212015.0 Protein structure
in Bioscience 4 sp (PSB)
Tiina Salminen, PhD, title of Docent (tiina.salminen@abo.fi)
Senior lecturer in structural biochemistry and bioinformatics
Structural Bioinformatics Laboratory, BioCity 3rd A floor
(www.abo.fi/fak/mnf/bkf/research/sbl)
Department of Biosciences
Åbo Akademi University
Pirkko Heikinheimo, PhD, title of Docent
University of Turku & University of Helsinki
Courses at Structural Bioinformatics
Laboratory (SBL)
Applied bioinformatics, comparative modeling, computer-
aided drug design
Applied Bioinformatics 8 sp
282001.0 Computer in Bioresearch (Applied Bioinformatics I) 2 sp:
Introduction to our computer system
www- course in Moodle
282002.0 Applied Bioinformatics 6 sp:
282003.0 Molecular modeling 4 sp
2010-2011: Protein structure in bioscience
283002.0 Structure-based drug design, 4 sp
2010-2011: Computer aided drug design
Course language is English but Swedish can be used in the
exam and project report
Dictionaries allowed and language is not taken into account
in grading
212015.0 Protein structure in Bioscience 4 sp
Sign-up Online:-17.01.2011:
Instructions on www-page: https://www.abo.fi/student/coursesbiosci
First register and then login with the e-mailed password
You must have an ÅA Student number to get your credits:
Fill in the Electronic JOO application (www.joopas.fi)
Sign-up for the exercises open after 18.1.2011 in Moodle
Do you have BioCity Magnetic Key?
The key can be programmed to allow access to this department
If you have an access to this department the time limit can be extended to
21.00 o’clock
If you wish that your key will be activated, please, contact me after this
lecture
212015.0 Protein Structure in Bioscience 4 sp
• Lectures (10 h)
• Computer exercises (10 h)
• Quiz (short exam): Amino acids & Terminology and principles of protein
structure (in the beginning of the 2ndsTutorial) – Material in Moodle
• Exam: 2-4 course exam dates:
1. Exam: 4.3 Friday 10.15-12.00
2. Exam 11.3 Friday 10.15-12.00
• Project work + report (10 h)
– will be done in pairs at your own time
Grade : ~ Quiz 10%+ Exam 70% + Project 20%
Literature
Course material in Moodle: http://moodle2.vasa.abo.fi/
BIOVET – Biovetenskap - Protein structure in bioscience
Moodle enrollment key: PSB2011
Course language is English
You may contact me in English, Swedish or Finnish
Exam/project can be done in English or Swedish
Literature
Liljas, A., Liljas, L., Piskur, J., Lindblom, G., Nissen, P.,
Kjeldgaard, M. (2009) Textbook Of Structural Biology
Xiong, J. (2006) Essential Bioinformatics
Höltje, H.-D., Sippl, W., Rognan, D., and Folkers, G. (2003)
Molecular Modeling. Basic Principles and Applications.
(Second edition); 3rd edition 2008
212015.0 Protein Structure in Bioscience
Lectures: Week 6
7.2 Monday:13.15-15.00 Aud Biokemi
Introduction
Quiz material: Terminology and Principles of protein structure
8.2 Tuesday:10.15-12.00 Aud Biokemi
3D Structure determination methods
9.2 Wednesday: 13.15-15.00 Aud Biokemi
Sequence alignment; Bodil presentation
Introduction to computer exercises
212015.0 Protein Structure in Bioscience
Computer exercises Obligatory!
Computer room, Biochemistry and Pharmacy, ÅA, BioCity 3rd floor
15 Linux/(Windows dual boot) workstations
Will be done alone or in pairs
Project work relies on the computer exercises!
5 Tutorials (1,2,3,4,5) – 3 groups (A,B,C=TERBIO, D)
Exercise 1:Searching and saving protein structure
Exercise 2:Quiz & Pymol: a program to visualise protein structures
Exercise 3: Analysis and comparison of enzymes structures: serine proteases
Exercise 4:Analysis and comparison of receptors structures: integrins
Exercise 5:Alpha-mannosidose mutant
Computer exercises
Sign-up in Moodle
Group C is available ONLY for University of Turku Health Bioscience students (TerBio).
Group D is designed for University of Turku Bioinformatics students (Note dates!)
15 places (18 in group C) available/exercise
Preferentially, choose the same group for all tutorials but you may choose a different group as
well!
212015.0 Protein Structure in Bioscience
Lectures: Week7
14.2 Monday:13.15-15.00 Aud Biokemi
Alpha-mannosidases
15.2 Tuesday: 10.15-12.00 Aud Biokemi
Integrins
Exam
You may choose one of the course exam dates
Sign-up in Moodle
Week 9
4.3 Friday 10.15-12.00 1. Exam Aud Biokemi
Week 10
11.3 Friday 10.15-12.00 2. Exam Aud Biokemi
3rd exam? Suggestions?
Projects – select in Moodle
Based on protein structures and related articles
Project submitted in Moodle
At your own time
Preferably in pairs (can be done alone)
Project descriptions in Moodle
Information in Moodle
You may work with your own protein of interest!
Send an email and tell about the protein
Week12
21.3 Monday Dead line for PROJECT REPORTS
Grade : ~ Quiz 10%+ Exam 70% + Project 20%
Projects – select in Moodle
Protein-Protein Interaction Inhibiting the Enzyme
Integrin Activity
Growth Hormone Receptor Cyclooxygenase-1
Haemoglobin HMG-CoA reductase
Type 5 phosphodiesterase
Protein-Ligand interaction Dihydrofolate reductase
α2A -adrenergic receptor β-lactamase
β2 adrenergic receptor HIV protease
β1-adrenergic receptor HIV reverse transcriptase
(pdb 1FK9)
Disease causing mutations Own project?
Projects – select in Moodle
E.g. Protein-Protein Interaction:
Integrin (PDB ID 3HI5, 3HI6)
Explain conformational changes upon ligand binding
Search for the structures from the protein structure database (PDB)
Search for the related article
Explain the desired details:
With figures (prepared with Pymol) and figure text
Supporting text: Introduction, Results, Concluding remarks, References
Focus on the requested data – you cannot explain everything!
Ask for help if you have a problem
21.2. and 22.2 in computer room (group D)
By email
Project report in a poster form
Use the example layout
Make the project report in a A4
poster form according to the
example (left) in Moodle
Why structural biology?
”In order to understand, we need to see.”
“Seeing is believing.”
James Watson 1964:
“Unfortunately, we cannot accurately describe at the
chemical level how a molecule functions unless we first
know its structure”
Why protein structures?
Proteins have key functional roles needed for life
Function by specific recognition of other molecules
Recognition leads to changes (shape, chemistry,
interactions) that lead to functional effects
Enzymes, receptors, hormones, transport proteins,
immunoglobulin, structural protein, motor proteins,
signaling proteins, storage proteins
Structures are valuable in interpreting
sequence-structure-function relationship
Find out the requirements for protein folding, stability,
dynamics and function
Predict the function of a protein
Explain the effect of polymorphism or other mutations
Establish new or modify old function e.g.
Increase stability (e.g.. thermostability in washing powders )
Modified enzymes in chemical processes
Analyze interactions
Protein –ligand interactions
Drug design – develop new compounds that bind to protein
Protein – protein interactions in biological processes
Explain the results from experimental studies
Design new experiments to test predictions
After this course the student:
is familiar with protein 3D structures, comparison and superposition of
3D structures, protein evolution, sequence alignment and sequence-
structure-function relationship
can critically utilize scientific literature and data deposited on protein
3D structures
knows how to relate published data on protein structures to its biological
function
can formulate a project report on the performed task