tertiary protein structure

Summary

Summary: The level of protein structure in which combinations of secondary protein structures (ALPHA HELICES; BETA SHEETS; loop regions, and AMINO ACID MOTIFS) pack together to form folded shapes. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure.

Top Publications

  1. Schlie K, Strecker T, Garten W. Maturation cleavage within the ectodomain of Lassa virus glycoprotein relies on stabilization by the cytoplasmic tail. FEBS Lett. 2010;584:4379-82 pubmed publisher
    ..Therefore, we postulate that the cytoplasmic domain is an important maturation factor stabilizing the overall conformation of the glycoprotein. ..
  2. Nakel K, Hartung S, Bonneau F, Eckmann C, Conti E. Four KH domains of the C. elegans Bicaudal-C ortholog GLD-3 form a globular structural platform. RNA. 2010;16:2058-67 pubmed publisher
    ..Instead, the KH1 domain mediates the direct interaction with the poly(A)-polymerase GLD-2, pointing to a function of the KH region as a protein-protein interaction platform. ..
  3. Bereau T, Bachmann M, Deserno M. Interplay between secondary and tertiary structure formation in protein folding cooperativity. J Am Chem Soc. 2010;132:13129-31 pubmed publisher
    ..Extending the results of lattice simulations and theoretical models, we have found that it is the interplay between secondary structure and the loss of non-native tertiary contacts that determines the nature of the transition. ..
  4. Cerda J. Molecular pathways during marine fish egg hydration: the role of aquaporins. J Fish Biol. 2009;75:2175-96 pubmed publisher
    ..The discovery of Aqp1b in teleosts provides an important insight into the molecular basis of the production of viable eggs in marine fish. ..
  5. Tsukada T, Pappas C, Moroz N, Antin P, Kostyukova A, Gregorio C. Leiomodin-2 is an antagonist of tropomodulin-1 at the pointed end of the thin filaments in cardiac muscle. J Cell Sci. 2010;123:3136-45 pubmed publisher
    ..Thus, Lmod2 antagonizes the function of Tmod1, and together, these molecules might fine-tune thin filament lengths. ..
  6. Ahmad M, Raut S, Pyaram K, Kamble A, Mullick J, Sahu A. Domain swapping reveals complement control protein modules critical for imparting cofactor and decay-accelerating activities in vaccinia virus complement control protein. J Immunol. 2010;185:6128-37 pubmed publisher
  7. Wu T, Manogaran A, Beauchamp J, Waring G. Drosophila vitelline membrane assembly: a critical role for an evolutionarily conserved cysteine in the "VM domain" of sV23. Dev Biol. 2010;347:360-8 pubmed publisher
    ..Found within the context of a putative thioredoxin active site (CXXS) C131, the critical cysteine in sV23, may play an important enzymatic role in isomerizing intermolecular disulfide bonds during eggshell assembly...
  8. Piccioli Z, McKee C, Leszczynski A, Onder Z, Hannah E, Mamoor S, et al. The nuclear localization of low risk HPV11 E7 protein mediated by its zinc binding domain is independent of nuclear import receptors. Virology. 2010;407:100-9 pubmed publisher
    ..Mutagenesis of Cys residues in these motifs changed the localization of the EGFP-11cE7/-11E7 mutants to cytoplasmic, suggesting that the zinc binding domain is essential for nuclear localization of 11E7. ..
  9. Beachy P, Hymowitz S, Lazarus R, Leahy D, Siebold C. Interactions between Hedgehog proteins and their binding partners come into view. Genes Dev. 2010;24:2001-12 pubmed publisher
    ..We review these results and discuss their implications for understanding Hh signaling in normal and disease states. ..

More Information

Publications62

  1. Thurison T, Lomholt A, Rasch M, Lund I, Nielsen H, Christensen I, et al. A new assay for measurement of the liberated domain I of the urokinase receptor in plasma improves the prediction of survival in colorectal cancer. Clin Chem. 2010;56:1636-40 pubmed publisher
    ..TR-FIA 4 has a functional sensitivity improved 4-fold over that of the previous uPAR(I) assay. The uPAR(I) concentration measured with TR-FIA 4 is an independent predictor of prognosis in CRC patients. ..
  2. Sadakata T, Shinoda Y, Sekine Y, Saruta C, Itakura M, Takahashi M, et al. Interaction of calcium-dependent activator protein for secretion 1 (CAPS1) with the class II ADP-ribosylation factor small GTPases is required for dense-core vesicle trafficking in the trans-Golgi network. J Biol Chem. 2010;285:38710-9 pubmed publisher
  3. Ma J, Martin J, Xue Y, Lor L, Kennedy Wilson K, Sinnamon R, et al. C-terminal region of USP7/HAUSP is critical for deubiquitination activity and contains a second mdm2/p53 binding site. Arch Biochem Biophys. 2010;503:207-12 pubmed publisher
    ..a. 425-491). We propose that the C-terminal domain of USP7 is responsible for maintaining the active conformation for catalysis and inhibitor binding, and contains the prime side of the proteolytic active site. ..
  4. Peters C, Brejc K, Belmont L, Bodey A, Lee Y, Yu M, et al. Insight into the molecular mechanism of the multitasking kinesin-8 motor. EMBO J. 2010;29:3437-47 pubmed publisher
    ..Our data reveal aspects of the molecular mechanism of kinesin-8 motors that contribute to their unique dual motile and depolymerising functions, which are adapted to control microtubule length. ..
  5. Yu Y, Chen Z, Li W, Cao H, Feng E, Yu F, et al. A nonproton ligand sensor in the acid-sensing ion channel. Neuron. 2010;68:61-72 pubmed publisher
    ..Thus, natural ligands beyond protons may activate ASICs under physiological and pathological conditions through the nonproton ligand sensor, serving for channel activation independent of abrupt and marked acidosis...
  6. Vo T, Letai A. BH3-only proteins and their effects on cancer. Adv Exp Med Biol. 2010;687:49-63 pubmed
    ..This chapter will discuss our current models of how BH3-only proteins function as well as their impact on carcinogenesis and cancer treatment. ..
  7. El Bakkouri M, Pow A, Mulichak A, Cheung K, Artz J, Amani M, et al. The Clp chaperones and proteases of the human malaria parasite Plasmodium falciparum. J Mol Biol. 2010;404:456-77 pubmed publisher
    ..Our data suggest the presence of a ClpCRP complex in the apicoplast of P. falciparum...
  8. Zehrmann A, Verbitskiy D, Härtel B, Brennicke A, Takenaka M. RNA editing competence of trans-factor MEF1 is modulated by ecotype-specific differences but requires the DYW domain. FEBS Lett. 2010;584:4181-6 pubmed publisher
    ..These do not recover RNA editing in protoplasts and regain only low levels in stable transformants. In MEF1, the DYW domain is thus required for full competence in RNA editing and its C-terminus has to be accessible. ..
  9. Yu J, Cheng W, Bustamante C, Oster G. Coupling translocation with nucleic acid unwinding by NS3 helicase. J Mol Biol. 2010;404:439-55 pubmed publisher
    ..The generic features of coupling single-stranded nucleic acid translocation with duplex unwinding presented in this work may apply generally to a class of helicases. ..
  10. Derrington I, Butler T, Collins M, Manrao E, Pavlenok M, Niederweis M, et al. Nanopore DNA sequencing with MspA. Proc Natl Acad Sci U S A. 2010;107:16060-5 pubmed publisher
    ..Passing DNA with a series of double-stranded sections through MspA provides proof of principle of a simple DNA sequencing method using a nanopore. These findings highlight the importance of MspA in the future of nanopore sequencing. ..
  11. Landreh M, Askarieh G, Nordling K, Hedhammar M, Rising A, Casals C, et al. A pH-dependent dimer lock in spider silk protein. J Mol Biol. 2010;404:328-36 pubmed publisher
    ..4 results in structural changes and alteration of charge-mediated interactions between subunits, thereby locking the spidroin NT dimer into a tight entity important for aggregation and silk formation. ..
  12. Reddy V, Natchiar S, Stewart P, Nemerow G. Crystal structure of human adenovirus at 3.5 A resolution. Science. 2010;329:1071-5 pubmed publisher
  13. Fan A, Jian W, Shi C, Ma Y, Wang L, Peng D, et al. Production and characterization of monoclonal antibody against Mycobacterium tuberculosis RpfB domain. Hybridoma (Larchmt). 2010;29:327-32 pubmed
  14. Sekulic N, Bassett E, Rogers D, Black B. The structure of (CENP-A-H4)(2) reveals physical features that mark centromeres. Nature. 2010;467:347-51 pubmed publisher
    ..Our results indicate that CENP-A marks centromere location by restructuring the nucleosome from within its folded histone core. ..
  15. Sohn J, Grant R, Sauer R. Allostery is an intrinsic property of the protease domain of DegS: implications for enzyme function and evolution. J Biol Chem. 2010;285:34039-47 pubmed publisher
    ..Thus, substrate binding alone may have regulated the activities of ancestral DegS trimers with subsequent fusion of the protease domain to a PDZ domain, resulting in ligand-mediated regulation. ..
  16. Bolstad H, Botelho D, Wood M. Proteomic analysis of protein-protein interactions within the Cysteine Sulfinate Desulfinase Fe-S cluster biogenesis system. J Proteome Res. 2010;9:5358-69 pubmed publisher
    ..By comparison with previous analysis of SufE, we demonstrate that there is some overlap in the CsdE and SufE interactomes. ..
  17. Harris J, Epting K, Kelly R. N-terminal fusion of a hyperthermophilic chitin-binding domain to xylose isomerase from Thermotoga neapolitana enhances kinetics and thermostability of both free and immobilized enzymes. Biotechnol Prog. 2010;26:993-1000 pubmed publisher
    ..These interactions likely also played a role in modifying active site structure, thereby diminishing substrate-binding affinities and generating higher turnover rates in the unbound fusion protein...
  18. Liu Y, Huo Z, Yan B, Lin X, Zhou Z, Liang X, et al. Prolyl hydroxylase 3 interacts with Bcl-2 to regulate doxorubicin-induced apoptosis in H9c2 cells. Biochem Biophys Res Commun. 2010;401:231-7 pubmed publisher
    ..Thus, PHD3 upregulation may be partially responsible for DOX-induced cardiomyocyte apoptosis via its interaction with Bcl-2. Inhibition of PHD3 is likely to be cardioprotective against apoptosis in some heart disorders. ..
  19. Wiemuth D, Lott J, Ly K, Ke Y, Teesdale Spittle P, Snyder P, et al. Interaction of serum- and glucocorticoid regulated kinase 1 (SGK1) with the WW-domains of Nedd4-2 is required for epithelial sodium channel regulation. PLoS ONE. 2010;5:e12163 pubmed publisher
    ..Further, SGK lacking a PY motif failed to stimulate ENaC activity in the presence of Nedd4-2. Binding of Nedd4-2 WW-domains to SGK is necessary for SGK-induced ENaC activity. ..
  20. Reuter M, Caswell C, Lukomski S, Zipfel P. Binding of the human complement regulators CFHR1 and factor H by streptococcal collagen-like protein 1 (Scl1) via their conserved C termini allows control of the complement cascade at multiple levels. J Biol Chem. 2010;285:38473-85 pubmed publisher
  21. Shi M, Zheng M, Liu Z, Hu Z, Huang Y, Chen J, et al. DCC is specifically required for the survival of retinal ganglion and displaced amacrine cells in the developing mouse retina. Dev Biol. 2010;348:87-96 pubmed publisher
    ..Thus, our findings suggest that DCC is a key regulator for the survival of specific types of neurons during retinal development and that DCC-P3 domain is essential for this developing event. ..
  22. Muskotál A, Seregélyes C, Sebestyén A, Vonderviszt F. Structural basis for stabilization of the hypervariable D3 domain of Salmonella flagellin upon filament formation. J Mol Biol. 2010;403:607-15 pubmed publisher
    ..Because D3 is a largely independent part of flagellin, its replacement by heterologous proteins or domains might offer a promising approach for creation of various fusion proteins possessing polymerization ability. ..
  23. Catterall W. Ion channel voltage sensors: structure, function, and pathophysiology. Neuron. 2010;67:915-28 pubmed publisher
    ..The emerging structural model for voltage sensor function opens the way to development of a new generation of ion-channel drugs that act on voltage sensors rather than blocking the pore. ..
  24. Herrera E, Tenckhoff S, Gomara M, Galatola R, Bleda M, Gil C, et al. Effect of synthetic peptides belonging to E2 envelope protein of GB virus C on human immunodeficiency virus type 1 infection. J Med Chem. 2010;53:6054-63 pubmed publisher
    ..We also show how GBV-C E2 domains notably decrease cellular membrane fusion and interfere with the HIV-1 infectivity in a dose-dependent manner, highlighting their potential utility in future anti-HIV-1 therapies. ..
  25. Pang S, Berry R, Chen Z, Kjer Nielsen L, Perugini M, King G, et al. The structural basis for autonomous dimerization of the pre-T-cell antigen receptor. Nature. 2010;467:844-8 pubmed publisher
    ..This unusual dual-chaperone-like sensing function of pre-T? represents a unique mechanism in nature whereby developmental quality control regulates the expression and signalling of an integral membrane receptor complex. ..
  26. Gakh O, Bedekovics T, Duncan S, Smith D, Berkholz D, Isaya G. Normal and Friedreich ataxia cells express different isoforms of frataxin with complementary roles in iron-sulfur cluster assembly. J Biol Chem. 2010;285:38486-501 pubmed publisher
    ..We suggest that the levels of both isoforms are relevant to FRDA pathophysiology and that the FXN(81-210)/FXN(42-210) molar ratio should provide a useful parameter to optimize FXN augmentation and replacement therapies...
  27. Negoda A, Negoda E, Reusch R. Resolving the native conformation of Escherichia coli OmpA. FEBS J. 2010;277:4427-37 pubmed
    ..The results suggest that the narrow pore is a folding intermediate, and demonstrate the decisive roles of cOHB-modification, disulfide bond formation and temperature in folding OmpA into its native large-pore configuration. ..
  28. Dupont D, Madsen J, Hartmann R, Tavitian B, Duconge F, Kjems J, et al. Serum-stable RNA aptamers to urokinase-type plasminogen activator blocking receptor binding. RNA. 2010;16:2360-9 pubmed publisher
    ..uPA-scavenging 2'-fluoro-pyrimidine-modified RNA aptamers represent a novel promising principle for interfering with the pathological functions of the uPA system. ..
  29. Aylett C, Wang Q, Michie K, Amos L, Lowe J. Filament structure of bacterial tubulin homologue TubZ. Proc Natl Acad Sci U S A. 2010;107:19766-71 pubmed publisher
    ..Filaments of ParM, the actin-like partitioning protein, are also double helical. We suggest that convergent evolution shapes these different types of cytomotive filaments toward a general mechanism for plasmid separation. ..
  30. van Dijk A, van Ham R. Conserved and variable correlated mutations in the plant MADS protein network. BMC Genomics. 2010;11:607 pubmed publisher
  31. Lindman S, Hernandez Garcia A, Szczepankiewicz O, Frohm B, Linse S. In vivo protein stabilization based on fragment complementation and a split GFP system. Proc Natl Acad Sci U S A. 2010;107:19826-31 pubmed publisher
  32. Zhu F, Hummer G. Pore opening and closing of a pentameric ligand-gated ion channel. Proc Natl Acad Sci U S A. 2010;107:19814-9 pubmed publisher
    ..The mechanical work of opening the pore is performed primarily on the M2-M3 loop. Strong interactions of this short and conserved loop with the extracellular domain are therefore crucial to couple ligand binding to channel opening. ..
  33. Dellarole M, Sánchez I, de Prat Gay G. Thermodynamics of cooperative DNA recognition at a replication origin and transcription regulatory site. Biochemistry. 2010;49:10277-86 pubmed publisher
    ..This is in surprising agreement with previous results for this domain, which revealed a strong coupling between global dynamics and DNA recognition. ..
  34. Umehara T, Nakamura Y, Wakamori M, Ozato K, Yokoyama S, Padmanabhan B. Structural implications for K5/K12-di-acetylated histone H4 recognition by the second bromodomain of BRD2. FEBS Lett. 2010;584:3901-8 pubmed publisher
    ..These results provide a structural basis for the recognition of two different patterns of the histone acetylation status by a single bromodomain. ..
  35. Marín E, Bodelon G, Fernández L. Comparative analysis of the biochemical and functional properties of C-terminal domains of autotransporters. J Bacteriol. 2010;192:5588-602 pubmed publisher
    ..These observations suggest that the AT ?-barrel without its ?-helix cannot form a stable hydrophilic channel in the OM for protein translocation. The implications of our data for an understanding of AT secretion are discussed. ..
  36. Luo W, Wang X, Kashtan C, Borza D. Alport alloantibodies but not Goodpasture autoantibodies induce murine glomerulonephritis: protection by quinary crosslinks locking cryptic ?3(IV) collagen autoepitopes in vivo. J Immunol. 2010;185:3520-8 pubmed publisher
    ..Crosslinking of alpha3alpha4alpha5NC1 hexamers represents a novel mechanism averting autoantibody binding and subsequent tissue injury by posttranslational modifications of an autoantigen...
  37. Out A, Tops C, Nielsen M, Weiss M, van Minderhout I, Fokkema I, et al. Leiden Open Variation Database of the MUTYH gene. Hum Mutat. 2010;31:1205-15 pubmed publisher
    ..This open-access repository allows all involved to quickly share all variants encountered and communicate potential consequences, which will be especially useful to classify variants of uncertain significance...
  38. Peng Z, He Y, Yang Y, Zhu R, Bai J, Li Y, et al. Autoproteolysis of the SEA module of rMuc3 C-terminal domain modulates its functional composition. Arch Biochem Biophys. 2010;503:238-47 pubmed publisher
  39. Motojima Miyazaki Y, Yoshida M, Motojima F. Ribosomal protein L2 associates with E. coli HtpG and activates its ATPase activity. Biochem Biophys Res Commun. 2010;400:241-5 pubmed publisher
    ..The ATPase of HtpG at increasing concentration of L2 indicated that an L2 molecule bound to a dimer HtpG with apparent K(D) of 0.3 ?M at 100mM KCl and 3.3 ?M at 200 mM KCl. ..
  40. Tran N, Dang H, Tuteja R, Tuteja N. A single subunit MCM6 from pea forms homohexamer and functions as DNA helicase. Plant Mol Biol. 2010;74:327-36 pubmed publisher
    ..This discovery should make an important contribution to a better understanding of DNA replication in plants. ..
  41. Isom D, Castaneda C, Cannon B, Velu P, Garcia Moreno E B. Charges in the hydrophobic interior of proteins. Proc Natl Acad Sci U S A. 2010;107:16096-100 pubmed publisher
  42. Kutlar F, Redding Lallinger R, Meiler S, Bakanay S, Borders L, Kutlar A. A new sickling variant 'Hb S-Wake ?[(Glu6Val-Asn139 Ser)]' found in a compound heterozygote with Hb S ?(Glu6Val) coinherited with homozygous ?-thalassemia-2: phenotype and molecular characteristics. Acta Haematol. 2010;124:120-4 pubmed publisher
    ..The patient also carried a single Hb S mutation in trans allele, leading to Hb SS-Wake disease. He had coinherited homozygous ?(+)-thalassemia (-?(3.7)/-?(3.7)) simultaneously which resulted in multiple globin gene abnormalities. ..
  43. Wang J, Horenstein N, Stokes C, Papke R. Tethered agonist analogs as site-specific probes for domains of the human ?7 nicotinic acetylcholine receptor that differentially regulate activation and desensitization. Mol Pharmacol. 2010;78:1012-25 pubmed publisher
    ..This insight may provide a new approach for drug development. ..
  44. Casteel D, Smith Nguyen E, Sankaran B, Roh S, Pilz R, Kim C. A crystal structure of the cyclic GMP-dependent protein kinase I{beta} dimerization/docking domain reveals molecular details of isoform-specific anchoring. J Biol Chem. 2010;285:32684-8 pubmed publisher
    ..Our structure provides molecular details of this unique leucine/isoleucine zipper, revealing specific hydrophobic and ionic interactions that mediate dimerization and demonstrating the topology of the GKAP interaction surface. ..
  45. Haurwitz R, Jinek M, Wiedenheft B, Zhou K, Doudna J. Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science. 2010;329:1355-8 pubmed publisher
    ..The RNA recognition mechanism identified here explains sequence- and structure-specific processing by a large family of CRISPR-specific endoribonucleases. ..
  46. Grace C, Perrin M, Gulyas J, Rivier J, Vale W, Riek R. NMR structure of the first extracellular domain of corticotropin-releasing factor receptor 1 (ECD1-CRF-R1) complexed with a high affinity agonist. J Biol Chem. 2010;285:38580-9 pubmed publisher
    ..Rivier, C., Perrin, M., Koerber, S. C., Sutton, S., Corrigan, A., Lahrichi, S. L., Craig, A. G., Vale, W., and Rivier, J. (1995) Proc. Natl. Acad. Sci. U.S.A. 92, 10575-10579). ..
  47. Blain K, Kwiatkowski W, Choe S. The functionally active Mistic-fused histidine kinase receptor, EnvZ. Biochemistry. 2010;49:9089-95 pubmed publisher
  48. D Avanzo N, Cheng W, Doyle D, Nichols C. Direct and specific activation of human inward rectifier K+ channels by membrane phosphatidylinositol 4,5-bisphosphate. J Biol Chem. 2010;285:37129-32 pubmed publisher
    ..This raises the interesting hypothesis that PIP(2) activation of eukaryotic channels reflects an evolutionary adaptation of the channel to the appearance of PIP(2) in the eukaryotic cell membrane. ..
  49. Zhang J, Ravichandran K, Garrison J. A key role for the phosphorylation of Ser440 by the cyclic AMP-dependent protein kinase in regulating the activity of the Src homology 2 domain-containing Inositol 5'-phosphatase (SHIP1). J Biol Chem. 2010;285:34839-49 pubmed publisher
    ..The inhibitory effect of Sp-cAMPS was absent in cells expressing the S440A mutant of SHIP1. These results suggest that activation of SHIP1 by PKA via phosphorylation on Ser(440) is an important regulatory event in hematopoietic cells. ..
  50. Mao Y, Xu X, Xu W, Ishida Y, Leal W, Ames J, et al. Crystal and solution structures of an odorant-binding protein from the southern house mosquito complexed with an oviposition pheromone. Proc Natl Acad Sci U S A. 2010;107:19102-7 pubmed publisher
    ..This study shows that CquiOBP binds MOP in an unprecedented fashion using both a small central cavity for the lactone head group and a long hydrophobic channel for its tail. ..
  51. Khambati H, Moraes T, Singh J, Shouldice S, Yu R, Schryvers A. The role of vicinal tyrosine residues in the function of Haemophilus influenzae ferric-binding protein A. Biochem J. 2010;432:57-64 pubmed publisher
    ..Collectively, these results demonstrate that the presence of a twin-tyrosine motif common to many periplasmic iron-binding proteins is critical for initially capturing the ferric ion released by the outer-membrane receptor complex. ..
  52. Haffke M, Menzel A, Carius Y, Jahn D, Heinz D. Structures of the nucleotide-binding domain of the human ABCB6 transporter and its complexes with nucleotides. Acta Crystallogr D Biol Crystallogr. 2010;66:979-87 pubmed publisher
    ..Structural comparison with other structurally characterized NBDs and full-length ABC transporters gives the first insight into the possible catalytic mechanism of ABCB6 and the role of the N-terminal helix alpha(1) in full-length ABCB6...
  53. Sugishima M, Okamoto Y, Noguchi M, Kohchi T, Tamiaki H, Fukuyama K. Crystal structures of the substrate-bound forms of red chlorophyll catabolite reductase: implications for site-specific and stereospecific reaction. J Mol Biol. 2010;402:879-91 pubmed publisher
    ..The geometrical arrangement of RCC and the carboxy groups of Glu154 and Asp291 in RCCR would appear to be essential for the stereospecificity of the RCCR reaction. ..