Schedule Protein Engineering 2017 (1BG301)Monday, Monday, 28 August – Friday, 27 October SLU: Monday, 28 August – Monday, 30 October

The course is given together with SLU course, ”Protein Technology” (BI1163). Blue text marks the UU-specific events. A separate printed version will be distributed to the SLU students.Req: x indicates a compulsory part of the course.

Teachers (in alphabetical order of first name, except SM and JS):Sherry Mowbray (SM) Jerry Ståhlberg, SLU (JS)Adrian Suarez Covarrubias (ASC) Benjamin Schmuck, SLU (BKMS)Annette Roos (AR) Mikolaj Chmielarz (MC)Annika Söderholm (AS) Lena Henriksson, IBG (LH)Dirk Hasse (DH) Ylva Adolfsson, IBG (YA)Gunilla Carlsson (GC)Sanjeewani Sooriyaarachchi (SS)Sebastian Deindl (SD)Yashraj Kulkarni (YK)

First Week Req.Monday August 2812:15-14:00 Course presentation, goals, grading and

organization. Check email addresses to use. Ylva and Jerry will take attendance (at kl 13:00). Lena presents DiaNa at kl 13:30.

BMC: A3:117a SM, JS, YA, LH

x

14:15-16:00 Assign and take photographs of groups; exercise on reading a paper. SM will send

BMC: A3:117a SM x

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email with self-study questions today; each student should email answers to SM at a later date (specified on schedule below).

Tuesday August 2910:15-12:00 Lecture: Protein Structure/Function 1 BMC: A7:115 SM13:15-17:00 Exercise: Protein Structure/Function 1;

checking computer accounts, starting to use graphics program

BMC: A11:009b/A11:015b

SM, JS, YK, BKMS

x

Wednesday August 3010:15-12:00 Lecture: Protein Structure/Function 2;

introduction to lab protein, and to extra credit project on pKas.

BMC: A7:115 SM

13:15-17:00 Exercise: Protein Structure/Function 1, continued (allows extra time if needed; this computer lab session is not compulsory).

BMC: A11:009b/A11:015b

SM, YK, BKMS

Thursday August 3110:15-12:00 Lecture: Binding and catalysis;

introduction to lab proteinBMC: A3:117a JS

13:15-17:00 Exercise: Protein structure/function 2, binding and catalysis.

BMC: A11:009b/A11:015b

JS, YK, BKMS

x

Friday September 110:15-12:00 Lecture: Enzyme kinetics and inhibition;

students should remember to buy a notebook (to use on Thursday next week)

BMC: A3:117a JS

13:15-17:00 Exercise: Enzyme kinetics and inhibition BMC: A11:009b/A11:015b

SM, JS, AS x

Second WeekMonday September 410:15-12:00 Lecture: Sequence and structure

comparisonsBMC: A3:117a JS

13:15-17:00 Exercise: Sequence and structure comparisons

BMC: A11:009b/A11:015b

JS, YK, MC x

Tuesday September 510:15-12:00 Lecture: Stability BMC: A3:117a SD13:15-17:00 Exercise: Stability

Email kinetics answers any time before midnight tonight (to SM).

BMC: A11:009b/A11:015b

SD, YK, MC x

Wednesday September 610:15-12:00 Lecture: Constructs for expression BMC: A3:117a ASC13:15-17:00 Send SM answers to self-study questions

any time before midnight today. Bring lab notebooks tomorrow!

BMC: A11:009b/A11:015b

SM

Thursday September 710:15-12:00 Lecture: Mutation with a purpose; BMC: A3:117a SM x

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explanation of how wet lab will work, and how lab notebook should look.

13:15-17:00 Exercise: Design mutations(Start using your lab notebook! Remember, you’ll hand the notebook in later for grading; grading criteria are on the website. Leave space for the table of contents at the front; include descriptions of mutants and primers you designed.)

BMC: A11:009b/A11:015b

SM, AR, JS, YK

x

Friday September 810:15-12:00 Lecture: Mutagenesis methods for the wet

labBMC: B8:001 ASC x

13:15-17:00 Exercise: Design primers; use your lab notebook to describe your plan!

BMC: A11:009b/A11:015b

ASC, YK, SS, DH

x

Third WeekMonday September 1110:15-12:00 Lecture: Heterologous expression BMC: A7:103 ASC13:15-17:00 Get take-home examination by email.

Computer lab booked for your convenience.

BMC: A11:009b/A11:015b

SM

Tuesday September 1210:15-12:00 Lecture: Protein purification BMC: A7:103 JS13:15-16:00 Exercise: Protein purification strategies BMC:

A11:009b/A11:015b

JS, SM, YK, BKMS

x

16:00-17:00 Exercise: Protein purification reports; note that tomorrow’s events are at the EBC!

BMC: A11:009b/A11:015b

JS, SM, YK, BKMS

x

Wednesday September 13 9:15-12:00 Present mutations planned for wet lab.

Note this is at EBC!EBC: Lindahlsalen

SM, ASC and company

x

12:15-13:15 Meeting for UU kursombud EBC: Sal 2 (Swedish) or Sal 3 (English)

Thursday September 1410:15-12:00 Lecture: Storage and analysis of protein

samples I.BMC: A5:001 SD

13:15-15:00 Lecture: Storage and analysis of protein samples II.

BMC: A9:001 SD

Friday September 1510:15-13:00 Presentation of biosciences research at

SLU, including lunchSLU Biocenter, A-241

JS

13:15-15:00 Lecture: Industrial enzymes SLU Biocenter A-241

JS

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Fourth WeekMonday September 1810:15-12:00 GLP, safety introduction, reminders on

keeping individual lab notebooks; grading criteria are on the website!

BMC: B7:101a ASC, SS, DH x

13:15-17:00 Lab BMC: B5:1, lab 1

ASC, SS, DH x

Tuesday September 199:00-17:00 Lab BMC: B5:1, lab

1ASC, SS, DH x

Wednesday September 209:00-10.00 Lab, inoculate cultures, 1 h. Teachers will

start the 37 °C incubation in the afternoon.BMC: B5:1, lab 1

ASC, SS, DH x

10:15-12:00 Lecture: Drug design, and membrane proteins.

BMC: A9:001 SM

Send in take-home examination by email by midnight today.

BMC: A11:009b/A11:015b, booked 13-17

SM (send in exam)

Thursday September 219:00-17:00 Lab BMC: B5:1, lab

1ASC, SS, DH x

Friday September 229:00-17:00 Lab BMC: B5:1, lab

1ASC, SS, DH x

Fifth WeekMonday September 259:00-17:00 Lab BMC: B5:1, lab

1ASC, SS, DH x

Tuesday September 269:00-17:00 Lab BMC: B5:1, lab

1ASC, SS, DH x

Wednesday September 279:00-12:00 Lab BMC: B5:1, lab

1ASC, SS, DH x

Afternoon UU course info daySLU course info day

Thursday September 289:00-17:00 Lab BMC: B5:1, lab

1ASC, SS, DH x

Friday September 299:00-17:00 Lab BMC: B5:1, lab

1ASC, SS, DH x

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Sixth WeekMonday October 29:00-late? Lab, start cleanup. BMC: B5:1, lab

1ASC, SS, DH x

Tuesday October 39:00- late? Lab: assay day, finish cleanup. GC will

give an introduction at the beginning.BMC: B5:1, lab 1

SM, AR, GC, JS, ASC, AS

x

Wednesday October 410:00-12:00 Book a time with one of us to check your

assay results and calculations. We will come at times agreed on, but will not be there continuously.

BMC: A11:009b/A11:015b

SM, AR, GC, AS?

13:00-15:00 Student Conference in Science and Technology

At EBC?

Thursday October 510:00-17:00 Book times with us…

Adrian’s workshop on sequencing results is at kl 11.

BMC: A11:009b/A11:015b

SM, AR, GC, ASC, AS?

Friday October 610:15-17:00 Book times with us… Send your

presentation to SM BEFORE kl 18 on Sunday!

BMC: A11:009b/A11:015b

SM, AR, GC, AS?

x

Seventh WeekMonday October 99:15-16:00 Present lab results (Groups 1-6 from kl 9-

12, then Groups 7-12 from kl 13-16)BMC: A7:111 SM and

companyx

Hand in lab notebook for grading SM xTuesday October 10Morning Study for exam13.15-14.00 Lecture: X-ray crystallography and

validationBMC: B7:111a SM

14:15-17:00 Exercise: X-ray crystallography BMC: A11:009b/A11:015b

SM, YK, BKMS

x

Wednesday October 11Morning Study for exam12:15-13:15 Meeting for UU kursombud EBC: Sal 2

(Swedish) or Sal 3 (English)

Thursday October 12Morning Study for exam13.00-15.00 Exam BMC: B8 SM xFriday October 1310:15-12:00 Self-grading of exam. Project startup. BMC: A1:111a SM x

Work on projects

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Eighth WeekMonday October 16

Work on projectsTuesday October 17

Work on projectsWednesday October 18

Work on projectsThursday October 19

Work on projects13:00-15:00 Visit to GE Healthcare (Linus Laurin)Friday October 20

Work on projects

Ninth WeekMonday October 23

Work on projects SMTuesday October 24

Work on projects SMWednesday October 2510:15-17:00 Work on projects; send your presentation

to SM before kl 18 today.SM

Thursday October 269:15-12:15 Present projects, section 1. You need to

attend the whole session your group is in.BMC: A5:001 SM, ASC,

othersx

13:00-17:00 Present projects, section 2. You need to attend the whole session your group is in.

BMC: A5:001 SM, ASC, others

x

Friday October 2710:00-13:00 Present projects, section 3. You need to

attend the whole session your group is in.BMC: A5:001 SM, ASC,

othersx

13-15 Course evaluation and DiaNa report (can be filled in whenever/wherever you like, but the computer rooms are booked for this time today)

BMC: A11:009b/A11:015b

SM

Grading UU: (see course web pages for details of grading in each part of the course)Each assignment is graded, and points are given. The assignments are then returned to you, with comments and/or correct answers. A pass for any specific item is 50%; you will need to redo items you do not pass.

The points are combined in the end as follows:

Theoretical block (7 ETCS, 47%):Grading: 0-100% on self-study questions for computer labs (individual, 5%)Grading: 0-100% on kinetics exercise (individual, 5%)Grading: pass/fail on purification exercise (group, 5%)Grading: 0-100% on take-home exam (individual, 16%)Grading: 0-100%on final exam (individual, 16%)

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Lab block (5 ECTS, 33%):Grading: 0-100% on presentation of mutations planned in the lab (group, 8%)Grading: 0-100% on presentation of lab results (group, 15%)Grading: 0-100% on lab notebook (individual, 10%)

Project block (3 ECTS, 20%):Grading: 0-100% on project (group, 20%)

For the final grade, 0-65 = fail, 66-75 = 3, 76-84 = 4, 85-100 = 5.

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