Answers.Body: <p>From your title, you are after better immobilisation, i.e. your enzyme behaves poorly when bound.</p>
  <ul>
  <li>Poor thermostability: Engineering enzymes for better thermostability, involves predicting mutations that improve its Gibbs free energy (∆G, negative potential = better). Finding mutations that improve a protein by going through the mutational landscape is called scanning.
  Rosetta <code>pmut_scan</code> is a command line tool to do this, while <a href="https://pross.weizmann.ac.il/step/pross-terms/" rel="nofollow noreferrer">Pross</a> is a really nice webapp that also does it.</li>
  <li>Poor catalysis: if your attachment is close to the active site, that is a design flaw and you need to attach on the other terminus or within a loop. Circular permutation may be an option.</li>
  <li>Aggregation: your enzyme aggregates due to pI close to 7 (see <a href="https://web.expasy.org/protparam/" rel="nofollow noreferrer">protparam</a>) or has a face that is hydrophobic (see the APBS plugin shipped within PyMOL). Rosetta <code>supercharge</code> is great at suggesting mutations to decrease the pI, but if doing it crudely by changing Gln -&gt; Gln &amp; Asn -&gt; Asp, do check for surface exposure.</li>
  </ul>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-10-05T10:09:14.667Z
Answers.LastActivityDate: 2023-09-18T16:00:51.237Z
Answers.LastEditDate: 2023-09-18T16:00:51.237Z
Answers.UserDisplayName: Matteo Ferla
Body: <p>Noob here. I get that I should  deduce what characteristics the ideal new enzyme should meet, and then use tools such as PDB and blast to compare to the old enzymes, and use other tools such as pymol, but I have no idea on how to approach this. Where should I look for tutorials?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-15T16:13:10.777Z
Comments.Text: Please consider the answer and upvoting/accepting. It's good for site stats and its a good answer IMO.
Comments.UserDisplayName: M__
Tags: <phylogenetics><blast><pdb><pymol>
Title: How do you search for new enzymes that are more stable for handling, immobilization?
ThreadText: # How do you search for new enzymes that are more stable for handling, immobilization?
  
  (Asked by: username_0 on 2021-10-04)
  
  Noob here. I get that I should deduce what characteristics the ideal new enzyme should meet, and then use tools such as PDB and blast to compare to the old enzymes, and use other tools such as pymol, but I have no idea on how to approach this. Where should I look for tutorials?
  
  **Tags:** phylogenetics, blast, pdb, pymol
  
  > **Comments:**
  > **username_1**: Please consider the answer and upvoting/accepting. It's good for site stats and its a good answer IMO.  
  
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  ## 1 answers
  
  ### Answer by username_2 on 2021-10-05. Score: 1
  
  From your title, you are after better immobilisation, i.e. your enzyme behaves poorly when bound.
  
  * Poor thermostability: Engineering enzymes for better thermostability, involves predicting mutations that improve its Gibbs free energy (∆G, negative potential = better). Finding mutations that improve a protein by going through the mutational landscape is called scanning.
    Rosetta `pmut_scan` is a command line tool to do this, while [Pross](https://pross.weizmann.ac.il/step/pross-terms/) is a really nice webapp that also does it.
  * Poor catalysis: if your attachment is close to the active site, that is a design flaw and you need to attach on the other terminus or within a loop. Circular permutation may be an option.
  * Aggregation: your enzyme aggregates due to pI close to 7 (see [protparam](https://web.expasy.org/protparam/)) or has a face that is hydrophobic (see the APBS plugin shipped within PyMOL). Rosetta `supercharge` is great at suggesting mutations to decrease the pI, but if doing it crudely by changing Gln -> Gln & Asn -> Asp, do check for surface exposure.
  
  
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