Protein complexes

This study determines the interaction between RBPs and target-RNA complexes from public data of the ENCODE project and identifies mutations associated with Mendelian diseases that could disrupt the RBP-RNA interactions.

8p viharuno 03-01-2025 1 1   Download

Phức hợp tương thích mô chính (Major Histocompatibility Complex, MHC) hay ở người còn được gọi kháng nguyên bạch cầu người (Human Leucocyte Antigen, HLA) là một nhóm gene mã hoá cho các protein trình diện kháng nguyên trên bề mặt tế bào của đa số động vật có xương sống. Những protein này đóng vai trò quan trọng trong tổ chức miễn dịch của cơ thể cũng như những cơ chế giao tiếp giữa các tế bào.

44p huynhhuuviet 11-06-2011 473 55   Download

The thesis is structured as follows: In Chapter 1, the scientific literature is summarized within the scope of this study. Chapter 2 provides a comprehensive overview of the principles of the applied computational approaches in this study. Chapter 3 identifies the important residues of the LsIA/α7 nAChR complex that affect the interactions between the toxin and the membrane protein due to C-terminal carboxylation of LsIA. The effects of C-terminal modification of LsIA on interactions with α3β2 nAChR, involved in cardiovascular diseases, were also investigated in Chapter 4.

234p runthenight04 02-02-2023 11 3   Download

In this paper, we present a novel global protein-protein interaction network alignment algorithm, which is enhanced with an extended large neighborhood search heuristics. Evaluated on benchmark datasets of yeast, fly, human and worm, the proposed algorithm outperforms state-of-the-art algorithms. Furthermore, the complexity of ours is polynomial, thus being scalable to large biological networks in practice.

11p tamynhan4 06-09-2020 15 4   Download

The K103N substitution is a frequently observed HIV-1 RT mutation in patients who do not respond to combinationtherapy. The drugs Efavirenz, MSC194 and PNU142721 belong to the recent generation of NNRTIs characterized by an improved resistance profile to the most common single point mutations within HIV-1 RT, including the K103N mutation. In the present study we present structural observations from Efavirenz in complex with wild-type protein and the K103N mutant and PNU142721 and MSC194 in complex with the K103N mutant.

8p system191 01-06-2013 41 4   Download

Trehalose metabolism is an essential component of the stress response in yeast cells. In this work we show that the products of the principal genes involved in trehalose metabolism in Schizosaccharomyces pombe, tps1+ (coding for trehalose6-P synthase, Tps1p), ntp1+ (encoding neutral trehalase, Ntp1p) and tpp1+ (that codes for trehalose-6-P phosphatase, Tpp1p), interact in vitro with each other and with themselves to form protein complexes. Disruption of the gene tps1+ blocks the activation of the neutral trehalase induced by heat shock but not by osmotic stress.

9p system191 01-06-2013 28 4   Download

The human immunodeficiency virus type 1, HIV-1, genome encodes a highly conserved regulatory gene product, Vpr (96 amino acids), which is incorporated into virions in quantities equivalent to those of the viral Gag protein. In infected cells, Vpr is believed to function during the early stages of HIV-1 replication (such as transcription of the proviral genome and migration of preintegration nuclear complex), blocks cells in G2 phase and triggers apoptosis.

10p system191 01-06-2013 46 4   Download

The plastid transcription kinase (PTK), a component of the major RNA polymerase complex from mustard chloroplasts, has been implicated in redox-mediated regulation of plastid gene expression. A cloning strategy to define the PTK gene(s) resulted in the isolation of a full-length cDNA for a protein with overall high homology with the a subunit of cytosolic casein kinase (CK2) that contained an N-terminal extension for a putative plastid transit peptide.

9p system191 01-06-2013 46 4   Download

This study addresses the interactions between the adaptor protein Shb and components involved in T cell signalling, including SLP-76, Gads, Vav and ZAP70. We show that both SLP-76 and ZAP70 co-immunoprecipitate with Shb in Jurkat T cells and that Shb and Vav co-immunoprecipitate when cotransfected in COS cells. We also demonstrate, utilizing fusion protein constructs, that SLP-76, Gads and Vav associate independently of each other to different domains or regions, of Shb.

10p system191 01-06-2013 37 5   Download

Guanosine triphosphate nucleotide analogues such as GppNHp (also named GMPPNP) or GTPcS are widely used to stabilize rapidly hydrolyzing protein-nucleotide complexes and to investigate biochemical reaction pathways. Here we describe the chemical synthesis of guanosine 5¢-O-(c-amidotriphosphate) (GTPcNH2) and a new synthesis of guanosine 5¢-O-(c-fluorotriphosphate) (GTPcF). The two nucleotides were characterized using NMR spectroscopy and isothermal titration calorimetry. Chemical shift data on 31P, 19F and 1H NMR resonances are tabulated.

9p system191 01-06-2013 32 5   Download

The high-pressure stopped-flow technique is applied to study the CO binding in cytochrome P450cam (P450cam) bound with homologous substrates (1R-camphor, camphane, norcamphor and norbornane) and in the substrate-free protein. The activation volume DV # of the CO on-rate is positive for P450cam bound with substrates that do not contain methyl groups. The kon rate constant for these substrate complexes is in the order of 3 · 106 M)1Æs)1. In contrast, P450cam complexed with substrates carrying methyl groups show a negative activation volume and a low kon rate constant of % 3 · 104 M)1Æs)1. ...

8p system191 01-06-2013 40 4   Download

Many groups of proteins play important roles in the cell’s response to various stresses. The molecular chaperone GroEL of Escherichia coli represents one such highly conserved family of stress proteins. We have observed that isolated GroEL complexes from stationary cultures contain various polypeptides that can be released from the chaperonin by GroES and/or ATP, and identified two such polypeptides as the proteins GatY and UP12.

9p system191 01-06-2013 31 3   Download

Laboratory for Phytopathology and Plant Protection, Katholieke Universiteit Leuven, Belgium; 2Institut de Pharmacologie et Biologie Structurale, UMR-CNRS 5089, Toulouse Cedex, France; 3Rega Institute, Laboratory of Molecular Immunology, Katholieke Universiteit Leuven, Belgium Fruits of elderberry (Sambucus nigra) express small quantities of a type-2 ribosome-inactivating protein with an exclusive specificity towards the NeuAc(a2,6)Gal/GalNAc disaccharide and a unique molecular structure typified by the occurrence of a disulfide bridge between the B-chains of two adjacent protomers....

10p system191 01-06-2013 43 3   Download

The serpins are of general protein chemical interest due to their ability to undergo a large conformational change consisting of the insertion of the reactive centre loop (RCL) as strand 4 of the central b sheet A. To make space for the incoming RCL, the ‘shutter region’ opens by the b strands 3A and 5A sliding apart over the underlying a helix B. Loop insertion occurs during the formation of complexes of serpins with their target serine proteinases and during latency transition. This type of loop insertion is unique to plasminogen activator inhibitor-1 (PAI-1).

10p system191 01-06-2013 42 4   Download

DNA transactions in eukaryotes require that proteins gain access to target sequences packaged in chromatin. Further, interactions between distinct nucleoprotein complexes are often required to generate higher-order structures. Here, we employed two prokaryotic site-specific recombination systems to investigate how chromatin packaging affects the assembly of nucleoprotein structures of different complexities at more than 30 genomic loci. The dynamic nature of chromatin permitted protein–DNA and DNA–DNA interactions for sites of at least 34 bp in length.

7p system191 01-06-2013 53 4   Download

Oligomerization into multimeric complexes is a prerequisite for the chaperone function of almost all a-crystallin type heat shock proteins (a-Hsp), but the molecular details of complex assembly are poorly understood. The a-Hsp proteins from Bradyrhizobium japonicum are suitable bacterial models for structure-function studies of these ubiquitous stress proteins. They fall into two distinct classes, A and B, display chaperone activity in vitro and form oligomers of  24 subunits.

9p research12 01-06-2013 50 6   Download

A splicing factor SF2/ASF is a natural substrate for the kinase activity of human topoisomerase I. This study demonstrates that SF2/ASF inhibits DNA cleavage by human topoisomerase I induced by the anti-cancer agent camptothecin. The inhibition is independent of the phosphorylation status of SF2/ASF. We show that the inhibition did not result from binding of SF2/ASF to DNA that would hinder interactions between topoisomerase I and DNA. Neither it was a consequence of a loss of sensitivity of the enzyme to camptothecin.

7p research12 01-06-2013 39 5   Download

The regulator of ubiquitous kinase (Ruk) protein, also known as CIN85 or SETA, is an adaptor-type protein belonging to the CD2AP/CMS family. It was found in complexes with many signaling proteins, including phos1 phoinositol (PtdIns) 3-kinase (EC 2.7.1.137), Cbl, GRB2, p130Cas and Crk. Functional analysis of these interactions, implicated Ruk in the regulation of apoptosis, receptor endocytosis and cytoskeletal rearrangements.

7p research12 01-06-2013 28 4   Download

Telomerase is a specialized reverse transcriptase responsible for synthesizing telomeric DNA at the ends of chromosomes. Six subunits composing the telomerase complex have been cloned: hTR (human telomerase RNA), TEP1 (telomerase-associated protein 1), hTERT (human telomerase reverse transcriptase), hsp90 (heat shock protein 90), p23, and dyskerin. In this study, we investigated the role of each the telomerase subunit on the activity of telomerase.

9p research12 01-06-2013 28 3   Download

Cloning and over-expression of human glucose 6-phosphate dehydrogenase (Glc6P dehydrogenase) has for the first time allowed a detailed kinetic study of a preparation that is genetically homogeneous and in which all the protein molecules are of identical age. The steady-state kinetics of the recombinant enzyme, studied by fluorimetric initial-rate measurements, gave converging linear Lineweaver–Burk plots as expected for a ternary-complex mechanism.

8p research12 01-06-2013 64 4   Download