Course catalogue doctoral education - HT18

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Title Understanding and fighting disease using structural biology
Course number 3047
Programme 1-Ingår i flera program
Language English
Credits 3.0
Date 2018-04-09 -- 2018-04-20
Responsible KI department Institutionen för biovetenskaper och näringslära
Specific entry requirements The course will be limited to 12-14 participants decided by the course responsible persons
Purpose of the course The course will first introduce X-ray crystallography, electron microscopy (EM) and nuclear magnetic resonance spectroscopy (NMR), the three main methodologies used to experimentally determine the three-dimensional structure of proteins. Doctoral candidates will then be introduced to molecular dynamics (MD) simulations, analyze how point mutations can cause diseases at the molecular level and gain a basic understanding of the structure-based drug design process.
Intended learning outcomes By following this course, doctoral candidates will learn how the three-dimensional structure of proteins is determined, and how this information can be used to both understand human disease at the molecular level and facilitate the rational development of novel therapeutics.

In particular, Ph.D. candidates will be able to understand the most important biochemical and biophysical properties of proteins and, based on this knowledge, learn to choose and apply protocols for expressing and purifying proteins for structural studies. Following the practicals, the candidates will also be able to bioinformatically analyze protein sequences and structures in order to predict their characteristics and functions.

At the end of the X-ray crystallography module, Ph.D. candidates will be able to read a protein crystallization diagram; list the different crystallization techniques; understand diffraction basics; describe the data collection, processing and refinement procedures; explain the phase problem and its solution by experimental phasing or molecular replacement; validate crystal structures downloaded from the Protein Data Bank.

The electron microscopy module of the course will provide an introduction to the basics of EM. This knowledge will provide a foundation for understanding the technique and its applications. At the end of the module, the candidates will be able to understand the basics concepts of EM and its differences from other structure determination techniques; list the advantages and limitations of EM for structure determination; describe the overall functioning and instrumentation of an electron microscope; explain the interaction of electrons with the sample and the process of image formation; understand the principles of 3D reconstruction from projection images; compare the process of model building in EM with other structure determination techniques.

The NMR lecture will provide a basic overview of the information that one can obtain by spectroscopically probing the chemical environment of atomic nuclei. Doctoral candidates will understand how an NMR machine is built, what chemical shifts are, and what are the differences between 1-D, 2-D and 3-D NMR experiments. They will then be introduced to the concept of assignments, and how this can be combined with MD simulations to produce a set of molecular models consistent with distance restraints derived from experimental measurements. Towards this goal, an introduction to MD simulations will be given. Finally, the differences between NMR-derived models and those obtained by the other techniques will be discussed. Thus, at the end of the lecture, the PhD candidates will be able to list the advantages and limitations of all methods presented and compare protein structures obtained through these different approaches.

After the last lecture, the doctoral candidates will be able to give recent examples describing how human mutations can cause diseases by affecting the structure of proteins and their ability to perform their biological function. They will also have gained a basic knowledge of how lead compounds/drugs bind to their molecular targets, and how structural biology can be of high medical relevance by allowing to optimize the affinity and specificity of this interaction.
Contents of the course Theoretical: The lectures will open with an introduction to protein structure and function (1), followed by a presentation of protein expression and purification strategies (2). Then the theoretical background needed for understanding X-ray crystallography (3), EM (4) and NMR as well as MD simulations (5) will be given. At the end, we will go through examples of how gene mutations can lead to diseases and explain how knowledge of molecular structures can contribute to drug discovery (6). Practical: The Ph.D. candidates will work through six projects during the two weeks: (1) analysis of protein structure elements and properties using PyMOL; (2) protein purification; (3) protein structure determination by X-ray crystallography; (4) protein structure determination by EM; (5) comparison of protein structures obtained by X-ray crystallography, EM and NMR using PyMOL; (6) analysis of structure-function relationship for a selection of medically relevant proteins.
Teaching and learning activities Lectures, laboratory work, presentation and discussion of current biomedically relevant research in the field of structural biology.
Compulsory elements Seminar presentations and laboratory work are compulsory. If a Ph.D. candidate misses a practical exercise, they will be given a chance to complete it at another occasion set by the organizers.
Examination Reports from practical exercises and journal club-like presentations of scientific articles describing protein structure of biomedical interest. ILOs will be studied both theoretically and through practical exercises. Each ILO will be tested through questionnaires that have to be submitted in electronic form at the end of each day.
Literature and other teaching material Compendium containing a selection of recent structural biology studies relevant for biomedicine; protocols for practical work.
Number of students 8 - 10
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) date for registration as a doctoral student (priority given to earlier registration date).
More information The course is given jointly by the doctoral programmes in Neuroscience, Development and regeneration, Metabolism and endocrinology and Tumor Biology and Oncology. See: http://ki.se/en/staff/doctoral-programmes.
Additional course leader Course responsible: Hans Herbert and Luca Jovine.
Earlier evaluation of the course Not available
Course responsible Hans Hebert
Institutionen för biovetenskaper och näringslära

Hans.Hebert@ki.se
Contact person Luca Jovine
Institutionen för biovetenskaper och näringslära

Luca.Jovine@ki.se


Carsten Mim
Institutionen för biovetenskaper och näringslära

carsten.mim@ki.se