Experts and Doctors on protein binding in Salt Lake City, Utah, United States

Summary

Locale: Salt Lake City, Utah, United States
Topic: protein binding

Top Publications

  1. Stewart R, Semerjian J, Schmidt C. Highly processive motility is not a general feature of the kinesins. Eur Biophys J. 1998;27:353-60 pubmed
    ..We conclude that a degree of processivity as high as that of kinesin, where a single dimer can move over distances on the order of one micrometer, may not be a general mechanistic feature of the kinesin superfamily. ..
  2. Clemons W, Gowda K, Black S, Zwieb C, Ramakrishnan V. Crystal structure of the conserved subdomain of human protein SRP54M at 2.1 A resolution: evidence for the mechanism of signal peptide binding. J Mol Biol. 1999;292:697-705 pubmed
  3. Fleischer T, Yun U, Ayer D. Identification and characterization of three new components of the mSin3A corepressor complex. Mol Cell Biol. 2003;23:3456-67 pubmed
    ..Finally, all three SAPs bind to the HDAC-interaction domain (HID) of mSin3A, suggesting that the HID functions as the assembly interface for the mSin3A corepressor complex. ..
  4. Cobine P, Pierrel F, Leary S, Sasarman F, Horng Y, Shoubridge E, et al. The P174L mutation in human Sco1 severely compromises Cox17-dependent metallation but does not impair copper binding. J Biol Chem. 2006;281:12270-6 pubmed
    ..They further suggest that defective Cox17-mediated copper metallation of Sco1, as well as the subsequent failure of Cu(A) site maturation, is the basis for the inefficient assembly of the cytochrome c oxidase complex in SCO1 patients. ..
  5. Mitra D, Parnell E, Landon J, Yu Y, Stillman D. SWI/SNF binding to the HO promoter requires histone acetylation and stimulates TATA-binding protein recruitment. Mol Cell Biol. 2006;26:4095-110 pubmed
    ..We have detected SWI/SNF binding at the HO TATA region, and our results suggest that SWI/SNF, either directly or indirectly, facilitates TBP binding at HO. ..
  6. Stuchell Brereton M, Skalicky J, Kieffer C, Karren M, Ghaffarian S, Sundquist W. ESCRT-III recognition by VPS4 ATPases. Nature. 2007;449:740-4 pubmed
    ..Thus, our studies reveal how the VPS4 ATPases recognize their CHMP substrates to facilitate the membrane fission events required for the release of viruses, endosomal vesicles and daughter cells. ..
  7. Li L, Bagley D, Ward D, Kaplan J. Yap5 is an iron-responsive transcriptional activator that regulates vacuolar iron storage in yeast. Mol Cell Biol. 2008;28:1326-37 pubmed
    ..These results show that Yap5 is an iron-sensing transcription factor and that iron regulates transcriptional activation. ..
  8. De Domenico I, Lo E, Ward D, Kaplan J. Hepcidin-induced internalization of ferroportin requires binding and cooperative interaction with Jak2. Proc Natl Acad Sci U S A. 2009;106:3800-5 pubmed publisher
    ..These results provide a molecular explanation for the dominant inheritance of hepcidin resistant iron overload disease. ..
  9. Whitby F, Xia G, Pickart C, Hill C. Crystal structure of the human ubiquitin-like protein NEDD8 and interactions with ubiquitin pathway enzymes. J Biol Chem. 1998;273:34983-91 pubmed
    ..One such residue, Ala-72 (Arg in ubiquitin), is shown to perform a key role in selecting against reaction with the ubiquitin E1 enzyme, thereby acting to prevent the inappropriate diversion of NEDD8 into ubiquitin-specific pathways. ..

More Information

Publications175 found, 100 shown here

  1. Luo W, Gangwal K, Sankar S, Boucher K, Thomas D, Lessnick S. GSTM4 is a microsatellite-containing EWS/FLI target involved in Ewing's sarcoma oncogenesis and therapeutic resistance. Oncogene. 2009;28:4126-32 pubmed publisher
    ..These data also suggest a novel therapeutic resistance mechanism, in which the central oncogenic abnormality directly regulates a resistance gene. ..
  2. Peterson C, Stoltzman C, Sighinolfi M, Han K, Ayer D. Glucose controls nuclear accumulation, promoter binding, and transcriptional activity of the MondoA-Mlx heterodimer. Mol Cell Biol. 2010;30:2887-95 pubmed publisher
    ..Our experiments establish the mechanistic circuitry by which cells sense and respond transcriptionally to various intracellular glucose levels. ..
  3. Lin Z, Reilly C, Antemano R, Hughen R, Marett L, Concepcion G, et al. Nobilamides A-H, long-acting transient receptor potential vanilloid-1 (TRPV1) antagonists from mollusk-associated bacteria. J Med Chem. 2011;54:3746-55 pubmed publisher
    ..While the activities were modest, we propose a new mechanism of action and a new site of binding for these inhibitors that may spur development of related analogues for treatment of pain. ..
  4. Buczek P, Orr R, Pyper S, Shum M, Kimmel E, Ota I, et al. Binding linkage in a telomere DNA-protein complex at the ends of Oxytricha nova chromosomes. J Mol Biol. 2005;350:938-52 pubmed
  5. Stadtmueller B, Ferrell K, Whitby F, Heroux A, Robinson H, Myszka D, et al. Structural models for interactions between the 20S proteasome and its PAN/19S activators. J Biol Chem. 2010;285:13-7 pubmed publisher
    ..In the case of the PAN and 19S activators, a penultimate tyrosine/phenylalanine residue contacts the proteasome Gly-19 carbonyl oxygen to stabilize the open conformation...
  6. Palanker L, Necakov A, Sampson H, Ni R, Hu C, Thummel C, et al. Dynamic regulation of Drosophila nuclear receptor activity in vivo. Development. 2006;133:3549-62 pubmed
  7. Navratilova I, Papalia G, Rich R, Bedinger D, Brophy S, Condon B, et al. Thermodynamic benchmark study using Biacore technology. Anal Biochem. 2007;364:67-77 pubmed
    ..This benchmark study also provides insights into the opportunities and challenges in carrying out thermodynamic studies using optical biosensors. ..
  8. Van Horn W, Ogilvie M, Flynn P. Use of reverse micelles in membrane protein structural biology. J Biomol NMR. 2008;40:203-11 pubmed publisher
    ..These results establish the effectiveness of reverse micelle based studies of membrane proteins, and illustrate that membrane proteins solubilized by reverse micelles are compatible with high resolution solution NMR techniques. ..
  9. Zhang Y, Soto J, Park K, Viswanath G, Kuwada S, Abel E, et al. Nuclear receptor SHP, a death receptor that targets mitochondria, induces apoptosis and inhibits tumor growth. Mol Cell Biol. 2010;30:1341-56 pubmed publisher
    ..Thus, SHP regulates a mechanism by which apoptotic signals can mediate local control of mitochondrial function and apoptosis, which in turn may limit tumorigenesis. ..
  10. Hill J, Demarest B, Gorsi B, Smith M, Yost H. Heart morphogenesis gene regulatory networks revealed by temporal expression analysis. Development. 2017;144:3487-3498 pubmed publisher
    ..This dataset provides an essential resource for future studies on the genetic/epigenetic pathways implicated in congenital heart defects and the mechanisms of cardiac transcriptional regulation. ..
  11. Soss S, Flynn P. Functional implications for a prototypical K-turn binding protein from structural and dynamical studies of 15.5K. Biochemistry. 2007;46:14979-86 pubmed
    ..Flexibility in fast time scale motions and the observation of limited intermediate and slow motions further characterize the free protein and may suggest local contributions to recognition and binding. ..
  12. De Domenico I, Zhang T, Koening C, Branch R, London N, Lo E, et al. Hepcidin mediates transcriptional changes that modulate acute cytokine-induced inflammatory responses in mice. J Clin Invest. 2010;120:2395-405 pubmed publisher
    ..The results of our study suggest a new function for hepcidin in modulating acute inflammatory responses. ..
  13. Chow K, Elgort S, Dasso M, Ullman K. Two distinct sites in Nup153 mediate interaction with the SUMO proteases SENP1 and SENP2. Nucleus. 2012;3:349-58 pubmed
    ..While SENP1 and SENP2 share many characteristics, we show here that SENP1 levels are influenced by the presence of Nup153, whereas SENP2 is not sensitive to changes in Nup153 abundance. ..
  14. Kim H, Jeong M, Na U, Winge D. Flavinylation and assembly of succinate dehydrogenase are dependent on the C-terminal tail of the flavoprotein subunit. J Biol Chem. 2012;287:40670-9 pubmed publisher
    ..The impaired assembly of SDH with the C-terminal Sdh1 mutants suggests that FAD binding is important to stabilize the Sdh1 conformation enabling association with Sdh2 and the membrane anchor subunits. ..
  15. Eubanks L, Poulter C. Rhodobacter capsulatus 1-deoxy-D-xylulose 5-phosphate synthase: steady-state kinetics and substrate binding. Biochemistry. 2003;42:1140-9 pubmed
    ..These results are consistent with an ordered mechanism for DXP synthase where pyruvate binds before GAP/d-glyceraldehyde...
  16. Roberts D, Stewart A, Huff J, Cairns B. The RNA polymerase III transcriptome revealed by genome-wide localization and activity-occupancy relationships. Proc Natl Acad Sci U S A. 2003;100:14695-700 pubmed
    ..These studies reveal new aspects of the kinetics, dynamics, and targets of the Pol III system. ..
  17. Kaltenbach L, Romero E, Becklin R, Chettier R, Bell R, Phansalkar A, et al. Huntingtin interacting proteins are genetic modifiers of neurodegeneration. PLoS Genet. 2007;3:e82 pubmed
    ..These studies demonstrate that high-throughput screening for protein interactions combined with genetic validation in a model organism is a powerful approach for identifying novel candidate modifiers of polyglutamine toxicity. ..
  18. Escobar H, Crockett D, Reyes Vargas E, Baena A, Rockwood A, Jensen P, et al. Large scale mass spectrometric profiling of peptides eluted from HLA molecules reveals N-terminal-extended peptide motifs. J Immunol. 2008;181:4874-82 pubmed
    ..In addition, these results expand the knowledge about the identity of anchor positions in HLA class I-associated peptides that can be used for characterization of HLA class I motifs. ..
  19. Strait K, Stricklett P, Kohan R, Kohan D. Identification of two nuclear factor of activated T-cells (NFAT)-response elements in the 5'-upstream regulatory region of the ET-1 promoter. J Biol Chem. 2010;285:28520-8 pubmed publisher
    ..Thus, NFAT appears to be an important regulator of ET-1 transcription in IMCD cells, and thus, it may play a role in controlling blood pressure through ET-1 regulation of renal salt excretion. ..
  20. Moore C, Shahrokh K, Sontum S, Cheatham T, Yost G. Improved cytochrome P450 3A4 molecular models accurately predict the Phe215 requirement for raloxifene dehydrogenation selectivity. Biochemistry. 2010;49:9011-9 pubmed publisher
    ..Thus, the improved structural model predicted novel enzyme-substrate interactions that control the selective dehydrogenation of raloxifene to its protein-binding intermediate. ..
  21. Larrieu Lahargue F, Welm A, Thomas K, Li D. Netrin-4 activates endothelial integrin {alpha}6{beta}1. Circ Res. 2011;109:770-4 pubmed publisher
    ..The ?6?1 integrin is a netrin-4 receptor in lymphatic endothelium and consequently represents a potential target to inhibit netrin-4-induced metastatic dissemination. ..
  22. Vachali P, Besch B, Gonzalez Fernandez F, Bernstein P. Carotenoids as possible interphotoreceptor retinoid-binding protein (IRBP) ligands: a surface plasmon resonance (SPR) based study. Arch Biochem Biophys. 2013;539:181-6 pubmed publisher
    ..These results suggest that further studies should be carried out to evaluate whether IRBP has a physiologically relevant role in binding lutein and zeaxanthin in the interphotoreceptor matrix...
  23. Leavitt J, Gogokhia L, Gilcrease E, Bhardwaj A, Cingolani G, Casjens S. The tip of the tail needle affects the rate of DNA delivery by bacteriophage P22. PLoS ONE. 2013;8:e70936 pubmed publisher
    ..These findings suggest that the needle plays a role in phage P22 DNA delivery by controlling the kinetics of DNA ejection into the host. ..
  24. Bursavich M, Dastrup D, Shenderovich M, Yager K, Cimbora D, Williams B, et al. Novel Mps1 kinase inhibitors: from purine to pyrrolopyrimidine and quinazoline leads. Bioorg Med Chem Lett. 2013;23:6829-33 pubmed publisher
    ..These new single-digit nanomolar leads provide the basis for developing potent, novel Mps1 inhibitors with improved drug-like properties. ..
  25. Blanchfield L, Sabatino J, Lawrence L, Evavold B. NFM Cross-Reactivity to MOG Does Not Expand a Critical Threshold Level of High-Affinity T Cells Necessary for Onset of Demyelinating Disease. J Immunol. 2017;199:2680-2691 pubmed publisher
  26. Bibikov S, Barnes L, Gitin Y, Parkinson J. Domain organization and flavin adenine dinucleotide-binding determinants in the aerotaxis signal transducer Aer of Escherichia coli. Proc Natl Acad Sci U S A. 2000;97:5830-5 pubmed
    ..One or both regions probably also play important roles in transmitting stimulus-induced conformational changes to the C-terminal flagellar signaling domain to trigger aerotactic behavioral responses. ..
  27. Renfranz P, Siegrist S, Stronach B, Macalma T, Beckerle M. Molecular and phylogenetic characterization of Zyx102, a Drosophila orthologue of the zyxin family that interacts with Drosophila Enabled. Gene. 2003;305:13-26 pubmed
  28. Pornillos O, Higginson D, Stray K, Fisher R, Garrus J, Payne M, et al. HIV Gag mimics the Tsg101-recruiting activity of the human Hrs protein. J Cell Biol. 2003;162:425-34 pubmed
    ..HIV-1 Gag apparently mimics this Hrs activity, and thereby usurps Tsg101 and other components of the MVB vesicle fission machinery to facilitate viral budding. ..
  29. Ruone S, Rhoades A, Formosa T. Multiple Nhp6 molecules are required to recruit Spt16-Pob3 to form yFACT complexes and to reorganize nucleosomes. J Biol Chem. 2003;278:45288-95 pubmed
    ..These results suggest that Nhp6 and the related high mobility group B proteins may have a general role in promoting rearrangements of chromatin by initiating the destabilization of core nucleosomal structure. ..
  30. Liu J, Durrant D, Yang H, He Y, Whitby F, Myszka D, et al. The interaction between tBid and cardiolipin or monolysocardiolipin. Biochem Biophys Res Commun. 2005;330:865-70 pubmed
    ..None of the single mutations can abolish the ability of tBid to target to mitochondria and to induce cytochrome c release, suggesting that positive-charged residues in helices 4-6 may not be required for mitochondrial targeting of tBid. ..
  31. Ball J, Dimaano C, Bilak A, Kurchan E, Zundel M, Ullman K. Sequence preference in RNA recognition by the nucleoporin Nup153. J Biol Chem. 2007;282:8734-40 pubmed
    ..This information adds a new dimension to the interfaces that can contribute to recognition in mRNA export cargo selection and fate. ..
  32. Goeres D, Van Norman J, Zhang W, Fauver N, Spencer M, Sieburth L. Components of the Arabidopsis mRNA decapping complex are required for early seedling development. Plant Cell. 2007;19:1549-64 pubmed
    ..Furthermore, the severe block to postembryonic development in vcs and tdt and the accompanying accumulation of embryonic mRNAs indicate that decapping is important for the embryo-to-seedling developmental transition. ..
  33. Zumbrennen K, Hanson E, Leibold E. HOIL-1 is not required for iron-mediated IRP2 degradation in HEK293 cells. Biochim Biophys Acta. 2008;1783:246-52 pubmed
    ..These data demonstrate that HOIL-1 is not required for iron-dependent degradation of IRP2 in HEK293 cells, and suggest that a HOIL-1 independent mechanism is used for IRP2 degradation in most cell types. ..
  34. Morita E, Sandrin V, Chung H, Morham S, Gygi S, Rodesch C, et al. Human ESCRT and ALIX proteins interact with proteins of the midbody and function in cytokinesis. EMBO J. 2007;26:4215-27 pubmed
    ..These experiments suggest that the ESCRT pathway may be recruited to facilitate analogous membrane fission events during HIV budding, MVB vesicle formation, and the abscission stage of cytokinesis. ..
  35. Voth W, Yu Y, Takahata S, Kretschmann K, Lieb J, Parker R, et al. Forkhead proteins control the outcome of transcription factor binding by antiactivation. EMBO J. 2007;26:4324-34 pubmed
    ..Thus Fkh proteins, which function initially to activate SWI5 and ACE2, subsequently function as Swi5-specific antiactivators. ..
  36. Decher N, Gonzalez T, Streit A, Sachse F, Renigunta V, Soom M, et al. Structural determinants of Kvbeta1.3-induced channel inactivation: a hairpin modulated by PIP2. EMBO J. 2008;27:3164-74 pubmed publisher
    ..Taken together, our findings indicate that inactivation of Kv1.5 is mediated by an equilibrium binding of the N terminus of Kvbeta1.3 between phosphoinositides (PIPs) and the inner pore region of the channel. ..
  37. Wang X, Xu R, Lu Z. A peptide-targeted delivery system with pH-sensitive amphiphilic cell membrane disruption for efficient receptor-mediated siRNA delivery. J Control Release. 2009;134:207-13 pubmed publisher
    ..This novel targeted delivery system holds a great promise for systemic and targeted delivery of therapeutic siRNA. ..
  38. Christensen D, Klevit R. Dynamic interactions of proteins in complex networks: identifying the complete set of interacting E2s for functional investigation of E3-dependent protein ubiquitination. FEBS J. 2009;276:5381-9 pubmed publisher
    ..Defining the set of E2s that interact with other RING and U-box E3s will open the door for predictive models and lead to a better understand of substrate ubiquitination. ..
  39. Krishna V, Ayton G, Voth G. Role of protein interactions in defining HIV-1 viral capsid shape and stability: a coarse-grained analysis. Biophys J. 2010;98:18-26 pubmed publisher
  40. Paulsen R, Seth P, Swayze E, Griffey R, Skalicky J, Cheatham T, et al. Inhibitor-induced structural change in the HCV IRES domain IIa RNA. Proc Natl Acad Sci U S A. 2010;107:7263-8 pubmed publisher
  41. Zhou T, Zhang Y, Macchiarulo A, Yang Z, Cellanetti M, Coto E, et al. Novel polymorphisms of nuclear receptor SHP associated with functional and structural changes. J Biol Chem. 2010;285:24871-81 pubmed publisher
    ..This study suggests that genetic variations in SHP are common among human subjects and the Lys-170 residue plays a key role in controlling SHP ubiquitination and acetylation associated with SHP protein stability and repressive function. ..
  42. Heo J, Livnat Levanon N, Taylor E, Jones K, Dephoure N, Ring J, et al. A stress-responsive system for mitochondrial protein degradation. Mol Cell. 2010;40:465-80 pubmed publisher
    ..We demonstrate that Vms1 is a required component of an evolutionarily conserved system for mitochondrial protein degradation, which is necessary to maintain mitochondrial, cellular, and organismal viability. ..
  43. Muthusamy V, Kannan S, Sadhaasivam K, Gounder S, Davidson C, Boeheme C, et al. Acute exercise stress activates Nrf2/ARE signaling and promotes antioxidant mechanisms in the myocardium. Free Radic Biol Med. 2012;52:366-76 pubmed publisher
    ..Our findings suggest the basis for a nonpharmacological approach to activate Nrf2/ARE signaling, which might be a potential therapeutic target to protect the heart from oxidative stress-induced cardiovascular complications. ..
  44. Wee Y, Roundy K, Weis J, Weis J. Interferon-inducible transmembrane proteins of the innate immune response act as membrane organizers by influencing clathrin and v-ATPase localization and function. Innate Immun. 2012;18:834-45 pubmed publisher
    ..These data suggest that the Ifitm proteins help stabilize v-ATPase complexes in cellular membranes which, in turn, facilitates the appropriate subcellular localization of clathrin. ..
  45. Vanhille D, Nussenzveig R, Glezos C, Perkins S, Agarwal A. Best practices for use of the HEMOX analyzer in the clinical laboratory: quality control determination and choice of anticoagulant. Lab Hematol. 2012;18:17-9 pubmed
    ..Use of the correct anticoagulant and strict control of buffer pH are 2 parameters that need to be accounted for in best-practices use of this hemoximeter and before determining P(50). ..
  46. Kang J, Shen Z, Lim J, Handa H, Wells L, Tantin D. Regulation of Oct1/Pou2f1 transcription activity by O-GlcNAcylation. FASEB J. 2013;27:2807-17 pubmed publisher
    ..We also, for the first time, identify specific Oct1 ubiquitination sites. The findings suggest that Oct1 integrates metabolic and stress signals via O-GlcNAc modification to regulate target gene activity. ..
  47. Krishnan R, Tsubery H, Proschitsky M, Asp E, Lulu M, Gilead S, et al. A bacteriophage capsid protein provides a general amyloid interaction motif (GAIM) that binds and remodels misfolded protein assemblies. J Mol Biol. 2014;426:2500-19 pubmed publisher
    ..Taken together, our studies show that g3p(N1N2) acts as a general amyloid interaction motif. ..
  48. Vachali P, Li B, Besch B, Bernstein P. Protein-Flavonoid Interaction Studies by a Taylor Dispersion Surface Plasmon Resonance (SPR) Technique: A Novel Method to Assess Biomolecular Interactions. Biosensors (Basel). 2016;6: pubmed publisher
    ..The interactions of flavonoids with HSA and GSTP1 were studied successfully using this novel SPR assay method. The new method is compatible with both kinetic and equilibrium analyses. ..
  49. Kim E, Panushka J, Meyer T, Ide N, Carlisle R, Baker S, et al. Biogenesis of the Flagellar Switch Complex in Escherichia coli: Formation of Sub-Complexes Independently of the Basal-Body MS-Ring. J Mol Biol. 2017;429:2353-2359 pubmed publisher
    ..FliM does not multimerize efficiently by itself but does so in the presence of FliG. Thus, pre-assemblies of the switch-complex proteins can form in the cytosol and might function as intermediates in assembly. ..
  50. Burke P, Schooler K, Wiley H. Regulation of epidermal growth factor receptor signaling by endocytosis and intracellular trafficking. Mol Biol Cell. 2001;12:1897-910 pubmed
    ..In addition, ligand loss is the proximal cause of EGFR inactivation. Thus, regulated trafficking could potentially influence the pattern as well as the duration of signal transduction. ..
  51. Koppisch A, Fox D, Blagg B, Poulter C. E. coli MEP synthase: steady-state kinetic analysis and substrate binding. Biochemistry. 2002;41:236-43 pubmed
    ..Fosmidomycin was an uncompetitive inhibitor against NADPH and gave a pattern representative of slow, tight-binding competitive inhibition against DXP. These results are consistent with an ordered mechanism where NADPH binds before DXP. ..
  52. Singer J, Shaw J. Mdm20 protein functions with Nat3 protein to acetylate Tpm1 protein and regulate tropomyosin-actin interactions in budding yeast. Proc Natl Acad Sci U S A. 2003;100:7644-9 pubmed
    ..These combined results strongly suggest that Mdm20p-dependent, N-terminal acetylation of Tpm1p by the NatB complex is required for Tpm1p association with, and stabilization of, actin filaments and cables. ..
  53. Bhosale P, Larson A, Frederick J, Southwick K, Thulin C, Bernstein P. Identification and characterization of a Pi isoform of glutathione S-transferase (GSTP1) as a zeaxanthin-binding protein in the macula of the human eye. J Biol Chem. 2004;279:49447-54 pubmed
    ..These results indicate that GSTP1 is a specific XBP in human macula that interacts with (3R,3'S-meso)-zeaxanthin and dietary (3R,3'R)-zeaxanthin in contrast to apparently weaker interactions with (3R,3'R,6'R)-lutein. ..
  54. Taluja A, Bae Y. Role of a novel multifunctional excipient poly(ethylene glycol)-block-oligo(vinyl sulfadimethoxine) in controlled release of lysozyme from PLGA microspheres. Int J Pharm. 2008;358:50-9 pubmed publisher
    ..Manipulation of such polyelectrolyte-protein complexation may play a role in protein-controlled delivery. ..
  55. McCullough L, Rawlins R, Olsen A, Xin H, Stillman D, Formosa T. Insight into the mechanism of nucleosome reorganization from histone mutants that suppress defects in the FACT histone chaperone. Genetics. 2011;188:835-46 pubmed publisher
  56. Paul K, Carlquist W, Blair D. Adjusting the spokes of the flagellar motor with the DNA-binding protein H-NS. J Bacteriol. 2011;193:5914-22 pubmed publisher
    ..The present findings provide an integrated, structurally grounded framework for understanding the roughly opposing effects of these motility regulators. ..
  57. Dahlem T, Hoshijima K, Jurynec M, Gunther D, Starker C, Locke A, et al. Simple methods for generating and detecting locus-specific mutations induced with TALENs in the zebrafish genome. PLoS Genet. 2012;8:e1002861 pubmed publisher
    ..In all, it takes about two weeks to create a target-specific TALEN and generate growing embryos that harbor an array of germ line mutations at a pre-specified locus. ..
  58. Keener J, Babst M. Quality control and substrate-dependent downregulation of the nutrient transporter Fur4. Traffic. 2013;14:412-27 pubmed publisher
    ..We propose that the LID-degron system is a conserved, chaperone-independent mechanism responsible for conformation-induced downregulation of many cell-surface transporters under physiological and pathological conditions. ..
  59. Han K, Ayer D. MondoA senses adenine nucleotides: transcriptional induction of thioredoxin-interacting protein. Biochem J. 2013;453:209-18 pubmed publisher
    ..We propose that this mechanism serves as a checkpoint to restore metabolic homoeostasis. ..
  60. Saayman S, Lazar D, Scott T, Hart J, Takahashi M, Burnett J, et al. Potent and Targeted Activation of Latent HIV-1 Using the CRISPR/dCas9 Activator Complex. Mol Ther. 2016;24:488-98 pubmed publisher
    ..CRISPR-mediated gene activation represents a novel system which provides enhanced efficiency and specificity in a targeted latency reactivation strategy and represents a promising approach to a "functional cure" of HIV/AIDS. ..
  61. Morton K, Alazraki N, Datz F, Taylor A, Winge D, Lynch R. Uptake of cadmium-109, a metallothionein-binding radiometal, by tumors in mice as a function of the transformed phenotype. Invest Radiol. 1988;23:200-4 pubmed
    ..We conclude that metals that bind to MT may be useful for imaging or radiotherapy of cancer...
  62. Gamble T, Vajdos F, Yoo S, Worthylake D, Houseweart M, Sundquist W, et al. Crystal structure of human cyclophilin A bound to the amino-terminal domain of HIV-1 capsid. Cell. 1996;87:1285-94 pubmed
    ..Side by side association of these strips may allow capsid to form the surface of the viral core. Cyclophilin A could then function by weakening the association between capsid strips, thereby promoting disassembly of the viral core. ..
  63. Yoo S, Myszka D, Yeh C, McMurray M, Hill C, Sundquist W. Molecular recognition in the HIV-1 capsid/cyclophilin A complex. J Mol Biol. 1997;269:780-95 pubmed
    ..These studies reveal that the active site of CypA, which can catalyze the isomerization of proline residues in vitro, also functions as a sequence-specific, protein-binding motif in HIV-1 replication. ..
  64. Day Y, Baird C, Rich R, Myszka D. Direct comparison of binding equilibrium, thermodynamic, and rate constants determined by surface- and solution-based biophysical methods. Protein Sci. 2002;11:1017-25 pubmed
  65. Pornillos O, Alam S, Davis D, Sundquist W. Structure of the Tsg101 UEV domain in complex with the PTAP motif of the HIV-1 p6 protein. Nat Struct Biol. 2002;9:812-7 pubmed
    ..The structure reveals the molecular basis of HIV PTAP late domain function and represents an attractive starting point for the design of novel inhibitors of virus budding. ..
  66. Wang B, Alam S, Meyer H, Payne M, Stemmler T, Davis D, et al. Structure and ubiquitin interactions of the conserved zinc finger domain of Npl4. J Biol Chem. 2003;278:20225-34 pubmed
    ..Our studies reveal the structure of this versatile class of protein binding domains and provide a means for identifying the subset of NZF domains likely to bind ubiquitin. ..
  67. Kloeker S, Major M, Calderwood D, Ginsberg M, Jones D, Beckerle M. The Kindler syndrome protein is regulated by transforming growth factor-beta and involved in integrin-mediated adhesion. J Biol Chem. 2004;279:6824-33 pubmed
    ..Additionally, kindlerin is required for normal cell spreading. Taken together, these data suggest a role for kindlerin in mediating cell processes that depend on integrins. ..
  68. Stuchell M, Garrus J, Muller B, Stray K, Ghaffarian S, McKinnon R, et al. The human endosomal sorting complex required for transport (ESCRT-I) and its role in HIV-1 budding. J Biol Chem. 2004;279:36059-71 pubmed
    ..Taken together, these experiments define new components of the human ESCRT-I complex and characterize several TSG101 protein/protein interactions required for HIV-1 budding and infectivity. ..
  69. Du X, Hlady V, Britt D. Langmuir monolayer approaches to protein recognition through molecular imprinting. Biosens Bioelectron. 2005;20:2053-60 pubmed
    ..Template assessment, however, was complicated by the presence of an irreversibly bound protein fraction, which AFM revealed to be locally ordered protein clusters. ..
  70. Kondo Okamoto N, Ohkuni K, Kitagawa K, McCaffery J, Shaw J, Okamoto K. The novel F-box protein Mfb1p regulates mitochondrial connectivity and exhibits asymmetric localization in yeast. Mol Biol Cell. 2006;17:3756-67 pubmed
    ..We propose that Mfb1p operates in a novel pathway regulating mitochondrial tubular connectivity. ..
  71. De Domenico I, Ward D, Musci G, Kaplan J. Evidence for the multimeric structure of ferroportin. Blood. 2007;109:2205-9 pubmed
    ..These results support the hypothesis that the dominant inheritance of Fpn-iron overload disease is due to the dominant-negative effects of mutant Fpn proteins. ..
  72. Kiefer J, Smith P, Mango S. PHA-4/FoxA cooperates with TAM-1/TRIM to regulate cell fate restriction in the C. elegans foregut. Dev Biol. 2007;303:611-24 pubmed
    ..We propose that restriction of early blastomeres to the pharyngeal fate depends on both repression of ectodermal genes and activation of pharyngeal genes by PHA-4. ..
  73. Pierrel F, Bestwick M, Cobine P, Khalimonchuk O, Cricco J, Winge D. Coa1 links the Mss51 post-translational function to Cox1 cofactor insertion in cytochrome c oxidase assembly. EMBO J. 2007;26:4335-46 pubmed
    ..coa1Delta cells also display a mitochondrial copper defect suggesting that Coa1 may have a direct link to copper metallation of CcO. ..
  74. Kondo Okamoto N, Shaw J, Okamoto K. Tetratricopeptide repeat proteins Tom70 and Tom71 mediate yeast mitochondrial morphogenesis. EMBO Rep. 2008;9:63-9 pubmed
    ..Our data indicate an unexpected role for Tom70 in recruitment of soluble proteins to the mitochondrial surface, and indicate that Tom71 has a specialized role in Mfb1-mediated mitochondrial morphogenesis. ..
  75. Dimaano C, Jones C, Hanono A, Curtiss M, Babst M. Ist1 regulates Vps4 localization and assembly. Mol Biol Cell. 2008;19:465-74 pubmed
    ..The activity of the MVB pathway might be in part determined by outcome of these two competing activities. ..
  76. Bonkowsky J, Wang X, Fujimoto E, Lee J, Chien C, Dorsky R. Domain-specific regulation of foxP2 CNS expression by lef1. BMC Dev Biol. 2008;8:103 pubmed publisher
    ..The foxP2 enhancers we identified will allow dissection of foxP2's role during CNS development. ..
  77. Yu Y, Blair S, Gillespie D, Jensen R, Myszka D, Badran A, et al. Direct DNA methylation profiling using methyl binding domain proteins. Anal Chem. 2010;82:5012-9 pubmed publisher
    ..Fitting skew normal probability density functions to our data, we estimate an accuracy of 97.5% for our method in identifying methylated CpG loci, which can be improved through optimization of probe design and surface density. ..
  78. Romney S, Newman B, Thacker C, Leibold E. HIF-1 regulates iron homeostasis in Caenorhabditis elegans by activation and inhibition of genes involved in iron uptake and storage. PLoS Genet. 2011;7:e1002394 pubmed publisher
    ..These data show that HIF-1 regulates intestinal iron homeostasis during iron deficiency by activating and inhibiting genes involved in iron uptake and storage. ..
  79. Baron R, Vellore N. LSD1/CoREST is an allosteric nanoscale clamp regulated by H3-histone-tail molecular recognition. Proc Natl Acad Sci U S A. 2012;109:12509-14 pubmed publisher
    ..This study underscores the importance of receptor flexibility for future epigenetic drug discovery. ..
  80. Reaz S, Mossalam M, Okal A, Lim C. A single mutant, A276S of p53, turns the switch to apoptosis. Mol Pharm. 2013;10:1350-9 pubmed publisher
    ..Higher induction apoptosis than wild-type p53 makes A276S an attractive candidate for therapy to eradicate cancer. ..
  81. Hone A, Ruiz M, Scadden M, Christensen S, Gajewiak J, Azam L, et al. Positional scanning mutagenesis of ?-conotoxin PeIA identifies critical residues that confer potency and selectivity for ?6/?3?2?3 and ?3?2 nicotinic acetylcholine receptors. J Biol Chem. 2013;288:25428-39 pubmed publisher
    ..The results of these studies provide molecular insights into designing ligands that selectively target ?6?2* nAChRs. ..
  82. Perera R, Fleming A, Peterson A, Heemstra J, Burrows C, White H. Unzipping of A-Form DNA-RNA, A-Form DNA-PNA, and B-Form DNA-DNA in the α-Hemolysin Nanopore. Biophys J. 2016;110:306-314 pubmed publisher
    ..This study identifies key differences between A- and B-form duplex unzipping that will be important in the design of future probe-based methods for detecting DNA or RNA. ..
  83. Tang H, Braun T, Blair D. Motility protein complexes in the bacterial flagellar motor. J Mol Biol. 1996;261:209-21 pubmed
    ..Torque generation in the flagellar motor is thus likely to involve interactions between these two protein complexes. ..
  84. Billin A, Eilers A, Coulter K, Logan J, Ayer D. MondoA, a novel basic helix-loop-helix-leucine zipper transcriptional activator that constitutes a positive branch of a max-like network. Mol Cell Biol. 2000;20:8845-54 pubmed
    ..We propose that Mlx, like Max, functions as the center of a transcription factor network. ..
  85. Garrus J, von Schwedler U, Pornillos O, Morham S, Zavitz K, Wang H, et al. Tsg101 and the vacuolar protein sorting pathway are essential for HIV-1 budding. Cell. 2001;107:55-65 pubmed
    ..These observations suggest that retroviruses bud by appropriating cellular machinery normally used in the Vps pathway to form multivesicular bodies. ..
  86. Mayer P, Xiang T, Niemi R, Anderson B. A hydrophobicity scale for the lipid bilayer barrier domain from peptide permeabilities: nonadditivities in residue contributions. Biochemistry. 2003;42:1624-36 pubmed
    ..5 to -2.2 kcal/mol). These nonadditivities may be rationalized by considering the effects of peptide length and N-methylation on membrane-induced intramolecular hydrogen bonding leading to various folded conformations. ..
  87. Alam S, Sun J, Payne M, Welch B, Blake B, Davis D, et al. Ubiquitin interactions of NZF zinc fingers. EMBO J. 2004;23:1411-21 pubmed
    ..Thus, the NZF is a versatile protein recognition domain that is used to bind ubiquitylated proteins during vacuolar protein sorting, and probably many other biological processes. ..
  88. Eide E, Woolf M, Kang H, Woolf P, Hurst W, Camacho F, et al. Control of mammalian circadian rhythm by CKIepsilon-regulated proteasome-mediated PER2 degradation. Mol Cell Biol. 2005;25:2795-807 pubmed
    ..Cell culture-based biochemical assays combined with measurement of cell-based rhythm complement genetic studies to elucidate basic mechanisms controlling the mammalian clock. ..
  89. F rster A, Masters E, Whitby F, Robinson H, Hill C. The 1.9 A structure of a proteasome-11S activator complex and implications for proteasome-PAN/PA700 interactions. Mol Cell. 2005;18:589-99 pubmed publisher
    ..Surprisingly, biochemical observations implicate an equivalent interaction for the unrelated ATP-dependent activators PAN and PA700...
  90. Kaadige M, Ayer D. The polybasic region that follows the plant homeodomain zinc finger 1 of Pf1 is necessary and sufficient for specific phosphoinositide binding. J Biol Chem. 2006;281:28831-6 pubmed
  91. Coyne H, Ciofi Baffoni S, Banci L, Bertini I, Zhang L, George G, et al. The characterization and role of zinc binding in yeast Cox4. J Biol Chem. 2007;282:8926-34 pubmed
    ..The Zn(II) ion is buried within the domain, consistent with its role in structural stability. Potential functions of this matrix-facing subunit are discussed. ..
  92. Rigby K, Zhang L, Cobine P, George G, Winge D. characterization of the cytochrome c oxidase assembly factor Cox19 of Saccharomyces cerevisiae. J Biol Chem. 2007;282:10233-42 pubmed
    ..Cysteinyl residues important for Cu(I) binding are also shown to be important for the in vivo function of Cox19. Thus, a correlation exists in the ability to bind Cu(I) and in vivo function. ..