1. Protein Evolution: Introduction to Protein Structure and Function http://tinyurl.com/7hplr7 http://tinyurl.com/ protEvolEllsEmblSept2009 Please open the link to the session pages:

2. Protein Evolution: Introduction to Protein Structure and Function Ricardo Rodriguez de la Vega, Aidan Budd and Francesca Diella EMBL Heidelberg, Germany Tuesday 29th September 2009 budd@embl.dediella@embl.devega@embl.de

3. Introduction We are computational biologists working at EMBL Exercises use DATA and SOFTWARE that is available to EVERYONE WITHOUT COST via the internet exactly the same data we work with as researchers Teaching using sequence and structural data thus: is cheap/affordable brings students very close to the everyday work of scientific researchers

4. Understanding/Studying Evolution Two main questions in most evolutionary studies: 1. What was the form of my system of interest at some point in the past? E.g. was the common ancestor of birds and mammals warm-blooded? 2. How (i.e. which changes occurred, and why those particular changes) did the system change over evolutionary time? E.g. did a recent or an ancient gene dupilcation give mice two hemoglobin-alpha-chain genes? To ask interesting evolutionary questions, you need to understand as well as possible the system as it is today

5. Protein Structure

6. Primary Protein Structure Protein Primary Structure: Sequence of amino acids making up polypeptide chains

7. Primary Protein Structure image: Wikimedia Commons Proteins: One (or more) polypeptides Different amino acids have different R groups Two ends of peptide are chemically different N-H C=O Peptides Polymers of amino-acids linked by peptide bonds

8. Primary Protein Structure 20 different amino acids specified by genetic code Polypeptide/protein sequence given using 20-letter alphabet “words” e.g.: YISCT image: Wikimedia Commons Different chemistry of termini makes TIS different from SIT Tyrosine - Isoleucine - Serine = TIS

9. Primary Protein Structure Protein Primary Structure: Sequence of amino acids making up polypeptide chains 1. SDNVLIT 2. SNDIVLT 3. TLVIDNS 4. TVLIENS Quiz Which sequence best describes this peptide? http://tinyurl.com/ckhyhy

10. Peptide Structure repeating backbone units different sidegroups terminals different chemically diversity of backbone structure (helix, sheet, loop) flexibility of structure how much space these atoms take up (spheres representation) PyMOL demonstrations using short peptide regions to show:

11. Secondary Structure the two kinds of regular/repeating secondary protein structure alpha-helices beta sheets most globular protein structure made up of these structures cartoon representations PyMOL demonstrations of short regions of peptide chain to show: Secondary Structure Local 3D orientation of peptide chain - compare later to tertiary structure

12. Tertiary Structure tertiary protein structure with both sheets and helices hemoglobin protein structure with different representations sticks spheres cartoons (often the best to get impression of overall structure) function involves binding things for hemoglobin, this is haem 3D fold of protein allows stable positioning of chemical groups to make interactions possible PyMOL demonstrations of: Tertiary Structure Global description of 3D structure of a polypeptide chain

13. Quaternary Structure interaction of 4 hemoglobin chains to form the functional tetramer PyMOL demonstration to show: Quaternary Structure The arrangement of several folded polypeptides to form a multi-unit complex

14. Intrinsically Unstructured Proteins Lots of the proteome is NOT globluar/intrinsically stably-structured! BUT it is still functional and hence important e.g.: specifying protein-protein interactions transporting proteins around the cell FHA domain interacting with phosphothreonine (PDB: 1k3q)

15. Intrinsically Unstructured Proteins Approximately 25% of human proteins have >50 residues of disordered sequence

16. Sequence Alignments Protein Sequence Alignment Set of protein sequences lined up against each other so that “similar” residues in different sequences are placed in the same column Sequences are aligned by choosing where to insert gaps for best agreement between the sequences Demo Using JalView we see how agreement changes when gaps are placed differently Key tools for analysing protein structure and evolution Shows that protein sequences have clearly changed/evolved between different organisms etc.

17. Conclusion Evolution of protein sequence: What sequence did the ancestral proteins have? Which amino acid changes occured to yield extant sequences? Which genetic events (point mutations? recombinations? gene duplications?) occurred during the evolution of the sequences? Evolution of protein structure: Did the ancestral protein have the same quaternary structure as the extant proteins? How much did the secondary structure change from the ancestral protein structure to the extant structures? Do different amino acid changes happen at same frequency in different kinds of secondary structural elements? We can now formulate interesting questions about protein structure/sequence evolution e.g.: