Answers.Body: <p>The word topology gets used in two different contexts.</p>
  <h2>Common case: the geometric configuration of the protein (=fold)</h2>
  <p>In common non-computational biochemistry parlance it is just the standard English meaning of topology and just geometry, in the case of protein it means protein fold:</p>
  <p><a href="https://en.wikipedia.org/wiki/Protein_fold_class" rel="nofollow noreferrer">https://en.wikipedia.org/wiki/Protein_fold_class</a></p>
  <p>Wiktionary (<a href="https://en.wiktionary.org/wiki/topology" rel="nofollow noreferrer">https://en.wiktionary.org/wiki/topology</a>) say:</p>
  <blockquote>
  <p>The branch of mathematics dealing with those properties of a geometrical object (of arbitrary dimensionality) that are unchanged by continuous deformations (such as stretching, bending, etc., without tearing or gluing)</p>
  </blockquote>
  <p>In the of protein, unchanged by small changes in length or amino acid sequence identity —no proteases or meat-glue ligase required!</p>
  <h2>Computational (Bio)chemistry</h2>
  <p>Topology has a technical jargon definition in computational biochemistry and computational chemistry.</p>
  <p>In computational chemistry how the connections of a molecule are configured, expressed as a graph network <a href="https://en.wikipedia.org/wiki/Graph_theory" rel="nofollow noreferrer">https://en.wikipedia.org/wiki/Graph_theory</a>, is referred to as topology. For example isopropanol and n-propanol have same number of heavy atom (<em>nodes</em>) and these will have the same hybridisation, but the network will have different connectivities (<em>vertices</em>).
  The topology definition generally runs off <em>atom types</em> more so than elements, these combine the element and hybridisation and other properties specific to a certain element in a molecule —e.g. amine vs. amide nitrogen vs. tryptophan ring nitrogens are different.
  The 3D embedding of said molecule is not part of its topology. Things get a bit problematic as ideal bond lengths, angles and dihedrals in dihedral space (i.e. not in cartesian space) go into the 'configuration' file (topology file) for several forcefield systems. And in others still there may be constraints or restraints specified.</p>
  <p>In computational biochemistry, this holds true for ligands. But with proteins there is less. The connectivity within each amino acids is preset in stone: where one to use the allo isomer of threonine as opposed to the threo one would need to define a non-canonical amino acid. So by topology of a protein it is intended the connectivity of the amino acids in chains, e.g. primary sequence devoid of cartesian coordinates.
  The word topology appears often in the context of ligands: these require custom definitions (=topologies) required to use a ligand not parameterised in the force field used, a common source of trouble.</p>
  <h2>See also</h2>
  <ul>
  <li><a href="https://manual.gromacs.org/documentation/2019/reference-manual/topologies.html" rel="nofollow noreferrer">https://manual.gromacs.org/documentation/2019/reference-manual/topologies.html</a></li>
  <li><a href="https://mdtraj.org/1.9.4/api/generated/mdtraj.Topology.html" rel="nofollow noreferrer">https://mdtraj.org/1.9.4/api/generated/mdtraj.Topology.html</a></li>
  </ul>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-05-22T18:30:51.143Z
Answers.Text: I am actually talking about protein modeling and simulation. :)
Answers.UserDisplayName: user366312
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-05-23T10:27:45.053Z
Answers.Text: I have amended my answer, but I should warn that by virtue of being used just to mean configuration/definition in compbiochem, there are a hundred and one cases where my answer is 100% wrong due to the layers of complexity.
Answers.UserDisplayName: Matteo Ferla
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-05-22T18:24:31.760Z
Answers.LastActivityDate: 2022-05-23T10:24:18.947Z
Answers.LastEditDate: 2022-05-23T10:24:18.947Z
Answers.UserDisplayName: Matteo Ferla
Body: <p>What does it mean by &quot;topology&quot; in the case of secondary and tertiary structures of proteins?</p>
  <p>N.B. I am not talking about DNA/RNA/genomics. I am talking about protein folding, as it relates to protein modeling and simulation.</p>
  
Tags: <proteins>
Title: What does it mean by "topology" in the case of secondary and tertiary structures of proteins?
ThreadText: # What does it mean by "topology" in the case of secondary and tertiary structures of proteins?
  
  (Asked by: username_0 on 2022-05-22)
  
  What does it mean by "topology" in the case of secondary and tertiary structures of proteins?
  
  N.B. I am not talking about DNA/RNA/genomics. I am talking about protein folding, as it relates to protein modeling and simulation.
  
  **Tags:** proteins
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2022-05-22. Score: 2 | Accepted answer
  
  The word topology gets used in two different contexts.
  
  ## Common case: the geometric configuration of the protein (=fold)
  
  In common non-computational biochemistry parlance it is just the standard English meaning of topology and just geometry, in the case of protein it means protein fold:
  
  <https://en.wikipedia.org/wiki/Protein_fold_class>
  
  Wiktionary (<https://en.wiktionary.org/wiki/topology>) say:
  
  > The branch of mathematics dealing with those properties of a geometrical object (of arbitrary dimensionality) that are unchanged by continuous deformations (such as stretching, bending, etc., without tearing or gluing)
  
  In the of protein, unchanged by small changes in length or amino acid sequence identity —no proteases or meat-glue ligase required!
  
  ## Computational (Bio)chemistry
  
  Topology has a technical jargon definition in computational biochemistry and computational chemistry.
  
  In computational chemistry how the connections of a molecule are configured, expressed as a graph network <https://en.wikipedia.org/wiki/Graph_theory>, is referred to as topology. For example isopropanol and n-propanol have same number of heavy atom (*nodes*) and these will have the same hybridisation, but the network will have different connectivities (*vertices*).
  The topology definition generally runs off *atom types* more so than elements, these combine the element and hybridisation and other properties specific to a certain element in a molecule —e.g. amine vs. amide nitrogen vs. tryptophan ring nitrogens are different.
  The 3D embedding of said molecule is not part of its topology. Things get a bit problematic as ideal bond lengths, angles and dihedrals in dihedral space (i.e. not in cartesian space) go into the 'configuration' file (topology file) for several forcefield systems. And in others still there may be constraints or restraints specified.
  
  In computational biochemistry, this holds true for ligands. But with proteins there is less. The connectivity within each amino acids is preset in stone: where one to use the allo isomer of threonine as opposed to the threo one would need to define a non-canonical amino acid. So by topology of a protein it is intended the connectivity of the amino acids in chains, e.g. primary sequence devoid of cartesian coordinates.
  The word topology appears often in the context of ligands: these require custom definitions (=topologies) required to use a ligand not parameterised in the force field used, a common source of trouble.
  
  ## See also
  
  * <https://manual.gromacs.org/documentation/2019/reference-manual/topologies.html>
  * <https://mdtraj.org/1.9.4/api/generated/mdtraj.Topology.html>
  
  > **Comments:**
  > **username_0**: I am actually talking about protein modeling and simulation. :)  
  > **username_1**: I have amended my answer, but I should warn that by virtue of being used just to mean configuration/definition in compbiochem, there are a hundred and one cases where my answer is 100% wrong due to the layers of complexity.  
  
  ---
  
  