Protein Classification Wei Chen Apr. 9, 2002 CISC 889: Bioinformatics 4/9/2002 Protein Classification - Wei Chen

About This Presentation Introduction Review of protein structure Terminology Representation Further Materials Conclusion 4/9/2002 Protein Classification - Wei Chen

Sequence V.S. Structure – 1 Amino Acid Sequence Protein 3D Structure relationship ? 4/9/2002 Protein Classification - Wei Chen

Sequence V.S. Structure – 2 June, 2000 PDB 12500 SwissProt 86500 Sequence/Structure Ratio 7 : 1 Now 17679 101602 6 : 1 4/9/2002 Protein Classification - Wei Chen

Eukaryotic RNA Processing: Nucleus 4/9/2002 Protein Classification - Wei Chen

Transcription & Translation Side groups Chaperone Proteins Membranes Hydrogen bonds (between amino acids) 4/9/2002 Protein Classification - Wei Chen

Protein Classification - Wei Chen 20 Amino Acids A b c d 4/9/2002 Protein Classification - Wei Chen

Review of protein structure – 1 4/9/2002 Protein Classification - Wei Chen

Protein Classification - Wei Chen Terminology – 1 -helix -sheet Loop – regions of a protein chain which are, (1) between -helix & -sheet; (2) of various lengths & 3D configuration; (3) on the surface of the structure. Coil – region of secondary structure that is NOT a helix, a sheet, or a recognizable turn. 4/9/2002 Protein Classification - Wei Chen

Protein Classification - Wei Chen Terminology – 2 4/9/2002 Protein Classification - Wei Chen

Protein Classification - Wei Chen Finite State Automata 4/9/2002 Protein Classification - Wei Chen

Protein Classification - Wei Chen Flow Chart 4/9/2002 Protein Classification - Wei Chen

Supplementary Materials For Structure: http://www.rcsb.org/pdb/ (Brookhaven Protein Data Bank, PDB) 4/9/2002 Protein Classification - Wei Chen

Protein Classification - Wei Chen Further Materials 4/9/2002 Protein Classification - Wei Chen

Protein Classification - Wei Chen The Ramachandran Plot glycine van der Waals radi 4/9/2002 Protein Classification - Wei Chen

Protein Classification - Wei Chen cosq -sinq = [ x cosq + y sinq, -x sinq + y cosq ] [x,y] [ ] Demo sinq cosq y q x’ y’ y1 q x1 x z 4/9/2002 Protein Classification - Wei Chen

Protein Classification - Wei Chen References http://www.cryst.bbk.ac.uk/PPS95/course/3_geometry/rama.html http://mathworld.wolfram.com/Root-Mean-square.html Methods for Displaying Macromolecular Structural Uncertainty: Application to the Globins - Russ Altman, et al. 4/9/2002 Protein Classification - Wei Chen