Course catalogue doctoral education - VT24

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Title Protein Structure, Function and Disease
Course number 5561
Programme Neurovetenskap
Language English
Credits 4.5
Date 2022-09-15 -- 2022-12-08
Responsible KI department Institutionen för biovetenskaper och näringslära
Specific entry requirements Completed Master studies in the field of biochemistry, biotechnology, biomedicine, biophysics, chemical neuroscience or related subjects.
Purpose of the course The course deals with the molecular properties of proteins concerning their molecular structure and implementation in biology as well as protein misfolding and the relation to neurodegenerative diseases. It covers the general architecture of proteins, the relation of structure to function and mechanisms of regulations of protein function. It includes recent insights into the molecular mechanisms of protein aggregation and the link to neurodegenerative diseases. Moreover, it gives an overview about recent developments within methods for protein structure and dynamics determination, in particular X-ray crystallography, electron microscopy and nuclear magnetic resonance. The course will also train the participants to prepare scientific presentations and critically assess research literature.
Intended learning outcomes At the end of the course the students are expected to be able to:
• Understand how protein architecture is related to protein function
• Explain how protein dynamics, catalysis, binding sites and cofactors determine the protein structure-function relationship
• Identify and discuss control mechanisms of protein function, including competitive binding and cooperativity of ligands, post-translational modification and enzyme reactions
• Understand the principles and apply some tools for sequence alignment, homology modeling and structure prediction methods from protein sequence
• Show up-to-date knowledge of the working principles for major methods for protein structure and dynamics determination as well as microscopic nucleation mechanisms underlying protein aggregation
Contents of the course The course is divided into two parts.
The first part of the course is based on the course book “Protein Structure and Function” and related research articles and consists of:
• Protein structure (from primary to quaternary structure, protein stability and protein flexibility, etc.)
• From structure to function (binding sites, catalysis, cofactors, etc.)
• Control of protein function (mechanisms of regulation, binding ligands, post-translational modifications, etc.)
• Deriving protein function from sequence (sequence alignment, homology modeling, structure prediction, etc.)

The second part is based on lectures from the course directors and from invited specialists in the field, including
• Neurodegenerative disorders and protein misfolding
• Molecular mechanisms of protein aggregation
• Recent developments in protein structure and dynamics methods, including
o X-ray crystallography
o Electron microscopy
o Nuclear magnetic resonance
Teaching and learning activities The course consists of
• Student presentations of research articles related to Chapters in the course book. If suitable examples from the student’s own research can be included.
• Questions for student presentations by students (two students are assigned as “opponents” for each presentation) and audience
• Written tasks, including practical of bioinformatics tools, related to the content of the Chapters, which are handed in before each session
• Presentations by several invited specialists of the field
Compulsory elements Attendance of lectures, student presentations and exercise sessions is compulsory. Absence needs to be compensated for by a written task related to the lecture subject in agreement with the course director. Further, the students need to submit written tasks and perform one scientific presentation about a research article.
Examination The course content will be examined by written tasks as well as student presentations and oral examination of the topic by the course directors.
Literature and other teaching material Mandatory reading:
1. Gregory A Petsko, Dagmar Ringe
Protein Structure and Function
Oxford University Press Inc
ISBN: 9780878936632
224 pages
2. Additional lecture material (will be provided)
Number of students 8 - 15
Selection of students Selection will be based on 1) the relevance of the course syllabus for the applicant's doctoral project (according to written motivation), 2) start date of doctoral studies (priority given to earlier start date)
More information The course lectures will be held on a mainly bi-weekly basis (ca. 2-3 h for 9 occasions), distributed throughout the course period. The course will take place on Thursdays at Neo, Karolinska Institutet, Flemingsberg.
Additional course leader Dr. Axel Abelein, axel.abelein@ki.se Dr. Henrik Biverstål, henrik.biverstal@ki.se Prof. Jan Johansson, janne.johansson@ki.se
Latest course evaluation Not available
Course responsible Axel Abelein
Institutionen för biovetenskaper och näringslära

axel.abelein@ki.se
Contact person -