Journal of Molecular Biology

article

Concurrent Interactions Contribute to the Raised pK _a of His18 in Barnase

Martine Prévost

Journal of Molecular Biology > 1996 > 260 > 1 > 99-110

To understand the source of the stability due to a charged His side-chain located at the C terminus of an α-helix in barnase, we computed the stabilization free energy, upon ionization of the His side-chain, in the native protein, the Leu94 mutant, and a ''pseudo-native'' protein, using free energy molecular dynamics simulations.We show that there are a number of interactions that can individually...

article

A Zinc-binding Domain Involved in the Dimerization of RAG1

Karla K. Rodgers, Zimei Bu, Karen G. Fleming, David G. Schatz, more

Journal of Molecular Biology > 1996 > 260 > 1 > 70-84

Recombination-activating gene 1 (RAG1), as well asRAG2, are the only lymphoid-specific genes required for V(D)J recombination. RAG1 protein contains a C ₃ HC ₄ zinc-binding motif (zinc ring finger) that binds two zinc ions. We have found that RAG1 contains additional zinc-binding motifs in the form of two separate C ₂ H ₂ zinc finger sequences. One of the zinc fingers,...

article

TheBacillus subtilisDNA Replication Terminator

M. T. Smith, C. J. de Vries, D. B. Langley, G. F. King, more

Journal of Molecular Biology > 1996 > 260 > 1 > 54-69

The recent discovery of theBacillus subtilisplasmid terminatorTerLS20 with bidirectional fork arrest activity has provided the opportunity to probe further the structural and functional features ofB. subtilisreplication terminators in general. The minimalTerIandTerLS20 terminators each comprise two 13 nt segments flanking a central trinucleotide, which is almost completely conserved in all terminators...

article

Three-dimensional Structure of Scaffolding-containing Phage P22 Procapsids by Electron Cryo-microscopy

Pamela A. Thuman-Commike, Barrie Greene, Joanita Jakana, Venkataram B. V. Prasad, more

Journal of Molecular Biology > 1996 > 260 > 1 > 85-98

The procapsids of bacterial viruses are the products of the polymerization of coat and scaffolding subunits, as well as the precursors in DNA packaging. Electron cryo-microscopy has been used to study the three-dimensional structures of bacteriophage P22 procapsids containing wild-type and mutant scaffolding proteins. The scaffolding mutant structure has been resolved to 19 Å resolution and agrees...

article

Sequence-specific DNA Binding of the Phage Mu C Protein : Footprinting Analysis Reveals Altered DNA Conformation Upon Protein Binding

V. Ramesh, V. Nagaraja

Journal of Molecular Biology > 1996 > 260 > 1 > 22-33

Themomgene of bacteriophage Mu, which codes for a DNA modification function, is regulated in a complex manner at both transcriptional and translational levels. The phage-encoded C protein functions as an activator ofmomtranscription. Themompromoter has features of an activator-dependent weak promoter, and the C binding site is located upstream and overlapping the -35 region and includes the palindromic...

article

Nucleolin is a Sequence-specific RNA-binding Protein: Characterization of Targets on Pre-ribosomal RNA

Laurence Ghisolfi-Nieto, Gérard Joseph, Francine Puvion-Dutilleul, François Amalric, more

Journal of Molecular Biology > 1996 > 260 > 1 > 34-53

Nucleolin is an abundant nucleolar protein, which plays an essential, but largely unknown role in ribosome biogenesis. Nucleolin contains four consensus RNA-binding domains (CS-RBD), the presence of which suggests that the molecular function of this protein is likely reflected by its RNA-binding properties. Indeed, by immunocytological analysis performed on ribosomal transcription units, we have found...

article

The Effect of Nucleosome Phasing Sequences and DNA Topology on Nucleosome Spacing

Thiemo A. Blank, Peter B. Becker

Journal of Molecular Biology > 1996 > 260 > 1 > 1-8

The distances between the nucleosomes in eukaryotic chromatin that define the nucleosome repeat length are not universally constant, but vary between different cell types and activity states. We have previously established in a cell-free system that nucleosome spacing is essentially governed by electrostatic principles, most likely through charge neutralisation of linker DNA by cations either free...

article

Role of Capsid Structure and Membrane Protein Processing in Determining the Size and Copy Number of Peptides Displayed on the Major Coat Protein of Filamentous Bacteriophage

Pratap Malik, Tamsin D. Terry, Lalitha R. Gowda, Amagoia Langara, more

Journal of Molecular Biology > 1996 > 260 > 1 > 9-21

Filamentous bacteriophage virions can be engineered to display small foreign peptides in the N-terminal regions of all 2700 copies of the major coat protein (pVIII), but larger peptides can be accommodated only in hybrid virions, in which modified and wild-type coat protein subunits are interspersed. The copy number of peptides accepted in hybrid virions is generally believed to be related to peptide...

article

Intron-encoded, Antisense Small Nucleolar RNAs: The Characterization of Nine Novel Species Points to Their Direct Role as Guides for the 2'-O-ribose Methylation of rRNAs

Monique Nicoloso, Liang-Hu Qu, Bernard Michot, Jean-Pierre Bachellerie

Journal of Molecular Biology > 1996 > 260 > 2 > 178-195

A growing number of small nucleolar RNAs (snoRNAs) are intron-encoded, contain the characteristic box C (UGAUGA) and box D (CUGA) motifs and exhibit long complementarities to conserved sequences in mature rRNAs. We have identified nine additional members of this family, U32 to U40. All but one are encoded in introns of ribosomal protein genes in vertebrates: U32 to U35 in rpL13a, U36 in rpL7a and...

article

Kinetic Discrimination in the Folding of Intramolecular Triple Helices

Richard W. Roberts, Donald M. Crothers

Journal of Molecular Biology > 1996 > 260 > 2 > 135-146

We report a study of the physical properties of oligonucleotide intramolecular Pyr.Pur.Pyr triplexes modeled afterH-form DNA. The experiments utilized a set of palindromic pyrimidine strands which form triplexes when combined with complementary purine strands. Triplexes of this nature have two possible isomers, one where the 3' half of the pyrimidine strand acts as the third strand (Y3) or one where...

article

NMR Structure of the J-domain and the Gly/Phe-rich Region of theEscherichia coliDnaJ Chaperone

Maurizio Pellecchia, Thomas Szyperski, Daniel Wall, Costa Georgopoulos, more

Journal of Molecular Biology > 1996 > 260 > 2 > 236-250

The recombinant N-terminal 107-amino acid polypeptide fragment 2 - 108 of the DnaJ molecular chaperone ofEscherichia coli, which contains the J-domain (residues 2 to 76) and the Gly/Phe-rich region (residues 77 to 108), was uniformly labeled with nitrogen-15 and carbon-13. The complete NMR solution structure of the J-domain was determined with the program DIANA on the basis of 682 nuclear Overhauser...

article

A Thermostable 35-Residue Subdomain within Villin Headpiece

James C. McKnight, Don S. Doering, Paul T. Matsudaira, Peter S. Kim

Journal of Molecular Biology > 1996 > 260 > 2 > 126-134

The actin-bundling protein villin contains, at its extreme C terminus, a compact f-actin binding domain called ''headpiece''. This 76-amino acid domain from chicken is highly thermostable. Here, we show that the stable folded structure in headpiece is localized to a subdomain formed by the C-terminal 35 residues. The subdomain, denoted HP-35, is monomeric and retains high thermostability, with aT...

article

The Motile Major Sperm Protein (MSP) fromAscaris suumis a Symmetric Dimer in Solution

Andreas Haaf, Jonathan G. P. Butler, Helen M. Kent, Ian M. Fearnley, more

Journal of Molecular Biology > 1996 > 260 > 2 > 251-260

The major sperm protein (MSP) ofAscaris suummediates amoeboid motility by forming an extensive intermeshed system of cytoskeletal filaments analogous to that formed by actin in many amoeboid cells. We have used a combination of biochemical and NMR methods to show that, in contrast to actin, MSP exists in solution as a symmetrical dimer. This result has important implications for the mechanism of both...

article

Helix Rigidity of DNA: The Meroduplex as an Experimental Paradigm

Karin R. Hagerman, Paul J. Hagerman

Journal of Molecular Biology > 1996 > 260 > 2 > 207-223

The intrinsic rigidity of the DNA helix is generally believed to arise primarily from vertical base-stacking interactions; however, relatively little experimental information exists regarding the relationship between the thermodynamic stability of base-stacking interactions and the mechanical rigidity imparted by such interactions. To address this issue, the solution conformations of complexes formed...

article

Localized DNA Flexibility Contributes to Target Site Selection by DNA-bending Proteins

Anne Grove, Aldo Galeone, Luciano Mayol, Peter E. Geiduschek

Journal of Molecular Biology > 1996 > 260 > 2 > 120-125

Certain DNA-binding proteins function as architectural elements by bending DNA. We have studied the binding of three such proteins, the prokaryotic HU and integration host factor (IHF) and the eukaryotic HMG1, to DNA in which flexibility is enhanced by tandem mismatches and by substituting 5-hydroxymethyluracil (hmU) for thymine (T). IHF and HU have higher affinity for DNA with two 4-nt loops than...

article

Assessment of Protein Fold Predictions from Sequence Information: The Predicted α/β Doubly Wound Fold of the von Willebrand Factor Type A Domain is Similar to its Crystal Structure

Yvonne J. K. Edwards, Stephen J. Perkins

Journal of Molecular Biology > 1996 > 260 > 2 > 277-285

The fold of the von Willebrand Factor type A domain (vWF-A) was predicted to be similar to an α/β doubly wound fold in the GTP-binding domain of ras-p21, despite the lack of sequence or functional similarity. This was subsequently confirmed by the vWF-A crystal structure from complement receptor type 3. The prediction is now reviewed. The vWF-A secondary structure was predicted with 62 to 75% accuracy...

article

The Use of Amino Acid Patterns of Classified Helices and Strands in Secondary Structure Prediction

Zhan-Yang Zhu, Tom L. Blundell

Journal of Molecular Biology > 1996 > 260 > 2 > 261-276

Elements of secondary structure from known protein three-dimensional structures have been classified with respect to their environments in tertiary structures. The size of the solvent-inaccessible face of an α-helix and the accessibility patterns on the two sides of a β-strand have been used to classify the secondary structures. For each class, we have derived a sequence template, giving the amino...

article

On the Connection Between Inherent DNA Flexure and Preferred Binding of Hydroxymethyluracil- containing DNA by the Type II DNA-binding Protein TF1

Anne Grove, Aldo Galeone, Luciano Mayol, Peter E. Geiduschek

Journal of Molecular Biology > 1996 > 260 > 2 > 196-206

TF1 is a member of the family of type II DNA-binding proteins, which also includes the bacterial HU proteins and theEscherichia coliintegration host factor (IHF). Distinctive to TF1, which is encoded by theBacillus subtilisbacteriophage SPO1, is its preferential binding to DNA in which thymine is replaced by 5-hydroxymethyluracil (hmU), as it is in the phage genome. TF1 binds to preferred sites within...

article

CytR/cAMP-CRP Nucleoprotein Formation inE. coli: The CytR Repressor Binds its Operator as a Stable Dimer in a Ternary Complex with cAMP-CRP

Hans-Henrik Kristensen, Poul Valentin-Hansen, Lotte Soøgaard-Andersen

Journal of Molecular Biology > 1996 > 260 > 2 > 113-119

The CytR repressor protein relies on protein-protein interactions to the cAMP-CRP complex to bind its operators with sufficiently high affinity to repress transcription. Here, the quaternary structure of CytR and the mechanism underlying the cooperative binding of CytR and cAMP-CRP have been analyzed. Using a modified Ferguson analysis in which protein-DNA complexes are separated in a non-denaturing...

article

Nuclear Magnetic Resonance Solution Structure of the Human Hsp40 (HDJ-1) J-domain

Yan Qiu Qian, Dinshaw Patel, F-Ulrich Hartl, Damian J. McColl

Journal of Molecular Biology > 1996 > 260 > 2 > 224-235

The J-domain is a highly conserved domain found in all members of the DnaJ family of molecular chaperones. The three-dimensional structure of a recombinant, uniformly ¹ ⁵ N-labeled 77-residue polypeptide containing the complete J-domain from human Hsp40 (HDJ-1) has been determined by nuclear magnetic resonance (NMR) spectroscopy in solution. On the basis of 876 upper distance constraints...

INFONA - science communication portal

Journal of Molecular Biology

Concurrent Interactions Contribute to the Raised pK _a of His18 in Barnase

A Zinc-binding Domain Involved in the Dimerization of RAG1

TheBacillus subtilisDNA Replication Terminator

Three-dimensional Structure of Scaffolding-containing Phage P22 Procapsids by Electron Cryo-microscopy

Sequence-specific DNA Binding of the Phage Mu C Protein : Footprinting Analysis Reveals Altered DNA Conformation Upon Protein Binding

Nucleolin is a Sequence-specific RNA-binding Protein: Characterization of Targets on Pre-ribosomal RNA

The Effect of Nucleosome Phasing Sequences and DNA Topology on Nucleosome Spacing

Role of Capsid Structure and Membrane Protein Processing in Determining the Size and Copy Number of Peptides Displayed on the Major Coat Protein of Filamentous Bacteriophage

Intron-encoded, Antisense Small Nucleolar RNAs: The Characterization of Nine Novel Species Points to Their Direct Role as Guides for the 2'-O-ribose Methylation of rRNAs

Kinetic Discrimination in the Folding of Intramolecular Triple Helices

NMR Structure of the J-domain and the Gly/Phe-rich Region of theEscherichia coliDnaJ Chaperone

A Thermostable 35-Residue Subdomain within Villin Headpiece

The Motile Major Sperm Protein (MSP) fromAscaris suumis a Symmetric Dimer in Solution

Helix Rigidity of DNA: The Meroduplex as an Experimental Paradigm

Localized DNA Flexibility Contributes to Target Site Selection by DNA-bending Proteins

Assessment of Protein Fold Predictions from Sequence Information: The Predicted α/β Doubly Wound Fold of the von Willebrand Factor Type A Domain is Similar to its Crystal Structure

The Use of Amino Acid Patterns of Classified Helices and Strands in Secondary Structure Prediction

On the Connection Between Inherent DNA Flexure and Preferred Binding of Hydroxymethyluracil- containing DNA by the Type II DNA-binding Protein TF1

CytR/cAMP-CRP Nucleoprotein Formation inE. coli: The CytR Repressor Binds its Operator as a Stable Dimer in a Ternary Complex with cAMP-CRP

Nuclear Magnetic Resonance Solution Structure of the Human Hsp40 (HDJ-1) J-domain

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