03 - classfolds1

03 - classfolds1 - Classifying and Comparing Structures A...

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Unformatted text preview: Classifying and Comparing Structures A major area of work is the comparison of proteins at the structural level. By seeing how structures relate to each other we can gain insights into their likely function, evolution (relationships) and the principles of protein structure. Most proteins are made from different units called domains (sometimes modules) which form distinct shapes. Major efforts to classify these have been the data bases SCOP (Structural Classification of Proteins) and CATH (Class, Architecture, Topology, Homology). Underlying Ideas A protein’s structure can reveal its function and evolutionary history. We require a knowledge of the structure and relationships (comparisons) with other proteins. This needs knowledge of the range of folds that proteins use and knowledge of many structures (databases). As in most of bioinformatics we gather an extensive amount of data on sequence and structure, integrate it with biological (functional) data and analyse it to find similarities and patterns so we can identify homologues and infer and understand function. How Can We Assess Homology Strong sequence similarity is considered sufficient evidence for common ancestry (or homology). Close structural AND! functional similarity is also accepted as sufficient evidence for common ancestry (distant homology) between proteins that lack significant sequence similarity. Neither structural similarity nor functional similarity alone is considered to be strong evidence for common ancestry. Never confuse similarity (and its levels) with homology. A level of similarity can be evidence for homology. Similarity Without Homology Proteins of independent origin may have similar structures due to physico-chemical reasons. They may evolve similar functions due to functional selection – a protein evolves to perform a function that is required. If descendants of the same ancestor had different functions and different structures, how would we detect their common ancestry? Structural similarity among (seemingly) unrelated proteins implies convergent or parallel evolution – resulting in analogues or analogous structures or folds. Fold Classification can be difficult – often requires expert manual intervention. Consider the major secondary structural elements in the same arrangement with the same topological connections....
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This note was uploaded on 07/29/2010 for the course BIOC BIOC2811 taught by Professor Dr.q.hao during the Summer '10 term at HKU.

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03 - classfolds1 - Classifying and Comparing Structures A...

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