Protein Evolution:Introduction to Protein Structure and Function

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http://tinyurl.com/protEvolEllsEmblSept2009

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Protein Evolution:Introduction to Protein Structure and Function

Ricardo Rodriguez de la Vega, Aidan Budd and Francesca Diella

EMBL Heidelberg, GermanyTuesday 29th September 2009

budd@embl.de diella@embl.devega@embl.de

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

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

Protein Structure

Primary Protein Structure

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

Primary Protein Structure

image: Wikimedia Commons

Proteins:One (or more) polypeptides

Different amino acids have different R groups

Two ends of peptide are chemically differentN-HC=O

PeptidesPolymers of amino-acids linked by peptide bonds

Primary Protein Structure

20 different amino acids specified by genetic codePolypeptide/protein sequence given using 20-letter alphabet “words” e.g.:

YISCTimage: Wikimedia Commons

Different chemistry of termini makes TIS different from SIT

Tyrosine - Isoleucine - Serine = TIS

Primary Protein Structure

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

1. SDNVLIT 2. SNDIVLT 3. TLVIDNS 4. TVLIENS

QuizWhich sequence best describes this peptide?

http://tinyurl.com/ckhyhy

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:

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 StructureLocal 3D orientation of peptide chain - compare later to tertiary structure

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 StructureGlobal description of 3D structure of a polypeptide chain

Quaternary Structure

• interaction of 4 hemoglobin chains to form the functional tetramer

PyMOL demonstration to show:

Quaternary StructureThe arrangement of several folded polypeptides to form a multi-unit complex

Intrinsically Unstructured Proteins

QuickTime™ and aPNG decompressor

are needed to see this picture.

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)

Intrinsically Unstructured Proteins

Approximately 25% of human proteins have >50 residues of disordered sequence

Sequence Alignments

Protein Sequence AlignmentSet 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

DemoUsing 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.

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.: