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Welcome to the Pubget Medical Subject Headings (MESH) browser. Click on a topic or subtopic below to explore related papers. In the gold box is the most recent paper about the current MESH term, and below are 20 related papers.
Amino Acid Motifs (1):
Recent article
Amino Acid Motifs
Abstract
We analyzed P30 derivatives having epitope tags engineered at various locations to demonstrate that posttranslational processing occurred in P30. Several potential cleavage sites predicted in silico were examined, and a processing-defective mutant was created to explore P30 maturation further. Our r...
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PMID: 21821772
PDF is available here.
PDF is available here.
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Endocrinology (152)10 2011
Abstract
We characterized to which GRE GR binds in the rat hippocampus. Using a position-specific scoring matrix, we identified evolutionary-conserved putative GREs from a microarray based set of hippocampal target genes. Using chromatin immunoprecipitation, we were able to confirm GR binding to 15 out of a...
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PMID: 21846803
PDF is available here.
PDF is available here.
Abstract
We developed a program to parse sequences according to predicted topology and then analyze topologically related regions. This approach identified three conserved motifs that served as the basis for subsequent mutagenesis and functional studies. This work reveals that several inter-transmembrane loo...
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PMID: 21812456
PDF is available here.
PDF is available here.
Abstract
We determined the structure of Phytophthora capsici AVR3a4, a close homolog of P. infestans AVR3a. Our structural and functional analyses reveal that the effector domain of AVR3a contains a conserved, positively charged patch and that this region, rather than the RXLR domain, is required for binding...
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PMID: 21821794
PDF is available here.
PDF is available here.
Abstract
We report that dUTPase, an essential nucleotide pyrophosphatase, uses a C-terminal P-loop-like sequence in a unique mechanism for substrate discrimination and efficient hydrolysis. Our spectroscopy and transient kinetics results on human dUTPase mutants combined with previous structural studies indi...
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PMID: 21831832
PDF is available here.
PDF is available here.
Abstract
We have solved the crystal structure of the RNA recognition and leucine-rich repeat motifs of TAP bound to one symmetrical half of the CTE RNA. L-shaped conformations of protein and RNA are involved in a mutual molecular embrace on complex formation. We have monitored the impact of structure-guided...
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PMID: 21822283
PDF is available here.
PDF is available here.
Abstract
We describe crystallographic and biochemical analyses of filament nucleation by VopL. The WH2 element of VopL does not nucleate on its own and requires the VCD for activity. The VCD forms a U-shaped dimer in the crystal, stabilized by a terminal coiled coil. Dimerization of the WH2 motifs contribute...
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PMID: 21873984
PDF is available here.
PDF is available here.
Abstract
We demonstrate that the proteolysis of human NANOG is regulated by the ubiquitin-proteasomal pathway. The inhibition of proteasome activity by proteasome inhibitor MG132 showed increase in protein levels of endogenous NANOG in a dose-dependent manner in human ESCs (hESCS). We demonstrated that the i...
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PMID: 21299413
PDF is available here.
PDF is available here.
Avian Diseases (55)3 2011
Abstract
Toll-like receptors (TLRs), a family of transmembrane and cytosolic proteins, detect microbial patterns, initiating innate immune responses in various organisms. Although they are abundant, genetic characterization and functional differences of TLRs in economically important avian sp...
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PMID: 22017051
PDF is available here.
PDF is available here.
Abstract
We show that a previously uncharacterized member of the I-BAR subfamily, Pinkbar, is specifically expressed in intestinal epithelial cells, where it localizes to Rab13-positive vesicles and to the plasma membrane at intercellular junctions. Notably, the BAR domain of Pinkbar does not induce membrane...
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PMID: 21743456
PDF is available here.
PDF is available here.
Abstract
We test this hypothesis by comparing vulva induction in two genetically tractable nematodes, Caenorhabditis elegans and Pristionchus pacificus. Previous work indicated that the vulva is induced by epidermal growth factor (EGF)/RAS and WNT signaling in Caenorhabditis and Pristionchus, respectively. H...
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PMID: 21814488
PDF is available here.
PDF is available here.
Abstract
We have performed fluorescence polarisation assays to indirectly measure relative binding affinity, and applied computational simulations to interrogate the behaviour of the eight human BRC-RAD51 complexes, as well as a suite of BRC cancer-associated mutations. Our computational approaches encompass...
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PMID: 21789034
PDF is available here.
PDF is available here.
Abstract
We present a new computational sampling approach to obtain reasonable loop backbone models, so-called the Pareto Optimal Sampling (POS) method. The rationale of the POS method is to sample the function space of multiple, carefully-selected scoring functions to discover an ensemble of diversified str...
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PMID: 21702492
PDF is available here.
PDF is available here.
Abstract
We report here that clusters of charged amino acids in the TR hormone-binding domain are required for this enhanced mode of coactivator recruitment and that mutations in these charge clusters, by disrupting TRβ2 coactivator binding, are a molecular basis for pituitary resistance to thyroid hormone,...
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PMID: 21622532
PDF is available here.
PDF is available here.
Abstract
We have examined whether 3Cl-AHPC acts as an agonist and increases SHP activity in the repression of bile acid biosynthetic CYP7A1 and CYP8B1 genes and delineated the underlying mechanisms. Contrary to this expectation, micromolar concentrations of 3Cl-AHPC increased CYP7A1 expression but indirectly...
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PMID: 21566081
PDF is available here.
PDF is available here.
Abstract
We were able to identify a new immunostimulatory, non-uridine-rich TLR7 motif that is present in many published siRNAs. Interestingly, the activity of this motif is dependent on the backbone chemistry. Phosphorothioate ORNs containing the motif did not stimulate immune activation, whereas phosphodie...
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PMID: 21749297
PDF is available here.
PDF is available here.
Abstract
Receptor proteins at the cell surface regulate the ability of natural killer cells to recognize and kill a variety of aberrant target cells. The structural features determining the function of natural killer receptor proteins 1 (NKR-P1s) are largely unknown. In the present work, refi...
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PMID: 20839018
PDF is available here.
PDF is available here.
Abstract
The structure of ent-copalyl diphosphate synthase reveals three α-helical domains (α, β and γ), as also observed in the related diterpene cyclase taxadiene synthase. However, active sites are located at the interface of the βγ domains in ent-copalyl diphosphate synthase but exc...
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PMID: 21602811
PDF is available here.
PDF is available here.
Abstract
The movement of the small ribosomal subunit (30S) relative to the large ribosomal subunit (50S) during translation is widely known, but many molecular details and roles of rRNA and proteins in this process are still undefined, especially in solution models. The functional relationship of modified nuc...
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PMID: 21557607
PDF is available here.
PDF is available here.
Abstract
We propose a model whereby an N-terminal signal sequence, xLxxKN, directs ABCA transporters to a post-Golgi vesicular sorting station where additional signals may be required for selective delivery of individual transporters to final subcellular destinations....
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PMID: 21586796
PDF is available here.
PDF is available here.
Abstract
We have used a FLNa-deficient human melanoma cell line (M2) and its derivative line (A7) that stably expresses FLNa to demonstrate that SH2B1β and FLNa are required for maximal PRL-dependent cell ruffling. We have found that in addition to two actin-binding domains, SH2B1β has a FLNa-binding domai...
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PMID: 21566085
PDF is available here.
PDF is available here.
Abstract
We investigate whether GRα isoform-specific differences in the regulation of antiapoptotic genes contribute to this resistant phenotype. We now show that GRα-D, unlike the other receptor isoforms, does not inhibit the activity of a nuclear factor κB (NF-κB)-responsive reporter gene and does not...
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PMID: 21527497
PDF is available here.
PDF is available here.
DNA Repair (10)5 2011
Abstract
We use two protein footprinting techniques, limited proteolysis and oxidative surface mapping, coupled with mass spectrometry to identify amino acids involved along the DNA-binding surface of the Pms1-NTD. Limited proteolysis experiments elucidated several basic residues that were protected in the p...
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PMID: 21354867
PDF is available here.
PDF is available here.
Abstract
X-ray absorption and resonance Raman spectroscopies show that CmlA, the β-hydroxylase of the chloramphenicol biosynthetic pathway, contains a (μ-oxo)-(μ-1,3-carboxylato)diiron(III) cluster with 6-coordinate iron centers and 3 - 4 His ligands. This active site is found within a uni...
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PMID: 21506543
PDF is available here.
PDF is available here.
Abstract
The structure-based design of small-molecule inhibitors of protein-ligand and protein-protein interfaces is a key component of drug discovery. The underlying protein interactions can be regarded based on structural similarity of the secondary structure elements: similarities around t...
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PMID: 21554076
PDF is available here.
PDF is available here.
Abstract
We performed a large scale analysis of the phosphoproteome in mouse embryonic stem (mES) cells. Using multiplex strategies, we detected 4581 proteins and 3970 high confidence distinct phosphosites in 1642 phosphoproteins. Notably, 22 prominent phosphorylated stem cell marker proteins with 39 novel p...
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PMID: 21149613
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1808)9 2011
Abstract
We assessed the microscopic interactions between ALPS and two phospholipid membranes at different degrees of lipid packing by explicit molecular dynamics (MD). Simulations were performed within loosely packed membranes composed of a mixture of dioleoylphosphatidylcholine (DOPC)/dioleoylglycerol (DOG...
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PMID: 21600869
PDF is available here.
PDF is available here.
Abstract
We identified the protein that specifically binds to the URE1 sequence (EhURE1BP). This protein contains five SNase domains and one Tudor motif, and has 21% identity and 36% similarity to the multifunctional eukaryotic protein known as the protein containing Tudor and staphyloccocal nuclease-like do...
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PMID: 21447339
PDF is available here.
PDF is available here.
Abstract
We focus on 'crosstalk manipulation' - the microbial strategies that instigate, subvert or disrupt the molecular signalling crosstalk between receptors of the innate immune system. This proactive interference undermines host defences and contributes to microbial adaptive fitness and persistent infec...
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PMID: 21350579
PDF is available here.
PDF is available here.
Abstract
We develop a general multiscale molecular simulation approach for the calculation of diffusion rates and determination of pathways by which substrate or inhibitor gases can reach the protein active site. Combining kinetic data from both equilibrium simulations and enhanced sampling, we construct a m...
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PMID: 21341658
PDF is available here.
PDF is available here.
Abstract
We describe our structural and biochemical research designed to understand the sequence-to-function relationship in EFCaBPs. The first structural goal was to define conformational changes induced by binding Ca(2+), and our group and others established that solution NMR spectroscopy is well suited fo...
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PMID: 21314091
PDF is available here.
PDF is available here.
Abstract
The haemopexin fold is present in almost all life forms and is utilized for carrying out diverse physiological functions. The structure of CP4, a haemopexin-fold protein from cow pea (Vigna unguiculata), was determined at 2.1 Å resolution. The protein exists as a monomer both in solution and in t...
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PMID: 21301085
PDF is available here.
PDF is available here.
Cell Cycle (10)3 2011
Abstract
We found that CK1ε has unique enzymatic activity on the serine residue in the DSG motif using a β-catenin N-terminal region as a substrate. We then examined whether CK1ε has activity on the DSG motif of Cdc25A. We found CK1ε directly phosphorylated Ser82 without any prior phosphorylation of Cdc2...
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PMID: 21252624
PDF is available here.
PDF is available here.
Molecular Cell (41)2 2011
Abstract
We asked if, during B cell activation, AID also induces DNA breaks at genes other than IgH genes. Using a nonbiased genome-wide approach, we have identified hundreds of reproducible, AID-dependent DSBs in mouse splenic B cells shortly after induction of CSR in culture. Most interestingly, AID induce...
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PMID: 21255732
PDF is available here.
PDF is available here.
Abstract
We propose a new, purely computational method for finding putative associations between transcription factors and motifs. This method is based on a linear model that combines sequence information with expression data. We present various methods for model parameter estimation and show, via experiment...
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PMID: 21297945
PDF is available here.
PDF is available here.
Abstract
We have used an evolutionary approach to study DIA1 and DIA1R. We found DIA1 conserved from cnidarians to humans, indicating DIA1 evolution coincided with the development of the first primitive synapses. Nematodes lack a DIA1 homologue, indicating Caenorhabditis elegans is not suitable for studying...
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PMID: 21283809
PDF is available here.
PDF is available here.
Abstract
We develop and test a novel method that identifies potential targeting motifs using a discriminative approach based on hidden Markov models (discriminative HMMs). These models search for motifs that are present in a compartment but absent in other, nearby, compartments by utilizing an hierarchical s...
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PMID: 21233524
PDF is available here.
PDF is available here.
Abstract
From the studies reported here, we show that mutations of the Y- and LL-motifs, which effectively eliminate the amphipathic nature of the lytic peptide 2 (LLP2) domain or disrupt YW and LL motifs in a region spanning residues 795-803 (YWWNLLQYW), just C-terminal of LLP2, can dramatically interfere w...
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PMID: 21569545
PDF is available here.
PDF is available here.
Abstract
We aimed to characterize these RNA-helicases in more detail. Here, we demonstrate that UAP56 and URH49 exhibit an intrinsic CRM1-independent nucleocytoplasmic shuttling activity. Extensive mapping studies identified distinct regions within UAP56 or URH49 required for (i) intranuclear localization (U...
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PMID: 21799930
PDF is available here.
PDF is available here.
Abstract
We report that along with the classical catalytic residues, an active site "aromatic triad", namely residues F12, F13, and Y79, is critical for cell survival in the presence of the alkylating agent methyl methanesulfonate (MMS). Strains expressing dinB alleles with single point mutations in the arom...
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PMID: 21614131
PDF is available here.
PDF is available here.
Abstract
We determined the first crystal structures of two remotely related, imelysin-like proteins. The Psychrobacter arcticus structure was determined at 2.15 Å resolution and contains the canonical imelysin fold, while higher resolution structures from the gut bacteria Bacteroides ovatus, in two crystal...
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PMID: 21799754
PDF is available here.
PDF is available here.
Abstract
We investigated the possible role of other viral capsid proteins on the FX/HSPG-mediated cellular uptake of HAdV5-based vectors. Using CAR- and CD46-negative CHO cells varying in HSPG expression, we confirmed that FX bound to serotype 5 hexon protein and to HAdV5 and HAdV5F35 virions via its Gla-dom...
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PMID: 21637339
PDF is available here.
PDF is available here.
Abstract
We performed parallel quantitative proteomic and phosphoproteomic analyses of hESCs during differentiation initiated by a diacylglycerol analog or transfer to media that had not been conditioned by feeder cells. We profiled 6521 proteins and 23,522 phosphorylation sites, of which almost 50% displaye...
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PMID: 21406692
PDF is available here.
PDF is available here.
Abstract
We present a computational approach for predicting the DFG-out inactive conformation using the DFG-in active structures, and develop related conformational selection protocols for the uses of the predicted DFG-out models in the binding pose prediction and virtual screening of type-II ligands. With t...
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PMID: 21818358
PDF is available here.
PDF is available here.
Abstract
We defined the important residues and domains of the Arabidopsis YUC1 FMO, a key enzyme in auxin biosynthesis. We previously showed that simultaneous inactivation of YUC1 and its homologue YUC4 caused severe defects in vascular and floral development. We mutagenized the yuc4 mutant and screened for...
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PMID: 21205174
PDF is available here.
PDF is available here.
Abstract
We have identified an additional kinase, CrdS, which directly regulates the phosphorylation state of CrdA. Both epistasis and in vitro phosphotransfer assays indicate that CrdS functions as part of the Che3 pathway and, in addition to CheA3, serves to regulate CrdA phosphorylation in M. xanthus. We...
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PMID: 21810965
PDF is available here.
PDF is available here.
Abstract
Ilf3 and NF90, two proteins containing double-stranded RNA-binding domains, are generated by alternative splicing and involved in several functions. Their heterogeneity results from posttranscriptional and posttranslational modifications. Alternative splicing of exon 3, coding for a 13 aa N-terminal...
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PMID: 21811582
PDF is available here.
PDF is available here.
Abstract
These results identify potentially important residues for the substrate recognition of CCHL....
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PMID: 21380436
PDF is available here.
PDF is available here.
Abstract
We evaluated the putative neurorigenerative properties of RADA16-4G-BMHP1 SAP, proved to enhance in vitro neural stem cells survival and differentiation. This SAP (RADA16-I) has been functionalized with a bone marrow homing motif (BMHP1) and optimized via the insertion of a 4-glycine-spacer that ame...
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PMID: 21611127
PDF is available here.
PDF is available here.
Virology Journal (8)1 2011
Abstract
We analyse the effect of these differences upon the binding of Influenza A virus NS1 protein to a range of cellular proteins involved in polarity and signal transduction....
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PMID: 21247458
PDF is available here.
PDF is available here.
Abstract
We show that a strain carrying a deletion of cre-1 has increased cellulolytic activity and increased expression of cellulolytic genes during growth on crystalline cellulose (Avicel). Constitutive expression of cre-1 complements the phenotype of a N. crassa Δcre-1 strain grown on Avicel, and also re...
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PMID: 21980519
PDF is available here.
PDF is available here.
American Surgeon (12) 2011
Abstract
Abstract
The Hpn and HspA proteins from H. pylori are significant for nickel homeostasis and protect the cells from higher concentrations of external metal ions. Both proteins have a unique histidine- and cysteine-rich domain at the C terminus. The interactions of Ni(2+), Bi(3+), Zn(2+) and Cd(2+) ions with C...
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PMID: 21503353
PDF is available here.
PDF is available here.
Abstract
We have demonstrated that the half-lives of HIV-derived peptides in cytosol from primary human cells were highly variable and sequence dependent, and significantly affected the efficiency of cell recognition by CD8⁺ T cells. Furthermore, multiple clinical isolates of HLA-associated HIV epitope var...
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PMID: 21555856
PDF is available here.
PDF is available here.
Abstract
Binding of calcium ions (Ca²⁺) to proteins can have profound effects on their structure and function. Common roles of calcium binding include structure stabilization and regulation of activity. It is known that diverse families--EF-hands being one of at least twelve--use a Dx[DN]xDG linear motif t...
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PMID: 21720552
PDF is available here.
PDF is available here.
Abstract
We analyzed the binding mode of recently reported 1-(1-(benzo[b]thiophen-2-yl)cyclohexyl)piperidine (BTCP) analogues using computer modeling methods. This led us to conclude that the analogues occupy a different region of the active site than the diaryl sulfide-based class of inhibitors. A combinati...
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PMID: 21275053
PDF is available here.
PDF is available here.
Abstract
Abstract
We report here a designer self-assembling peptide nanofiber scaffold developed specifically for nerve tissue engineering. We synthesized a peptide FGL-RADA containing FGL (EVYVVAENQQGKSKA), the motif of neural cell adhesion molecule (NCAM), and then attended to make a FGL nanofiber scaffold (FGL-NS)...
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PMID: 20878982
PDF is available here.
PDF is available here.
Abstract
We report an SVM method, SMpred, to identify structural motifs from single protein structure without using sequence and structural homologs. SMpred method was trained and tested using 132 proteins domains containing 581 motifs. SMpred method achieved 78.79% accuracy with 79.06% sensitivity and 78.53...
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PMID: 20919755
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (285)48 2010
Abstract
These results indicate that the cysteine-containing sensor II plays a critical role in redox sensing and the nucleotide and partner binding functions of torsinA and suggest that loss of this function of torsinA contributes to the development of DYT1 dystonia....
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PMID: 20861018
PDF is available here.
PDF is available here.