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Structural Homology, Protein (0):
Recent article
Structural Homology, Protein
Abstract
We present a subquadratic running time algorithm capable of computing an alignment that optimizes one of the most widely used measures of protein structure similarity, defined as the number of pairs of residues in two proteins that can be superimposed under a predefined distance cutoff. The algorith...
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PMID: 21714130
PDF is available here.
PDF is available here.
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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
A homology model for pig liver esterase was generated on the basis of human carboxyl esterase (hCE) and subjected to extensive molecular dynamics simulations. By virtual mutations the isoenzymes PLE1-6 and APLE were obtained, and the PLE1 trimer was built from the respective model of...
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PMID: 20862595
PDF is available here.
PDF is available here.
Abstract
We present the new software tools RINerator and RINalyzer for the automatized generation, 2D visualization, and interactive analysis of residue interaction networks, and highlight their use in different application scenarios....
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PMID: 21345680
PDF is available here.
PDF is available here.
Abstract
We have analysed the chemokine receptor genes from the genomes of 16 vertebrate species, and classify them into 29 orthologous groups using phylogenetic and comparative genomic analyses. The results reveal a continuous gene birth and death process during the vertebrate evolution and an interesting e...
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PMID: 21295066
PDF is available here.
PDF is available here.
Abstract
Pea encodes eukaryotic translation initiation factor eIF4E (eIF4E(S)), which supports the multiplication of Pea seed-borne mosaic virus (PSbMV). In common with hosts for other potyviruses, some pea lines contain a recessive allele (sbm1) encoding a mutant eIF4E (eIF4E(R)) that fails to interact funct...
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PMID: 21283665
PDF is available here.
PDF is available here.
Abstract
We report the biochemical and biophysical characterization of the three Cdv proteins from the hyperthermophilic archaeon Metallospherae sedula.
Using sucrose density gradient ultracentrifugation and negative staining electron microscopy, we evidenced for the first time that CdvA form...
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PMID: 21760923
PDF is available here.
PDF is available here.
Abstract
We have refined the crystal structure of a recombinant plant-type Fd I from the blue green alga Aphanothece sacrum (AsFd-I) at 1.46 Å resolution on the basis of the synchrotron radiation data. Incorporating the revised amino-acid sequence, our analysis corrects the 3D structure previously reported;...
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PMID: 21760931
PDF is available here.
PDF is available here.
Abstract
Iron is one of the most important minor elements in the shells of bivalves. This study was designed to investigate the involvement of ferritin, the principal protein for iron storage, in shell growth. A novel ferritin subunit (Fth1) cDNA from the freshwater pearl mussel (Hyriopsis cu...
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PMID: 21818403
PDF is available here.
PDF is available here.
Abstract
Tuberculosis (TB) continues to pose a serious challenge to human health afflicting a large number of people throughout the world. In spite of the availability of drugs for the treatment of TB, the non-compliance to 6-9 months long chemotherapeutic regimens often results in the emergence of multidrug...
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PMID: 21818324
PDF is available here.
PDF is available here.
Abstract
The PWWP domain was first identified as a structural motif of 100-130 amino acids in the WHSC1 protein and predicted to be a protein-protein interaction domain. It belongs to the Tudor domain 'Royal Family', which consists of Tudor, chromodomain, MBT and PWWP domains. While Tudor, chromodomain and MB...
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PMID: 21720545
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (285)45 2010
Abstract
We report crystallization of recombinant Pz-peptidase A in complex with two phosphinic peptide inhibitors (PPIs) that also function as inhibitors of TOP and determination of the crystal structure of these complexes at 1.80-2.00 Å resolution. The most striking difference between Pz-peptidase A and...
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PMID: 20817732
PDF is available here.
PDF is available here.
EMBO Reports (11)11 2010
Abstract
We have determined the crystal structure of the zinc-finger domain of zebrafish Nanos, for the first time revealing that Nanos adopts a novel zinc-finger structure. In addition, Nanos has a conserved basic surface that is directly involved in RNA binding. Our results provide the structural basis for...
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PMID: 20948543
PDF is available here.
PDF is available here.
Abstract
We show that serine 197 (S197) in the cytoplasmic tail of Ig-α is phosphorylated upon B-cell antigen receptor activation, and that this modification inhibits the signal output of the B-cell antigen receptor. Surprisingly, we found that the well-known protein tyrosine kinase Syk (spleen tyrosine kin...
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PMID: 20940318
PDF is available here.
PDF is available here.
Abstract
I (THLGC) and II (PCHGS), were detected by multiple alignments. Real-time PCR analysis showed that Cgisp is expressed in a wide range of tissues, with adductor muscle exhibiting the top expression level, suggesting its biological function of energy transduction. The GFP tagging Cgisp indicated a mit...
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PMID: 19876765
PDF is available here.
PDF is available here.
Hearing Research (268)1-2 2010
Abstract
We have overcome these obstacles by generating otoconial matrix proteins by recombinant techniques. In the present study, we evaluated the effects of recombinant Otoconin 90 (OC90), the principal soluble matrix protein upon calcite crystal growth patterns in vitro. Our findings highlight multiple ef...
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PMID: 20595020
PDF is available here.
PDF is available here.
Abstract
We describe a highly refined homology model of L. donovani chagasi DHFR-TS based on available crystallographic structures by using the Homology module of Insight II. Structural refinement and minimization of the generated L. donovani chagasi DHFR-TS model employed the Discover 3 module of Insight II...
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PMID: 20174846
PDF is available here.
PDF is available here.
Abstract
It is widely acknowledged that the H(1) receptor antagonists have important therapeutic significance in the treatment of various allergic disorders, but little was known about the binding mode between the receptor and antagonists since the crystal structure of G-protein coupling rece...
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PMID: 20179978
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (285)34 2010
Abstract
We have used a modular approach to determine the crystal structures of the structured domains in the EBF family. The DNA binding domain reveals a striking resemblance to the DNA binding domains of the Rel homology superfamily of transcription factors but contains a unique zinc binding structure, ter...
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PMID: 20592035
PDF is available here.
PDF is available here.
Abstract
We use antibodies as a model system to investigate strategies for more robustly predicting loop conformations when the protein model contains errors in the conformations of side chains and protein backbone surrounding the loop in question. Specifically, our test system consists of partial models of...
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PMID: 20602354
PDF is available here.
PDF is available here.
Abstract
Retroviral integrases are vital enzymes in the viral life cycle and thus are important targets for antiretroviral drugs. The structure of the catalytic core domain of the integrase from human foamy virus, which is related to HIV-1, has been solved. The structure of the protein is presented in two di...
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PMID: 20693659
PDF is available here.
PDF is available here.
Abstract
Uracil N-glycosylase (Ung) is the most thoroughly studied of the group of uracil DNA-glycosylase (UDG) enzymes that catalyse the first step in the uracil excision-repair pathway. The overall structure of the enzyme from Mycobacterium tuberculosis is essentially the same as that of the enzyme from ot...
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PMID: 20693660
PDF is available here.
PDF is available here.
Abstract
We built a homology model of Asp kinase using the crystallized Asp kinase from M. Jannaschii, as template structures (2HMF and 3C1M). After the molecular dynamics refinement, the optimized homology model was assessed as a reliable structure by PROCHECK, ERRAT, WHAT-IF, PROSA2003 and VERIFY-3D. The r...
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PMID: 20140471
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1798)8 2010
Abstract
We solved the structure of the entire transmembrane domain (TM1234) of the beta2 subunit. We found that TM1234 formed a four-helix bundle in the absence of the extracellular and intracellular domains. The structure exhibited many similarities to those previously determined for the Torpedo nAChR and...
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PMID: 20441771
PDF is available here.
PDF is available here.
Abstract
A full-length complementary DNA (cDNA; designated Hc-stp-1) encoding a serine/threonine phosphatase (Hc-STP-1) was isolated from Haemonchus contortus, a strongylid nematode parasite of small ruminants. Hc-stp-1 was shown to be transcribed in males of both adults and fourth-stage larvae, but not in f...
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PMID: 20153820
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (285)29 2010
Abstract
We present the first three-dimensional structure of beta2m from bony fish grass carp (Ctid-beta2m), resolved at 2.1 A. The key structural differences between this new structure and previously published structures are two new hydrogen bonds at positions Ile(37) and Glu(38) in strand C and Lys(66) in...
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PMID: 20444690
PDF is available here.
PDF is available here.
Abstract
We used large datasets from both fungi and vertebrates to perform a comprehensive comparison of the TMDs of proteins from different organelles. We find that TMDs are not generic but have organelle-specific properties with a dichotomy in TMD length between the early and late parts of the secretory pa...
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PMID: 20603021
PDF is available here.
PDF is available here.
Plant Physiology (153)3 2010
Abstract
We report on the isolation and characterization of two novel genes both encoding hydroxycinnamoyl-coenzyme A quinate transferases (HQT) from artichoke. The recombinant proteins (HQT1 and HQT2) were assayed after expression in Escherichia coli, and both showed higher affinity for quinate over shikima...
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PMID: 20431089
PDF is available here.
PDF is available here.
Virus Research (151)1 2010
Abstract
We show that A33 has most likely evolved from a C-type lectin-like protein. Comparison of the three-dimensional A33 model to the X-ray structures of distant cellular homologues revealed that A33 retained the key residues required for adopting the C-type lectin-like fold. Our results provide insights...
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PMID: 20302896
PDF is available here.
PDF is available here.
Journal of Molecular Biology (399)4 2010
Abstract
We show that this approach results in successful modelling of the ligand and key binding-site residues of angiotensin-converting enzyme 2 (ACE2) from its homologue ACE, which is not possible via conventional homology modelling or by homology modelling followed by docking. Several other difficult tar...
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PMID: 20434455
PDF is available here.
PDF is available here.
Abstract
We explore the range of applicability of such information by analyzing the extent to which the location of binding sites on protein surfaces is conserved among structural neighbors. We find, as expected, that interface conservation is most significant among proteins that have a clear evolutionary re...
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PMID: 20534496
PDF is available here.
PDF is available here.
Biochemistry (Washington) (49)23 2010
Abstract
We show that Mycobacterium tuberculosis UvrD1 more efficiently inhibited the strand exchange promoted by its cognate RecA, compared to noncognate Mycobacterium smegmatis or Escherichia coli RecA proteins. The M. tuberculosis UvrD1(Q276R) mutant lacking the helicase and ATPase activities was able to...
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PMID: 20455546
PDF is available here.
PDF is available here.
Abstract
We have examined the importance of hinge conformation to the proximity of these lysines and their ability to undergo intramolecular and intermolecular crosslinks using homology models. The results, counter intuitively, indicate that the more open hinge conformations favor intramolecular crosslinking...
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PMID: 20457133
PDF is available here.
PDF is available here.
Abstract
We have determined the structure of the EC1-EC2 domains of cadherin 23 (CDH23), which binds to protocadherin 15 (PCDH15) to form tip links of mechanosensory hair cells. Unlike classical cadherins, the CDH23 N terminus contains polar amino acids that bind Ca(2+). The N terminus of PCDH15 also contain...
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PMID: 20498078
PDF is available here.
PDF is available here.
Abstract
We present the crystal structure of human Rae1 in complex with the Gle2-binding sequence (GLEBS) of Nup98 at 1.65 A resolution. Rae1 forms a seven-bladed beta-propeller with several extensive surface loops. The Nup98 GLEBS motif forms an approximately 50-A-long hairpin that binds with its C-terminal...
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PMID: 20498086
PDF is available here.
PDF is available here.
Molecular Diversity (14)2 2010
Abstract
We have recently reported the MD simulations of a potent CB ligand at bovine rhodopsin-based CB1 and CB2 receptors (Durdagi et al., Bioorg Med Chem 16:7377-7387, 2008). In this present study, a homology modeling study based on the beta2-adrenergic receptor for both CB1 and CB2 receptors was performe...
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PMID: 19536636
PDF is available here.
PDF is available here.
Biophysical Journal (98)8 2010
Abstract
We created homology models of 5-HT3AB receptors and docked 5-HT and granisetron into AB, BA, and BB interfaces. To test whether ligands bind in any or all of these interfaces, we mutated amino acids that are important for agonist and antagonist binding in the 5-HT3A subunit to their corresponding re...
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PMID: 20409468
PDF is available here.
PDF is available here.
Abstract
Designing selective cyclin-dependent kinase 4 (CDK4) inhibitors is an area of intense research to develop potential anticancer drugs. The molecular basis governing the selective inhibition of CDK4 by lig17 (6-bromo-8-cyclopentyl-2-(5-piperazin-1-yl-pyridin-2-ylamino)-8H-pyrido[2,3-d]pyrimidin-7-one)...
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PMID: 20153225
PDF is available here.
PDF is available here.
Abstract
Penicillin amidase from Alacaligenes faecalis is an attractive biocatalyst for hydrolysis of penicillin G for production of 6-aminopenicillanic acid, which is used in the synthesis of semi-synthetic beta-lactam antibiotics. Recently a mutant of this enzyme with extended C-terminus of the A-chain com...
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PMID: 20224955
PDF is available here.
PDF is available here.
Abstract
We report the backbone resonance assignments of the 34 kDa LpxC from Escherichia coli in complex with the antibiotic L-161,240 using multidimensional, multinuclear NMR experiments. The (1)H chemical shifts of complexed L-161,240 are also determined....
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PMID: 19941092
PDF is available here.
PDF is available here.
Abstract
We present the NMR backbone assignments of human UCH-L1, thus enabling future solution-state NMR spectroscopic studies on the structure and function of this important protein....
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PMID: 20012716
PDF is available here.
PDF is available here.
Abstract
We report (1)H, (13)C, and (15)N chemical shift assignments of murine IL-3 comprising residues 33-156 (SWISS-PROT accession number: P01586), in which the only mutation is an alanine substitution of Cys105. The mIL-3 construct used in the present study was engineered by eliminating residues 27-32 of...
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PMID: 20174897
PDF is available here.
PDF is available here.
Journal of Experimental Biology (213)Pt 7 2010
Abstract
We show that they regulate tick physiological functions that may be related to A. americanum tick feeding success as revealed by RNAi-mediated dual silencing of AamIGFBP-rP6S and AamIGFBP-rP6L or AamIGFBP-rP1 alone, which caused a reduction in blood meal size compared to the controls. Additionally,...
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PMID: 20228352
PDF is available here.
PDF is available here.
Abstract
We found a novel mutation in a highly conserved residue in the T-box DNA binding domain (I121M) segregating with CHD in a three generation kindred. Four mutation carriers revealed cardiac phenotypes in terms of cribriform ASDII, large patent foramen ovale or cardiac valve defects. Interestingly, ter...
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PMID: 19762328
PDF is available here.
PDF is available here.
Abstract
An insect antifreeze protein gene Mpafp149 was cloned by the RT-PCR approach from the desert beetle Microdera punctipennis dzungarica. Sequence analysis revealed that this gene encoding a protein of 120 amid acids and this protein showed 65-76% homology with other insect antifreeze proteins, the ded...
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PMID: 19562508
PDF is available here.
PDF is available here.
Abstract
A series of 5-ureidobenzofuranones was discovered as potent and selective inhibitors of mTOR with good cellular activity. Molecular modeling studies revealed several hydrogen bond interactions of the ureido group with the enzyme at the ATP-binding site. Furthermore, modeling showed that the ureido g...
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PMID: 20188551
PDF is available here.
PDF is available here.
Abstract
We have determined the conformation of the ECL2 of the angiotensin II type 1 receptor by reporter-cysteine accessibility mapping in different receptor states (i.e. empty, agonist-bound and antagonist-bound). We introduced cysteines at each position of ECL2 of an N-terminal epitope-tagged receptor su...
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PMID: 20299456
PDF is available here.
PDF is available here.
Abstract
Neuropeptide S (NPS) is a 20-residue peptide of great interest due to its potential involvement in several biological processes such as arousal, anxiety, and food intake. The NPS receptor belongs to the rhodopsin-like G-protein-coupled receptor superfamily, and several polymorphisms...
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PMID: 20087922
PDF is available here.
PDF is available here.
Chemmedchem (5)3 2010
Abstract
Neuropeptide S (NPS) is a 20-residue peptide of great interest due to its potential involvement in several biological processes such as arousal, anxiety, and food intake. The NPS receptor belongs to the rhodopsin-like G-protein-coupled receptor superfamily, and several polymorphisms...
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PMID: 20087922
PDF is available here.
PDF is available here.
Chemmedchem (5)3 2010
Abstract
Neuropeptide S (NPS) is a 20-residue peptide of great interest due to its potential involvement in several biological processes such as arousal, anxiety, and food intake. The NPS receptor belongs to the rhodopsin-like G-protein-coupled receptor superfamily, and several polymorphisms...
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PMID: 20087922
PDF is available here.
PDF is available here.
Chemmedchem (5)3 2010
Abstract
Neuropeptide S (NPS) is a 20-residue peptide of great interest due to its potential involvement in several biological processes such as arousal, anxiety, and food intake. The NPS receptor belongs to the rhodopsin-like G-protein-coupled receptor superfamily, and several polymorphisms...
|
PMID: 20087922
PDF is available here.
PDF is available here.
Chemmedchem (5)3 2010
Abstract
Neuropeptide S (NPS) is a 20-residue peptide of great interest due to its potential involvement in several biological processes such as arousal, anxiety, and food intake. The NPS receptor belongs to the rhodopsin-like G-protein-coupled receptor superfamily, and several polymorphisms...
|
PMID: 20087922
PDF is available here.
PDF is available here.
Chemmedchem (5)3 2010
Abstract
Neuropeptide S (NPS) is a 20-residue peptide of great interest due to its potential involvement in several biological processes such as arousal, anxiety, and food intake. The NPS receptor belongs to the rhodopsin-like G-protein-coupled receptor superfamily, and several polymorphisms...
|
PMID: 20087922
PDF is available here.
PDF is available here.
Chemmedchem (5)3 2010
Abstract
Neuropeptide S (NPS) is a 20-residue peptide of great interest due to its potential involvement in several biological processes such as arousal, anxiety, and food intake. The NPS receptor belongs to the rhodopsin-like G-protein-coupled receptor superfamily, and several polymorphisms...
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PMID: 20087922
PDF is available here.
PDF is available here.
Chemmedchem (5)3 2010
Abstract
Neuropeptide S (NPS) is a 20-residue peptide of great interest due to its potential involvement in several biological processes such as arousal, anxiety, and food intake. The NPS receptor belongs to the rhodopsin-like G-protein-coupled receptor superfamily, and several polymorphisms...
|
PMID: 20087922
PDF is available here.
PDF is available here.
Chemmedchem (5)3 2010
Abstract
Neuropeptide S (NPS) is a 20-residue peptide of great interest due to its potential involvement in several biological processes such as arousal, anxiety, and food intake. The NPS receptor belongs to the rhodopsin-like G-protein-coupled receptor superfamily, and several polymorphisms...
|
PMID: 20087922
PDF is available here.
PDF is available here.
Chemmedchem (5)3 2010
Abstract
Neuropeptide S (NPS) is a 20-residue peptide of great interest due to its potential involvement in several biological processes such as arousal, anxiety, and food intake. The NPS receptor belongs to the rhodopsin-like G-protein-coupled receptor superfamily, and several polymorphisms...
|
PMID: 20087922
PDF is available here.
PDF is available here.
Chemmedchem (5)3 2010
Abstract
Neuropeptide S (NPS) is a 20-residue peptide of great interest due to its potential involvement in several biological processes such as arousal, anxiety, and food intake. The NPS receptor belongs to the rhodopsin-like G-protein-coupled receptor superfamily, and several polymorphisms...
|
PMID: 20087922
PDF is available here.
PDF is available here.
Chemmedchem (5)3 2010
Abstract
Neuropeptide S (NPS) is a 20-residue peptide of great interest due to its potential involvement in several biological processes such as arousal, anxiety, and food intake. The NPS receptor belongs to the rhodopsin-like G-protein-coupled receptor superfamily, and several polymorphisms...
|
PMID: 20087922
PDF is available here.
PDF is available here.
Chemmedchem (5)3 2010
Abstract
Neuropeptide S (NPS) is a 20-residue peptide of great interest due to its potential involvement in several biological processes such as arousal, anxiety, and food intake. The NPS receptor belongs to the rhodopsin-like G-protein-coupled receptor superfamily, and several polymorphisms...
|
PMID: 20087922
PDF is available here.
PDF is available here.