Current Opinion in Structural Biology

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Sequences and topology - Genome and proteome informatics

Peer Bork, David Eisenberg

Current Opinion in Structural Biology > 2000 > 10 > 3 > 341-342

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Protein structure prediction in the postgenomic era

David T Jones

Current Opinion in Structural Biology > 2000 > 10 > 3 > 371-379

As the number of completely sequenced genomes rapidly increases, the postgenomic problem of gene function identification becomes ever more pressing. Predicting the structures of proteins encoded by genes of interest is one possible means to glean subtle clues as to the functions of these proteins. There are limitations to this approach to gene identification and a survey of the expected reliability...

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Simulation of the structure and dynamics of nonhelical RNA motifs

Martin Zacharias

Current Opinion in Structural Biology > 2000 > 10 > 3 > 311-317

Computer simulation methods are increasingly being used to study possible conformations and dynamics of structural motifs in RNA. Recent results of molecular dynamics simulations and continuum solvent studies of RNA structures and RNA-ligand complexes show promising agreement with experimental data. Combined with the ongoing progress in the experimental characterization of RNA structure and thermodynamics,...

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Allosteric nucleic acid catalysts

Garrett A Soukup, Ronald R Breaker

Current Opinion in Structural Biology > 2000 > 10 > 3 > 318-325

Endowing nucleic acid catalysts with allosteric properties provides new prospects for RNA and DNA as controllable therapeutic agents or as sensors of their cognate effector compounds. The ability to engineer RNA catalysts that are allosterically regulated by effector binding has been propelled by the union of modular rational design principles and powerful combinatorial strategies.

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Fitting peptides into the RNA world

Alan D Frankel

Current Opinion in Structural Biology > 2000 > 10 > 3 > 332-340

The structures of several peptide-RNA complexes have been reported in the past year, underscoring the diverse nature of RNA structure and protein interactions. In general, specific peptide conformations are stabilized by the surrounding RNA framework; this is strikingly similar to how peptides are stabilized upon interaction with proteins.

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NMR solution structure determination of RNAs

Emilia T Mollova, Arthur Pardi

Current Opinion in Structural Biology > 2000 > 10 > 3 > 298-302

During the past several years, there have been significant advances in NMR solution structure determination of macromolecules. The ability to easily measure residual dipolar couplings, to directly detect NH...N hydrogen bonding interactions and to study much larger macromolecules by the application of heteronuclear experiments that select narrow lines in 2D and 3D spectra of isotopically labeled molecules...

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Annotating eukaryote genomes

Suzanna Lewis, Michael Ashburner, Martin G Reese

Current Opinion in Structural Biology > 2000 > 10 > 3 > 349-354

The Genome Annotation Assessment Project tested current methods of gene identification, including a critical assessment of the accuracy of different methods. Two new databases have provided new resources for gene annotation: these are the InterPro database of protein domains and motifs, and the Gene Ontology database for terms that describe the molecular functions and biological roles of gene products...

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The i-motif in nucleic acids

Maurice Guéron, Jean-Louis Leroy

Current Opinion in Structural Biology > 2000 > 10 > 3 > 326-331

Seven years after the discovery of the DNA i-motif, partial explanations for its occurrence have been uncovered, possibly involving CH...O hydrogen bonds across the narrow grooves. Investigations of its biological significance have been encouraged by the demonstration and description of the intramolecular i-motif structure of human telomeric and centromeric sequences, by the recent observation of...

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Nucleic acids - Theory and experiment

Paul J Hagerman, Ignacio Tinoco

Current Opinion in Structural Biology > 2000 > 10 > 3 > 275-278

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Structural biology - Paper alert

Máire Convery, Caitrı́ona Dennis, Siân Rowsell, Brian Kuhlman, more

Current Opinion in Structural Biology > 2000 > 10 > 3 > 265-271

A selection of interesting papers that were published in the two months before our press date in major journals most likely to report significant results in structural biology.

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Modeling DNA deformations

Wilma K Olson, Victor B Zhurkin

Current Opinion in Structural Biology > 2000 > 10 > 3 > 286-297

Recent developments have been made in modeling double-helical DNA at four levels of three-dimensional structure: the all-atom level, whereby an oligonucleotide duplex is surrounded by a shroud of solvent molecules; the base-pair level, with explicit backbone atoms; the mesoscopic level, that is, a few hundred base pairs, with the local duplex conformation described by knowledge-based harmonic energy...

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Nucleic acids - Sequences and topology

Judith Murray-Rust, Jeremy H Lakey, Eric D Scheeff

Current Opinion in Structural Biology > 2000 > 10 > 3 > 273-274

A selection of World Wide Web sites relevant to reviews published in this issue of Current Opinion in Structural Biology.

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Genome data: what do we learn?

William C Nierman, Jonathan A Eisen, Robert D Fleischmann, Claire M Fraser

Current Opinion in Structural Biology > 2000 > 10 > 3 > 343-348

Genome sequence information has continued to accumulate at a spectacular pace during the past year. Details of the sequence and gene content of human chromosome 22 were published. The sequencing and annotation of the first two Arabidopsis thaliana chromosomes was completed. The sequence of chromosome 3 from Plasmodium falciparum, the second sequenced malaria chromosome, was reported, as was that of...

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tructural genomics of microbes: an objective

Sung-Hou Kim

Current Opinion in Structural Biology > 2000 > 10 > 3 > 380-383

A comparison of the genome sequences of more than 20 microorganisms reveals that a large fraction of the genes have unknown functions. Determining the structures of the proteins coded by these genes may provide additional key information in an effort to uncover the molecular functions of such proteins and new protein fold patterns. Using existing technology, it is possible to obtain a complete sequence...

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Exploitation of gene context

Martijn Huynen, Berend Snel, Warren Lathe, Peer Bork

Current Opinion in Structural Biology > 2000 > 10 > 3 > 366-370

Recently, a number of techniques have been proposed that use completely sequenced genomes for the function prediction of individual proteins encoded therein. They use the fusion of genes, their conserved location in operons or merely their co-occurrence in genomes to predict the existence of functional interactions between the proteins they encode. This type of information complements functional features...

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Calculating nucleic acid secondary structure

Michael Zuker

Current Opinion in Structural Biology > 2000 > 10 > 3 > 303-310

New results for calculating nucleic acid secondary structure by free energy minimization and phylogenetic comparisons have recently been reported. A complete set of DNA energy parameters is now available and the RNA parameters have been improved. Although databases of RNA secondary structures are still derived and expanded using computer-assisted, ad hoc comparative analysis, a number of new computer...

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The nature of the universal ancestor and the evolution of the proteome

W Ford Doolittle

Current Opinion in Structural Biology > 2000 > 10 > 3 > 355-358

The past year has seen several attempts to reconstruct the proteome of the universal ancestor of all life on the basis of comparisons of contempory genomes. However, increasing evidence for lateral gene transfer could mean that such attempts are based on an incorrect understanding of evolution.

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From fold to function

John Moult, Eugene Melamud

Current Opinion in Structural Biology > 2000 > 10 > 3 > 384-389

A number of recent advances have been made in deriving function information from protein structure. A fold relationship to an already characterized protein will often allow general information about function to be deduced. More detailed information can be obtained using sequence relationships to already studied proteins. Methods of deducing function directly from structure, without the use of evolutionary...

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Single-molecule studies of DNA mechanics

Carlos Bustamante, Steven B Smith, Jan Liphardt, Doug Smith

Current Opinion in Structural Biology > 2000 > 10 > 3 > 279-285

During the past decade, physical techniques such as optical tweezers and atomic force microscopy were used to study the mechanical properties of DNA at the single-molecule level. Knowledge of DNA's stretching and twisting properties now permits these single-molecule techniques to be used in the study of biological processes such as DNA replication and transcription.

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Computational genetics: finding protein function by nonhomology methods

Edward M Marcotte

Current Opinion in Structural Biology > 2000 > 10 > 3 > 359-365

During the past year, computational methods have been developed that use the rapidly accumulating genomic data to discover protein function. The methods rely on properties shared by functionally related proteins other than sequence or structural similarity. Instead, these 'nonhomology' methods analyze patterns such as domain fusion, conserved gene position and gene co-inheritance and coexpression...

INFONA - science communication portal

Current Opinion in Structural Biology

Sequences and topology - Genome and proteome informatics

Protein structure prediction in the postgenomic era

Simulation of the structure and dynamics of nonhelical RNA motifs

Allosteric nucleic acid catalysts

Fitting peptides into the RNA world

NMR solution structure determination of RNAs

Annotating eukaryote genomes

The i-motif in nucleic acids

Nucleic acids - Theory and experiment

Structural biology - Paper alert

Modeling DNA deformations

Nucleic acids - Sequences and topology

Genome data: what do we learn?

tructural genomics of microbes: an objective

Exploitation of gene context

Calculating nucleic acid secondary structure

The nature of the universal ancestor and the evolution of the proteome

From fold to function

Single-molecule studies of DNA mechanics

Computational genetics: finding protein function by nonhomology methods

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