Current Opinion In Structural Biology Research Articles

Site-specific molecular design and its relevance to pharmacogenomics and chemical biology.

The emergence of the new discipline of pharmacogenomics reflects the growing convergence of chemical and genomic space. The massive information-driven growth in both computational chemistry and structural biology is leading to unprecedented opportunities in both chemical and biological design. In this paper we relate current opinion in structural biology to recent developments in computational drug design. Sequence information now permits protein structure prediction and, together with experimental protein structure determination, a complete database of ligand-binding sites and protein-protein interactions can be assembled. When aligned with site exploration and virtual screening, this information provides a foundation for structure-based pharmacogenomics. In association with chemical genomics, structure-based design will allow major new insights into a compound's biological and pharmaceutical properties.

Web alert: Proteins Catalysis and regulation

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

Biophysical methods

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

Web alert: Engineering and design: Membrane proteins: Lipids

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

Nucleic acids: Sequences and topology

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

Theory and simulation: Macromolecular assemblages: Web alert

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

Folding and binding: Protein–nucleic acid interactions: Web alert

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

Catalysis and regulation: Proteins: Web alert

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

Carbohydrates and glycoconjugates Biophysical methods: Web alert

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

Carbohydrates and glycoconjugates Biophysical methods Web alert

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

Nucleic acids sequences and topology web alert

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

Modeling cytochrome P450 14α demethylase ( Candida albicans) from P450cam

The tertiary structure of cytochrome P450 14α demethyl-ase—Candida albicans (P450 CA) is modeled on the basis of sequence alignment with two closely related proteins and the cristallographic structure of Pseudomonas putida P450cam. The secondary structure prediction system used combines the information from several algorithms and trains the data to offer an optimized prediction of the known P450cam. The trained algorithm was then used to predict the secondary structure of the other P450 sequences. The prediction of the surface coil regions was aided by an alignment between P450 CA and the homologous sequences P450 I4a demethylase—Saccharomyes cerevisiae (66 SD) and P450 14α demethylase—Candida tropicalis (72 SD). The prediction and alignment information was combined to establish an alignment between P450 CA and P450cam, and to assign full secondary structure to the target protein. This secondary structure was folded from the template of P450cam and the predicted structure was relaxed by molecular dynamics. Model checking highlighted minor adjustments in the alignment, correctly orienting hydrophobic and hydrophilic side chains. The model offers explanations for several known experimental results and suggests further investigations that may prove fruitful in understanding the structure and mechanisms of the P450 family (Porter, T.D. and Coon, M.J. Minireview cytochrome P450. J. Biol. Chem. 1991, 266, 13469-13472. Waterman, M.R. Cytochrome P450 cellular distribution and structural considerations. Current Opinion in Structural Biology 1992, 2, 384-387. Aoyama, Y., Yoshida, Y., Sonondo, Y. and Sato, Y. Structural analysis of the interaction between the side-chain of substrates and the active site of lanosterol 14α demethylase (P450 14DM) of yeast. Biochim. Biophys. Acta 7992, 1122, 251-255.).

Protein engineering strategies in examining protein folding intermediates: Current opinion in Structural Biology 1993, 3:594–600

Mutagenesis has proven to be a powerful tool for examining the structures and stabilities of intermediates which appear during the folding of globular proteins. Combining site-directed mutagenesis with other, more classical, methods of protein chemistry, such as chemical labeling and cleavage, has advanced the investigation of these transient, marginally stable species. The high cooperativity of the folding reaction has been reduced by mutagenesis to produce a series of reactions involving stable, highly populated, partially folded forms. New insights into inherently slow processes, such as proline isomerization reactions and disulfide bond rearrangements, have also resulted from protein engineering experiments.

Non-covalent protein assembly: Current opinion in structural biology 1993, 3:549–554

The aminoacyl-tRNA synthetases are diverse proteins which offer a unique opportunity to investigate protein assembly and evolution. Non-covalent assembly of tRNA synthetases has been achieved by association of the core acceptor-stem binding catalytic domain with a domain that facilitates interactions with more distal parts of the tRNA molecule. The core catalytic domain has also been dissected into pieces which can be reassembled through complementary chain-packing interactions. Current evidence suggests the possibility of assemblages of polypeptides as intermediates in the early development of long single-chain aminoacyl-tRNA synthetases.

Phase topology and percolation in multi-phase lipid bilayers: is the biological membrane a domain mosaic?: Current Opinion in Structural Biology 1993, 3:482–488

The recent literature provides strong evidence that phase separations do occur in biological membranes. Phase co-existence, as microscopic domains, raises important questions with regard to domain connectivity, phase percolation, long-range translational diffusion, lateral segregation of membrane components and efficiency of bimolecular reactions that occur in membranes. It also provides a basis for understanding several documented structural and dynamic aspects of this important cellular structure. It is suggested that changes between different phase ‘landscapes’ in a membrane may function as switching mechanisms for physiologically important events in a cell.

Phage display of peptides and protein domains: Current opinion in structural biology 1993, 3:572–579

Phage display of peptides and proteins is a versatile and promising tool for protein engineering and drug discovery programs because of the vast libraries of sequences that can be rapidly screened for biological function. Over the past year, reports have appeared in which these libraries have been used to investigate the binding properties of a variety of receptors. Several functional protein domains have also been displayed. A novel selection scheme using both protein and peptide display has been devised for determining protease cleavage specificity.

The structure of photosystem I: Current Opinion in Structural Biology 1993, 3:508–514

The cofactors and polypeptides that comprise the photosystem I reaction center are now largely known, and the functions of the low molecular mass polypeptides are rapidly becoming elucidated. We can expect significant progress in the study of the reaction center components because of two experimental advances: the determination of the three-dimensional structure of the cyanobacterial photosystem I complex, and the successful application of site-specific mutagenesis of the photosystem I polypeptides.

The erythrocyte anion transporter (band 3): Current Opinion in Structural Biology 1993, 3:515–523

Band 3 is the best characterized member of a multi-gene anion exchanger family. Multiple promoters within each gene produce a variety of tissue-specific transcripts. The cell-surface expression of band 3 in oocytes is promoted by glycophorin A, which might act as a molecular chaperone. Several band 3 variants have been characterized, including a transport-defective form found in ovalocytic erythrocytes that contains a nine-amino-acid deletion bordering the membrane domain. The roles of the various oligomeric forms of band 3 and interactions between band 3 subunits and between the cytosolic and membrane domains continue to draw the attention of many researchers. The recent production of two-dimensional crystalline arrays of band 3 provides hope that the vast amount of kinetic, biophysical and chemical information available on this transport system will soon be put on a firm structural footing.

Metalloprotein design: Current Opinion in Structural Biology 1993, 3:585–588

The design of proteins with desired or novel properties remains a very challenging area of research. Metal ions have certain characteristics which make them particularly suitable for use in such studies. Many different approaches ranging from de novo design to the recombination of existing metal-based modules are being pursued. Some important successes have been achieved but much is left to do in terms of the characterization of the novel species prepared to date and the extension of lessons learned to more complex systems.

Bacterial porins: lessons from three high-resolution structures: Current Opinion in Structural Biology 1993, 3:501–507

The structures of a porin from Rhodobacter capsulatus and two porins from Escherichia coli provide a wealth of information regarding the structure and function of transmembrane pores and extend our rather limited knowledge of the structure of membrane proteins in general. There are also implications for methods used to investigate the topology and properties of membrane proteins and for algorithms used to predict their structure.