Plant Proteomics Tutorial and Online Resources. Manish Raizada University of Guelph

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1 Plant Proteomics Tutorial and Online Resources Manish Raizada University of Guelph

2 A Brief Introduction to Proteins -A. Structural proteins make large structures (eg. microtubule cables to pull chromosomes apart during mitosis/meiosis) protein cables From Biochemistry and Molecular Biology of Plants (W.Gruissem, B. Buchanan and R.Jones p.236 ASPP, Rockville MD, B. Enzymes - catalyze biochemical reactions - the key to life demo Rather than 2 reactive molecules trying to find each other by random diffusion, an enzyme binds both molecules in close proximity at its active site. The enzyme positions the two molecules in place, thus decreasing the activation energy required for the chemical reaction to proceed. From Biology of Plants p. 80 (P.Raven, R.Evert, S. Eichhorn) Worth Publishers, New York, 1992 From Introduction to Protein Structure p.206 C. Branden and J. Tooze Garland Publishing, New York, 1999 Slide 2.2

3 How does an enzyme function? Enzymes - Because biochemical molecules come in different sizes, shapes, with different surface charges (charged, polar, hydrophobic), then in order for proteins to grab onto them, they must form a "glove", a pocket at the active site containing the appropriate charges. It must have a second pocket to grab onto a second molecule Molecule 1 Molecule 2 Enzyme Enzyme + molecules Change in Protein Conformation After binding the two substrates, the enzyme may need to change its shape in order to position them closer together. In addition, the chemistry may need to be protected from the aqueous environment -- for example, a charged molecule may be more attracted to water than to the second molecule involved in the biochemical reaction. In such a case, the charged molecule needs to be hidden away from the outside of the protein into a hydrophobic pocket inside the protein. Because the binding site of the molecule must be near the surface of the protein, the binding must cause a change in conformation of the protein such that the bound molecule is rotated into a cavity inside the protein. hydrophobic hydrophobic hydrophobic hydrophobic protective cavity H 2 0 charged Pictures from M. Raizada H 2 0 H 2 0 H 2 0

4 How do herbicides, pesticides or pharmaceuticals work?: 1. The chemical mimics the real substrate and competes for the enzyme active site. Enzyme native herbicide substrate (eg. nitrogen metabolism) 2. The chemical binds elsewhere to the enzyme, and because of its charge, alters the conformation of the enzyme, causing it to be no longer functional. - Enzyme-herbicide binding Native enzyme Enzyme + herbicide In addition, other molecules (phosphate groups, sugars, lipids) can bind onto proteins and alter its conformation, thus either activating its function or preventing its function. Inactive enzyme Charged phosphate Activated enzyme **Hence, small molecules can be used to switch on/off enzymes**. Source of pictures: M. Raizada

5 How does an enzyme fold? demo -Parts of the protein interact with other parts of the protein (eg. plus to negative, hydrophobic to hydrophobic) to create loops. -After substrate binding, the local charge might be altered, causing the active site to be more attracted to another internal region of the protein, hence causing a change in protein conformation. + Hydrophobic - stretches + - Hydrophobic stretches + - *+ uncharged region Source of cartoonss: M. Raizada Substrate-binding alters local protein charge Positive attracted to negative, causes change in conformation From Introduction to Protein Structure p.56 C. Branden and J. Tooze Garland Publishing, New York, 1999

6 Amino Acids and Proteins To facilitate the binding of molecules and changes in protein conformation, proteins have an arsenal of 20 amino acid building-blocks, each with a unique size, shape and charge. + P P H P P H H - P P From Biochemistry and Molecular Biology of Plants (W.Gruissem, B. Buchanan and R.Jones p.360 ASPP, Rockville MD, 2000 P * P H H H H What charges can amino acids have? + positive charged - negative P polar H hydrophobic * very flexible

7 Amino acids join together through peptide bonds that can rotate. Why is this useful? rotate From An Introduction to Genetic Analysis (6th ed) A.J. Griffiths et al., page346 W.H. Freeman and Co., New York, 1996 rotate

8 By placing these at particular places relative to each other in a 3-dimensional chain, they can form the binding sites necessary to bind molecules for biochemistry or bind one another to form large structures. Specific amino acids bond to specific regions of the reactant molecule. From Introduction to Protein Structure p C. Branden and J. Tooze Garland Publishing, New York, 1999

9 Regular Arrangement of Amino Acids Creates Secondary Structures

10 Protein enzymes can adopt multiple shapes by folding. Protein Folding To review, what are the molecular functions of an enzyme? Therefore, why are the shapes of proteins important? How many different protein shapes (unique folds) are there in all of life? Is this a surprise? TIM Barrel - Rubisco Horsheshow - RNasin Beta roll - transcription factor Beta barrell - GFP

11 Bonds between amino acids can create elaborate secondary and higher order scaffolds upon which or within which the biochemistry can be performed. alpha-helix scaffold beta-sheet scaffold From Biochemistry and Molecular Biology of Plants (W.Gruissem, B. Buchanan and R.Jones) p ASPP, Rockville MD, 2000 Alpha/beta scaffold structures create pocket for enzyme active site From Introduction to Protein Structure p.73 C. Branden and J. Tooze Garland Publishing, New York, 1999

12 Predicting How a Protein to Fold is Tricky Excellent Review: Fersht and Daggett (2002) Cell 108:

13 Interior of proteins tend to be hydrophobic. The outside of the protein is called the surface-exposed or aqueous-exposed side. There are ~1000 folds in ALL of nature!!!!! Proteins are fragile, based on small-large numbers of amino acid contacts to stabilize structure. Any particular protein has multiple ways that it can fold predicting the correct one is the holy grail of molecular biology!!!

14 Post-Translation and Folding Correct 3-D protein folding: -to create correct enzyme active site and shape -only <1000 folds in all of life!!! -DNA is rigid, but amino acid peptide bonds can rotate, so many combinations -other protein complexes (chaperones) assist in folding in a destabilizing aqueous environment --chaperonin From Biochemistry and Molecular Biology of Plants (W.Gruissem, B. Buchanan and R.Jones p Any change in the local charge or size can cause changes in protein conformation or binding to DNA, etc.. 2. The addition or loss of small molecules (phosphates, lipids, glucose) can be used as an on/off switch for protein activity.

15 Proteins interact with other proteins: Interactome of Yeast From Tyers and Mann (2003) Nature 422:

16 Proteins are basically a carbon scaffold upon which charged or hydrophobic surfaces exist to create precise pockets/interaction surfaces to conduct biochemistry or create scaffold polymers. C - carbon scaffold, unreactive N,O,P,S - precise decorations to make reactive

17 Protein Tutorials Scenario: You isolate a peptide from Arabidopsis Chloroplasts from immunoprecipitation. You conduct peptide sequencing: GAVLSGKFCSQSIVQDYELLAASGPRKLSEATVSSS 1. You want to identify this gene. Perform a BLAST search: What are: Blastn? Blastp? Tplastn? Which type of Blast search do you need to perform? Copy and paste the above amino acid sequence here. On the next window, scroll down to Organisms, and select Arabidopsis. Then hit Format above.. What is the protein? Before you close this window, highlight and copy the full amino acid sequence 2. Has this gene been studied in Arabidopsis? 1.If so, what is the name of the gene? 2. What chromosome is located on? 3. Do TDNA insertion alleles exist? Are there publications? 4. What does the enzyme do? Highlight and copy the full amino acid sequence from Genbank Go to Under Analysis Tools, perform a BLAST Search Choose BlastP, for Dataset, choose: AGI (Proteins) Paste the amino acid sequence, then Run Blast. Choose the sequence with the best homology score (e.g. zero) Click on the TAIR link ( Result At4g )

18 3. Find the protein features of phytoene desaturase from Arabidopsis in the UniProt Database, the world s largest catalog of proteins: Go to text search, type in phytoene desaturase Choose: CRTI_ARATH Note the Synonym is EC What is this? 4. What is the precise chemical reaction performed by phytoene desaturase? Use the IUBMB Enzyme Nomenclature Database, determine Type in phytoene desaturase What does E.C enzyme class do? Click on E.C homepage at the bottom of the page above What are the 4 main categories in which enzymes are classified? (E.C.#) Go to: 5. What is the 3D Structure of this enzyme? Go back to UniProt: Find phytoene desaturase CRT1_ARATH again. What is the 3D protein structure of this enzyme? Scroll down to Database Cross-References, click PFAM link: PF01593 What is the 3D structure? Also check PDB, Protein Databank, the world s Largest database of 3D protein structures: Type in Phytoene Desaturase and hit search. Are there any hits? Try just Desaturase Click on any image. For display options, click WebMol, grant this session, then once Downloaded, click on protein and scroll to rotate For fun, Search PDB again, but for Rubisco. Take a look at the structure.

19 Additional Links of Protein Interest E.C. Number - Enzymes are given a 4 digit universal number tag, called the E.C. number based on function: Excellent 3D Visualization Programs (requires free download of Chime Software) Mac Requires Netscape, not IE: Protein Explorer Review of Chemistry (for Biology) Review of Primary, Secondary, Tertiary Protein Structure: Nice article on the importance of correct protein folding: Introduction to Protein Folding Introduction to Enzymes: Databases that cluster proteins into families based on 3D structure and function: SCOP (Structural Classification of Proteins) SUPFAM Databases of Enzyme Function and Links: Expasy (also has lots of online molecular biology programs)

20 Useful Online Protein and Plant Proteomics Databases, Software and Reviews: UniProt: World s Largest catalog of proteins Check links from igap: Proteome 3D protein structure and domain assignment. Genome Biol. (2003): 4, R51 (July 28) MIPS: Analysis and annotation of protein - contains software. Nucl. Acids. Res. (2004) Jan 1: 32 AMPDB: Arabidopsis Mitochondrial Protein Database Nucl. Acids. Res. (2005) 1, 33 D PlantsP: Plant protein phosphorylation database: Plant Cell (2004) 16, Organelle DB: A database to proteins localized to organelles and subcellular Structures in diverse Eukaryotes (25,000 proteins, 60 organelles or structures) Nucl. Acids. Res. (2005) 1, 33 D (Database Issue) AtNoPDB: Arabidopsis nucleolar protein database. Nucl Acid Res.(2005) 1, D PHYTOPROT: Clustering of plant proteins in families. Nucl. Acid. Res. (2004): 32: D Good Reviews: Van Wijk, K.J. (2001) Challenges and prospects of plant proteomics. Plant Physiol. 126, Kersten et al. (2002) Large-scale plant proteomics. Plant Mol. Biol. 48, Borevitz and Ecker (2004) Plant genomics: the third wave. Annu Rev Genomics Hum Genet. 2004;5:

21 Proteins Need to be Localized to the Correct Compartment References for Online Software and Database Localization Programs: O Emanuelsson, H Nielsen, and G von Heijne ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites Protein Sci., May 1999; 8: A. I. Schein, J. C. Kissinger, and L. H. Ungar Chloroplast transit peptide prediction: a peek inside the black box Nucleic Acids Res., August 15, 2001; 29(16): e R. Schwacke, A. Schneider, E. van der Graaff, K. Fischer, E. Catoni, M. Desimone, W. B. Frommer, U.-I. Flugge, and R. Kunze ARAMEMNON, a Novel Database for Arabidopsis Integral Membrane Proteins Plant Physiology, January 1, 2003; 131(1): I. Westerlund, G. von Heijne, and O. Emanuelsson LumenP--A neural network predictor for protein localization in the thylakoid lumen Protein Sci., October 1, 2003; 12(10): V. A. Eyrich and B. Rost META-PP: single interface to crucial prediction servers Nucleic Acids Res., July 1, 2003; 31(13):

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