Expected Preparations:

  Biomolecules:
The molecules of life; The genetic code; Nucleic acids; Amino acids; Protein folding; Post-translational modifications and protein biochemistry; Membrane proteins; Biological function.
   [BIN]
Abstractions 		 
  If you are not already familiar with the prior knowledge listed above, you need to prepare yourself from other information sources.   The units listed above are part of this course and contain important preparatory material.  
Keywords: Structure determination; X-ray crystallography; NMR; EM
Objectives:

This unit will …

  • review methods of determining the high-resolution 3D-structure of biomolecules;

  • discuss the consequences (and limitations) of these approaches;

  • introduce principles of the computational analysis of structure coordinates.

 Outcomes:

After working through this unit you …

  • can name the main experimental approaches for structure determination and list their relative merits;

  • apply your knowledge of structure quality metrics to choose structures that are most suitable for analysis;

  • appreciate the importance of stereo vision to understand 3D-structures;

  • can name various approaches to analyze 3D-coordinate sets including bond-, angle- and deihedral angle features, cumputing accessible surfaces, and mapping properties to surfaces.

Deliverables:

Time management: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.

Journal: Document your progress in your Course Journal. Some tasks may ask you to include specific items in your journal. Don’t overlook these.

Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.

Evaluation:

NA: This unit is not evaluated for course marks.

Contents

Experimental determination of the 3D-structure of biomolecules has provided amazing insight into biological mechanisms. In this unit we review principles of structure determination, how structure is abstracted and stored, tools and principles for visualizing structure, and how the analysis of structure provides a spatial map of features and properties.

 

How could the search for ultimate truth have revealed so hideous and visceral-looking an object?
Max Perutz  (on his first glimpse of the Hemoglobin structure)

 

Task…

 

Questions, comments

If in doubt, ask! If anything about this contents is not clear to you, do not proceed but ask for clarification. If you have ideas about how to make this material better, let’s hear them. We are aiming to compile a list of FAQs for all learning units, and your contributions will count towards your participation marks.

Improve this page! If you have questions or comments, please post them on the Quercus Discussion board with a subject line that includes the name of the unit.

References

Page ID: BIN-SX-Concepts

Author:
Boris Steipe ( <boris.steipe@utoronto.ca> )
Created:
2017-08-05
Last modified:
2022-09-14
Version:
1.1
Version History:
–  1.1 Maintenance
–  1.0 First live version
–  0.1 First stub
Tagged with:
–  Unit
–  Live
–  Has lecture slides

 

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