Genomes and Genes
Experts and Doctors on ligands in Anguilla
- Yu B, Qin Z, Wijewickrama G, Edirisinghe P, Bolton J, Thatcher G. Comparative methods for analysis of protein covalent modification by electrophilic quinoids formed from xenobiotics. Bioconjug Chem. 2009;20:728-41 pubmed publisher..For study of the protein targets of electrophilic metabolites formed by in situ oxidative bioactivation, the COATag is both sensitive and specific and does not appear to suffer from poor cell permeability. ..
- Ďuriš A, Daïch A, Santos C, Fleury L, Ausseil F, Rodriguez F, et al. Asymmetric Synthesis and Binding Study of New Long-Chain HPA-12 Analogues as Potent Ligands of the Ceramide Transfer Protein CERT. Chemistry. 2016;22:6676-86 pubmed publisher..In silico studies were used to rationalized these trends, leading to a model of protein recognition coherent with the stronger binding of (1R,3S)-syn HPAs. ..
- Han H, Bennett R, Hurley L. Inhibition of unwinding of G-quadruplex structures by Sgs1 helicase in the presence of N,N'-bis[2-(1-piperidino)ethyl]-3,4,9,10-perylenetetracarboxylic diimide, a G-quadruplex-interactive ligand. Biochemistry. 2000;39:9311-6 pubmed..The G-quadruplex structures may, in turn, disrupt some critical cellular events such as DNA replication, transcription regulation, and telomere maintenance. ..
- Kil K, Poutiainen P, Zhang Z, Zhu A, Kuruppu D, Prabhakar S, et al. Synthesis and evaluation of N-(methylthiophenyl)picolinamide derivatives as PET radioligands for metabotropic glutamate receptor subtype 4. Bioorg Med Chem Lett. 2016;26:133-9 pubmed publisher..Therefore, [(11)C]11 will be a useful radioligand to investigate mGlu4 in different biological applications. ..
- Grate D, Wilson C. Inducible regulation of the S. cerevisiae cell cycle mediated by an RNA aptamer-ligand complex. Bioorg Med Chem. 2001;9:2565-70 pubmed..These results are consistent with a model in which translational initiation is blocked by ligand-induced conformational changes in the 5'-UTR. ..
- Duchardt Ferner E, Gottstein Schmidtke S, Weigand J, OhlenschlÃ¤ger O, Wurm J, Hammann C, et al. What a Difference an OH Makes: Conformational Dynamics as the Basis for the Ligand Specificity of the Neomycin-Sensing Riboswitch. Angew Chem Int Ed Engl. 2016;55:1527-30 pubmed publisher..The remarkable specificity of this riboswitch is thus based on structural dynamics rather than static structural differences. In this respect, the neomycin riboswitch is a model for many of its natural counterparts. ..
- Vigerust D, Vick S, Shepherd V. Characterization of functional mannose receptor in a continuous hybridoma cell line. BMC Immunol. 2012;13:51 pubmed publisher..This cell line provides an important cell model for other researchers for the study of human MR biology and host-pathogen interactions. ..
- Nakamura M, Nara T. Gene regulation of mammalian desaturases. Biochem Soc Trans. 2002;30:1076-9 pubmed..Available data suggest that the induction of desaturases by PPs may be a compensatory response to an increased demand for unsaturated fatty acids because PPs increase fatty acid degradation and induce proliferation of peroxisomes. ..
- Cowart M, Gfesser G, Bhatia K, Esser R, Sun M, Miller T, et al. Fluorescent benzofuran histamine H(3) receptor antagonists with sub-nanomolar potency. Inflamm Res. 2006;55 Suppl 1:S47-8 pubmed
- Vanhooke J, Benning M, Bauer C, Pike J, DeLuca H. Molecular structure of the rat vitamin D receptor ligand binding domain complexed with 2-carbon-substituted vitamin D3 hormone analogues and a LXXLL-containing coactivator peptide. Biochemistry. 2004;43:4101-10 pubmed..Electrostatic and hydrophobic interactions between the peptide and the LBD stabilize the active receptor conformation. This stablization appears necessary for crystal growth. ..
- Amaro R, Baron R, McCammon J. An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J Comput Aided Mol Des. 2008;22:693-705 pubmed publisher..Finally, we outline potential methodological improvements that we anticipate will assist future development. ..
- Cassina V, Torsello A, Tempestini A, Salerno D, Brogioli D, Tamiazzo L, et al. Biophysical characterization of a binding site for TLQP-21, a naturally occurring peptide which induces resistance to obesity. Biochim Biophys Acta. 2013;1828:455-60 pubmed publisher..Furthermore we observed that the distribution of these binding sites on the surface was relatively uniform. ..
- Kane C, Coe N, Vanlandingham B, Krieg P, Bernlohr D. Expression, purification, and ligand-binding analysis of recombinant keratinocyte lipid-binding protein (MAL-1), an intracellular lipid-binding found overexpressed in neoplastic skin cells. Biochemistry. 1996;35:2894-900 pubmed
- Golbraikh A, Tropsha A. Beware of q2!. J Mol Graph Model. 2002;20:269-76 pubmed..We emphasize that the external validation is the only way to establish a reliable QSAR model. We formulate a set of criteria for evaluation of predictive ability of QSAR models. ..
- Li S, Zhu R, Xiao K, Yu J. Ligand-Enabled Arylation of γ-C-H Bonds. Angew Chem Int Ed Engl. 2016;55:4317-21 pubmed publisher..Various γ-aryl-α-amino acids were prepared from natural amino acids using this method. The influence of ligand structure on reactivity was also systematically investigated. ..
- Paasonen L, Sharma S, Braun G, Kotamraju V, Chung T, She Z, et al. New p32/gC1qR Ligands for Targeted Tumor Drug Delivery. Chembiochem. 2016;17:570-5 pubmed publisher..This compound provides a lead for the development of p32-targeted affinity ligands that circumvent some of the limitations of peptide-based probes in guided drug delivery. ..
- Saelim N, John L, Wu J, Park J, Bai Y, Camacho P, et al. Nontranscriptional modulation of intracellular Ca2+ signaling by ligand stimulated thyroid hormone receptor. J Cell Biol. 2004;167:915-24 pubmed..We conclude that T3-bound mitochondrial targeted TRs acutely modulate IP3-mediated Ca2+ signaling by increasing mitochondrial metabolism independently of transcriptional activity. ..
- Bhattacherjee P, Paterson C, Percicot C. Studies on receptor binding and signal transduction pathways of unoprostone isopropyl. J Ocul Pharmacol Ther. 2001;17:433-41 pubmed
- Seong J, Wang L, Oh D, Yun O, Maiti K, Li J, et al. Ala/Thr(201) in extracellular loop 2 and Leu/Phe(290) in transmembrane domain 6 of type 1 frog gonadotropin-releasing hormone receptor confer differential ligand sensitivity and signal transduction. Endocrinology. 2003;144:454-66 pubmed..Collectively, these results demonstrate the presence of three types of GnRHR in amphibians, and suggest species- and type-specific ligand recognition and different signaling pathways in frog GnRHRs. ..
- Huang N, Kalyanaraman C, Irwin J, Jacobson M. Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screening. J Chem Inf Model. 2006;46:243-53 pubmed..We also present anecdotal but encouraging results assessing the ability of the rescoring method to predict specificity of inhibitors for structurally related proteins. ..
- Wang L, Oh D, Bogerd J, Choi H, Ahn R, Seong J, et al. Inhibitory activity of alternative splice variants of the bullfrog GnRH receptor-3 on wild-type receptor signaling. Endocrinology. 2001;142:4015-25 pubmed..Collectively, these results suggest that alternative splicing of the bfGnRHR-3 primary transcript plays a role in fine-tuning GnRH receptor function in amphibians. ..
- Flaveny C, Murray I, Chiaro C, Perdew G. Ligand selectivity and gene regulation by the human aryl hydrocarbon receptor in transgenic mice. Mol Pharmacol. 2009;75:1412-20 pubmed publisher..These discoveries imply that there may be a significant degree of structural divergence between mAHR and hAHR ligands and highlights the importance of the hAHR transgenic mouse as a model to study the hAHR in vivo. ..
- Ivanenkov Y, Veselov M, Chufarova N, Majouga A, Kudryavceva A, Ivachtchenko A. Non-dopamine receptor ligands for the treatment of Parkinson's disease. Insight into the related chemical/property space. Mol Divers. 2016;20:345-65 pubmed publisher..This review thoroughly describes the chemical space of non-dopamine receptor ligands in terms of diversity, isosteric/bioisosteric morphing, and molecular descriptors. ..
- Baig M, Ahmad K, Roy S, Ashraf J, Adil M, Siddiqui M, et al. Computer Aided Drug Design: Success and Limitations. Curr Pharm Des. 2016;22:572-81 pubmed..Finally, we discuss the principles and concepts of molecular docking, pharmacophores and other methods used in computer-aided drug design. ..
- Xu M, Wang Z, Locksley R. Innate immune responses in peptidoglycan recognition protein L-deficient mice. Mol Cell Biol. 2004;24:7949-57 pubmed..In contrast to its critical role in immunity in flies, PGRP-L is largely dispensable for mammalian immunity against bacteria and fungi. ..
- Konecny R, Trylska J, Tama F, Zhang D, Baker N, Brooks C, et al. Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids. Biopolymers. 2006;82:106-20 pubmed..Favorable binding to the swollen form suggests that Ca(2+) ions can induce the capsid contraction and stabilize the native form. ..
- Taylor B, Dadia N, Yang C, Krishnan S, Badr M. Peroxisome proliferator-activated receptor agonists inhibit inflammatory edema and hyperalgesia. Inflammation. 2002;26:121-7 pubmed..We conclude that systemic administration of potent PPARalpha and PPARgamma agonists exert anti-hyperalgesic and/or antiinflammatory actions in vivo, possibly by interfering with the initiation of inflammation. ..
- Koulakov A, Tsigankov D. A stochastic model for retinocollicular map development. BMC Neurosci. 2004;5:30 pubmed..including bifurcation in heterozygous Isl2/EphA3 knock-ins. The model is based on known chemical labels, axonal repulsion/competition, and stochasticity. Possible mapping in Isl2/EphB knock-ins is also discussed. ..
- Kang J, Nan X, Jin M, Youn S, Ryu Y, Mah S, et al. Recognition of lipopeptide patterns by Toll-like receptor 2-Toll-like receptor 6 heterodimer. Immunity. 2009;31:873-84 pubmed publisher..The structures of the TLR2-lipoteichoic acid and the TLR2-PE-DTPA complexes demonstrate that a precise interaction pattern of the head group is essential for a robust immune response by TLR2 heterodimers. ..
- Gardea Torresdey J, Arteaga S, Tiemann K, Chianelli R, Pingitore N, Mackay W. Absorption of copper(II) by creosote bush (Larrea tridentata): use of atomic and x-ray absorption spectroscopy. Environ Toxicol Chem. 2001;20:2572-9 pubmed..The results of this study indicate that creosote bush may provide a useful and novel method of removing copper(II) from contaminated soils in an environmentally friendly manner...
- Yu W, Liu C, Liu Y, Zhang N, Xu W. Mannan-modified solid lipid nanoparticles for targeted gene delivery to alveolar macrophages. Pharm Res. 2010;27:1584-96 pubmed publisher..One major problem with SLN is the lack of cell-targeting ability. In the present study, a mannan-based PE-grafted ligand was synthesized and used for the surface modification of DNA-loaded cationic SLN to prepare Man-SLN-DNA...
- Schluckebier G, Zhong P, Stewart K, Kavanaugh T, Abad Zapatero C. The 2.2 A structure of the rRNA methyltransferase ErmC' and its complexes with cofactor and cofactor analogs: implications for the reaction mechanism. J Mol Biol. 1999;289:277-91 pubmed publisher..A model for the transition-state based on the atomic details of the active site is consistent with a one-step methyl-transfer mechanism and might serve as a first step towards the design of potent Erm inhibitors...
- Krishnamoorthy N, Gajendrarao P, Thangapandian S, Lee Y, Lee K. Probing possible egress channels for multiple ligands in human CYP3A4: a molecular modeling study. J Mol Model. 2010;16:607-14 pubmed publisher..Our modeling study for multiple ligand-channeling of CYP3A4 could be very helpful to gain new insights into channel selectivity of CYP3A4. ..
- Davis P, Mousa S, Cody V, Tang H, Lin H. Small molecule hormone or hormone-like ligands of integrin ?V?3: implications for cancer cell behavior. Horm Cancer. 2013;4:335-42 pubmed publisher..This refinement of up-down control at the level of discrete receptors is not a function of the use of ?v?3 antibody or RGD peptides that occlude regions of the integrin. ..
- Hudson B, Martinez Yamout M, Dyson H, Wright P. Solution structure and acetyl-lysine binding activity of the GCN5 bromodomain. J Mol Biol. 2000;304:355-70 pubmed
- Pizzuti M, Minnaard A, Feringa B. Catalytic enantioselective addition of organometallic reagents to N-formylimines using monodentate phosphoramidite ligands. J Org Chem. 2008;73:940-7 pubmed publisher..Under the reaction conditions, partial oxidation of the phosphoramidite ligand to the corresponding phosphoric amide was detected. A preliminary study on the origin and the effect on the catalytic addition reaction is presented. ..
- Larsen T, Wedekind J, Rayment I, Reed G. A carboxylate oxygen of the substrate bridges the magnesium ions at the active site of enolase: structure of the yeast enzyme complexed with the equilibrium mixture of 2-phosphoglycerate and phosphoenolpyruvate at 1.8 A resolution. Biochemistry. 1996;35:4349-58 pubmed..The structure provides a candid view of the catalytic machinery of enolase. ..
- Yan Y, Munshi S, Leiting B, Anderson M, Chrzas J, Chen Z. Crystal structure of Escherichia coli UDPMurNAc-tripeptide d-alanyl-d-alanine-adding enzyme (MurF) at 2.3 A resolution. J Mol Biol. 2000;304:435-45 pubmed..As such, catalysis is not feasible and significant domain closure is expected upon substrate binding. ..
- Lee K, Lee Y, Shim I, Joung J, Oh Y. Direct synthesis and bonding origins of monolayer-protected silver nanocrystals from silver nitrate through in situ ligand exchange. J Colloid Interface Sci. 2006;304:92-7 pubmed..In addition, systematic studies revealed that the silver nanocrystals synthesized through in situ ligand exchange were stabilized through bidentate bridging of carboxyl groups in dodecanoic acid...
- Heck G, Pintro V, Pereira R, de Ávila M, Levin N, De Azevedo W. Supervised Machine Learning Methods Applied to Predict Ligand- Binding Affinity. Curr Med Chem. 2017;24:2459-2470 pubmed publisher..Recent developments in this area indicate that building scoring functions targeted to the biological systems of interest shows superior predictive performance, when compared with other approaches. ..
- Iram S, Cronan J. Unexpected functional diversity among FadR fatty acid transcriptional regulatory proteins. J Biol Chem. 2005;280:32148-56 pubmed..coli and S. enterica proteins. The significance of these findings is discussed in view of the protein sequences and the physiological niches occupied by these organisms. ..
- Gent J, Braakman I. Low-density lipoprotein receptor structure and folding. Cell Mol Life Sci. 2004;61:2461-70 pubmed..In this review, we will elaborate on the structural aspects of the LDLR and its folding pathway and compare it to other LDLR family members. ..
- Zhuo H, Payan F, Qian M. Crystal structure of the pig pancreatic alpha-amylase complexed with rho-nitrophenyl-alpha-D-maltoside-flexibility in the active site. Protein J. 2004;23:379-87 pubmed..The crystal structure was refined at 2.4 A resolution to an R factor of 17.55% (Rfree factor of 23.32%). ..
- Hart P, Deep S, Taylor A, Shu Z, Hinck C, Hinck A. Crystal structure of the human TbetaR2 ectodomain--TGF-beta3 complex. Nat Struct Biol. 2002;9:203-8 pubmed
- Chen M, Celik A, Georgeson K, Harmon C, Yang Y. Molecular basis of melanocortin-4 receptor for AGRP inverse agonism. Regul Pept. 2006;136:40-9 pubmed..Our results also indicate that the residues D90 in TM2 and D298 in TM7 of hMC4R are involved in not only NDP-MSH mediated receptor activation but also AGRP mediated inverse agonism. ..
- Rajah R, Lee K, Cohen P. Insulin-like growth factor binding protein-3 mediates tumor necrosis factor-alpha-induced apoptosis: role of Bcl-2 phosphorylation. Cell Growth Differ. 2002;13:163-71 pubmed..These findings confirm that IGFBP-3 is essential for TNF-alpha-induced apoptosis in PC-3 cells and that this IGFBP-3 effect includes the inactivation of Bcl-2 through serine phosphorylation. ..
- Wu S, Chen M, Rozengurt E. Genomic organization, expression, and function of bitter taste receptors (T2R) in mouse and rat. Physiol Genomics. 2005;22:139-49 pubmed
- Kolakowski L, Jung B, Nguyen T, Johnson M, Lynch K, Cheng R, et al. Characterization of a human gene related to genes encoding somatostatin receptors. FEBS Lett. 1996;398:253-8 pubmed..A repeat polymorphism of the form (CA)n was discovered in the 5'-untranslated region (UTR) of the gene and SLC-1 was mapped to chromosome 22, q13.3. ..
- Roberts G, Thorsteinsson M, Kerby R, Lanzilotta W, Poulos T. CooA: a heme-containing regulatory protein that serves as a specific sensor of both carbon monoxide and redox state. Prog Nucleic Acid Res Mol Biol. 2001;67:35-63 pubmed..The recent solution of the crystal structure of the CO-free (transcriptionally inactive) form of CooA has allowed insights into the mechanism by which both proteins respond to their specific small-molecule effectors. ..
- Luther S, Ansel K, Cyster J. Overlapping roles of CXCL13, interleukin 7 receptor alpha, and CCR7 ligands in lymph node development. J Exp Med. 2003;197:1191-8 pubmed..These findings indicate that CXCL13 and CCR7 ligands promote accumulation of CD4+ CD3- IL-7R alpha hi cells, delivering IL-7R alpha-dependent LT alpha 1 beta 2 signals critical for LN development. ..
- Larsen T, Benning M, Wesenberg G, Rayment I, Reed G. Ligand-induced domain movement in pyruvate kinase: structure of the enzyme from rabbit muscle with Mg2+, K+, and L-phospholactate at 2.7 A resolution. Arch Biochem Biophys. 1997;345:199-206 pubmed..The position and liganding of K+ are unaffected by the different conformations of the subunits. The side chain of Arg 72, Mg2+, and K+ provides a locus of positive charge for the phosphate moiety of the analog in the closed subunit. ..
- Parks D, Blanchard S, Bledsoe R, Chandra G, Consler T, Kliewer S, et al. Bile acids: natural ligands for an orphan nuclear receptor. Science. 1999;284:1365-8 pubmed..These results provide evidence for a nuclear bile acid signaling pathway that may regulate cholesterol homeostasis. ..
- Chigaev A, Zwartz G, Buranda T, Edwards B, Prossnitz E, Sklar L. Conformational regulation of alpha 4 beta 1-integrin affinity by reducing agents. "Inside-out" signaling is independent of and additive to reduction-regulated integrin activation. J Biol Chem. 2004;279:32435-43 pubmed..Based on this result and differences in the kinetics of integrin activation, we conclude that conformational activation of VLA-4 by inside-out signaling is independent of and additive to reduction-regulated integrin activation. ..
- Rice J, Schohn A, Bessette P, Boulware K, Daugherty P. Bacterial display using circularly permuted outer membrane protein OmpX yields high affinity peptide ligands. Protein Sci. 2006;15:825-36 pubmed..CPX bacterial display thus provides a highly effective method for screening peptide libraries to rapidly generate ligands with high affinity and specificity. ..
- Lanier L. NKG2D. J Biol Regul Homeost Agents. 2003;17:338-40 pubmed
- Sablin S, Ramsay R. Substrates but not inhibitors alter the redox potentials of monoamine oxidases. Antioxid Redox Signal. 2001;3:723-9 pubmed..In contrast, stable products and inhibitors did not cause a shift in potential and did not prevent the formation of semiquinone. ..
- Getz W. A kinetic model of the transient phase in the response of olfactory receptor neurons. Chem Senses. 1999;24:497-508 pubmed..The sensitivity of model output to various model parameters is investigated and changes to parameters are discussed that would improve the ability of ORNs to follow rapidly pulsed stimuli...
- Xue C, Luo W, Ding Q, Liu S, Gao X. Quantitative structure-activity relationship studies of mushroom tyrosinase inhibitors. J Comput Aided Mol Des. 2008;22:299-309 pubmed publisher..We believe that the QSAR models built here provide important information necessary for the design of novel tyrosinase inhibitors. ..
- Gianneschi N, Ghadiri M. Design of molecular logic devices based on a programmable DNA-regulated semisynthetic enzyme. Angew Chem Int Ed Engl. 2007;46:3955-8 pubmed
- Axtell R, Webb M, Barnum S, Raman C. Cutting edge: critical role for CD5 in experimental autoimmune encephalomyelitis: inhibition of engagement reverses disease in mice. J Immunol. 2004;173:2928-32 pubmed..Our studies indicate that CD5 regulates survival of activated T cells and provides a target for treatment of T cell-dependent autoimmune diseases such as multiple sclerosis. ..
- Shao L, Moloney D, Haltiwanger R. Fringe modifies O-fucose on mouse Notch1 at epidermal growth factor-like repeats within the ligand-binding site and the Abruptex region. J Biol Chem. 2003;278:7775-82 pubmed..These findings provide insight into potential mechanisms by which Fringe action on Notch receptors may influence both the affinity of Notch-ligand binding and cell-autonomous inhibition of Notch signaling by ligand. ..
- Gestwicki J, Kiessling L. Inter-receptor communication through arrays of bacterial chemoreceptors. Nature. 2002;415:81-4 pubmed..These results demonstrate that the entire array is involved in sensing. This mode of information exchange has general implications for the processing of signals by cellular receptors. ..
- Lau H, Yu M, Fontana A, Stoeckert C. Prevention of islet allograft rejection with engineered myoblasts expressing FasL in mice. Science. 1996;273:109-12 pubmed..Thus, the FasL signal provided site- and immune-specific protection of islet allografts. ..
- Raman C. CD5, an important regulator of lymphocyte selection and immune tolerance. Immunol Res. 2002;26:255-63 pubmed..I and others, reviewed here, now provide clear evidence that CD5 is a key regulator of immune tolerance and that alterations of its activity can promote development of autoreactivity. ..
- Roy A, Tyagi R, Song C, Lavrovsky Y, Ahn S, Oh T, et al. Androgen receptor: structural domains and functional dynamics after ligand-receptor interaction. Ann N Y Acad Sci. 2001;949:44-57 pubmed..Xenobiotic ligands, considered as selective androgen receptor modulators (SARMs), can modulate AR activity by inhibiting either its nuclear translocation or its subnuclear clustering and subsequent transactivation function. ..
- Ruan T, Davis S, Powell B, Harbeck C, Habdas J, Habdas P, et al. Lowering the overall charge on TMPyP4 improves its selectivity for G-quadruplex DNA. Biochimie. 2017;132:121-130 pubmed publisher..We conclude that lowering the charge on TMPyP4 to 3+ can achieve the desired balance between stabilizing ability, affinity, and high selectivity required for an excellent quadruplex ligand. ..
- Durand I, Green R. Cloning of a chick A3 adenosine receptor: characterization of ligand binding and receptor-effector coupling of chick A1 and A3 adenosine receptors. Naunyn Schmiedebergs Arch Pharmacol. 2001;363:81-6 pubmed..While both receptors coupled to the inhibition of adenylyl cyclase, we were unable to detect coupling of either receptor to phospholipase C or D. ..