Protein structure concepts and its related computation problem 朱家漢主講

1. Protein structure concepts and its related computation problem Speaker: Chia Han Chu (PHD candidate) 21/07/2009 nthu CSBB lab

19. General concepts for structural bioinformatics Sequence Structure Analysis Classification Function Prediction Modelling Design Engineering 21/07/2009 nthu CSBB lab

24. Structure Databases 21/07/2009 nthu CSBB lab

36. Structure Classification Databases Information comes from Murzin,A., Brenner,S.E., Hubbard,T.J.P. and Chothia,C. (1995) SCOP: a Structural Classification of Proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540 and Wiki. 21/07/2009 nthu CSBB lab Family : Clear evolutionary relationship Proteins are clustered together into families on the basis of one of two criteria that imply their having a common evolutionary origin. Criteria 1 : All proteins that have residue identities of 30% and greater . Criteria 2 : Proteins with lower sequence identities but whose functions and structures are very similar . For example, globins with sequence identities of 15%. Superfamily : Probable common evolutionary origin Families , whose proteins have low sequence identities but whose structures and, in many cases, functional features suggest that a common evolutionary origin is probable, are placed together in superfamilies . Example actin, the ATPase domain of the heat-shock protein and hexokinase Fold : Major Structural Similarity Superfamilies and families are defined as having a common fold if their proteins have same major secondary structures in same arrangement with the same topological connections . Advantage There may, however, be cases where a common evolutionary origin is obscured by the extent of the divergence in sequence, structure and function. In these cases, it is possible that the discovery of new structures, with folds between those of the previously known structures, will make clear their common evolutionary relationship. Class (1) α- helical domains (2) β- sheet domains (3) α/β domains which consist of from " beta-alpha-beta " structural units or "motifs" that form mainly parallel β- sheets (4) α+β domains formed by independent α- helices and mainly antiparallel β- sheets (5) multi-domain proteins (for those with domains of different fold and for which no homologues are known at present) (6)membrane and cell surface proteins and peptides (7)small proteins (8)coiled-coil proteins (9)low-resolution protein structures (10)peptides and fragments (11)designed proteins of non-natural sequence

56. Translation X Y 21/07/2009 nthu CSBB lab

57. Rotation X Y 21/07/2009 nthu CSBB lab

58. Scale X Y 21/07/2009 nthu CSBB lab

75. RMSD v.s. Similarity measure RMSD dissimilarity measure  emphasizes differences  smaller support STRUCTAL ’s similarity measure  emphasizes similarities  larger support 21/07/2009 nthu CSBB lab Gap penalty

80. Dali An intra-molecular distance plot for myoglobin 21/07/2009 nthu CSBB lab

82. VAST 21/07/2009 nthu CSBB lab

84. Recommanded books 21/07/2009 nthu CSBB lab

85. Recommanded books 21/07/2009 nthu CSBB lab

86. Thank you for your attention! 21/07/2009 nthu CSBB lab