BIN-SX-Concepts

Concepts of Molecular Structure

 

Keywords:  Structure determination - X-ray crystallography, NMR, EM

 

 

 

Abstract

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.

 

This unit ...

Prerequisites

You need the following preparation before beginning this unit. If you are not familiar with this material from courses you took previously, you need to prepare yourself from other information sources:

• Biomolecules: The molecules of life; nucleic acids and amino acids; the genetic code; protein folding; post-translational modifications and protein biochemistry; membrane proteins; biological function.

You need to complete the following units before beginning this one:

• BIN-Abstractions (Abstractions for Bioinformatics)

 

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

Evaluation: NA

This unit is not evaluated for course marks.

 

Contents

 

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:

• Read the introductory notes on principles behind the determination of macromolecular 3D structure.

 

 

Further reading, links and resources

 

Notes

 

Self-evaluation

 

 

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If in doubt, ask! If anything about this learning unit is not clear to you, do not proceed blindly but ask for clarification. Post your question on the course mailing list: others are likely to have similar problems. Or send an email to your instructor.

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About ...
 
Author:

Boris Steipe <boris.steipe@utoronto.ca>

Created:

2017-08-05

Modified:

2017-09-26

Version:

1.0.1

Version history:

• 1.0.1 Fixed typo in PDF link
• 1.0 First live version
• 0.1 First stub

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