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[PPS] Principles of Protein Structure

The principles governing protein structure are covered in most biochemistry courses. The module reviews this knowledge and places it in the context of the subsequent work on structure determination. The module is also a suitable introduction for students from non-biological sciences who may wish to study structural biology.

Lecturer

Dr Muhammed Sayed, Department of Biotechnology (UWC), is a protein crystallographer who completed his post-doctoral studies under Professor Tom Blundell at Cambridge University. He will supervise the web-courses in protein structure and protein crystallography. His goal is to develop protein crystallography as a practical discipline.

Main Outcomes:

The ability to:

  • understand the physical and chemical principles which determine protein structure
  • describe and discuss the structures of one or more selected proteins in detail
  • present information about protein structure in the form of a website

Main Content

  • Primary Structure
  • Protein Geometry and Secondary Structure
  • Motifs and Domains
  • Tertiary and Quaternary Structure
  • Protein Synthesis
  • Protein Bioinformatics
  • Overview of Molecular Forces in Proteins
  • Protein Interactions
  • Molecular Immunology
  • In-depth study of a protein of the student’s choice
  • Structures of Membrane Proteins
  • Web Authoring

This module descriptor document also can be downloaded as an MS-Word document.

Home Department: Biotechnology (UWC)
Module description (Header): Principles of Protein Structure
Generic module name: Structural Biology
Alpha-numeric code: STB705
Credit Value: 10 Credits
Duration: 8 Weeks
Module Type: P
Level: 8
Prerequisites: None
Co-requisites: None
Prohibited combinations: None
Learning time breakdown (hours):
Contact with lecturer/tutor: 30
Assignments & tasks: 20
Tests & examinations: 0
Practicals: 0
Selfstudy: 50
Project: 10
Total Learning Time 100
Methods of Student Assessment: Oral presentations, assignments and webpage design. Moderation will be internal.
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Online Course

The following course material has been developed by the School of Crystallography, Birkbeck College, University of London and has been made available under licence to Professor B T Sewell, for students in the Structural Biology Course.

This module provides a systematic treatment of protein structure and integrates web and computer resources to create a novel teaching environment. Students should work through the material at their own pace and tutorials will be held regularly.

The course is modular and specific outcomes are listed in each section.

Dr Sayed’s lectures are copyright and available to registered students only. You may not copy them or distribute them in the original or modified form:

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Assessment

Students are required to construct a website describing a protein of their choice. The website should contain a description of the protein’s structure and function as well as diagrams that both give insight into the structure and function and display the student’s technological expertise. It is important that the student’s use the techniques outlined in the web-course and lectures to describe the protein and that relevant questions regarding the protein’s design are posed and answered. Some examples of such questions are given below.

Haemoglobin

  • How could we estimate experimentally the amount of helix in haemoglobin in solution?
  • How could we predict where the helices are from sequence? Are there features of the sequence that indicate an a-helical structure?
  • How is the haem bound? Could the globin fold without the haem?
  • What sequences are conserved in the evolution of the globin family and why?
  • Why is the haemoglobin tetramer symmetrical? What advantage does it have in function?
  • Are a-helical proteins particularly suited to allosteric effects? If so, why?
  • How does the mutation Valb7Glu lead to cell sickling? Why is it dependent on the state of oxygenation?

HIV Proteinase

  • Why is the Asp-Thr/Ser-Gly motif conserved?
  • Why is HIV proteinase a dimer?
  • What evolutionary relationship does HIV proteinase have with pepsin?
  • How has knowledge of the structure and catalytic mechanism been helpful in the design of AIDS antivirals?
  • How do single mutations lead to resistance to proteinase inhibitors? How has the pharmaceutical industry responded to this challenge?

Fibroblast Growth Factor Receptor

  • Could we predict that the domains of the receptor have immunoglobulin-like b-structures? What stabilises such domains and why are they so common in cell surface proteins?
  • How have the receptors evolved? Is it by gene duplication? If so, what from?
  • How is the b-trefoil structure formed? What stabilises such structures? Where else are b-trefoil structures found?
  • What kind of interactions are involved in the FGF:FGFR binary complex?
  • How does heparin bind to the FGF:FGFR complex? Is it mainly through ionic interactions?
  • How does the receptor signal? Is it through conformational changes or just by bringing molecules together?
  • How do the mutations found in Apert’s syndrome affect the assembly of the receptor complex and consequently cell signalling?

Judging Criteria

  • Completeness of the description of the protein’s structure and function – 30%
  • Neatness, layout and accessibility – 20%
  • Technological expertise displayed – 10%
  • Clarity of graphics displays and the quality of insights displayed – 20%
  • Formulation of questions and the quality of the answers – 20%
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References

The primary reference for the course is Branden and Tooze. Additional specific references are given in each section.

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