当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > Structure, function, and dynamics of the dimerization and DNA-binding domain of oncogenic transcription factor v-Myc.

Structure, function, and dynamics of the dimerization and DNA-binding domain of oncogenic transcription factor v-Myc.

Abstract：

:The protein product (c-Myc) of the protooncogene c-myc is a transcriptional regulator playing a key role in cellular growth, differentiation, and apoptosis. Deregulated myc genes, like the transduced retroviral v-myc allele, are oncogenic and cause cell transformation. The C-terminal bHLHZip domain of v-Myc, encompassing protein dimerization (helix-loop-helix, leucine zipper) and DNA contact (basic region) surfaces, was expressed in bacteria as a highly soluble p15(v-myc )recombinant protein. Dissociation constants (K(d)) for the heterodimer formed with the recombinant bHLHZip domain of the Myc binding partner Max (p14(max)) and for the Myc-Max-DNA complex were estimated using circular dichroism (CD) spectroscopy and quantitative electrophoretic mobility shift assay (EMSA). Multi-dimensional NMR spectroscopy was used to characterize the solution structural and dynamic properties of the v-Myc bHLHZip domain. Significant secondary chemical shifts indicate the presence of two separated alpha-helical regions. The C-terminal leucine zipper region forms a compact alpha-helix, while the N-terminal basic region exhibits conformational averaging with substantial alpha-helical content. Both helices lack stabilizing tertiary side-chain interactions and represent exceptional examples for loosely coupled secondary structural segments in a native protein. These results and CD thermal denaturation data indicate a monomeric state of the v-Myc bHLHZip domain. The (15)N relaxation data revealed backbone mobilities which corroborate the existence of a partially folded state, and suggest a "beads-on-a-string" motional behaviour of the v-Myc bHLHZip domain in solution. The preformation of alpha-helical regions was confirmed by CD thermal denaturation studies, and quantification of the entropy changes caused by the hydrophobic effect and the reduction of conformational entropy upon protein dimerization. The restricted conformational space of the v-Myc bHLHZip domain reduces the entropy penalty associated with heterodimerization and allows rapid and accurate recognition by the authentic Myc binding partner Max.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Fieber W,Schneider ML,Matt T,Kräutler B,Konrat R,Bister K

doi

10.1006/jmbi.2001.4537

keywords:

subject

Has Abstract

pub_date

2001-04-13 00:00:00

pages

1395-410

issue

5

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(01)94537-1

journal_volume

307

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Topological frustration and the folding of interleukin-1 beta.

    abstract：:The cytokine, interleukin-1beta (IL-1beta), adopts a beta-trefoil fold. It is known to be much slower folding than similarly sized proteins, despite having a low contact order. Proteins are sufficiently well designed that their folding is not dominated by local energetic traps. Therefore, protein models that encode on...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.11.074

    authors： Gosavi S,Chavez LL,Jennings PA,Onuchic JN

    更新日期：2006-03-31 00:00:00

  • The molecular defect leading to Fabry disease: structure of human alpha-galactosidase.

    abstract：:Fabry disease is an X-linked lysosomal storage disease afflicting 1 in 40,000 males with chronic pain, vascular degeneration, cardiac impairment, and other symptoms. Deficiency in the lysosomal enzyme alpha-galactosidase (alpha-GAL) causes an accumulation of its substrate, which ultimately leads to Fabry disease sympt...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.01.035

    authors： Garman SC,Garboczi DN

    更新日期：2004-03-19 00:00:00

  • Predicting absolute ligand binding free energies to a simple model site.

    abstract：:A central challenge in structure-based ligand design is the accurate prediction of binding free energies. Here we apply alchemical free energy calculations in explicit solvent to predict ligand binding in a model cavity in T4 lysozyme. Even in this simple site, there are challenges. We made systematic improvements, be...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.06.002

    authors： Mobley DL,Graves AP,Chodera JD,McReynolds AC,Shoichet BK,Dill KA

    更新日期：2007-08-24 00:00:00

  • Characterization of Warfarin Inhibition Kinetics Requires Stabilization of Intramembrane Vitamin K Epoxide Reductases.

    abstract：:Intramembrane enzymes are often difficult for biochemical characterization. Human vitamin K epoxide reductase (VKOR) is the target of warfarin. However, this intramembrane enzyme becomes insensitive to warfarin inhibition in vitro, preventing the characterization of inhibition kinetics for decades. Here we employ stru...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2020.05.009

    authors： Li S,Liu S,Yang Y,Li W

    更新日期：2020-08-21 00:00:00

  • Design, characterization, and structure of a biologically active single-chain mutant of human IFN-gamma.

    abstract：:A mutant form of human interferon-gamma (IFN-gamma SC1) that binds one IFN-gamma receptor alpha chain (IFN-gamma R alpha) has been designed and characterized. IFN-gamma SC1 was derived by linking the two peptide chains of the IFN-gamma dimer by a seven-residue linker and changing His111 in the first chain to an aspart...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.3734

    authors： Landar A,Curry B,Parker MH,DiGiacomo R,Indelicato SR,Nagabhushan TL,Rizzi G,Walter MR

    更新日期：2000-05-26 00:00:00

  • Crystal structure of muconate lactonizing enzyme at 3 A resolution.

    abstract：:The crystal structure of muconate lactonizing enzyme has been solved at 3 A resolution, and an unambiguous alpha-carbon backbone chain trace made. The enzyme contains three domains; the central domain is a parallel-stranded alpha-beta barrel, which has previously been reported in six other enzymes, including triose ph...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(87)90723-6

    authors： Goldman A,Ollis DL,Steitz TA

    更新日期：1987-03-05 00:00:00

  • Crystal Structure and Directed Evolution of Specificity of NlaIV Restriction Endonuclease.

    abstract：:Specificity engineering is challenging and particularly difficult for enzymes that have the catalytic machinery and specificity determinants in close proximity. Restriction endonucleases have been used as a paradigm for protein engineering, but successful cases are rare. Here, we present the results of a directed evol...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2019.04.010

    authors： Czapinska H,Siwek W,Szczepanowski RH,Bujnicki JM,Bochtler M,Skowronek KJ

    更新日期：2019-05-17 00:00:00

  • Structure of the connector of bacteriophage T7 at 8A resolution: structural homologies of a basic component of a DNA translocating machinery.

    abstract：:The three-dimensional structure of the bacteriophage T7 head-to-tail connector has been obtained at 8A resolution using cryo-electron microscopy and single-particle analysis from purified recombinant connectors. The general morphology of the T7 connector is that of a 12-folded toroidal homopolymer with a channel that ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.02.005

    authors： Agirrezabala X,Martín-Benito J,Valle M,González JM,Valencia A,Valpuesta JM,Carrascosa JL

    更新日期：2005-04-15 00:00:00

  • Structure of selenophosphate synthetase essential for selenium incorporation into proteins and RNAs.

    abstract：:Selenophosphate synthetase (SPS) catalyzes the activation of selenide with adenosine 5'-triphosphate (ATP) to generate selenophosphate, the essential reactive selenium donor for the formation of selenocysteine (Sec) and 2-selenouridine residues in proteins and RNAs, respectively. Many SPS are themselves Sec-containing...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.08.042

    authors： Itoh Y,Sekine S,Matsumoto E,Akasaka R,Takemoto C,Shirouzu M,Yokoyama S

    更新日期：2009-02-06 00:00:00

  • Structure-function analysis of the acyl carrier protein synthase (AcpS) from Mycobacterium tuberculosis.

    abstract：:We have solved the crystal structure of the acyl carrier protein synthase (AcpS) from Mycobacterium tuberculosis (Mtb) at 1.95 A resolution. AcpS, a 4-phosphopantetheinyl transferase, activates two distinct acyl carrier proteins (ACPs) that are present in fatty acid synthase (FAS) systems FAS-I and FAS-II, the ACP-I d...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.08.065

    authors： Dym O,Albeck S,Peleg Y,Schwarz A,Shakked Z,Burstein Y,Zimhony O

    更新日期：2009-11-06 00:00:00

  • Predictive QM/MM Modeling of Modulations in Protein-Protein Binding by Lysine Methylation.

    abstract：:Lysine methylation is a key regulator of protein-protein binding. The amine group of lysine can accept up to three methyl groups, and experiments show that protein-protein binding free energies are sensitive to the extent of methylation. These sensitivities have been rationalized in terms of chemical and structural fe...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2020.166745

    authors： Rahman S,Wineman-Fisher V,Al-Hamdani Y,Tkatchenko A,Varma S

    更新日期：2021-02-05 00:00:00

  • Structure-guided identification of a laminin binding site on the laminin receptor precursor.

    abstract：:The 37/ 67-kDa human laminin receptor (LamR) is a cell surface receptor for laminin, prion protein, and a variety of viruses. Because of its wide range of ligands, LamR plays a role in numerous pathologies. LamR overexpression correlates with a highly invasive cell phenotype and increased metastatic ability, mediated ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2010.10.028

    authors： Jamieson KV,Hubbard SR,Meruelo D

    更新日期：2011-01-07 00:00:00

  • Adrm1, a putative cell adhesion regulating protein, is a novel proteasome-associated factor.

    abstract：:We have identified Adrm1 as a novel component of the regulatory ATPase complex of the 26 S proteasome: Adrm1 was precipitated with an antibody to proteasomes and vice versa. Adrm1 co-migrated with proteasomes on gel-filtration chromatography and non-denaturing polyacrylamide gel electrophoresis. Adrm1 has been describ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.06.011

    authors： Jørgensen JP,Lauridsen AM,Kristensen P,Dissing K,Johnsen AH,Hendil KB,Hartmann-Petersen R

    更新日期：2006-07-28 00:00:00

  • A novel calmodulin-like gene from the nematode Caenorhabditis elegans.

    abstract：:A novel gene from the nematode Caenorhabditis elegans was isolated by hybridization with a human calmodulin complementary DNA probe. This gene, cal-1, is present at one copy per haploid genome. In-situ hybridization of the cloned gene to metaphase chromosomes allowed us to assign it to the nematode linkage group IV. T...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(86)90002-1

    authors： Salvato M,Sulston J,Albertson D,Brenner S

    更新日期：1986-08-05 00:00:00

  • Rz/Rz1 lysis gene equivalents in phages of Gram-negative hosts.

    abstract：:Under usual laboratory conditions, lysis by bacteriophage lambda requires only the holin and endolysin genes, but not the Rz and Rz1 genes, of the lysis cassette. Defects in Rz or Rz1 block lysis only in the presence of high concentrations of divalent cations. The lambda Rz and Rz1 lysis genes are remarkable in that R...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.08.045

    authors： Summer EJ,Berry J,Tran TA,Niu L,Struck DK,Young R

    更新日期：2007-11-09 00:00:00

  • Determining the Limitations and Benefits of Noise in Gene Regulation and Signal Transduction through Single Cell, Microscopy-Based Analysis.

    abstract：:Stochastic fluctuations, termed "noise," in the level of biological molecules can greatly impact cellular functions. While biological noise can sometimes be detrimental, recent studies have provided an increasing number of examples in which biological noise can be functionally beneficial. Rather than provide an exhaus...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2017.03.007

    authors： Harton MD,Batchelor E

    更新日期：2017-04-21 00:00:00

  • Exploring the structural dynamics of the E.coli chaperonin GroEL using translation-libration-screw crystallographic refinement of intermediate states.

    abstract：:Large rigid-body domain movements are critical to GroEL-mediated protein folding, especially apical domain elevation and twist associated with the formation of a folding chamber upon binding ATP and co-chaperonin GroES. Here, we have modeled the anisotropic displacements of GroEL domains from various crystallized stat...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.07.015

    authors： Chaudhry C,Horwich AL,Brunger AT,Adams PD

    更新日期：2004-09-03 00:00:00

  • Filamentous phage IKe mRNAs conserve form and function despite divergence in regulatory elements.

    abstract：:As a means of determining whether there has been selection to conserve the basic pattern of filamentous phage mRNAs, the major mRNAs representing genes II to VIII have been defined for a phage distantly related to the Ff group specific for Escherichia coli hosts bearing F pili. Phage IKe has a genome with 55% identity...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0766

    authors： Stump MD,Madison-Antenucci S,Kokoska RJ,Steege DA

    更新日期：1997-02-14 00:00:00

  • Crystallization of recA protein from Proteus mirabilis.

    abstract：:The recA protein from Proteus mirabilis, which is homologous to the Escherichia coli protein, forms crystals in the orthorhombic space group P2(1)2(1)2(1). There are two 38,000 molecular weight subunits in the asymmetric unit and the unit cell dimensions are a = 57.5, b = 127.0 and c = 157.0 A. ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(86)90486-9

    authors： Weber IT,Steitz TA

    更新日期：1986-03-05 00:00:00

  • The crystal structure of glutamine-binding protein from Escherichia coli.

    abstract：:The crystal structure of the glutamine-binding protein (GlnBP) from Escherichia coli in a ligand-free "open" conformational state has been determined by isomorphous replacement methods and refined to an R-value of 21.4% at 2.3 A resolution. There are two molecules in the asymmetric unit, related by pseudo 4-fold screw...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1006/jmbi.1996.0509

    authors： Hsiao CD,Sun YJ,Rose J,Wang BC

    更新日期：1996-09-20 00:00:00

  • Discovery of ANTAR-RNAs and their Mechanism of Action in Mycobacteria.

    abstract：:Non-coding RNAs play pivotal roles in bacterial signaling. However, RNAs from certain phyla (specially high-GC actinobacteria) still remain elusive. Here, by re-engineering the existing genome-wide search approach, we discover a family of structurally conserved RNAs that are present ubiquitously across actinobacteria,...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2020.05.003

    authors： Mehta D,Koottathazhath A,Ramesh A

    更新日期：2020-06-26 00:00:00

  • Crystal structure of human ribosomal protein L10 core domain reveals eukaryote-specific motifs in addition to the conserved fold.

    abstract：:A phylogenetically conserved ribosomal protein L16p/L10e organizes the architecture of the aminoacyl tRNA binding site on the large ribosomal subunit. Eukaryotic L10 also exhibits a variety of cellular activities, and, in particular, human L10 is known as a putative tumor suppressor, QM. We have determined the 2.5-A c...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.01.003

    authors： Nishimura M,Kaminishi T,Takemoto C,Kawazoe M,Yoshida T,Tanaka A,Sugano S,Shirouzu M,Ohkubo T,Yokoyama S,Kobayashi Y

    更新日期：2008-03-21 00:00:00

  • Dual modes of modification of hepatitis A virus 3C protease by a serine-derived beta-lactone: selective crystallization and formation of a functional catalytic triad in the active site.

    abstract：:Hepatitis A virus (HAV) 3C proteinase is a member of the picornain cysteine proteases responsible for the processing of the viral polyprotein, a function essential for viral maturation and infectivity. This and its structural similarity to other 3C and 3C-like proteases make it an attractive target for the development...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.09.074

    authors： Yin J,Bergmann EM,Cherney MM,Lall MS,Jain RP,Vederas JC,James MN

    更新日期：2005-12-09 00:00:00

  • The 1.9 A resolution structure of phospho-serine 46 HPr from Enterococcus faecalis.

    abstract：:The histidine-containing phosphocarrier protein HPr is a central component of the phosphoenolpyruvate:sugar phosphotransferase system (PTS), which transfers metabolic carbohydrates across the cell membrane in many bacterial species. In Gram-positive bacteria, phosphorylation of HPr at conserved serine 46 (P-Ser-HPr) p...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.4166

    authors： Audette GF,Engelmann R,Hengstenberg W,Deutscher J,Hayakawa K,Quail JW,Delbaere LT

    更新日期：2000-11-03 00:00:00

  • Replication stress-induced genome instability: the dark side of replication maintenance by homologous recombination.

    abstract：:Homologous recombination (HR) is an evolutionary-conserved mechanism involved in a subtle balance between genome stability and diversity. HR is a faithful DNA repair pathway and has been largely characterized in the context of double-strand break (DSB) repair. Recently, multiple functions for the HR machinery have bee...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2013.04.023

    authors： Carr AM,Lambert S

    更新日期：2013-11-29 00:00:00

  • The solution structure of the native K50 Bicoid homeodomain bound to the consensus TAATCC DNA-binding site.

    abstract：:The solution structure of the homeodomain of the Drosophila morphogenic protein Bicoid (Bcd) complexed with a TAATCC DNA site is described. Bicoid is the only known protein that uses a homeodomain to regulate translation, as well as transcription, by binding to both RNA and DNA during early Drosophila development; in ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.12.007

    authors： Baird-Titus JM,Clark-Baldwin K,Dave V,Caperelli CA,Ma J,Rance M

    更新日期：2006-03-10 00:00:00

  • RNA-DNA hybrid formation at a bacteriophage T4 replication origin.

    abstract：:The bacteriophage T4 replication origins ori(uvsY) and ori(34) each contain two distinct components: a T4 middle-mode promoter that is strictly required for replication and a downstream region of about 50 bp that is required for maximal levels of replication. Here, we present evidence that structure of the downstream ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0844

    authors： Carles-Kinch K,Kreuzer KN

    更新日期：1997-03-14 00:00:00

  • Electrostatic mechanism of chromatin folding.

    abstract：:We describe a theoretical analysis of cation binding in the nucleosome, and in chromatin as it folds, using Manning's polyelectrolyte theory. The theory accounts remarkably well, even quantitatively, both for the interaction of histone charges with DNA in chromatin, and for the essential features of the folding proces...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(90)90081-V

    authors： Clark DJ,Kimura T

    更新日期：1990-02-20 00:00:00

  • Translational control and differential RNA decay are key elements regulating postsegregational expression of the killer protein encoded by the parB locus of plasmid R1.

    abstract：:The parB locus of plasmid R1, which mediates plasmid stability via postsegregational killing of plasmid-free cells, encodes two genes, hok and sok. The hok gene product is a potent cell-killing protein. The hok gene is regulated at the translational level by the sok gene-encoded repressor, a small anti-sense RNA compl...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(88)90096-4

    authors： Gerdes K,Helin K,Christensen OW,Løbner-Olesen A

    更新日期：1988-09-05 00:00:00

  • Structural analysis of the group II intron splicing factor CRS2 yields insights into its protein and RNA interaction surfaces.

    abstract：:Chloroplast RNA splicing 2 (CRS2) is a nuclear-encoded protein required for the splicing of nine group II introns in maize chloroplasts. CRS2 functions in the context of splicing complexes that include one of two CRS2-associated factors (CAF1 and CAF2). The CRS2-CAF1 and CRS2-CAF2 complexes are required for the splici...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.10.032

    authors： Ostheimer GJ,Hadjivassiliou H,Kloer DP,Barkan A,Matthews BW

    更新日期：2005-01-07 00:00:00