The alternatively folded state of the antibody C(H)3 domain.

Abstract:

:The C(H)3 domain of antibodies is characterized by two antiparallel beta-sheets forming a disulfide-linked sandwich-like structure. At acidic pH values and low ionic strength, C(H)3 becomes completely unfolded. The addition of salt transforms the acid-unfolded protein into an alternatively folded state exhibiting a characteristic secondary structure. The transition from native to alternatively folded C(H)3 is a fast reaction. Interestingly, this reaction involves the formation of a defined oligomer consisting of 12-14 subunits. Association is completely reversible and the native dimer is quantitatively reformed at neutral pH. This alternatively folded protein is remarkably stable against thermal and chemical denaturation and the unfolding transitions are highly cooperative. With a t(m) of 80 degrees C, the stability of the alternatively folded state is comparable to that of the native state of C(H)3. The defined oligomeric structure of C(H)3 at pH 2 seems to be a prerequisite for the cooperative unfolding transitions.

journal_name

J Mol Biol

authors

Thies MJ,Kammermeier R,Richter K,Buchner J

doi

10.1006/jmbi.2001.4707

keywords:

subject

Has Abstract

pub_date

2001-06-22 00:00:00

pages

1077-85

issue

5

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(01)94707-2

journal_volume

309

pub_type

杂志文章
  • A novel mutation in the neurofibromatosis type 1 (NF1) gene promotes skipping of two exons by preventing exon definition.

    abstract::Using a protein truncation assay, we have identified a new mutation in the neurofibromatosis type 1 (NF1) gene that causes a severe defect in NF1 pre-mRNA splicing. The mutation, which consists of a G to A transition at position +1 of the 5' splice site of exon 12a, is associated with the loss of both exons 11 and 12a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4561

    authors: Fang LJ,Simard MJ,Vidaud D,Assouline B,Lemieux B,Vidaud M,Chabot B,Thirion JP

    更新日期:2001-04-13 00:00:00

  • Evidence indicating proximity in the nucleosome between the histone H4 N termini and the globular domain of histone H1.

    abstract::Proteolysis of rat liver chromatin by the Arg-C peptidase, clostripain, is characterized by a progressive fragmentation of the N-terminal segments of the four core histones H2A, H2B, H3 and H4, until a well-defined limit digest is reached. This work addresses the case of histone H4. Two intermediate proteolytic sites ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1629

    authors: Banères JL,Essalouh L,Jariel-Encontre I,Mesnier D,Garrod S,Parello J

    更新日期:1994-10-14 00:00:00

  • Mechanism of strand cleavage and exchange in the Cre-lox site-specific recombination system.

    abstract::The bacteriophage P1 recombinase Cre mediates site-specific recombination between loxP sites. The loxP site consists of two 13 base-pair inverted repeats separated by an eight base-pair spacer region. When DNA containing the loxP site is incubated with Cre, specific cleavages occur within the spacer region, creating a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(85)90224-4

    authors: Hoess RH,Abremski K

    更新日期:1985-02-05 00:00:00

  • Structure of an archaeal RNA polymerase.

    abstract::Related multisubunit RNA polymerases (RNAPs) carry out gene transcription in all kingdoms of life. Since structural information is limited to bacterial and eukaryotic RNAPs, we determined the cryo-electron microscopic structure of the RNAP from the thermophilic archaeon Pyrococcus furiosus at 13 A resolution. Comparis...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.08.066

    authors: Kusser AG,Bertero MG,Naji S,Becker T,Thomm M,Beckmann R,Cramer P

    更新日期:2008-02-15 00:00:00

  • Conservation of organization in the specificity polypeptides of two families of type I restriction enzymes.

    abstract::We have identified the recognition sequence for the Citrobacter freundii restriction endonuclease CfrA, a member of the A-family of type I R-M enzymes. This bipartite target sequence differs in both its components from those of other type I enzymes. We determined the nucleotide sequence of its specificity gene (hsdS) ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(89)90001-6

    authors: Kannan P,Cowan GM,Daniel AS,Gann AA,Murray NE

    更新日期:1989-10-05 00:00:00

  • Kat6b Modulates Oct4 and Nanog Binding to Chromatin in Embryonic Stem Cells and Is Required for Efficient Neural Differentiation.

    abstract::Chromatin remodeling is fundamental for the dynamical changes in transcriptional programs that occur during development and stem cell differentiation. The histone acetyltransferase Kat6b is relevant for neurogenesis in mouse embryos, and mutations of this gene cause intellectual disability in humans. However, the mole...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2019.02.012

    authors: Cosentino MS,Oses C,Vázquez Echegaray C,Solari C,Waisman A,Álvarez Y,Petrone MV,Francia M,Schultz M,Sevlever G,Miriuka S,Levi V,Guberman A

    更新日期:2019-03-15 00:00:00

  • Structural insight into the dioxygenation of nitroarene compounds: the crystal structure of nitrobenzene dioxygenase.

    abstract::Nitroaromatic compounds are used extensively in many industrial processes and have been released into the environment where they are considered environmental pollutants. Nitroaromatic compounds, in general, are resistant to oxidative attack due to the electron-withdrawing nature of the nitro groups and the stability o...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.03.052

    authors: Friemann R,Ivkovic-Jensen MM,Lessner DJ,Yu CL,Gibson DT,Parales RE,Eklund H,Ramaswamy S

    更新日期:2005-05-20 00:00:00

  • Exploration of alternate catalytic mechanisms and optimization strategies for retroaldolase design.

    abstract::Designed retroaldolases have utilized a nucleophilic lysine to promote carbon-carbon bond cleavage of β-hydroxy-ketones via a covalent Schiff base intermediate. Previous computational designs have incorporated a water molecule to facilitate formation and breakdown of the carbinolamine intermediate to give the Schiff b...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2013.10.012

    authors: Bjelic S,Kipnis Y,Wang L,Pianowski Z,Vorobiev S,Su M,Seetharaman J,Xiao R,Kornhaber G,Hunt JF,Tong L,Hilvert D,Baker D

    更新日期:2014-01-09 00:00:00

  • Quaternary structure changes in aspartate transcarbamylase studied by X-ray solution scattering. Signal transmission following effector binding.

    abstract::The result of binding the effectors ATP and CTP to aspartate transcarbamylase was studied by X-ray solution scattering. Binding of substrate analogues produces a substantial change in the solution scattering curve, allowing us to monitor the proportion of the different quaternary structure states present in solution. ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(85)90190-1

    authors: Hervé G,Moody MF,Tauc P,Vachette P,Jones PT

    更新日期:1985-09-05 00:00:00

  • Sub-atomic resolution crystal structure of cholesterol oxidase: what atomic resolution crystallography reveals about enzyme mechanism and the role of the FAD cofactor in redox activity.

    abstract::The crystal structure of cholesterol oxidase, a 56kDa flavoenzyme was anisotropically refined to 0.95A resolution. The final crystallographic R-factor and R(free) value is 11.0% and 13.2%, respectively. The quality of the electron density maps has enabled modeling of alternate conformations for 83 residues in the enzy...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00054-8

    authors: Lario PI,Sampson N,Vrielink A

    更新日期:2003-03-07 00:00:00

  • DNA sequences, gene regulation and modular protein evolution in the Drosophila 68C glue gene cluster.

    abstract::The 68C locus of the Drosophila melanogaster polytene chromosomes contains the structural genes for three glue polypeptides (sgs-3, sgs-7 and sgs-8) synthesized in the larval salivary glands during the third larval instar. When the messenger RNAs for the glue polypeptides are being synthesized, the locus is puffed; th...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(83)80074-6

    authors: Garfinkel MD,Pruitt RE,Meyerowitz EM

    更新日期:1983-08-25 00:00:00

  • Effects of cobalt hexammine on folding and self-cleavage of the Neurospora VS ribozyme.

    abstract::We have investigated the effects of Co(NH3)6(3+), an analog of hexahydrated Mg2+, on folding and catalysis of the Neurospora VS ribozyme. Most of the metal ion-induced changes detected by chemical modification structure probing in either metal ion are similar, but occur at approximately 33-fold lower concentrations of...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4625

    authors: Maguire JL,Collins RA

    更新日期:2001-05-25 00:00:00

  • Transthyretin Interferes with Aβ Amyloid Formation by Redirecting Oligomeric Nuclei into Non-Amyloid Aggregates.

    abstract::The pathological Aβ aggregates associated with Alzheimer's disease follow a nucleation-dependent path of formation. A nucleus represents an oligomeric assembly of Aβ peptides that acts as a template for subsequent incorporation of monomers to form a fibrillar structure. Nuclei can form de novo or via surface-catalyzed...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2018.06.005

    authors: Nilsson L,Pamrén A,Islam T,Brännström K,Golchin SA,Pettersson N,Iakovleva I,Sandblad L,Gharibyan AL,Olofsson A

    更新日期:2018-08-17 00:00:00

  • Functional role of the "ionic lock"--an interhelical hydrogen-bond network in family A heptahelical receptors.

    abstract::Activation of family A G-protein-coupled receptors involves a rearrangement of a conserved interhelical cytoplasmic hydrogen bond network between the E(D)RY motif on transmembrane helix 3 (H3) and residues on H6, which is commonly termed the cytoplasmic "ionic lock." Glu134(3.49) of the E(D)RY motif also forms an intr...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.05.022

    authors: Vogel R,Mahalingam M,Lüdeke S,Huber T,Siebert F,Sakmar TP

    更新日期:2008-07-18 00:00:00

  • Probing a tRNA core that contributes to aminoacylation.

    abstract::The contribution of the tRNA "core" to aminoacylation is beginning to be recognized. One example is the core region of Escherichia coli tRNA(Cys), which has been shown by biochemical studies to be important for aminoacylation. This core has several layers of unusual base-pairs, which are revealed by the recent crystal...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3353

    authors: Hamann CS,Hou YM

    更新日期:2000-01-28 00:00:00

  • Crystallization of a DNA duplex 15-mer containing unpaired bases: d(CGCGAAATTTACGCG).

    abstract::Crystals of an almost self-complementary DNA 15-mer d(CGCGAAATTTACGCG) have been grown by the vapor diffusion technique at 4 degrees C. The space group is I222 with a = 37.3 A, b = 54.6 A and c = 104.8 A. Solution studies showed that the 15-mer forms a duplex with the extra adenine residue unpaired: (sequence; see tex...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(87)90503-1

    authors: Miller M,Wlodawer A,Appella E,Sussman JL

    更新日期:1987-06-20 00:00:00

  • Structural studies of cytochrome reductase. Improved membrane crystals of the enzyme complex and crystallization of a subcomplex.

    abstract::Membrane crystals of mitochondrial ubiquinol: cytochrome c reductase of improved size and long-range order and of the cytochrome bc1 subcomplex have been obtained by a dialysis method. The enzyme--Triton X-100 complex was mixed with Triton phospholipid micelles and the Triton slowly removed by dialysis for 48 hours at...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(83)80264-2

    authors: Hovmöller S,Slaughter M,Berriman J,Karlsson B,Weiss H,Leonard K

    更新日期:1983-04-05 00:00:00

  • Multiple sequence threading: an analysis of alignment quality and stability.

    abstract::Methods that compare a protein sequence directly to a structure can be divided into those that construct a molecular model (threading methods) and those that perform a sequence alignment with the structure encoded as a sequence of structural states (one-dimensional/three-dimensional (1D/3D) matching). The former take ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1008

    authors: Taylor WR

    更新日期:1997-06-27 00:00:00

  • Autonomous and reversible folding of a soluble amino-terminally truncated segment of the mouse prion protein.

    abstract::Prion diseases are assumed to be caused by the infectious isoform, PrPsc, of a single cellular surface protein, PrPc. PrPsc is an insoluble form of PrPc and is believed to possess a different three-dimensional fold. It may propagate by causing PrPc to adopt its own infectious conformation by an unknown mechanism. Stud...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0487

    authors: Hornemann S,Glockshuber R

    更新日期:1996-09-06 00:00:00

  • Crystal structure of metastasis-associated protein S100A4 in the active calcium-bound form.

    abstract::S100A4 (metastasin) is a member of the S100 family of calcium-binding proteins that is directly involved in tumorigenesis. Until recently, the only structural information available was the solution NMR structure of the inactive calcium-free form of the protein. Here we report the crystal structure of human S100A4 in t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.04.076

    authors: Pathuri P,Vogeley L,Luecke H

    更新日期:2008-10-31 00:00:00

  • Whither Ribosome Structure and Dynamics Research? (A Perspective).

    abstract::As high-resolution cryogenic electron microscopy (cryo-EM) structures of ribosomes proliferate, at resolutions that allow atomic interactions to be visualized, this article attempts to give a perspective on the way research on ribosome structure and dynamics may be headed, and particularly the new opportunities we hav...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2016.04.034

    authors: Frank J

    更新日期:2016-09-11 00:00:00

  • Binding mode prediction for a flexible ligand in a flexible pocket using multi-conformation simulated annealing pseudo crystallographic refinement.

    abstract::We describe multi-conformation simulated annealing-pseudo-crystallographic refinement (MCSA-PCR), a technique developed for predicting the binding mode of a flexible ligand in a flexible binding pocket. To circumvent the local-minimum problem efficiently, this method performs multiple independent cycles of simulated a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.5147

    authors: Ota N,Agard DA

    更新日期:2001-11-30 00:00:00

  • Structure-function analysis of a bacterial deoxyadenosine kinase reveals the basis for substrate specificity.

    abstract::Deoxyribonucleoside kinases (dNKs) catalyze the transfer of a phosphoryl group from ATP to a deoxyribonucleoside (dN), a key step in DNA precursor synthesis. Recently structural information concerning dNKs has been obtained, but no structure of a bacterial dCK/dGK enzyme is known. Here we report the structure of such ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.12.010

    authors: Welin M,Wang L,Eriksson S,Eklund H

    更新日期:2007-03-09 00:00:00

  • Crystal structure of the Mycobacterium tuberculosis dUTPase: insights into the catalytic mechanism.

    abstract::The structure of Mycobacterium tuberculosis dUTP nucleotidohydrolase (dUTPase) has been determined at 1.3 Angstrom resolution in complex with magnesium ion and the non-hydrolyzable substrate analog, alpha,beta-imido dUTP. dUTPase is an enzyme essential for depleting potentially toxic concentrations of dUTP in the cell...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.06.028

    authors: Chan S,Segelke B,Lekin T,Krupka H,Cho US,Kim MY,So M,Kim CY,Naranjo CM,Rogers YC,Park MS,Waldo GS,Pashkov I,Cascio D,Perry JL,Sawaya MR

    更新日期:2004-08-06 00:00:00

  • RNA Splicing: A New Paradigm in Host-Pathogen Interactions.

    abstract::RNA splicing brings diversity to the eukaryotic proteome. Different spliced variants of a gene may differ in their structure, function, localization, and stability influencing protein stoichiometry and physiological outcomes. Alternate spliced variants of different genes are known to associate with various chronic pat...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2019.03.001

    authors: Chauhan K,Kalam H,Dutt R,Kumar D

    更新日期:2019-04-05 00:00:00

  • Domain closure mechanism in transferrins: new viewpoints about the hinge structure and motion as deduced from high resolution crystal structures of ovotransferrin N-lobe.

    abstract::The crystal structure of holo hen ovotransferrin N-lobe refined at 1.65 A resolution has been obtained. The final model gave an R-factor of 0.173 in the resolution range between 10.0 and 1.65 A. The comparison of the structure with previous high-resolution apo and Fe(3+)-loaded, domain-opened intermediate structures p...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4719

    authors: Mizutani K,Mikami B,Hirose M

    更新日期:2001-06-15 00:00:00

  • p53 blocks RuvAB promoted branch migration and modulates resolution of Holliday junctions by RuvC.

    abstract::The Holliday junction is the central intermediate in homologous recombination. Branch migration of this four-stranded DNA structure is a key step in genetic recombination that affects the extent of genetic information exchanged between two parental DNA molecules. Here, we have constructed synthetic Holliday junctions ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.5408

    authors: Prabhu VP,Simons AM,Iwasaki H,Gai D,Simmons DT,Chen J

    更新日期:2002-03-08 00:00:00

  • Crystal structure of three consecutive laminin-type epidermal growth factor-like (LE) modules of laminin gamma1 chain harboring the nidogen binding site.

    abstract::The structure of three consecutive laminin-type EGF-like (LE) modules of mouse laminin gammma1 chain, gamma1III3-5 (positions 738 to 899), has been determined by multiple isomorphous replacement in a crystal of space group p6(4)22 (a=b=74.57 angstroms, c = 185.11 angstroms and gamma = 120 degrees). The crystal structu...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0191

    authors: Stetefeld J,Mayer U,Timpl R,Huber R

    更新日期:1996-04-05 00:00:00

  • Lambda phage protein Nu 1 contains the conserved DNA binding fold of repressors.

    abstract::Analysis of 64 lambda phage proteins revealed the presence of four strong variants of the conserved DNA binding fold of repressors. Three of them have been known from previous studies but the Nu 1 gene product is a new member of the family of proteins that may bind strongly to DNA in the repressor-like fashion. It is ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(86)90430-4

    authors: Kypr J,Mrázek J

    更新日期:1986-09-05 00:00:00

  • Attachment of tail fibers in bacteriophage T4 assembly. Identification of the baseplate protein to which tail fibers attach.

    abstract::A phage-neutralizing rabbit antiserum collected after immunization with tail-fiberless bacteriophage T4 particles was adsorbed with complete T4 phage. The resulting adsorbed serum inhibited tail fiber attachment in vitro. To identify the antigens against which this inhibitory activity was directed, blocking experiment...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(83)80059-x

    authors: Urig MA,Brown SM,Tedesco P,Wood WB

    更新日期:1983-09-15 00:00:00