SBNet - Graduate Course "Protein Structure & Analysis"

Biomedical Centre, Uppsala - 22-26 June, 1998

The course will be devoted to architecture and analysis of protein structures. In addition, experimental methods for investigating protein structure will be discussed (NMR, X-ray, EM, MS). The course will consist of lectures (open to all interested scientists and students; lecture hall A11), and a practical part (limited to 22 students and post-docs). Tutors include:

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Background and preparation

For the morning lectures of this course (presented by Prof. Carl-Ivar Brändén), the first edition of his book serves as an excellent introduction (the lectures will deal mostly with additions to the second edition of this book):

  C. Brändén & J. Tooze
  "Introduction to Protein Structure"
  Garland Publishing, Inc.
  New York and London, 1991
  ISBN 0-8153-0344-0 (hard cover)
  ISBN 0-8153-0270-3 (paperback)
All participants are strongly encouraged to read at least chapters 1-5 and 16-17 (and preferably the entire book) before the start of the course.

For some of the lectures additional course material will be handed out (e.g., literature list, reprints, book chapters).

Students who participate in the computer practicals are assumed to be familiar with the use of Netscape. Some experience with Rasmol or Chime is advantageous, but not strictly necessary (we'll provide a brief introduction at the start of the first practical).

Full-course participants

The following persons have been selected as participants in the full course (lectures plus practicals):

Number First name Last Name E-mail Affiliation Supervisor M/F
1 Patrik Andersson KI Otting (NMR) M
2 Gunnar Berglund UU Hajdu (X-ray) M
3 Enrique Carredano SLU Eklund (X-ray) M
4 Devapriya Choudhury SLU Eklund (X-ray) M
5 Michel Fodje LU Liljas (X-ray) M
6 Svenja Frischolz SU Lindberg (Cell Biol.) F
7 Talal Gariani UmU Eriksson (X-ray) M
8 Hongwei Guo GU Sjölin (X-ray) F
9 Nina Susanna Hakulinen Joensuu Univ. Rouvinen (X-ray) F
10 Niklas Hellgren KI Ladenstein (X-ray) M
11 Mohammed Homman KI Möller/Söderberg-Naudér M
12 Ying Liu Oslo Univ. Reichelt (Med. Fac.) F
13 Anders Magnusson KTH Holmquist/Hult (Biotechnol.) M
14 Winfried Meining KI Ladenstein (X-ray) M
15 Inés Muñoz SLU Ståhlberg (X-ray) F
16 Andrzej Poplawski UU Nordström (Microbiol.) M
17 Ulla Rütschi GU Rymo (Clin. Chem.) F
18 Ann-Charlotte Thuresson UU Virtanen (Med. Genet.) F
19 Valentina Burkow Vollan Tromsö Univ. Hough (X-ray) F
20 Erik Wallin SU von Heijne (Biochem.) M
21 Susanne Wisén UU Mannervik (Biochem.) F
22 Susanne Witt SU von Heijne (Biochem.) F
23 Ulla Elofsson LU ? F


We have booked hotel rooms for:

The hotel lies within walking distance from the railway station in Uppsala:

  "Basic Hotell"
  Kungsgatan 27
  753 21 Uppsala
  Phone: 018 - 4805000
  Fax:   018 - 4805050
We will pay the hotel bills, but any personal expenses (e.g., use of the telephone) you will have to pay yourself when you check out.

If you arrive by plane, you can use the direct bus connection from Arlanda Airport to Uppsala (get off at the railway station); cost 75 SEK.

Practical information

How to get to the Biomedical Centre (BMC) ? From central Uppsala, there are several buses that pass the Biomedical Centre ("Biomedicum", "Dag Hammarskjöldsväg"). Bus 16 leaves from the railway station, others (e.g., 12, 20) leave from the town centre.

For those travelling from Stockholm by car (E4): when you arrive in Uppsala, there is a roundabout ("Gnistarondellen"). Turn left in this roundabout ("Centrum/Sjukhus") and follow this road for 4.0 km. Then turn right (onto Dag Hammarskjöldsväg), go straight ahead in the roundabout, and take the first exit to the left. Immediately turn right onto the parking lot.

Getting into the BMC. When you are in front of the building (Dag Hammarskjöldsväg), you need to enter through entrance A11 (on the right). The entrances to the building will be locked for the Summer. However, on Monday morning between 8:30 and 9:00, Kristina Bäckbro will be at entrance A11 to let you in.

We have a number of entrance cards for the building (which will work for one week). These will be available to participants from outside Uppsala (there will be a 100 SEK deposit, which is refunded when you hand the card in again).

If you arrive later, use the telephone at the entrance and dial any of the following extensions to try and get in touch with someone who can come down and open the door for you: 4177, 4983, 4543, 4616, 4566, 4007, 4537, 4475, or 4008 (if you dial from a cellular phone, prefix 018-471 to each of these numbers). If you have no luck at all, and if you have access to a cellular phone, dial 070-494 1690 (Gerard's cellular phone).

Please, do NOT leave any of the outer doors open, as this will set off the alarm (and annoy a lot of people) !

Lectures and practicals. All lectures will be held in lecture hall A11 (entrance A11, then two floors up). All computer practicals will be held in the IBG Computer Lab ("Cellen"; entrance A11, in the basement).

Information for full-course participants only. Full-course participants can register between 8:30 and 9:00 on the Monday morning in the sitting area outside the lecture hall. You will receive a badge, course material, expense claim form (save tickets & receipts !), etc.

Lunch will be at the BMC Restaurant; you will receive lunch coupons which entitle you to a hot meal, including salad, and a drink or coffee. The location for the dinners on Monday to Thursday is "Bistro Blå" in Döbelnsgatan, conveniently located close to the BMC. The course dinner on Friday night will be at restaurant "Akropolis" (which has a very good Greek kitchen).

Those of you who attend >90% of all lectures and practicals will receive an "intygg" that states that you have participated in the course (40 hours), and that may be of use if you want to claim credit for the course at your home institute. Students who attend >90% of all lectures can also get an "intygg" (for 20 hours) if they notify the organisers in advance.


Morning sessions: 09:00 - 12:30 (incl. breaks)
Lunch (12:30 - 14:00)
Afternoon sessions: 14:00 - 17:30 (incl. breaks)
Dinner (18:00 - 20:00)
Evening lecture (20:00 - 21:00)

Monday, 22 June

I-1 - 09:00 - 09:40 (Binder A)

Motifs and domains 1

Carl-Ivar Brändén

The following literature will be handed out:
  • P. Bork, A.K. Downing, B. Kieffer, and I.D. Campbell (1996). Structure and distribution of modules in extracellular proteins. Q. Rev. Biophys. 29, 119-167.

I-2 - 09:50 - 10:30

Motifs and domains 2

Carl-Ivar Brändén

I-3 - 11:00 - 12:30

Practical I

Carl-Ivar Brändén & Tom Taylor

  1. SCOP and CATH
  2. Classify:
    • Staphylococcus nuclease
    • Elastase
    • Cytochrome b5
    • Adenosine deaminase
  3. Compare transducin and neuraminidase. Does neuraminidase have a seventh blade ?

I-4 - 14:00 - 15:30 (one short break) (Binder C/D)

X-ray for NMRists

Alwyn Jones

The following literature will be handed out:
  • T.A. Jones and M. Kjeldgaard (1997). Electron-density map interpretation. Meth. Enzymol. 277, 173-208.
  • G.J. Kleywegt and T.A. Jones (1997). Model building and refinement practice. Meth. Enzymol. 277, 208-230.

I-5 - 16:00 - 17:30 (one short break) (Binder E)

NMR for crystallographers

Paul Driscoll

A combined literature list for lectures I-5 and II-4 will be handed out.

I-6 - 20:00 - 21:00 (Binder F)

Structural properties of T-cell antigen CD2 revealed by NMR and X-ray analysis

Paul Driscoll

Tuesday, 23 June

II-1 - 09:00 - 09:40 (Binder G)

Transcription factors I

Carl-Ivar Brändén

The following literature will be handed out:
  • Brändén and Tooze: DNA recognition by eucaryotic transcription factors.

II-2 - 09:50 - 10:30 (Binder H)

Transcription factors II

Carl-Ivar Brändén

The following literature will be handed out:
  • Brändén and Tooze: Specific transcription factors belong to a few families.

II-3 - 11:00 - 12:30

Practical II

Carl-Ivar Brändén & Tom Taylor

  1. Make a topological comparison between p53 and immunoglobulin domains
  2. Find another transcription factor with similar topology

II-4 - 14:00 - 15:30 (one short break) (Binder I/J)

Analysis and validation of NMR models

Paul Driscoll

A combined literature list for lectures I-5 and II-4 will be handed out.

II-5 - 16:00 - 17:30 (one short break) (Binder K)

Refinement and validation of X-ray models

Gerard Kleywegt

The following literature will be handed out:
  • G.J. Kleywegt and T.A. Jones (1995). Where freedom is given, liberties are taken. Structure 3, 535-540.
  • G.J. Kleywegt and T.A. Jones (1996). Phi/psi-chology: Ramachandran revisted. Structure 4, 1395-1400.
How credible are those beautiful pictures of protein crystal structures that you see in Nature, Science, and Cell almost every week ? How much of a crystallographic protein model is based on experimental data, and how much on the imagination of the crystallographer ? What do you have to look for when you read a crystal structure paper in order to get some idea as to how reliable the model is ? Is a 3 Å model really equally trustworthy as a 1.2 Å one ?

II-6 - 20:00 - 21:00 (Binder L)

Electron microscopy for crystallographers and NMRists

Hans Hebert

The lecture will focus on applications of high resolution EM in structural biology. This discipline can be divided into electron crystallography of thin, ideally 2-D crystals at one extreme and single randomly oriented particles at the other. A fundamental question to be addressed is what kind of information we can expect from different types of specimens. Is it for example possible to obtain atomic models? The resolution level depends on several factors, such as specimen preparation, conditions for data collection and strategies for image processing which all will be discussed briefly during the lecture.

Wednesday, 24 June

III-1 - 09:00 - 09:40 (Binder M)

Receptors and signal transduction I

Carl-Ivar Brändén

The following literature will be handed out:
  • Brändén and Tooze: Signal transduction.

III-2 - 09:50 - 10:30 (Binder M)

Receptors and signal transduction II

Carl-Ivar Brändén

III-3 - 11:00 - 12:30

Practical III

Carl-Ivar Brändén & Tom Taylor

  1. Which TIM-barrel structures have a metal atom in the active site ?
  2. What are the ligands to the metal and from which loop regions do they come ?

III-4 - 14:00 - 15:00 lecture (Binder O)

III-4 - 15:30 - 17:30 practical

PDBsum and SAS - summaries, structural analyses and inter-relationships

Roman Laskowski

III-5 - 20:00 - 21:00 (Binder P/Q)

Mass spectrometry as a tool in protein research

Bengt Norén

With the development of new ionizations techniques in mass spectrometry it has become an indispensable tool in the protein research. The Matrix Assisted Laser Desorption/Ionization (MALDI) and Electrospray Ionization (ESI) are today the dominating techniques which coupled to the high sensitivity of MS instrumention allows protein identification in the femtomole and even attomole range. The presentation will give a glimpse of the recent development in protein MS with examples of some applications.

Thursday, 25 June

IV-2 - 09:00 - 09:40 (Binder N)

Other membrane proteins

Carl-Ivar Brändén

The following literature will be handed out:
  • Brändén and Tooze: Membrane proteins.

IV-1 - 09:50 - 10:30 (Binder R)

Proteins of the immune system

Carl-Ivar Brändén

IV-3 - 11:00 - 12:30

Practical IV

Carl-Ivar Brändén & Tom Taylor

(Continuation of yesterday's practical)

IV-4 - 14:00 - 15:00 lecture (Binder T)

IV-4 - 15:30 - 17:30 practical

CATH - classification of protein structures

Roman Laskowski

IV-5 - 20:00 - 21:00 (Binder U)

Mats Kihlén

Drug design

Friday, 26 June

V-1 - 09:00 - 09:40 (Binder B)

Folding and flexibility

Carl-Ivar Brändén

The following literature will be handed out:
  • Brändén and Tooze: Folding and flexibility.

V-2 - 09:50 - 10:30 (Binder X/Y/Z)

Prediction, engineering and design

Carl-Ivar Brändén

The following literature will be handed out:
  • Brändén and Tooze: Prediction, engineering and design.

V-3 - 11:00 - 12:30

Practical V

Gerard Kleywegt

Using tools accessible via the ProSAL (Protein Sequence Analysis Launcher) facility, try to find as much structural information as you can about the following protein:

You may use the following prepared page to start your searches from.

V-4 - 14:00 - 15:00 lecture (Binder Å/Ä/Ö)

V-4 - 15:30 - 17:30 practical

From sequence to structure

Roman Laskowski


Course dinner

Restaurant "Akropolis"

Web resources

  1. Structures
  2. Sequences
  3. Validation
  4. Literature
  5. Roman's practicals
  6. Miscellaneous
  7. Pre-prints

SBNet Latest update at 12 November, 1999.