Questions

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Specific questions for the MOL221 Computer Exercise

Here are the nine specific questions that you will work on in this exercise and the test proteins can be found here. Answers to the questions shall be presented in a Report in the form of a Powerpoint file (max 20 pages). Here are the guidelines for the Powerpoint Report.

(1) What is the biochemical reaction catalysed by the enzyme? Does it require any cofactors? Does it have any particular requirements for optimal function (e.g. temperature, pH, salt concentrations etc)?
http://www.uniprot.org/ (This site can most likely answer all the questions. Use other databases to confirm things annotated here if possible)
  • General annotation (name, function, …)
  • Uniprot accession number
  • Manual / automatic annotation
  • Uniprot abstract (protein summary)

and much more

http://brenda-enzymes.info (Search with ID found at Uniprot to be sure that you find the correct entry)
  • Name
  • EC number
  • Reaction catalysed
  • Word map
(2) What is the molecular composition of the enzyme? Is it monomeric, oligomeric, or is it embedded in a larger protein complex?
http://web.expasy.org/protparam/ (Use sequence or ID to predict protein parameters
  • Molecular Weight
  • Theoretical pI
  • Amino acid composition
  • Extinction coefficients
http://mips.helmholtz-muenchen.de (Click on Resources and Mammalian Protein Complexes (CORUM)). Note that http://www.uniprot.org/ may well have important information on protein complexes (check the "Interaction section")
  • Complex ID / Name
  • Complex Function
(3) Is the structure of the enzyme known? If so, does the structure reveal something about how the enzyme works? [this is a large question, and is not expected to be extensively covered]
http://www.rcsb.org/pdb/ (NB! Not all protein have a structure and usually only structured regions are in the solution structure)
  • PDB ID
  • Image of protein structure
  • Region covered
  • Method used
  • Resolution
http://www.ebi.ac.uk/pdbsum/ (Information about PDB entries).
  • Same as PDB
  • Ligand binding
  • Binding mechanism
  • Clefts, Pores, Interaction sites


(4) Where is it experssed in the organism (HUMAN only!!!)? Is it present in some organs or tissues than others?
http://www.ebi.ac.uk/gxa/home
  • Expression table
  • Map of where the protein (POI; protein-of-interest) is expressed (in human)
http://pax-db.org/ Protein Abundance Across Organisms
  • information on the relative abundance of proteins in different organisms and tissues. Data given in ppm: parts per million relative to all other protein molecules in the tissue type.


(5) Where in the cell is the enzyme localised? Is it cytoplasmic? Is it localised in a particular organelle (e.g. nucleus, mitochondia, plasma membrane), or is it secreted and/or associated with the surface of the cells? Are there isoforms of the enzyme with different localisations in the cells?
http://www.uniprot.org/
  • Much of this may be found in the Uniprot entry. It is otherwise possible to find this information in the scientific papers (see below), but that's very tedious and demanding task.
http://www.ncbi.nlm.nih.gov/pubmed (Collection of all (biomedical) publications)
  • This is a big job to look at. Focus on how this site work, and get a feeling how to search it (very specific search method [1]).


(6) Is there any data suggesting that the enzyme is post-translationally modified? (e.g. phosphorylation, acetylation, glycosylation, etc.)
http://www.phosphosite.org
  • Type of modification
  • Location of modification (residue number)
  • Is the modification implicated in function

Some of our proteins may have many modifications. If more than 5, report how many, and list the 5-10 first ones.

(7) Are there closely related enzymes in the human proteome? For this question, you must perform a sequence-based blastp search
"http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome"
(8) Is the enzyme conserved in evolution? I.e.: is it found in other organisms such as other vertebrates, chordates, insects, yeasts, and bacteria?
http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
(9) Are there interesting papers published about the enzyme during the last year (i.e. 2014 or 2015)
http://www.ncbi.nlm.nih.gov/pubmed
  • Try to find relevant information using advanced searches: MeSH, Timespan, or organism. Try to use the word map you found at Brenda enzymes enhance your search. Instructors will guide you on this task.
http://www.omim.org : On-line Inheritance in Man.

OMIM is rich source of information on human genes and gene products (e.g. proteins), with a perspective on genetic basis for disease, and has information on e.g.

  • gene (protein) function
  • biochemical features
  • molecular genetics
  • genetic variants

Note that OMIM sections are written in a chronological style.


Feel free to explore other web resources. Share your knowledge with your colleagues and instructors. Google is also a good source of information. Remember to write down where you found your information and how you searched.