation of gene expression. It is located on chromosome 22q11.2. SMARCB1 tumors have been found in various locations, including the sinonasal region, gastrointestinal tract, central nervous system (in atypical teratoid and rhabdoid tumors), and perirenal region (in malignant rhabdoid tumors) in both adults and children.

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Ebook "T-cell differentiation: Methods and protocols" provides protocols to successfully apply cutting-edge technologies to characterize the biology of T cells at an unprecedented level of complexity. Chapters guide readers through flow cytometry and fluorescence-activated cell sorting, the behaviour of single T cells after adoptive cell transfer (ACT), single cell gene expression by multiplex PCR, lentiviral transduction approaches, protocols to derive large numbers of early-differentiated memory T cells by using dedicated cytokines cocktails,...

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Ebook "Bacterial protein secretion systems: Methods and protocols" details protocols that cover the broad arsenal of techniques used to study a secretion system from A to Z. Chapters focus on identifying and localizing the different subunits, defining interactions within subunits, monitoring conformational changes, purifying and imaging of large complexes, defining the assembly pathway by fluorescence microscopy and the role of energy during assembly and/or secretion, identifying secreted effectors as well as reporters to follow effector transport.

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Ebook "Protein NMR: Methods and protocols" covers state-of-the-art applications of solid-state and solution nuclear magnetic resonance( NMR) spectroscopy to study protein structure, dynamics and interactions. Chapters detail various aspects of data acquisition and processing, determination of the structure, multi-timescale dynamics of entities ranging from individual proteins to large macromolecular complexes to intact viral assemblies.

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All mRNAs are bound in vivo by proteins to form mRNA–protein complexes (mRNPs), but changes in the composition of mRNPs during posttranscriptional regulation remain largely unexplored. Here, we have analyzed, on a transcriptome-wide scale, how microRNA-mediated repression modulates the associations of the core mRNP components eIF4E, eIF4G, and PABP and of the decay factor DDX6 in human cells.

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Recent large-scale studies revealed cell-type specific proteomes. However, protein complexes, the basic functional modules of a cell, have been so far mostly considered as static entities with well-defined structures. The co-expression of their members has not been systematically charted at the protein level.

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To live such complex lifestyles, they have evolved efficient signal transduction systems with numerous one- and two-component regulatory system along with a large array of chemosensory systems to perceive and integrate both external and internal cues.

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WD40 domains are abundant in eukaryotes, and they are essential subunits of large multiprotein complexes, which serve as scaffolds. WD40 proteins participate in various cellular processes, such as histone modification, transcription regulation, and signal transduction. WD40 proteins are regarded as crucial regulators of plant development processes. However, the systematic identification and analysis of WD40 proteins have yet to be reported in wheat.

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In plants, 14-3-3 proteins, also called GENERAL REGULATORY FACTORs (GRFs), encoded by a large multigene family, are involved in protein–protein interactions and play crucial roles in various physiological processes.

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Boolean models are increasingly used to study biological signaling networks. In a Boolean network, nodes represent biological entities such as genes, proteins or protein complexes, and edges indicate activating or inhibiting influences of one node towards another.

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Identification of protein complexes can help us get a better understanding of cellular mechanism. With the increasing availability of large-scale protein-protein interaction (PPI) data, numerous computational approaches have been proposed to detect complexes from the PPI networks.

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Amino acid replacement rate matrices are a crucial component of many protein analysis systems such as sequence similarity search, sequence alignment, and phylogenetic inference. Ideally, the rate matrix reflects the mutational behavior of the actual data under study; however, estimating amino acid replacement rate matrices requires large protein alignments and is computationally expensive and complex.

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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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Structural comparison of protein-protein interfaces provides valuable insights into the functional relationship between proteins, which may not solely arise from shared evolutionary origin. A few methods that exist for such comparative studies have focused on structural models determined at atomic resolution, and may miss out interesting patterns present in large macromolecular complexes that are typically solved by low-resolution techniques.

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Network query problem aligns a small query network with an arbitrarily large target network. The complexity of this problem grows exponentially with the number of nodes in the query network if confidence in the optimality of result is desired. Scaling this problem to large query and target networks remains to be a challenge.

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Proteins interact with a variety of other molecules such as nucleic acids, small molecules and other proteins inside the cell. Structure-determination of protein-protein complexes is challenging due to several reasons such as the large molecular weights of these macromolecular complexes, their dynamic nature, difficulty in purification and sample preparation.

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Microbial genomes at the National Center for Biotechnology Information (NCBI) represent a large collection of more than 35,000 assemblies. There are several complexities associated with the data: A great variation in sampling density since human pathogens are densely sampled while other bacteria are less represented; different protein families occur in annotations with different frequencies; and the quality of genome annotation varies greatly.

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Biological networks play an increasingly important role in the exploration of functional modularity and cellular organization at a systemic level. Quite often the first tools used to analyze these networks are clustering algorithms.

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