A protein structural motif that bends DNA

White, Stephen W.; Appelt, K.; Wilson, K.S.; Tanaka, Isao

doi:10.1002/prot.340050405

Cited by 155 publications

(114 citation statements)

References 47 publications

(10 reference statements)

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“…The HU proteins from Bacillus stearothermophilus and B. subtilis are homodimers of interlaced polypeptides containing 90 and 92 residues, respectively. The primary sequences of the two proteins are highly identical and the X-ray models show a high degree of structural conservation (White et al, 1989). The structural similarity permits the formation of heterodimers, which allows monitoring the slow interconversion between the two homodimeric species (Fig.…”

Section: Dynamics Of Assemblymentioning

confidence: 99%

Investigation of intact protein complexes by mass spectrometry

Heck

Heuvel

2004

Mass Spectrometry Reviews

553

554

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I. Introduction 00 II. Electrospray Ionization of Biomacromolecules 00 III. Mass Analyzers for Biomacromolecular Mass Spectrometry 00 A. Collisional Cooling and/or Focusing 00 B. Alternative Mass Analyzers 00 IV. Solution‐Phase Properties of Proteins Complexes 00 A. Protein–Protein Interactions 00 B. Cooperativity and Cofactors 00 C. Dynamics of Assembly 00 V. Gas‐Phase Properties of Protein Complexes 00 A. Tandem Mass Spectrometry 00 B. Charge Separation in Protein Dissociation 00 VI. Future Outlook 00 Acknowledgments 00 References 00 Mass spectrometry has grown in recent years to a well‐accepted and increasingly important complementary technique in structural biology. Especially electrospray ionization mass spectrometry is well suited for the detection of non‐covalent protein complexes and their interactions with DNA, RNA, ligands, and cofactors. Over the last decade, significant advances have been made in the ionization and mass analysis techniques, which makes the investigation of even larger and more heterogeneous intact assemblies feasible. These technological developments have paved the way to study intact non‐covalent protein–protein interactions, assembly and disassembly in real time, subunit exchange, cooperativity effects, and effects of cofactors, allowing us a better understanding of proteins in cellular processes. In this review, we describe some of the latest developments and several highlights. © 2004 Wiley Periodicals, Inc., Mass Spec Rev

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Section: Dynamics Of Assemblymentioning

confidence: 99%

Investigation of intact protein complexes by mass spectrometry

Heck

Heuvel

2004

Mass Spectrometry Reviews

553

554

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“…However, there are subtle differences in the mode of DNA recognition and interaction displayed by these repressors, the details of which will be discussed later. On the other hand, the three helix-turn-helix repressors listed in Table 1 Beese & Steitz (1991 Beese & Steitz (1991) Freemont et al (1988) Steitz (1990) White et al (1989) Sanderson et al (1990 Burlingame et al (1985) Richmond et al (1984 is involved in the regulation of tryptophan biosynthesis by binding as a dimer to three different operator sites in the presence of its corepressor L-tryptophan (Klig et al, 1988). Binding in the absence of L-tryptophan is weak and non-specific.…”

Section: Helix-turn-helix Proteinsmentioning

confidence: 99%

“…Protein HU (90 amino acids) binds nonspecifically to DNA as a dimer and is involved in the formation of nucleoprotein structures (the nucleoid) analogous to the nucleosomes found in eukaryotes. The crystal structure has been determined and shows HU to be composed of two distinct structures, namely a N-terminal helical region containing two ahelices and a C-terminal sheet region consisting mainly of a three-stranded antiparallel fl-sheet (Tanaka et al, 1984;White et al, 1989). The HU dimer is intertwined and forms a cleft bordered by two arm-like structures (one from each subunit) consisting of two antiparallel fl-strands (Fig.…”

Section: Beta Proteinsmentioning

confidence: 99%

“…have been proposed to interact with the DNA by inserting into the minor groove, although a major groove model is also possible (White et al, 1989). Although no co-crystal structure is available, HU has been shown to bend DNA, which, if the proposed model were correct, would result in a widening of the minor groove to accommodate the fl-ribbon structure.…”

Section: Beta Proteinsmentioning

confidence: 99%

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Structural aspects of protein-DNA recognition

Freemont

Lane

Sanderson

1991

Biochemical Journal

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“…1984;White et al, 1989). The solution structure of recombinant HU from B. stearothermophilus expressed in E. coli (Padas et al, 1992) was also determined using NMR (Vis et al, 1995).…”

Section: Introductionmentioning

confidence: 99%

Cloning, overproduction, purification and crystallization of the DNA binding protein HU from the hyperthermophilic eubacterium Thermotoga maritima

Christodoulou

Vorgias

1998

Acta Cryst D

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The humar gene encoding for the histonc-like DNA-binding protein HU from the hyperthermophilic eubacterium Thermotoga maritima was efficiently ovcrexpressed in Escherichia coli under the T7 promoter. The HU protein was purified using SPScpharosc ion-exchange and heparin-affinity chromatography and was successfully crystallized in ammonium sulfate. The crystals wcrc grown in the tctragonal form in space group P43 or P41 and have unit-cell dimensions a = b = 46.12, c= 77.56 A, a =/3 = y = 90. The crystals diffract X-rays to 1.6 A, resolution using synchrotron radiation and are suitable for determination of the HU structure at high resolution. AbbreviationsAmp, ampicillin; EDTA, ethylenediaminetetraacetic acid: E. coli, Escherichia coli; I PTG, isopropyl-/3-D-thiogalactopyranoside: LB, Luria Bertani (medium); NMR, nuclear magnetic resonance; OD¢,¢x~, absorption at 600nm: PAGE, polyacrylamide gel electrophoresis; PMSF, phenylmethylsulfonyl fluoride; SDS, sodium dodecyl sulfate; aa, amino acids. IntroductionThe nucleoid of the prokaryotic cell contains a number of abundant, low-molecular-weight and positively charged proteins classified as histone-like DNA-binding proteins. Among those proteins, HU has been identified as the major protein component of the nucleoid and has attracted considerable attention during the last two decades. In E. coli, HU (HU~e~) is the most abundant DNA-binding protein with "-~30 000 dimers per cell. It is a hetcrodimer consisting of homologous ot and/3 subunits each of 90 aa, which are encoded by the hupB and hupA genes, respectively, and are 70% identical in their sequence. HU appears to be a homodimer in all other bacterial species in which it has bccn studied (for review sec Drlica & Rouviere-Yaniv, 1987: Pettijohn, 1988). Up to now, several functions of HU have been found including: (i) HU binds with little sequence specificity to dsDNA, ssDNA and RNA (Rouvi6re-Yaniv & Gros, 1975): (ii) DNA-HU complexes condense into nuclcosome-like particles and can introduce negative supercoiling into a relaxed circular plasmid DNA in the presence of topoisomerase 1 (Rouvi~re-Yaniv et aL, 1979; Broyles & Pettijohn, 1986); (iii) the binding of the lac rcpressor as well as the binding of the cAMP receptor protein to the lac promoter is facilitated by HU (Flashner & Gralla, 1988): (iv) HU is required for transposition by bacteriophage Mu (Craigie et aL, 1985) and (v) HU in vitro plays a regulatory role in ~. DNA replication (Mensa-Wilmot et aL, 1989)..~ 1998 International Union of C.rystallography Printed in Great Britain -all rights reservedThe crystal structure of HU from Bacillus stearothermophilus has been solved (Tanaka et al.. 1984;White et al., 1989). The solution structure of recombinant HU from B. stearothermophilus expressed in E. coli (Padas et al., 1992) was also determined using NMR (Vis et al., 1995).The study of the structural properties responsible for the thermostability of HUs from mesophilic and thermophilic organisms attracted our attention in the past (Wilson et al., 1990)...

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A protein structural motif that bends DNA

Cited by 155 publications

References 47 publications

Investigation of intact protein complexes by mass spectrometry

Investigation of intact protein complexes by mass spectrometry

Structural aspects of protein-DNA recognition

Cloning, overproduction, purification and crystallization of the DNA binding protein HU from the hyperthermophilic eubacterium Thermotoga maritima

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