Protein sequencing finding sequences

Starting from the protein sequence (primary structure) several algorithms can be used to analyze the primary structure and to predict secondary structural elements like beta-strands, turns, and helices. The first algorithms from Chou and Fasman occurred already in 1978. The latest algorithms find e.g., that predictions of transmembrane... 

Proteins fold on a time scale from [is to s. Starting from a random coil conformation, proteins can find their stable fold quickly although the number of possible conformations is astronomically high. The protein folding problem is to predict the folding and the final structure of a protein solely from its sequence. 

New domains and their boundaries have been defined manually from sequence alone for literally hundreds of protein domains. Finding regions of similarity between proteins allows detection of domains. However, defining the exact boundaries of the domain is often a more difficult problem. Certain rules can be used to find the maximum size of a domain from pairwise comparisons of proteins in a related family. 

The use of DNA sequencing as a method of generating protein sequence data (53) has proven to be extremely fast and efficient and future technical developments such as automated DNA sequencing will further expedite the production of protein sequence data (53). Nevertheless, DNA sequencing often calls for a certain amount of protein sequence information for the procedure to be most efficient. From our own experience in the amino terminal protein sequencing of over 500 samples, we find that approximately 50% of all naturally occurring proteins have ammo termini which are blocked, thus precluding their... 

The transmembrane domain may be made up of one or many transmembrane elements. Generally, the transmembrane elements include 20-25 mostly hydrophobic amino acids. At the interface with aqueous medium, we often find hydrophilic amino acids in contact with the polar head groups of the phospholipids. In addition, they mediate distinct fixing of the transmembrane section in the phospholipid double layer. A sequence of 20-25 hydrophobic amino acids is seen as characteristic for membrane-spaiming elements. This property is used in analysis of protein sequences, to predict possible transmembrane elements in so-called hydropathy plots". 

To classify and find the category of protein sequences under investigation into families of related sequences... 

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