NMR solution structure of the C-terminal fragment 255-316 of thermolysin: a dimer formed by subunits having the native structure.

Abstract:

:The solution structure of the C-terminal fragment 255-316 of thermolysin has been determined by two-dimensional proton NMR methods. For this disulfide-free fragment there was a previous proposal according to which it would fold into a stable helical structure forming a dimer at concentrations above 0.06 mM. A complete assignment of the proton NMR resonances of the backbone and amino acid side chains of the fragment was first performed using standard sequential assignment methods. On the basis of 729 distance constraints derived from unambiguously assigned nuclear Overhauser effect (NOE) proton connectivities, the three-dimensional structure of a monomeric unit was then determined by using distance geometry and restrained molecular dynamic methods. The globular structure of fragment 255-316 of thermolysin in solution, composed of three helices, is largely coincident with that of the corresponding region in the crystallographic structure of intact thermolysin [Holmes, M. A., & Matthews, B. W. (1982) J. Mol. Biol. 160, 623-639]. This fact allowed identification as intersubunit of up to 52 NOE cross correlations, which were used to dock the two subunits into a symmetric dimer structure. The obtained dimeric structure served as the starting structure in a final restrained molecular dynamic calculation subjected to a total of 1562 distance constraints. In the resulting dimeric structure, the interface between the two subunits, of a marked hydrophobic character, coincides topologically with the one between the 255-316 fragment and the rest of the protein in the intact enzyme. The present work decisively shows that the thermolysin fragment 255-316 can attain a stable and nativelike structure independently of the rest of the polypeptide chain. Considering that the thermolysin molecule is constituted of two structural domains of equal size (residues 1-157 and 158-316), the results of this study show that autonomously folding units can be substantially smaller than entire domains.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Rico M,Jiménez MA,González C,De Filippis V,Fontana A

doi

10.1021/bi00253a023

subject

Has Abstract

pub_date

1994-12-13 00:00:00

pages

14834-47

issue

49

eissn

0006-2960

issn

1520-4995

journal_volume

33

pub_type

杂志文章
  • Detailed structural characterization of unbound protein phosphatase 1 inhibitors.

    abstract::Protein phosphatase 1 (PP1) is an essential and ubiquitous serine/threonine protein phosphatase that is regulated by more than 100 known inhibitor and targeting proteins. It is currently unclear how protein inhibitors distinctly and specifically regulate PP1 to enable rapid responses to cellular alterations. We demons...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi801308y

    authors: Dancheck B,Nairn AC,Peti W

    更新日期:2008-11-25 00:00:00

  • Phosphoinositide 3-kinase in rat liver nuclei.

    abstract::Biochemical and immunochemical data from the present investigation reveal the existence of a p85/p110 phosphoinositide 3-kinase (PI 3-kinase) in rat liver nuclei. 32P-Labeling of membrane phosphoinositides by incubating intact nuclei with [gamma-32P]ATP results in the formation of [32P]phosphatidyl-inositol 3,4, 5-tri...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi972551g

    authors: Lu PJ,Hsu AL,Wang DS,Yan HY,Yin HL,Chen CS

    更新日期:1998-04-21 00:00:00

  • Observation of multiple myosin subfragment 1-ADP-fluoroberyllate complexes by 19F NMR spectroscopy.

    abstract::Fluoroaluminate and fluoroberyllate are potent inhibitors of the ATPase activity of myosin. Inhibition requires the presence of ADP, and much evidence has accumulated to suggest that the tetrahedral fluoroaluminate and fluoroberyllate ions act as phosphate analogues, binding with high affinity at the active site in th...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00090a022

    authors: Henry GD,Maruta S,Ikebe M,Sykes BD

    更新日期:1993-10-05 00:00:00

  • NMR studies of DNA support the role of pre-existing minor groove variations in nucleosome indirect readout.

    abstract::We investigated how the intrinsic sequence-dependent properties probed via the phosphate linkages (BI ↔ BII equilibrium) influence the preferred shape of free DNA, and how this affects the nucleosome formation. First, this exploits NMR solution studies of four B-DNA dodecamers that together cover 39 base pairs of the ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi500504y

    authors: Xu X,Ben Imeddourene A,Zargarian L,Foloppe N,Mauffret O,Hartmann B

    更新日期:2014-09-09 00:00:00

  • Light-induced charge separation in Rhodopseudomonas viridis reaction centers monitored by Fourier-transform infrared difference spectroscopy: the quinone vibrations.

    abstract::Static FTIR light-induced difference spectra have been recorded for reaction centers from Rhodopseudomonas viridis in the following charge-separated states: P+QA(-)-PQA, P+QB(-)-PQB, I(-)-I, I-QA(-)-IQA, and I-QA(2-)-IQA. A comparison of the I(-)-I difference spectra with the I-QA(-)-IQA difference spectra reveals new...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00120a006

    authors: Buchanan S,Michel H,Gerwert K

    更新日期:1992-02-11 00:00:00

  • Binding of divalent magnesium by Escherichia coli phosphoribosyl diphosphate synthetase.

    abstract::The mechanism of binding of the substrates Mg x ATP and ribose 5-phosphate as well as Mg2+ to the enzyme 5-phospho-D-ribosyl (alpha-1-diphosphate synthetase from Escherichia coli has been analyzed. By use of the competive inhibitors of ATP and ribose 5-phosphate binding, alpha,beta-methylene ATP and (+)-1-alpha,2-alph...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi962610a

    authors: Willemoës M,Hove-Jensen B

    更新日期:1997-04-22 00:00:00

  • DNA-binding and oligomerization studies of the manganese(II) metalloregulatory protein MntR from Bacillus subtilis.

    abstract::The metalloregulatory protein MntR from Bacillus subtilis acts as a transcriptional regulator of manganese homeostasis. MntR is a member of a subfamily of DtxR-related proteins that perform analogous regulatory functions in a variety of pathogenic organisms. Metal ions activate MntR to bind DNA and repress the transcr...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0350248

    authors: Lieser SA,Davis TC,Helmann JD,Cohen SM

    更新日期:2003-11-04 00:00:00

  • Isolation and characterization of neutralizing single-chain antibodies against Xenopus mitogen-activated protein kinase kinase from phage display libraries.

    abstract::MAP kinase kinase (MAPKK) is a dual specificity protein kinase that phosphorylates and activates MAP kinase in vivo. In this study, four mouse monoclonal single-chain Fv (scFv) antibodies (Y1-6, Y1-7, Y3-6, and Y3-11) that can specifically bind to Xenopus MAPKK were isolated from combinatorial scFv-displaying phage li...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi960956f

    authors: Kosako H,Akamatsu Y,Tsurushita N,Lee KK,Gotoh Y,Nishida E

    更新日期:1996-10-08 00:00:00

  • Phenotypic regulation of the sphingosine 1-phosphate receptor miles apart by G protein-coupled receptor kinase 2.

    abstract::The evolutionarily conserved DRY motif at the end of the third helix of rhodopsin-like, class-A G protein-coupled receptors (GPCRs) is a major regulator of receptor stability, signaling activity, and β-arrestin-mediated internalization. Substitution of the DRY arginine with histidine in the human vasopressin receptor ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi501061h

    authors: Burczyk M,Burkhalter MD,Blätte T,Matysik S,Caron MG,Barak LS,Philipp M

    更新日期:2015-01-27 00:00:00

  • Effects of putative catalytic base mutation E211Q on ABCG2-mediated methotrexate transport.

    abstract::ABCG2 is a half-ATP binding cassette (ABC) drug transporter that consists of a nucleotide binding domain (NBD) followed by a transmembrane domain. This half-ABC transporter is thought to form a homodimer in the plasma membrane where it transports anticancer drugs across the biological membranes in an ATP-dependent man...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi900675v

    authors: Hou YX,Li CZ,Palaniyandi K,Magtibay PM,Homolya L,Sarkadi B,Chang XB

    更新日期:2009-09-29 00:00:00

  • Calcium regulation of calmodulin binding to and dissociation from the myo1c regulatory domain.

    abstract::Myo1c is an unconventional myosin involved in cell signaling and membrane dynamics. Calcium binding to the regulatory-domain-associated calmodulin affects myo1c motor properties, but the kinetic details of this regulation are not fully understood. We performed actin gliding assays, ATPase measurements, fluorescence sp...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi700894h

    authors: Manceva S,Lin T,Pham H,Lewis JH,Goldman YE,Ostap EM

    更新日期:2007-10-23 00:00:00

  • Active site of bee venom phospholipase A2: the role of histidine-34, aspartate-64 and tyrosine-87.

    abstract::In bee venom phospholipase A2, histidine-34 probably functions as a Brønsted base to deprotonate the attacking water. Aspartate-64 and tyrosine-87 form a hydrogen bonding network with histidine-34. We have prepared mutants at these positions and studied their kinetic properties. The mutant in which histidine-34 is cha...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9528412

    authors: Annand RR,Kontoyianni M,Penzotti JE,Dudler T,Lybrand TP,Gelb MH

    更新日期:1996-04-09 00:00:00

  • An aggregation-prone intermediate species is present in the unfolding pathway of the monomeric portal protein of bacteriophage P22: implications for portal assembly.

    abstract::The head of the P22 bacteriophage is interrupted by a unique dodecameric portal vertex that serves as a conduit for the entrance and exit of the DNA. Here, the in vitro unfolding/refolding processes of the portal protein of P22 were investigated at different temperatures (1, 25, and 37 degrees C) through the use of ur...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi700006d

    authors: Braga CA,Carvalho D,Lara FA,Cortines JR,Moore SD,Prevelige PE Jr,Foguel D

    更新日期:2007-06-26 00:00:00

  • Structure-function relationships in sorcin, a member of the penta EF-hand family. Interaction of sorcin fragments with the ryanodine receptor and an Escherichia coli model system.

    abstract::Sorcin, a 21.6 kDa cytosolic EF-hand protein which undergoes a Ca(2+)-induced translocation from cytoplasm to membranes, has been assigned to the newly defined penta EF-hand family. A molecular model of the C-terminal Ca(2+)-binding domain has been generated using as a template the X-ray coordinates of the correspondi...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi991648v

    authors: Zamparelli C,Ilari A,Verzili D,Giangiacomo L,Colotti G,Pascarella S,Chiancone E

    更新日期:2000-02-01 00:00:00

  • Tying up the Ends: Plasticity in the Recognition of Single-Stranded DNA at Telomeres.

    abstract::Telomeres terminate nearly exclusively in single-stranded DNA (ssDNA) overhangs comprised of the G-rich 3' end. This overhang varies widely in length from species to species, ranging from just a few bases to several hundred nucleotides. These overhangs are not merely a remnant of DNA replication but rather are the res...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.6b00496

    authors: Lloyd NR,Dickey TH,Hom RA,Wuttke DS

    更新日期:2016-09-27 00:00:00

  • Structure and Dynamics of RNA Repeat Expansions That Cause Huntington's Disease and Myotonic Dystrophy Type 1.

    abstract::RNA repeat expansions cause a host of incurable, genetically defined diseases. The most common class of RNA repeats consists of trinucleotide repeats. These long, repeating transcripts fold into hairpins containing 1 × 1 internal loops that can mediate disease via a variety of mechanism(s) in which RNA is the central ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.7b00252

    authors: Chen JL,VanEtten DM,Fountain MA,Yildirim I,Disney MD

    更新日期:2017-07-11 00:00:00

  • Activation-induced subcellular redistribution of G alpha(s) is dependent upon its unique N-terminus.

    abstract::The heterotrimeric G protein subunit, alpha(s), can move reversibly from plasma membranes to cytoplasm in response to activation by GPCRs or activating mutations. We examined the importance of the unique N-terminus of alpha(s) in this translocation in cultured cells. alpha(s) contains a single site for palmitoylation ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi025533u

    authors: Thiyagarajan MM,Bigras E,Van Tol HH,Hébert TE,Evanko DS,Wedegaertner PB

    更新日期:2002-07-30 00:00:00

  • Skp Trimer Formation Is Insensitive to Salts in the Physiological Range.

    abstract::Biogenesis of the Gram-negative outer membrane involves the chaperone seventeen kilodalton protein (Skp). A Skp trimer is currently thought to bind its unfolded outer membrane protein (uOMP) substrates. Using sedimentation equilibrium, we discovered that Skp is not an obligate trimer under physiological conditions and...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.5b00806

    authors: Sandlin CW,Zaccai NR,Fleming KG

    更新日期:2015-12-08 00:00:00

  • Two-dimensional 1H NMR studies of cytochrome c: hydrogen exchange in the N-terminal helix.

    abstract::The hydrogen exchange behavior of the N-terminal helical segment in horse heart cytochrome c was studied in both the reduced and the oxidized forms by use of two-dimensional nuclear magnetic resonance methods. The amide protons of the first six residues are not H bonded and exchange rapidly with solvent protons. The m...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00353a025

    authors: Wand AJ,Roder H,Englander SW

    更新日期:1986-03-11 00:00:00

  • Influence of sequence-dependent cytosine protonation and methylation on DNA triplex stability.

    abstract::To investigate cytosine protonation and its influence on the sequence-dependent thermal stability of DNA triplexes in detail, we have employed homo- and heteronuclear NMR experiments on specifically (15)N-labeled oligodeoxynucleotides that were designed to fold into intramolecular triple helices of the pyrimidine moti...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi992630n

    authors: Leitner D,Schröder W,Weisz K

    更新日期:2000-05-16 00:00:00

  • Mutational analysis of the roles in catalysis and substrate recognition of arginines 54 and 305, aspartic acid 309, and tryptophan 317 located at subsites 1 and 2 in glucoamylase from Aspergillus niger.

    abstract::The mutants Arg54-->Leu, Arg54-->Lys, Arg305-->Lys, Asp309-->Glu, and Trp317-->Phe, located at subsites 1 and 2 in glucoamylase from Aspergillus niger, provide insight into the importance of specific hydrogen bonds and hydrophobic interactions in substrate recognition, catalytic mechanism, and stability. As suggested ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00032a009

    authors: Frandsen TP,Christensen T,Stoffer B,Lehmbeck J,Dupont C,Honzatko RB,Svensson B

    更新日期:1995-08-15 00:00:00

  • Structural basis of the anionic interface preference and kcat* activation of pancreatic phospholipase A2.

    abstract::Pancreatic phospholipase A(2) (PLA2) shows a strong preference for the binding to the anionic interface and a consequent allosteric activation. In this paper, we show that virtually all the preference is mediated through 3 (Lys-53, -56, and -120) of the 12 cationic residues of bovine pancreatic PLA2. The lysine-to-met...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi000740k

    authors: Yu BZ,Poi MJ,Ramagopal UA,Jain R,Ramakumar S,Berg OG,Tsai MD,Sekar K,Jain MK

    更新日期:2000-10-10 00:00:00

  • Revealing the allosterome: systematic identification of metabolite-protein interactions.

    abstract::Small molecule allostery modifies protein function but is not easily discovered. We introduce mass spectrometry integrated with equilibrium dialysis for the discovery of allostery systematically (MIDAS), a method for identifying physiologically relevant, low-affinity metabolite-protein interactions using unmodified pr...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi201313s

    authors: Orsak T,Smith TL,Eckert D,Lindsley JE,Borges CR,Rutter J

    更新日期:2012-01-10 00:00:00

  • Solution structure of the DNA methyl phosphotriester repair domain of Escherichia coli Ada.

    abstract::The Escherichia coli Ada protein repairs methyl phosphotriesters in DNA by direct, irreversible methyl transfer to one of its own cysteine residues. The methyl-transfer process appears to be autocatalyzed by coordination of the acceptor residue, Cys-69, to a tightly bound zinc ion. Upon methyl transfer, Ada acquires t...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00214a003

    authors: Myers LC,Verdine GL,Wagner G

    更新日期:1993-12-28 00:00:00

  • The binding mechanism of pyoverdin with the outer membrane receptor FpvA in Pseudomonas aeruginosa is dependent on its iron-loaded status.

    abstract::In iron-deficient conditions, Pseudomonas aeruginosa secretes a major fluorescent siderophore named pyoverdin (Pvd), which after chelating iron(III) is transported back into the cell via its outer membrane receptor FpvA. FpvA is a TonB-dependent transport protein and has the ability to bind Pvd in its apo- or iron-loa...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi049768c

    authors: Clément E,Mesini PJ,Pattus F,Schalk IJ

    更新日期:2004-06-22 00:00:00

  • Probes of hydrogen tunneling with horse liver alcohol dehydrogenase at subzero temperatures.

    abstract::The temperature dependence of steady-state kinetics has been studied with horse liver alcohol dehydrogenase (HLADH) using protonated and deuterated benzyl alcohol as substrates in methanol/water mixtures between +3 and -50 degrees C. Additionally, the competitive isotope effects, k(H)/k(T) and k(D)/k(T), were measured...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi002075l

    authors: Tsai S,Klinman JP

    更新日期:2001-02-20 00:00:00

  • Kinetics of polymerization of a fluoresceinated derivative of complement protein C9 by the membrane-bound complex of complement proteins C5b-8.

    abstract::The fluorescence self-quenching by energy transfer of FITC-C9, a fluoresceinated derivative of human complement protein C9 [Sims, P.J. (1984) Biochemistry (preceding paper in this issue)], has been used to monitor the kinetics of C9 polymerization induced by the membrane-associated complex of complement proteins C5b-8...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00309a021

    authors: Sims PJ,Wiedmer T

    更新日期:1984-07-03 00:00:00

  • Contribution of structural peculiarities of onconase to its high stability and folding kinetics.

    abstract::Onconase (ONC) from Rana pipiens is the smallest member of the ribonuclease A (RNase A) superfamily. Despite a tertiary structure similar to RNase A, ONC is distinguished by an extremely high thermodynamic stability. In the present paper we have probed the significance of three structural regions, which exhibit struct...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0525223

    authors: Arnold U,Schulenburg C,Schmidt D,Ulbrich-Hofmann R

    更新日期:2006-03-21 00:00:00

  • Distinct reactions catalyzed by bacterial and yeast trans-aconitate methyltransferases.

    abstract::The trans-aconitate methyltransferase from the bacterium Escherichia coli catalyzes the monomethyl esterification of trans-aconitate and related compounds. Using two-dimensional (1)H/(13)C nuclear magnetic resonance spectroscopy, we show that the methylation is specific to one of the three carboxyl groups and further ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0022902

    authors: Cai H,Strouse J,Dumlao D,Jung ME,Clarke S

    更新日期:2001-02-20 00:00:00

  • Comparison of the effects of tropomyosin and troponin-tropomyosin on the binding of myosin subfragment 1 to actin.

    abstract::The effect of tropomyosin alone on the binding of myosin subfragment 1 (S-1) to actin was compared to that of troponin-tropomyosin, with and without Ca2+. Over a range of ionic strength and with different ligands (adenyl-5'-yl imidodiphosphate, pyrophosphate, and adenosine 5'-diphosphate), tropomyosin confers slight c...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00280a027

    authors: Williams DL Jr,Greene LE

    更新日期:1983-05-24 00:00:00