Difference between revisions of "BIN-SX-Concepts"

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<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce; font-size:300%; font-weight:400; color: #000000; width:100%;">
 
Concepts of Molecular Structure
 
Concepts of Molecular Structure
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<div style="padding:5px; margin-top:20px; margin-bottom:10px; background-color:#b3dbce; font-size:30%; font-weight:200; color: #000000; ">
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(Structure determination - X-ray crystallography, NMR, EM)
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</div>
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<div class="keywords">
 
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<b>Keywords:</b>&nbsp;
 
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Structure determination - X-ray crystallography, NMR, EM
 
 
</div>
 
</div>
  
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{{Smallvspace}}
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__TOC__
 
  
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<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce33; font-size:85%;">
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{{DEV}}
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<div style="font-size:118%;">
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<b>Abstract:</b><br />
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</div>
 
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<div id="ABC-unit-framework">
 
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== Abstract ==
 
 
<section begin=abstract />
 
<section begin=abstract />
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<!-- included from "../components/BIN-SX-Concepts.components.wtxt", section: "abstract" -->
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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.
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...
 
 
<section end=abstract />
 
<section end=abstract />
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</div>
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<!-- ============================  -->
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<hr>
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<table>
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== This unit ... ==
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<tr>
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=== Prerequisites ===
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<td style="padding:10px;">
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<!-- included from "../components/BIN-SX-Concepts.components.wtxt", section: "prerequisites" -->
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<b>Objectives:</b><br />
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<!-- included from "ABC-unit_components.wtxt", section: "notes-external_prerequisites" -->
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This unit will ...
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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:
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* review methods of determining the high-resolution 3D-structure of biomolecules;
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<!-- included from "FND-prerequisites.wtxt", section: "biomolecules" -->
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* discuss the consequences (and limitations) of these approaches;
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* introduce principles of the computational analysis of structure coordinates.
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</td>
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<td style="padding:10px;">
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<b>Outcomes:</b><br />
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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;
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* can name various approaches to analyze 3D-coordinate sets including bond-, angle- and deihedral angle features, cumputing accessible surfaces, and mapping properties to surfaces.
 +
</td>
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</tr>
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</table>
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<!-- ============================ -->
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<hr>
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<b>Deliverables:</b><br />
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<section begin=deliverables />
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<li><b>Time management</b>: 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.</li>
 +
<li><b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.</li>
 +
<li><b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li>
 +
<section end=deliverables />
 +
<!-- ============================  -->
 +
<hr>
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<section begin=prerequisites />
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<b>Prerequisites:</b><br />
 +
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:<br />
 
*<b>Biomolecules</b>: The molecules of life; nucleic acids and amino acids; the genetic code; protein folding; post-translational modifications and protein biochemistry; membrane proteins; biological function.
 
*<b>Biomolecules</b>: The molecules of life; nucleic acids and amino acids; the genetic code; protein folding; post-translational modifications and protein biochemistry; membrane proteins; biological function.
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<!-- included from "ABC-unit_components.wtxt", section: "notes-prerequisites" -->
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This unit builds on material covered in the following prerequisite units:<br />
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You need to complete the following units before beginning this one:
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*[[BIN-Abstractions|BIN-Abstractions (Abstractions for Bioinformatics)]]
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*[[BIN-Abstractions]]
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<section end=prerequisites />
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<!-- ============================  -->
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</div>
  
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{{Smallvspace}}
  
  
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=== Objectives ===
 
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...
 
  
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=== Outcomes ===
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__TOC__
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<!-- included from "../components/BIN-SX-Concepts.components.wtxt", section: "outcomes" -->
 
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...
 
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=== Deliverables ===
 
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<!-- included from "../components/BIN-SX-Concepts.components.wtxt", section: "deliverables" -->
 
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<!-- included from "ABC-unit_components.wtxt", section: "deliverables-time_management" -->
 
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*<b>Time management</b>: 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.
 
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<!-- included from "ABC-unit_components.wtxt", section: "deliverables-journal" -->
 
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*<b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.
 
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<!-- included from "ABC-unit_components.wtxt", section: "deliverables-insights" -->
 
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*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].
 
  
 
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=== Evaluation ===
 
=== Evaluation ===
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<b>Evaluation: NA</b><br />
 
<b>Evaluation: NA</b><br />
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:This unit is not evaluated for course marks.
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<div style="margin-left: 2rem;">This unit is not evaluated for course marks.</div>
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<div id="BIO">
 
 
== Contents ==
 
== Contents ==
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{{Task|1=
 
{{Task|1=
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*Read the introductory notes on {{ABC-PDF|BIN-SX-Components|principles behind the determination of macromolecular 3D structure}}.
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*Read the introductory notes on {{ABC-PDF|BIN-SX-Concepts|principles behind the determination of macromolecular 3D structure}}.
 
}}
 
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==Introduction==
 
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Where is the hidden beauty in structure, and where, the "ultimate truth"? In the previous assignments we have discovered homologues of APSES domain containing proteins in all fungal species. This makes the domain an ancient protein family that had already duplicated to several paralogues at the time when the cenancestor of all fungi lived, more than 600,000,000 years ago, in the [http://www.ucmp.berkeley.edu/fungi/fungifr.html Vendian period] of the Proterozoic era of Precambrian times.
 
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In this assignment we will explore its molecular structure.
 
  
  
 
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== Further reading, links and resources ==
 
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<!-- {{#pmid: 19957275}} -->
 
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<!-- <div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> -->
 
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== Notes ==
 
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== Self-evaluation ==
 
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=== Question 1===
 
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<b>If in doubt, ask!</b> 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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:2017-08-05
 
:2017-08-05
 
<b>Modified:</b><br />
 
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:2017-08-05
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:2020-09-22
 
<b>Version:</b><br />
 
<b>Version:</b><br />
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:0.1
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:1.1
 
<b>Version history:</b><br />
 
<b>Version history:</b><br />
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*1.1 Maintenance
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*1.0 First live version
 
*0.1 First stub
 
*0.1 First stub
 
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Latest revision as of 09:27, 25 September 2020

Concepts of Molecular Structure

(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.

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.

    • 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.

    This unit builds on material covered in the following prerequisite units:


     



     



     


    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:


     


     


    About ...
     
    Author:

    Boris Steipe <boris.steipe@utoronto.ca>

    Created:

    2017-08-05

    Modified:

    2020-09-22

    Version:

    1.1

    Version history:

    • 1.1 Maintenance
    • 1.0 First live version
    • 0.1 First stub

    CreativeCommonsBy.png This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.

    Retrieved from "http://steipe.biochemistry.utoronto.ca/abc/index.php?title=BIN-SX-Concepts&oldid=11696"