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1.
Background
PH domains represent one of the most common domains in the human proteome. These domains are recognized as important mediators of protein-phosphoinositide and protein-protein interactions. Phosphoinositides are lipid components of the membrane that function as signaling molecules by targeting proteins to their sites of action. Phosphoinositide based signaling pathways govern a diverse range of important cellular processes including membrane remodeling, differentiation, proliferation and survival. Myo-Inositol phosphates are soluble signaling molecules that are structurally similar to the head groups of phosphoinositides. These molecules have been proposed to function, at least in part, by regulating PH domain-phosphoinositide interactions. Given the structural similarity of inositol phosphates we were interested in examining the specificity of PH domains towards the family of myo-inositol pentakisphosphate isomers. 相似文献2.
Background
PDZ domain is a well-conserved, structural protein domain found in hundreds of signaling proteins that are otherwise unrelated. PDZ domains can bind to the C-terminal peptides of different proteins and act as glue, clustering different protein complexes together, targeting specific proteins and routing these proteins in signaling pathways. These domains are classified into classes I, II and III, depending on their binding partners and the nature of bonds formed. Binding specificities of PDZ domains are very crucial in order to understand the complexity of signaling pathways. It is still an open question how these domains recognize and bind their partners. 相似文献3.
Background
Copines are soluble, calcium-dependent membrane binding proteins found in a variety of organisms. Copines are characterized as having two C2 domains at the N-terminal region followed by an "A domain" at the C-terminal region. The "A domain" is similar in sequence to the von Willebrand A (VWA) domain found in integrins. The presence of C2 domains suggests that copines may be involved in cell signaling and/or membrane trafficking pathways. 相似文献4.
Background
The mechanism by which the signals are transmitted between receptor and effector domains in multi-domain signaling proteins is poorly understood. 相似文献5.
Background
FYVE domains have emerged as membrane-targeting domains highly specific for phosphatidylinositol 3-phosphate (PtdIns(3)P). They are predominantly found in proteins involved in various trafficking pathways. Although FYVE domains may function as individual modules, dimers or in partnership with other proteins, structurally, all FYVE domains share a fold comprising two small characteristic double-stranded β-sheets, and a C-terminal α-helix, which houses eight conserved Zn2+ ion-binding cysteines. To date, the structural, biochemical, and biophysical mechanisms for subcellular targeting of FYVE domains for proteins from various model organisms have been worked out but plant FYVE domains remain noticeably under-investigated. 相似文献6.
7.
Background
CC chemokine receptor proteins (CCR1 through CCR10) are seven-transmembrane G-protein coupled receptors whose signaling pathways are known for their important roles coordinating immune system responses through targeted trafficking of white blood cells. In addition, some of these receptors have been identified as fusion proteins for viral pathogens: for example, HIV-1 strains utilize CCR5, CCR2 and CCR3 proteins to obtain cellular entry in humans. The extracellular domains of these receptor proteins are involved in ligand-binding specificity as well as pathogen recognition interactions. 相似文献8.
Zsofia Szentpetery Andras Balla Yeun Ju Kim Mark A Lemmon Tamas Balla 《BMC cell biology》2009,10(1):67-20
Background
Phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P 2] is a critically important regulatory phospholipid found in the plasma membrane of all eukaryotic cells. In addition to being a precursor of important second messengers, PtdIns(4,5)P 2 also regulates ion channels and transporters and serves the endocytic machinery by recruiting clathrin adaptor proteins. Visualization of the localization and dynamic changes in PtdIns(4,5)P 2 levels in living cells is critical to understanding the biology of PtdIns(4,5)P 2. This has been mostly achieved with the use of the pleckstrin homology (PH) domain of PLCδ1 fused to GFP. Here we report on a comparative analysis of several recently-described yeast PH domains as well as the mammalian Tubby domain to evaluate their usefulness as PtdIns(4,5)P 2 imaging tools. 相似文献9.
10.
Background
Phosphorylation by protein kinases is central to cellular signal transduction. Abnormal functioning of kinases has been implicated in developmental disorders and malignancies. Their activity is regulated by second messengers and by the binding of associated domains, which are also influential in translocating the catalytic component to their substrate sites, in mediating interaction with other proteins and carrying out their biological roles.Result
Using sensitive profile-search methods and manual analysis, the human genome has been surveyed for protein kinases. A set of 448 sequences, which show significant similarity to protein kinases and contain the critical residues essential for kinase function, have been selected for an analysis of domain combinations after classifying the kinase domains into subfamilies. The unusual domain combinations in particular kinases suggest their involvement in ubiquitination pathways and alternative modes of regulation for mitogen-activated protein kinase kinases (MAPKKs) and cyclin-dependent kinase (CDK)-like kinases. Previously unexplored kinases have been implicated in osteoblast differentiation and embryonic development on the basis of homology with kinases of known functions from other organisms. Kinases potentially unique to vertebrates are involved in highly evolved processes such as apoptosis, protein translation and tyrosine kinase signaling. In addition to coevolution with the kinase domain, duplication and recruitment of non-catalytic domains is apparent in signaling domains such as the PH, DAG-PE, SH2 and SH3 domains.Conclusions
Expansion of the functional repertoire and possible existence of alternative modes of regulation of certain kinases is suggested by their uncommon domain combinations. Experimental verification of the predicted implications of these kinases could enhance our understanding of their biological roles.11.
Holger Conzelmann Julio Saez-Rodriguez Thomas Sauter Boris N Kholodenko Ernst D Gilles 《BMC bioinformatics》2006,7(1):34-15
Background:
Receptors and scaffold proteins possess a number of distinct domains and bind multiple partners. A common problem in modeling signaling systems arises from a combinatorial explosion of different states generated by feasible molecular species. The number of possible species grows exponentially with the number of different docking sites and can easily reach several millions. Models accounting for this combinatorial variety become impractical for many applications. 相似文献12.
Background
As important regulators of developmental and adult processes in metazoans, Fibroblast Growth Factor (FGF) proteins are potent signaling molecules whose activities must be tightly regulated. FGFs are known to play diverse roles in many processes, including mesoderm induction, branching morphogenesis, organ formation, wound healing and malignant transformation; yet much more remains to be learned about the mechanisms of regulation used to control FGF activity. 相似文献13.
Sylvie Elsen Georgios Efthymiou Panagiotis Peteinatos George Diallinas Panayotis Kyritsis Jean-Marc Moulis 《BMC microbiology》2010,10(1):271
Background
Ferredoxins are small iron-sulfur proteins belonging to all domains of life. A sub-group binds two [4Fe-4S] clusters with unequal and extremely low values of the reduction potentials. These unusual properties are associated with two specific fragments of sequence. The functional importance of the very low potential ferredoxins is unknown. 相似文献14.
Background
Calcium signaling plays a prominent role in plants for coordinating a wide range of developmental processes and responses to environmental cues. Stimulus-specific generation of intracellular calcium transients, decoding of calcium signatures, and transformation of the signal into cellular responses are integral modules of the transduction process. Several hundred proteins with functions in calcium signaling circuits have been identified, and the number of downstream targets of calcium sensors is expected to increase. We previously identified a novel, calmodulin-binding nuclear protein, IQD1, which stimulates glucosinolate accumulation and plant defense in Arabidopsis thaliana. Here, we present a comparative genome-wide analysis of a new class of putative calmodulin target proteins in Arabidopsis and rice. 相似文献15.
Background
The related proteins Boi1 and Boi2, which appear to promote polarized growth in S. cerevisiae, both contain a PH (pleckstrin homology) and an SH3 (src homology 3) domain. Previously, we gained evidence that a PH domain-bearing segment of Boi1, which we call Boi1-PH, is sufficient and necessary for function. In the current study, we investigate the binding of Boi1's PH domain to the acidic phospholipids PIP2 (phosphatidylinositol-4,5-bisphosphate) and PS (phosphatidylserine). 相似文献16.
João Pessoa Zsuzsa Sárkány Frederico Ferreira-da-Silva Sónia Martins Maria R Almeida Jianming Li Ana M Damas 《BMC plant biology》2010,10(1):30
Background
Arabidopsis thaliana transthyretin-like (TTL) protein is a potential substrate in the brassinosteroid signalling cascade, having a role that moderates plant growth. Moreover, sequence homology revealed two sequence domains similar to 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU) decarboxylase (N-terminal domain) and 5-hydroxyisourate (5-HIU) hydrolase (C-terminal domain). TTL is a member of the transthyretin-related protein family (TRP), which comprises a number of proteins with sequence homology to transthyretin (TTR) and the characteristic C-terminal sequence motif Tyr-Arg-Gly-Ser. TRPs are single domain proteins that form tetrameric structures with 5-HIU hydrolase activity. Experimental evidence is fundamental for knowing if TTL is a tetrameric protein, formed by the association of the 5-HIU hydrolase domains and, in this case, if the structural arrangement allows for OHCU decarboxylase activity. This work reports about the biochemical and functional characterization of TTL. 相似文献17.
Background
Human APPL1 and APPL2 are homologous RAB5 effectors whose binding partners include a diverse set of transmembrane receptors, signaling proteins, and phosphoinositides. APPL proteins associate dynamically with endosomal membranes and are proposed to function in endosome-mediated signaling pathways linking the cell surface to the cell nucleus. APPL proteins contain an N-terminal Bin/Amphiphysin/Rvs (BAR) domain, a central pleckstrin homology (PH) domain, and a C-terminal phosphotyrosine binding (PTB) domain. Previous structural and biochemical studies have shown that the APPL BAR domains mediate homotypic and heterotypic APPL-APPL interactions and that the APPL1 BAR domain forms crescent-shaped dimers. Although previous studies have shown that APPL minimal BAR domains associate with curved cell membranes, direct interaction between APPL BAR domains on cell membranes in vivo has not been reported.Methodology
Herein, we used a laser-scanning confocal microscope equipped with a spectral detector to carry out fluorescence resonance energy transfer (FRET) experiments with cyan fluorescent protein/yellow fluorescent protein (CFP/YFP) FRET donor/acceptor pairs to examine interactions between APPL minimal BAR domains at the subcellular level. This comprehensive approach enabled us to evaluate FRET levels in a single cell using three methods: sensitized emission, standard acceptor photobleaching, and sequential acceptor photobleaching. We also analyzed emission spectra to address an outstanding controversy regarding the use of CFP donor/YFP acceptor pairs in FRET acceptor photobleaching experiments, based on reports that photobleaching of YFP converts it into a CFP-like species.Conclusions
All three methods consistently showed significant FRET between APPL minimal BAR domain FRET pairs, indicating that they interact directly in a homotypic (i.e., APPL1-APPL1 and APPL2-APPL2) and heterotypic (i.e., APPL1-APPL2) manner on curved cell membranes. Furthermore, the results of our experiments did not show photoconversion of YFP into a CFP-like species following photobleaching, supporting the use of CFP donor/YFP acceptor FRET pairs in acceptor photobleaching studies. 相似文献18.
Background
High-throughput protein structure analysis of individual protein domains requires analysis of large numbers of expression clones to identify suitable constructs for structure determination. For this purpose, methods need to be implemented for fast and reliable screening of the expressed proteins as early as possible in the overall process from cloning to structure determination. 相似文献19.
Background
Measuring each protein's importance in signaling networks helps to identify the crucial proteins in a cellular process, find the fragile portion of the biology system and further assist for disease therapy. However, there are relatively few methods to evaluate the importance of proteins in signaling networks. 相似文献20.
Xiaoying Jian Patrick Brown Peter Schuck James M. Gruschus Andrea Balbo Jenny E. Hinshaw Paul A. Randazzo 《The Journal of biological chemistry》2009,284(3):1652-1663
ASAP1 is an Arf GTPase-activating protein (GAP) that functions on membrane
surfaces to catalyze the hydrolysis of GTP bound to Arf. ASAP1 contains a
tandem of BAR, pleckstrin homology (PH), and Arf GAP domains and contributes
to the formation of invadopodia and podosomes. The PH domain interacts with
the catalytic domain influencing both the catalytic and Michaelis constants.
Tandem BAR-PH domains have been found to fold into a functional unit. The
results of sedimentation velocity studies were consistent with predictions
from homology models in which the BAR and PH domains of ASAP1 fold together.
We set out to test the hypothesis that the BAR domain of ASAP1 affects GAP
activity by interacting with the PH and/or Arf GAP domains. Recombinant
proteins composed of the BAR, PH, Arf GAP, and Ankyrin repeat domains (called
BAR-PZA) and the PH, Arf GAP, and Ankyrin repeat domains (PZA) were compared.
Catalytic power for the two proteins was determined using large unilamellar
vesicles as a reaction surface. The catalytic power of PZA was greater than
that of BAR-PZA. The effect of the BAR domain was dependent on the N-terminal
loop of the BAR domain and was not the consequence of differential membrane
association or changes in large unilamellar vesicle curvature. The
Km for BAR-PZA was greater and the
kcat was smaller than for PZA determined by saturation
kinetics. Analysis of single turnover kinetics revealed a transition state
intermediate that was affected by the BAR domain. We conclude that BAR domains
can affect enzymatic activity through intraprotein interactions.The Bin, amphiphysin, RSV161/167
(BAR)2 domain is a
recently identified structural element in proteins that regulate membrane
trafficking
(1–7).
The BAR superfamily comprises three subfamilies: F-BAR, I-BAR, and BAR. The
BAR group can be further subdivided into BAR, N-BAR, PX-BAR, and
BAR-pleckstrin homology (PH). The BAR group domains consist of three bundled
α-helices that homodimerize to form a banana-shaped structure. The inner
curved face can bind preferentially to surfaces with similar curvatures. As a
consequence, BAR domains can function as membrane curvature sensors or as
inducers of membrane curvature. BAR domains also bind to proteins
(8,
9). Several proteins contain a
BAR domain immediately N-terminal to a PH domain, which also mediates
regulated membrane association
(10–13).
In the protein APPL1 (9), the
BAR-PH domains fold together forming a binding site for the small GTP-binding
protein Rab5. Arf GTPase-activating proteins (GAPs) are regulators of Arf
family GTP-binding proteins
(14–18).
Two subtypes of Arf GAPs have N-terminal BAR and PH domains similar to that
found in APPL1.Thirty-one genes encode Arf GAPs in humans
(16–18).
Each member of the family has an Arf GAP domain that catalyzes the hydrolysis
of GTP bound to Arf family GTP-binding proteins. The Arf GAPs are otherwise
structurally diverse. ASAP1 is an Arf GAP that affects membrane traffic and
actin remodeling involved in cell movement and has been implicated in
oncogenesis
(19–22).
ASAP1 contains, from the N terminus, BAR, PH, Arf GAP, Ankyrin repeat,
proline-rich, and SH3 domains.ASAP1 contains a BAR domain immediately N-terminal to a PH domain. The PH
domain of ASAP1 is functionally integrated with the Arf GAP domain and may
form part of the substrate binding pocket
(23,
24). The PH domain binds
specifically to phosphatidylinositol 4,5-bisphosphate (PIP2), a
constituent of the membrane, leading to stimulation of GAP activity by a
mechanism that is, in part, independent of recruitment to membranes
(23,
25). The BAR domain of ASAP1
is critical for in vivo function of ASAP1, but the molecular
functions of the BAR domain of ASAP1 have not been extensively characterized.
Hypotheses related to membrane curvature have been examined. Recombinant ASAP1
can induce the formation of tubules from large unilamellar vesicles, which may
be related to a function of ASAP1 in membrane traffic. The BAR domain might
also regulate GAP activity of ASAP1. We have considered two mechanisms based
on the known properties of BAR domains. First the BAR domain could regulate
association of ASAP1 with membrane surfaces containing the substrate
Arf1·GTP. The BAR domain could also affect GAP activity through an
intramolecular association. In one BAR-PH protein that has been crystallized
(APPL1), the two domains fold together to form a protein binding site
(9). In ASAP1, the PH domain is
functionally integrated with the GAP domain, raising the possibility that the
BAR domain affects GAP activity by folding with the PH domain.Here we compared the kinetics of recombinant proteins composed of the PH,
Arf GAP, and Ankyrin repeat
(PZA)3 or BAR, PH, Arf
GAP, and Ankyrin repeat (BAR-PZA) domains of ASAP1 to test the hypothesis that
the BAR domain affects enzymatic activity. We found kinetic differences
between the proteins that could not be explained by membrane association
properties. The results were consistent with a model in which the BAR domain
affects transition of ASAP1 through its catalytic cycle. 相似文献