Protein sequencing overview

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Mewes HW, Albermann K, Bahr M, Frishman D, Gleissner A, Hani J, Heuman K, Kleine K, Maierl A, Oliver SG, Pfeifer F, Zollner A Overview of the yeast genome. Nature 1997 387 7-65. Mewes HW, Albermann K, Heumann K, Liebl S, Pfeifer F MIPS A database for protein sequences, homology data and yeast genome information. Nucleic Acid Res 1997 35 28-30. Clarke L, Baum MP Functional analysis of a centromere from fission yeast A role for centromere-specific repeated DNA sequences. Mol Cell Biol 1990 10 1863-1872. 

This chapter is intended as a broad overview to give researchers with a prospective need for protein sequence analysis some feeling of the strengths/weaknesses of... 

In summary, the gene conservation option provides a compact overview on protein sequence similarities in all genomes included in a dedicated genome browser. 

Overview of the flow of information from mRNA to protein. The polarity of mRNA and protein sequences are analogous in that both are synthesized from left to right. 

The World Wide Web has transformed the way in which we obtain and analyze published information on proteins. What only a few years ago would take days or weeks and require the use of expensive computer workstations can now be achieved in a few minutes or hours using personal computers, both PCs and Macintosh, connected to the internet. The Web contains hundreds of sites of Interest to molecular biologists, many of which are listed in Pedro s BioMolecular Research Tools (http // www.fmi.ch/biology/research tools.html). Many sites provide free access to databases that make it very easy to obtain information on structurally related proteins, the amino acid sequences of homologous proteins, relevant literature references, medical information and metabolic pathways. This development has opened up new opportunities for even non-specialists to view and manipulate a structure of interest or to carry out amino-acid sequence comparisons, and one can now rapidly obtain an overview of a particular area of molecular biology. We shall here describe some Web sites that are of interest from a structural point of view. Updated links to these sites can be found in the Introduction to Protein Structure Web site (http // WWW.ProteinStructure.com/). 

Taking a final overview of proteins we have to observe how remarkably suitable they are as semi-soft materials. The different variety of sequences and the different ways their folds enable them to act in a variety of ways within the temperature range of water may well be unique. Remember that their value rests not just in structure but in structure associated with thermodynamically controlled features, i.e. concentration, mobility, and temperature. These structures are dynamic and are an essential feature of physical flow, e.g. of electrons and protons and metabolic activity and as such their connectivity is of the essence of energy uptake and degradation. 

It is clear that in this brief overview of molecular biology, we have not covered a number of important areas that have an important impact on the study of metalloproteins. These include molecular cloning and recombinant DNA technology, which allow proteins to be over-expressed and individual amino acids to be mutated to any other of the 19 protein amino acids genome and proteome analysis that enables the sequences of all the genes of the entire organisms to be determined, and the quantification, localization, interactions and, where possible, activities and identification of all of the proteins in an organism,... 

This overview presents some cases in which sequence profile-based methods have been able to predict nontrivial structural and evolutionary relationships between proteins and then discusses the current state of structural genomics as assesed using these methods. This discussion is not a comprehensive review of profile-based methods for sequence analysis and their application in structural genomics rather observations made with PSI-BLAST-constructed PSSMs are emphasized, and results produced by other methods are cited only as needed for discussion. 

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