User:Eric Martz/Introduction to Structural Bioinformatics I: Difference between revisions
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==Overview and Goals== | ==I. Overview and Goals== | ||
In these two classes, you will | In these two classes, you will | ||
# Be introduced to structural biology and structural bioinformatics. | # Be introduced to structural biology and structural bioinformatics. | ||
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# Email your .pptx file to '''emartz@microbio.umass.edu''' for grading.--> | # Email your .pptx file to '''emartz@microbio.umass.edu''' for grading.--> | ||
==Computer Lab Preparation ([https://www.bio.umass.edu/biology/bcrc BCRC])== | ==I. Computer Lab Preparation ([https://www.bio.umass.edu/biology/bcrc BCRC])== | ||
#Log in | #Log in | ||
#Run Firefox | #Run Firefox | ||
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#Take a look around Proteopedia. Click on the ''PDB codes'' below, or the ''Random'' links to see other molecules. | #Take a look around Proteopedia. Click on the ''PDB codes'' below, or the ''Random'' links to see other molecules. | ||
==Protein Structure and Structural Bioinformatics== | ==II. Protein Structure and Structural Bioinformatics== | ||
:<span style="font-size:130%">1. Amino acid '''sequence''' + protein chain '''conformation''' = protein '''function'''.</span> | :<span style="font-size:130%">1. Amino acid '''sequence''' + protein chain '''conformation''' = protein '''function'''.</span> | ||
::A. Conformation can be a '''stable fold''' or '''[[Intrinsically Disordered Protein|intrinsically unstructured]]'''. Both commonly exist in the same protein molecule. | ::A. Conformation can be a '''stable fold''' or '''[[Intrinsically Disordered Protein|intrinsically unstructured]]'''. Both commonly exist in the same protein molecule. | ||
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::E. Crystallographers publish the [[asymmetric unit]] of the crystal. It may be identical with the [[biological unit]] (the functional form of the molecule), or it may be only part of the biological unit, or it may contain multiple copies of the biological unit. | ::E. Crystallographers publish the [[asymmetric unit]] of the crystal. It may be identical with the [[biological unit]] (the functional form of the molecule), or it may be only part of the biological unit, or it may contain multiple copies of the biological unit. | ||
==Choose a Molecule to Explore== | ==III. Choose a Molecule to Explore== | ||
*Choose a molecule that includes '''protein and ligand'''. It may also include nucleic acid, but must have protein and ligand. | *Choose a molecule that includes '''protein and ligand'''. It may also include nucleic acid, but must have protein and ligand. | ||
*Be sure to note the '''4-character PDB code''' of the molecule you choose. The PDB code makes it easy to retrieve the molecule and information about it. Here are some ways to find a protein with known structure: | *Be sure to note the '''4-character PDB code''' of the molecule you choose. The PDB code makes it easy to retrieve the molecule and information about it. Here are some ways to find a protein with known structure: | ||
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# Search by molecule name or amino acid sequence at [http://www.pdb.org www.pdb.org], but remember that less than 10% of proteins have known structure. | # Search by molecule name or amino acid sequence at [http://www.pdb.org www.pdb.org], but remember that less than 10% of proteins have known structure. | ||
==Explore Your Molecule== | ==IV. Explore Your Molecule== | ||
===1. Start in Proteopedia=== | ===1. Start in Proteopedia=== | ||
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Most proteins have roughly equal numbers of positive and negative charges intermixed on their surfaces. Surface patches of exclusively positive charge often bind nucleic acids (negatively charged because of their phosphates). For example, examine the protein surface charges where the gal4 transcriptional regulator binds DNA ([[1d66]]). | Most proteins have roughly equal numbers of positive and negative charges intermixed on their surfaces. Surface patches of exclusively positive charge often bind nucleic acids (negatively charged because of their phosphates). For example, examine the protein surface charges where the gal4 transcriptional regulator binds DNA ([[1d66]]). | ||
==Powerpoint Report== | ==V. Powerpoint Report== | ||
Save your report with the filename yourLastName-565.pptx, for example <font color='red'><b>sandler-565.pptx</b></font>. When completed, your Powerpoint report is to be emailed to '''emartz@microbio.umass.edu''' for grading. | Save your report with the filename yourLastName-565.pptx, for example <font color='red'><b>sandler-565.pptx</b></font>. When completed, your Powerpoint report is to be emailed to '''emartz@microbio.umass.edu''' for grading. | ||
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===Section 8 - Optional: Contacts/Non-covalent Bonds=== | ===Section 8 - Optional: Contacts/Non-covalent Bonds=== | ||
==See Also== | ==VI. See Also== | ||
* [[User:Eric Martz/Introduction to Structural Bioinformatics]], a list of courses and workshops at various levels. | * [[User:Eric Martz/Introduction to Structural Bioinformatics]], a list of courses and workshops at various levels. | ||
==Notes and References== | ==VII. Notes and References== | ||
<references /> | <references /> | ||