Literature on the topological properties of folded proteins that has emerged as a field in its own right in the past decade is reviewed. Physics-based construction of coarse-grained models of proteins from knowledge of all-atom coordinates of the average structure is discussed. Once network is thus obtained with the node and link information, local motifs provide plethora of information on prot...

Most Ig receptors exist as multi-subunit complexes with a unique ligand binding alpha chain and a common signaling FcR gamma-chain. The myeloid Fc gamma RIIa (CD32) appears unique among FcR because both ligand-binding and signaling capacity are found in the alpha chain. Within the cytoplasmic tails of Fc gamma RIIa and FcR gamma-chain similar, but not identical, activatory motifs (ITAMs) have b...

*Correspondence to: Roger A. Garrett; Email: [email protected] Protospacer adjacent motifs (PAMs) were originally characterized for CRISPR-Cas systems that were classified on the basis of their CRISPR repeat sequences. A few short 2–5 bp sequences were identified adjacent to one end of the protospacers. Experimental and bioinformatical results linked the motif to the excision of protospacers an...

Among methyltransferases, KsgA and the reaction it catalyzes are conserved throughout evolution. However, the specifics of substrate recognition by the enzyme remain unknown. Here we report structures of Aquifex aeolicus KsgA, in its ligand-free form, in complex with RNA, and in complex with both RNA and S-adenosylhomocysteine (SAH, reaction product of cofactor S-adenosylmethionine), revealing ...

This paper presents a generalization of the notion of longest repeats with a block of k don’t care symbols introduced by [8] (for k fixed) to longest motifs composed of three parts: a first and last that parameterize match (that is, match via some symbol renaming, initially unknown), and a functionally equivalent central block. Such three-part motifs are called longest block motifs. Different t...

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-structur...