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Prospectus

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Design and Self-assembly of Biomolecules (DSB)

Course
2020-2021

Admission requirements

Elective course MSc Chemistry, MSc Life Science and Technology
Students with a BSc MST/LST or equivalent. Students with a BSc in other subjects should have knowledge of peptide/protein structure.

Description

This course is intended to give students an insight into peptide/protein design and self-assembly, and an introduction to membrane proteins (including their design) and DNA nanotechnology.
A brief recap of protein primary, secondary, tertiary and quaternary structure will be given at the beginning of the course, before the so-called ‘protein folding problem’ will be explained and discussed. The remainder of the course will focus on how researchers are designing and self-assembling peptides and proteins. Design principles for secondary structural elements will be presented, as will strategies for how these small peptides can be programmed to self-assemble into both discrete and extended assemblies. The course will then move on to protein design, focusing on three different strategies: de novo design (bottom-up design), protein redesign (top-down design), and computational design. Examples of applications for such designed and self-assembled systems will also be covered, meaning the course moves from the fundamentals of design through to applications.

Course Objectives

At the end of this course students:

Will be able to design elements of protein secondary structure such as α-helices, β-strands and polyproline type-II helices.
Will understand, through case-studies from the literature, how peptides and proteins can be programmed to self-assemble to form higher-order structures, and what kinds of functions such structures can fulfil.
Will be able to describe the advantages and disadvantages of de novo design, protein redesign, and computational design in creating new protein structures and functions.
Will have knowledge of the principles of DNA nanotechnology.
Will be able to critically evaluate a research paper and present this to the group.

Timetable

Schedule information can be found on the website of the programmes. Assignment deadlines are communicated via Brightspace.

Mode of instruction

Lectures and guest lectures. Students will give presentations in small groups on a relevant literature paper of their own choice.

Assessment method

Written exam (50%) If circumstances prevent a physical on-campus exam, assessment will take the form of an essay of 2000 words on the different approaches to protein design. Any changes to the assessment measures will be communicated via Brightspace a minimum of ten working days before the original scheduled exam date.
Group presentations (50%) Group presentations and lectures may be delivered online if necessitated by corona measures.
Several of the later lectures in the course will focus on recent literature. Students will benefit from reading, in advance, the papers that will be discussed during the lectures.

Reading list

All relevant literature will be provided on Brightspace at least seven days before the relevant lecture.

Registration

Register for this course via uSis

Contact

Dr. Aimee Boyle

Remarks

According to OER article 4.8, students are entitled to view their marked examination for a period of 30 days following the publication of the results of a written examination. Students should contact the lecturer to make an appointment for such an inspection session.