References

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215 403-410 Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST a new generation of protein database search programs. Nucleic Acids Res 25 3389-3402 Aravind L, Koonin EV (1999) Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. J Mol Biol 287 1023-1040 Aravind L,...

Jpred

Combet et al. (2000) Eyrich and Rost (2003) www.compbio.dundee.ac.uk www-jpred npsa-pbil.ibcp.fr cubic.bioc.columbia.edu meta number of moderately diverged sequences. Discard too strongly diverged sequences, which cannot be aligned with confidence and carefully refine the MSA in the most diverged regions. (3) If the particular algorithm does not accept MSA as an input, try to predict the secondary structure for the target and a few of its distant homologues and use the consensus pattern of...

Comparative Modeling

2.1 Sequence Gathering and Alignment Before, comparative molecular modeling, i.e. three-dimensional structure building, can be initiated, sequence alignment of the target and (at least) one template is necessary. However, the lower the sequence identity, the harder it is to detect similarity and to align sequences. While obvious at high sequence identity (above 30 ), the detection might not be straightforward at lower sequence identity. A prerequisite is generally to find and align close...

Sequence Analysis of the Processosome Components

I extracted sequences of yeast processome components listed in Fatica and Tollervey (2002) from GenBank. For comparative purposes, five other protein sets were prepared (1) complete yeast proteome, as distributed by NCBI (http www.ncbi.nlm.nih.gov). (2) Proteins localized throughout the nucleus, as determined by the high-throughput tagging project at Yale University (3) Proteins with nuclear localization, determined by various computational and in vivo approaches, from the MIPS Yeast database...

Bioinformatics Terminology Methodology and Applications to RNA MTases

Homology is defined as a synonym of common evolutionary origin, i.e., all genes that have arisen from a common ancestor are homologous. Genes in different species that originate from a single gene in the last common ances tor of these species are termed orthologs. Orthologous genes have often very similar biological roles in the present-day organisms. Homologues generated by gene duplication are termed paralogs - they often share the same generic function, such as the type of the reaction...

Internal Dynamics and NMR Structure Determination

3.1 Calculating NMR Parameters from Molecular Dynamics Simulations NMR is a rich source of structural data (inter-atomic distances, angles, and orientations), However, the sensitivity of all structural data obtainable from NMR experiments to internal dynamics makes them particularly difficult to interpret in structural terms. The measured quantities are averages over time and a large ensemble of structures, while in a standard structure calculation the lower and upper bounds refer to...

Traditional and Novel Approaches to Identification of New RNAModification Enzymes

The first RNA modification enzyme that was identified in the 1960s by Borek and coworkers was a tRNA MTase. Using RCRel mutants of E. coli which accumulate undermodified RNAs during methionine starvation, Borek's group showed for the first time that an AdoMet-dependent enzyme can mediate methylation in vitro of specific bases in macromolecular precursors of RNA, i.e., posttranscriptionally after polynucleotide synthesis, which at that time was not evident at all (Fleissner and Borek 1962). The...

Comparative Genomics an Emerging Tool to Identify Missing Genes

The data generated from genome sequencing programs (16 Archaea, 106 Bacteria and 18 Eukarya fully sequenced and published to date) has revealed how much we have yet to learn before understanding the roles of all the proteins in a cell. Even in the best genetically characterized organisms, a third of the genes have no assigned function (Blattner et al. 1997 Kunst et al. 1997). Systematic approaches such as structural genomics initiatives or systematic interaction mapping can lead to elucidation...

Finding Complex Modification Pathway Genes

Queuosine Biosynthetic Pathway

4.1 Finding Missing Steps in Known Pathways For many complex tRNA modifications such as queuosine, ms2i6A or Wyeo-sine, several biosynthetic steps are needed. Few pathways have yet been totally characterized and fully reconstituted in vitro. In the case of the synthesis of mnm5s2U34 (Fig. 5A), five enzymes have been characterized but at least one enzyme is still missing (Kambampati and Lauhon 2003). Gene clustering around the gidA, mnmE, and mnmA genes was analyzed. One candidate, gidB, clearly...

Generating Predictions Sequence Selection and Analysis

The basis for structure-conservation analysis is intuitively clear (Zharkov and Grollman 2002). Consider the situation in which a group of sequence-related proteins (orthologous, paralogous, or both) is divided into two or more functional subgroups. Then, residues conserved across all subgroups should be important for functions common to all proteins, whereas residues conserved in some subgroups, but not others, would be important only for functions of subgroups in which they are conserved. For...

Rosetta Folding Simulations Using a Fragment Library

The ROSETTA folding simulation algorithm uses Monte Carlo Fragment Insertion (MCFI) to predict the 3D structures of small proteins or protein fragments without the use of structural templates (Bonneau and Baker 2001 Bonneau et al. 2001 Simons et al. 1997,1999a, b). MCFI is a mostly downhill search in a knowledge-based energy landscape. Each MCFI move consists of replacing the backbone angles of segments of the chain with fragments in a library. ROSETTA has been successful in prediction...

References About Protein Structures

Agris PF (1996) The importance of being modified roles of modified nucleosides and Mg2+ in RNA structure and function. Prog Nucleic Acid Res Mol Biol 53 79-129 Ahn HJ, Kim HW, Yoon HJ, Lee BI, Suh SW, Yang JK (2003) Crystal structure of tRNA(m'G37)methyltransferase insights into tRNA recognition. EMBO J 22 25932603 Alexandrov A, Martzen MR, Phizicky EM (2002) Two proteins that form a complex are required for 7-methylguanosine modification of yeast tRNA. RNA 8 1253-1266 Altschul SF, Gish W,...

Introduction

The function of a protein is defined by its interactions with other molecules in its environment. The interactions can be either transient, such as proteinprotein interactions involved in intracellular signaling, or relatively stable, such as the protein-protein and protein-RNA interactions in ribosomes. A structural description of these interactions is an important step toward understanding the mechanisms of biochemical, cellular, and higher order biological processes. There is a need to...

Pharmacogenomic Applications

3.4.1 A Challenging Application the GPCRs With the single exception of bovine rhodopsin, there are no experimental 3D structures available for G-protein-coupled receptors GPCRs . GPCRs are membrane proteins hardly overexpressed or purified while their pharmacology is better characterized Bockaert and Pin 1999 . This situation has encouraged theoretical modeling of GPCRs and model evaluation using docking of well-characterized ligands and or directed mutagenesis Gershen-gorn and Osman 2001...