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

2. About This Presentation
Introduction
Review of protein structure
Terminology
Representation
Further Materials
Conclusion
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Protein Classification - Wei Chen

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

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

5. Eukaryotic RNA Processing: Nucleus
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Protein Classification - Wei Chen

6. Transcription & Translation
Side groups Chaperone Proteins Membranes
Hydrogen bonds (between amino acids)
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Protein Classification - Wei Chen

7. Protein Classification - Wei Chen
20 Amino Acids
A b c d
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Protein Classification - Wei Chen

8. Review of protein structure – 1
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Protein Classification - Wei Chen

9. 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.
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Protein Classification - Wei Chen

10. Protein Classification - Wei Chen
Terminology – 2
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Protein Classification - Wei Chen

11. Protein Classification - Wei Chen
Finite State Automata
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Protein Classification - Wei Chen

12. Protein Classification - Wei Chen
Flow Chart
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Protein Classification - Wei Chen

13. Supplementary Materials
For Structure: (Brookhaven Protein Data Bank, PDB)
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Protein Classification - Wei Chen

14. Protein Classification - Wei Chen
Further Materials
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Protein Classification - Wei Chen

15. Protein Classification - Wei Chen
The Ramachandran Plot
glycine
van der Waals radi
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Protein Classification - Wei Chen

16. 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
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Protein Classification - Wei Chen

17. Protein Classification - Wei Chen
References
Methods for Displaying Macromolecular Structural Uncertainty: Application to the Globins - Russ Altman, et al.
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Protein Classification - Wei Chen