Protein Sequence Motifs Involved in Intracellular Trafficking

1997 ◽  
pp. 59-83
Author(s):  
Silvia Biocca ◽  
Antonino Cattaneo
Keyword(s):  
Protein Sequence ◽  
Intracellular Trafficking ◽  
Sequence Motifs ◽  
Protein Sequence Motifs

scholarly journals Impact of VP1-Specific Protein Sequence Motifs on Adeno-Associated Virus Type 2 Intracellular Trafficking and Nuclear Entry

2012 ◽  
Vol 86 (17) ◽  
pp. 9163-9174 ◽  
Author(s):  
R. Popa-Wagner ◽  
M. Porwal ◽  
M. Kann ◽  
M. Reuss ◽  
M. Weimer ◽  
...  
Keyword(s):  
Virus Type ◽  
Protein Sequence ◽  
Intracellular Trafficking ◽  
Specific Protein ◽  
Sequence Motifs ◽  
Nuclear Entry ◽  
Adeno Associated Virus ◽  
Protein Sequence Motifs

Early Molecular Evolution

2006 ◽  
Vol 52 (3-4) ◽  
pp. 375-387 ◽  
Author(s):  
Edward N. Trifonov
Keyword(s):  
Molecular Evolution ◽  
Protein Sequence ◽  
Last Common Ancestor ◽  
Sequence Motifs ◽  
Molecular Events ◽  
Function Modules ◽  
Recent Developments ◽  
Module Size ◽  
Protein Sequence Motifs ◽  
Polypeptide Chains

Four fundamentally novel, recent developments make a basis for the Theory of Early Molecular Evolution. The theory outlines the molecular events from the onset of the triplet code to the formation of the earliest sequence/structure/function modules of proteins. These developments are: (1) Reconstruction of the evolutionary chart of codons; (2) Discovery of omnipresent protein sequence motifs, apparently conserved since the last common ancestor; (3) Discovery of closed loops—standard structural modules of modern proteins; (4) Construction of protein sequence space of module size fragments, with far-reaching evolutionary implications. The theory generates numerous predictions, confirmed by massive nucleotide and protein sequence analyses, such as existence of two distinct classes of amino acids, and their periodical distribution along the sequences. The emerging picture of the earliest molecular evolutionary events is outlined: consecutive engagement of codons, formation of the earliest short peptides, and growth of the polypeptide chains to the size of loop closure, 25-30 residues.

Deterministic Motif Mining in Protein Databases

2008 ◽  
pp. 116-140 ◽  
Author(s):  
Pedro Gabriel Ferreira ◽  
Paulo Jorge Azevedo
Keyword(s):  
Protein Sequence ◽  
Sequence Motif ◽  
Structural Level ◽  
Sequence Motifs ◽  
Motif Analysis ◽  
Level Information ◽  
Information Patterns ◽  
Definition Of ◽  
Protein Sequence Motifs ◽  
Related Proteins

Protein sequence motifs describe, through means of enhanced regular expression syntax, regions of amino-acids that have been conserved across several functionally related proteins. These regions may have an implication at the structural and functional level of the proteins. Sequence motif analysis can bring significant improvements towards a better understanding of the protein sequence-structure-function relation. In this chapter we review the subject of mining deterministic motifs from protein sequence databases. We start by giving a formal definition of the different types of motifs and the respective specificities. Then, we explore the methods available to evaluate the quality and interest of such patterns. Examples of applications and motif repositories are described. We discuss the algorithmic aspects and different methodologies for motif extraction. A briefly description on how sequence motifs can be used to extract structural level information patterns is also provided.

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