Bioinformatics Exercises
Over the last two decades, information has been gaining increasing importance in both
teaching and learning biochemistry. The most obvious case is the sequencing of the
human genome and many other complete genomes. In 1990, the determination of the
sequence of a protein was often the topic of a full publication in a peer-reviewed journal
such as Science, Nature, or The Journal of Biological Chemistry. Now entire genomes
are the topic of individual research papers. The term "bioinformatics" is a catch-all
phrase which generally refers to the use computers and computer science approaches to
the study of biological systems. The main chapters where this information is discussed
in the text are chapters 3 (Nucleotides, Nucleic Acids and Genetic Information), 5
(Proteins: Primary Structure), 6 (Proteins: Three-Dimensional Structure), 12 (Enzyme
Kinetics, Inhibition and Regulation) and 13 (Introduction to Metabolism). Here we
provide exercises appropriate to these chapters aimed at introducing the techniques of
bioinformatics that involve the use of computers, Internet-accessible databases and the
tools that have been developed to “mine” those databases.
General principles
Open ended questions. The exercises may include some questions that have definite
answers, but in many cases there will also be questions which may be answered in a
number of ways, depending on the approach you take or the topic you select.
2. Stable Internet Resources. As much as possible, the exercises will be based on well
established, stable web sites. If it is necessary to use less reliable sites and/or
resources, attempts have been made to provide multiple sites that perform similar
functions.
3. Here are the stable online resources that will be used most frequently:
1.
a.
b.
c.
d.
e.
f.
g.
h.
i.
Genbank (http://www.ncbi.nlm.nih.gov/)
Protein Data Bank (http://www.rcsb.org)
Expasy Proteomics Server (http://us.expasy.org/)
European Bioinformatics Institute (http://www.ebi.ac.uk/)
Pfam (http://www.sanger.ac.uk/Software/Pfam/)
SCOP (http://scop.mrc-lmb.cam.ac.uk/scop/)
CATH (http://www.biochem.ucl.ac.uk/bsm/cath/)
PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi)
PubMed Central (http://www.pubmedcentral.nih.gov/)
Answer key. Where a definite answer is known, it will be provided in an answer key.
For more open-ended questions, a typical correct answer will be presented.
5. Historical perspective. If historical resources are available online (including
PubMed), there may be questions designed to help students identify some of the
historical roots of biochemistry and molecular biology.
4.
Project 10: Drug Design and Cholesterol Medications
Resources
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The Nobel Foundation (http://www.nobelprize.org/)
KEGG: the Kyoto Encyclopedia of Genes and
Genomes (http://www.genome.jp/kegg/)
PubChem (http://pubchem.ncbi.nlm.nih.gov/), a
resource from the National Center for Biotechnology
Information that divides and links information for
bioassay, compound and substance for thousands of
metabolites. The image of cholesterol show here was taken from the PubChem
site.
PubMed Central (http://www.ncbi.nlm.nih.gov/pmc/), an archive of free full-text
articles from the life sciences provided by the National Center for Biotechnology
Information
The Protein Data Bank (http://www.rcsb.org/pdb/) is a repository of published
macromolecular structures.
Software
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ChemAxon MarvinSketch
(http://www.chemaxon.com/products/marvin/marvinsketch/)
Cholesterol is the most decorated molecule in the history of science. It was most
recently recognized in 1985, when Michael S. Brown and Joseph L. Goldstein received
the 1985 Nobel Prize in Physiology and Medicine
(http://www.nobelprize.org/nobel_prizes/medicine/laureates/1985/press.html), "for
their discoveries concerning the regulation of cholesterol metabolism". Visit the Nobel
Foundation web site (http://www.nobelprize.org/) to find at least one more prize that
was awarded for research on cholesterol.
Cholesterol is a hydrophobic molecule that tends to clump together in an aqueous
environment. This makes it quite effective as a contributor to the stability of
membranes; it also makes it potentially lethal if it accumulates in our bloodstreams. A
number of different approaches have been developed to reduce cholesterol levels in the
blood. In this exercise, we will explore two families of drugs that are used to treat
cholesterol: bile acid sequestrants and statins.
1. Bile Acid Sequestrants
The study of these medications is more of a focus on the application of analytical
methods to medicine than a bioinformatics challenge. Nonetheless, it is an interesting
study and will contrast markedly with the development of the statins. We will start by
finding out what they are, then we will consider how they work.
1. What is a bile acid?
a. Visit KEGG and search for “bile acid”. Explore the links there to find (1) the
metabolic starting point for bile acids synthesis and (2) the names of some
bile acids.
b. Use the name of one of these bile acids to find its structure at PubChem to
paste in here.
c. At PubChem, scroll down the page to find the section on Biosystems and
Pathways. Follow the links in this section to find out the metabolic role of
bile acids.
2. What is a bile acid sequestrant?
a. Use your favorite Internet search engine to search for “bile acid
sequestrants”. Report your findings.
b. Based on your search, what is the structure of one of these compounds?
c. Before it was used as a bile acid sequestrant, how was this material used in
the lab?
3. Continue your search to find more questions about bile acid sequestrants.
a. Identify three medically prominent bile acid reductants.
b. What is the goal of medical treatment with these compounds?
c. How do they work? If you are having difficulties finding answers to these
questions, you may wish to focus on sites like WebMD
(http://www.webmd.com/) or a major research hospital like The Mayo Clinic
(http://www.mayoclinic.com/).
d. You may have already answered this question - how does the action of bile
acid sequestrants relate to cholesterol metabolism?
2. Statins
Your study of how the bile acid sequestrants reduce blood cholesterol levels almost
certainly led you to consider the regulation of cholesterol synthesis. While the bile acid
sequestrants reduce cholesterol levels by drawing off products that are synthesized from
existing cholesterol, the statins are a newer group of cholesterol-lowering drugs that
directly reduce the synthesis of cholesterol.
1.
Section 7 of Chapter 20 covers cholesterol metabolism. Review this material to
find the enzyme that controls the rate of cholesterol synthesis. Continue reading
that section for a brief review of statins as inhibitors of this enzyme.
2.
3.
4.
Search the Protein Data Bank for structures of this enzyme that contain a bound
statin (just search for “statin”). When you find a structure that contains a statin
(e.g. 3CD0), scroll down the page to find the section labeled “Ligand Chemical
Component” or “External Ligand Annotations”. What is the binding affinity of the
statin to the enzyme? How does this compare to the binding affinity for the
substrate to the enzyme (see your textbook)?
Next, hover your mouse over the small chemical structure that is shown in the
box.
In the case of PDB entry 3CD0
(http://www.rcsb.org/pdb/explore/explore.do?structureId=3CD0), the structure
that appears looks like this.
Notice that the name of the ligand is given, but that no synonym is provided.
Search for a protein structure containing a statin that has a synonym (several of
these were published in 2001 - 2003). That means it is probably a commonly
prescribed medication. List the PDB id for the structure, the name of the statin and
the Kd for the statin. As an alternative, you can simply search the Internet for
statins to find some common medications. Under external ligand annotations, what
terms do they use to describe the binding affinity? What is the meaning of these
terms?
5. Use the name of the statin from the PDB entry to search PubChem to search for its
structure, which you should insert here. Explore the PubChem entry to find similar
molecules.
6. The history of the discovery and development of statins is documented in the
literature. Here are three references, but many more can be found on PubMed
Central.
Akira Endo. A Historical Perspective on the Discovery of Statins
(http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3108295/?tool=pmcentrez). Proc
Jpn Acad Ser B Phys Biol Sci. 2010; 86(5): 484–493.
Some valuable information can be found in a review of the book Triumph of the
Heart: the Story of Statins by Jie Jack Li, (Oxford University Press, 2009) in
Chemical & Engineering News
(http://pubs.acs.org/cen/books/87/8723books.html).
Lovastatin and beyond: the history of the HMG-CoA reductase inhibitors by
Jonathan A. Tobert in Nature Reviews Drug Discovery 2, 517-526 (July 2003).
Use these resources to answer the following questions.
a. Who discovered statins?
b. What was the original source of statins?
c. When was a statin first approved as a prescription drug? What was the name
of the drug? Are there any structures in the Protein Data Bank that contain
this statin?
d. Identify one or more additional statins that are currently legal to prescribe in
your country.
e. Find these statins on PubChem and compare their structures. How are they
similar and how are they different?