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Evolutionary Conservation is introduced at [[Introduction to Evolutionary Conservation]], and treated in somewhat greater depth in the article [[Conservation, Evolutionary]]. These describe how conservation patterns in 3D can help to identify functional sites in proteins. Proteopedia displays conservation patterns pre-calculated by [http://consurfdb.tau.ac.il ConSurfDB], when available. These are usually based on broad protein families that include sequences of proteins with multiple functions. Consequently, they usually '''obscure conservation''' present in a family of proteins with a single function (see [[Conservation%2C_Evolutionary#Caveats|Caveats]]). The present article describes the mechanisms utilized by the ConSurfDB and ConSurf servers, and how to use the latter to reveal conservation within a family of proteins with a single function.
<table align="right" class="wikitable" width=430><tr><td>
[[Image:2vaa-APD0.31-40degslow.gif]]
</td></tr><tr><td>
{{Template:ColorKey_ConSurf_NoYellow_NoGray}}
 
Conservation of amino acids non-covalently interacting with a peptide ({{Template:ColorKey_Element_C}} {{Template:ColorKey_Element_N}} {{Template:ColorKey_Element_O}}) in the groove of [https://www.youtube.com/watch?v=2ZakngfbHSo Major Histocompatibility Protein] Class I ([[2vaa]]). Conservation was '''not revealed''' until an [[#Average Pairwise Distance]] of 0.31 was achieved in a customized ConSurf Server job. [[#Examples|DETAILS BELOW]].
</td></tr></table>
Evolutionary Conservation is introduced at [[Introduction to Evolutionary Conservation]], and treated in somewhat greater depth in the article [[Conservation, Evolutionary]]. These describe how conservation patterns in 3D can help to identify functional sites in proteins. Proteopedia displays conservation patterns pre-calculated by [http://consurfdb.tau.ac.il ConSurfDB], when available. These are usually based on broad protein families that include sequences of proteins with multiple functions. Consequently, they usually '''obscure conservation''' present in a family of proteins with a single function (see [[Conservation%2C_Evolutionary#Caveats|Caveats]]).
 
The present article explains '''how to use options available at the ConSurf Server to reveal conservation within a group limited to proteins with a single function'''. Several [[#Examples|examples are presented]]. The mechanisms utilized by ConSurfDB and ConSurf Servers are also summarized.


==The Two ConSurf Servers==
==The Two ConSurf Servers==
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# Go to [http://consurfdb.tau.ac.il consurf'''db'''.tau.ac.il] (the DB, distinct from the ConSurf Server).
# Go to [http://consurfdb.tau.ac.il consurf'''db'''.tau.ac.il] (the DB, distinct from the ConSurf Server).
# Enter the [[PDB code]] (PDB ID) for the protein of interest. If you get "ERROR: No chains found" it means that this PDB entry was released after the most recent update of ConSurfDB, so you should use the ConSurf Server.
# Enter the [[PDB code]] (PDB ID) for the protein of interest. If you get "ERROR: No chains found" it means that this PDB entry was released after the most recent update of ConSurfDB, so you should [[ConSurf Quick Analysis Procedure|use the ConSurf Server]].
# Select the chain of interest. If you're not sure, get familiar with the structure using [http://firstglance.jmol.org FirstGlance].
# Select the chain of interest. If you're not sure, get familiar with the structure using [http://firstglance.jmol.org FirstGlance].
# Click the button '''Apply''', and wait for the results to load.
# Click the button '''Apply''', and wait for the results to load.
# Scroll down and click ''Homologues, Alignment, and Phylogeny''.
# Scroll down and click ''Homologues, Alignment, and Phylogeny''.
# Notice the number of sequences in the MSA (the number of "hits" upon which "calculations were conducted").
# Notice the number of sequences in the MSA (the number of "hits" upon which "calculations were conducted").
# '''To view the list of sequences in the multiple sequence alignment (MSA)''' from which the conservation pattern was determined, click on the count of hits upon which the calculations were conducted. (If fewer than 50 hits were used, it will probably be useful to do another run using a larger database: UniProt and NR are larger than the default UniProt90. Use the button "Select Run Parameters Manually".
# '''To view the list of sequences in the multiple sequence alignment (MSA)''' from which the conservation pattern was determined, click on the count of hits upon which the calculations were conducted. <!--(If fewer than 50 hits were used, it will probably be useful to do another run using a larger database: UniProt and NR are larger than the default UniProt90. Use the button "Select Run Parameters Manually".-->
# '''Get the Average Pairwise Distance (APD)''' by clicking "View Alignment Details". A value > ~1.1 suggests that proteins with multiple functions were included in the multiple sequence alignment, which obscures conservation related to the function of your query protein. See [[Interpreting ConSurf Results]], where the APD is explained.
# '''Get the Average Pairwise Distance (APD)''' by clicking "View Alignment Details". A value close to, or larger than 1.0 suggests that proteins with multiple functions were included in the multiple sequence alignment, which obscures conservation related to the function of your query protein. See [[Interpreting ConSurf Results]], where the APD is explained.


If the list includes proteins of functions that differ from that of the protein of interest, that tends to obscure patches of conservation that exist among proteins with the same function as the query protein of interest.
If the list includes proteins of functions that differ from that of the protein of interest, that tends to obscure patches of conservation that exist among proteins with the same function as the query protein of interest.
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When the [[Interpreting ConSurf Results|Average Pairwise Distance]] (APD) in the multiple sequence alignment (MSA) approaches or exceeds approximately 1.0, it is likely that proteins with multiple functions have been included in the MSA. To see conservation that reflects the function of the query protein, it is best to use an MSA with an APD in roughly the range 0.3-0.6. Sometimes, the ConSurf Server's result with default settings may give such a result. If not, you may wish to do additional ConSurf runs with the goal of reducing the APD.
When the [[Interpreting ConSurf Results|Average Pairwise Distance]] (APD) in the multiple sequence alignment (MSA) approaches or exceeds approximately 1.0, it is likely that proteins with multiple functions have been included in the MSA. To see conservation that reflects the function of the query protein, it is best to use an MSA with an APD in roughly the range 0.3-0.6. Sometimes, the ConSurf Server's result with default settings may give such a result. If not, you may wish to do additional ConSurf runs with the goal of reducing the APD.


Prior to 2022, the ConSurf Server enabled manual selection of sequences. Unfortunately, after a 2022 update to the ConSurf Server, this is no longer practical. Hence we are limited to adjusting run parameters "in the dark".
Prior to 2022, the ConSurf Server enabled manual selection of sequences. Unfortunately, after a 2022 update to the ConSurf Server, this is no longer practical. Hence we are limited to adjusting run parameters by trial and error "in the dark" until satisfactory results are obtained.


#Go to [http://consurf.tau.ac.il consurf.tau.ac.il], the ConSurf Server (distinct from ConSurf-DB).
#Go to [http://consurf.tau.ac.il consurf.tau.ac.il], the ConSurf Server (distinct from ConSurf-DB).
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#Upload each domain's PDB file to ConSurf as a separate job.
#Upload each domain's PDB file to ConSurf as a separate job.
</blockquote>
</blockquote>
==Examples==
<StructureSection load='' size='350' side='right' caption='' scene='39/399854/2vaa_consurf_halos_w274_y159/4'>
With default parameters, the ConSurf Server results have an average [[#Average Pairwise Distance]] (APD) of 1.00<ref name="APD">Tested with 20 arbitrarily selected proteins, mostly enzymes. Average of the average pairwise distance (APD) values: 1.00; range 0.82-1.42.</ref>, and an average of only a few "yellow" residues with insufficient data.<ref name="ISD">Tested with 20 arbitrarily selected proteins, mostly enzymes. Average number of amino acids with insufficient data ("yellow" in ConSurf): 3.5; range 0 to 16.</ref> For the examples below, it was necessary to [[#Limiting ConSurf Analysis to Proteins of a Single Function|customize the ConSurf Server job parameters]] in order to '''reveal conservation of key residues''' in proteins with the same function as the query.
These molecular scenes were obtained in [[FirstGlance in Jmol]], which offers many conveniences for analyzing ConSurf Server results. See [[Help:How to Insert a ConSurf Result Into a Proteopedia Green Link|How to Insert a ConSurf Result Into a Proteopedia Green Link]].
===Case #1: MHC===
The alpha chain of [https://www.youtube.com/watch?v=2ZakngfbHSo Major Histocompatibility Complex (MHC)] Class I protein has a groove that binds a wide range of peptides, and a small loop that binds CD8. Our example is [[2vaa]] (mouse H-2Kb).
<span style="float:right;">{{Template:ColorKey_ConSurf}}</span>
====ConSurf Server Default APD 1.1====
[[2vaa]] contains three chains. Here, (<scene name='39/399854/2vaa_consurf_halos_w274_y159/4'>restore initial scene, ConSurf Server default settings, APD 1.1</scene>)<ref name="consurfdefaults">Default ConSurf Server settings: UniRef90 database, excluding sequences with > 95% or < 35% identity with the query, MSA has 150 sequences sampled evenly from all unique sequence hits.</ref> ConSurf colors are applied only to the alpha chain (chain A), while the beta chain (chain B = &beta;-2 microglobulin) and the 8 amino acid peptide (chain P) are shown as gray backbone traces.
Conservation of important residues in the groove is obscured by inclusion in the MSA of proteins with different functions ([[#Example With Multiple Functions|see analysis above]]). The sides of the groove are variable due to many alleles that enable it to bind a wide range of peptide sequences. The only groove residue that is conserved at greater than level 7 is '''Tyr159''' (level 8), whose sidechain hydrogen bonds the main-chain oxygen of the amino-terminal peptide residue. Only a handful of surface residues are highly conserved (level 9), including '''Trp274''' involved in binding CD8.
====ConSurfDB APD 1.63====
ConSurfDB has a result (NOT SHOWN) with an '''APD of 1.63''', much higher than the APD 1.1 for the ConSurf Server with default settings. As expected, nothing in the contacts between the peptide and the groove shows high conservation in the ConSurfDB result, but Trp274 (the CD8 binding site) remains highly conserved.
====ConSurf Server Custom APD 0.51====
A custom consurf job resulting in an APD of 0.51<ref name="apd0.51">Custom ConSurf Server settings for APD 0.51 with 2vaa: UniRef90 database, excluding sequences with > 95% or '''< 50%''' identity with the query, MSA has 150 sequences sampled evenly from all unique sequence hits.</ref> (NOT SHOWN) had '''NO groove residues with conservation levels > 6'''. Trp274 was level 9.
====ConSurf Server Custom APD 0.31====
<span style="float:right;">{{Template:ColorKey_ConSurf_NoYellow_NoGray}}</span>
By default, ConSurf Server excludes from the multiple sequence alignment sequences with >95% identity, or <35% identity with the query sequence. Changing those limits to >98% and <70% reduced the default APD of 1.1 to 0.31<ref name="apd0.31">Custom ConSurf Server settings for APD 0.31 with 2vaa: UniRef90 database, excluding sequences with '''> 98% or < 70%''' identity with the query, MSA has 150 sequences sampled evenly from all unique sequence hits.</ref>. <scene name='39/399854/2vaa_apd_point31/3'>This result reveals high conservation of the following 4 key residues in the groove</scene> ({{Yelspan|yellow halos}}). With spin OFF, touch a residue to identify it.
* <span style="background-color:#961d54;color:white;padding:0.2em 0.4em 0.1em 0.4em;">Level 9:</span>
**Tyr7: hydrogen bonds to the amino terminus of the peptide. (Floor of the groove, hard to see.)
**Lys146: salt bridges to the carboxy terminus of the peptide.
* <span style="background-color:#ec6d96;color:white;padding:0.2em 0.4em 0.1em 0.4em;">Level 8:</span>
**Tyr84: hydrogen bonds to the peptide C-terminus.
**Thr143: hydrogen bonds to the peptide C-terminus. (Buried, hard to see.)
(Tyr159 was level 6. CD8 binding site Trp274 remains level 9.)
<scene name='39/399854/2vaa_peptide_contacts/1'>Here are all the polar residues contacting the peptide</scene>. Use the '''POPUP BUTTON''' to see details! (This scene is easily obtained in [http://firstglance.jmol.org FirstGlance]: Tools tab, click Contacts, check Label Contacts, and [[Help:How to Insert a ConSurf Result Into a Proteopedia Green Link|made into a Green Link]].)
Another custom ConSurf Server job<ref name="apd0.30">Custom ConSurf Server settings for APD 0.30 with 2vaa: UniRef90 database, excluding sequences with > 95% or < 35% identity with the query, MSA has '''250''' sequences '''closest''' to the query.</ref> gave an '''APD of 0.30''', but levels for the above 4 groove residues were 7-8. These lower levels can be accounted for by the highest expectation value<ref name="evalue" /> in the MSA, which was 10 to the power -141. In contrast, for the job with APD 0.31, the highest expectation value was 10 to the power -84.
===Case #2: UV Resistance Protein===
<scene name='39/399854/4dnw_consurf_apd-point48/1'>''Arabidopsis'' UVB-Resistance Protein UVR8</scene> [[4dnw]] is a homodimer with an <scene name='39/399854/4dnw_consurf_apd-point48/2'>unusual number of between-chain salt bridges</scene>. '''Are the between-chain salt bridges more conserved than the within-chain salt bridges?'''
[[FirstGlance in Jmol]] displays <scene name='39/399854/4dnw_consurf_apd-point48/2'>all salt bridges</scene> with one click (Tools tab), colored by conservation (if pre-processed by the ConSurf Server), and can list them, '''spreadsheet-ready, including conservation level numbers, and marking those between chains'''.
With the default ConSurf Server result '''APD 1.42''', and with a custom ConSurf Server result '''APD 0.91''', the salt-bridged residues have about '''average''' conservation. With a custom result '''APD 0.48''', the between-chain salt bridges have '''above-average''' conservation (7.6 vs. 6.8), while the within-chain salt bridges have below average conservation (6.3 vs. 6.8). In conclusion, when the multiple sequence alignment is limited to sequences closely related to the query (APD 0.48), '''between-chain salt bridged residues are more conserved than are within-chain salt bridged residues.''' The difference is '''statistically significant''' (p < 0.01<ref name="stats">With APD 0.48, mean conservation of between-chain salt bridged atoms is 7.57 &plusmn; 0.13 SEM. Subtracting 3 SEM (99% confidence limit) gives 7.18. This does not overlap with either 7.16 (the all-salt-bridged atoms mean + 3 SEM) or 6.82 (the mean for within-chain salt-bridged atoms + 3 SEM).</ref>).
<table class="wikitable" style="text-align:center;">
<tr>
  <td colspan=5>
Salt Bridges in [[4dnw]]
  </td>
</tr><tr>
  <td rowspan=2>
ConSurf [[#Average Pairwise Distance|APD]]
  </td>
  <td rowspan=2>
Level 9:<br>% of All Residues
  </td>
  <td colspan=3>
  <center>
Mean Conservation Levels &plusmn; SEM
  </center>
  </td>
</tr><tr>
  <td>
All Residues
  </td><td>
Salt Bridges Between Chains
  </td><td>
Salt Bridges Within Chains
  </td>
</tr><tr>
  <td>
1.42<ref name="consurfdefaults" />
  </td><td>
14%
  </td><td>
3.7
  </td><td>
3.5
  </td><td>
3.8
  </td>
</tr><tr>
  <td>
0.91<ref name="apd0.91">ConSurf settings for APD 0.91 with 4dnw: Clean UniProt, 35-95%, 200 sequences closest to query.</ref>
  </td><td>
16%
  </td><td>
5.4
  </td><td>
6.0
  </td><td>
5.0
  </td>
</tr><tr>
  <td>
0.48<ref name="apd0.48">ConSurf settings for APD 0.48 with 4dnw: Clean UniProt, 35-95%, 125 sequences closest to query.</ref>
  </td><td>
18%
  </td><td>
6.8 &plusmn; 0.12*
  </td><td>
7.6 &plusmn; 0.13*
  </td><td>
6.3 &plusmn; 0.17*
  </td>
</tr>
</table>
* *Averages are per atom for 88 between-chains salt-bridged atoms, and 140 within chain salt-bridged atoms. SEM's were calculated as standard deviation divided by the square root of the atom counts. Differences for APD 0.48 are statistically significant, p < 0.01<ref name="stats" />.
*Salt bridges are Lys or Arg sidechain nitrogens within 4.0 &Aring; of Asp or Glu sidechain oxygens.
Examples of conserved patches on other proteins, revealed by ConSurf, will be found in the articles on
*[[Lac repressor]]
*[[Avian Influenza Neuraminidase, Tamiflu and Relenza]]
*[[Mechanosensitive channels: opening and closing]]
</StructureSection>
==Conclusion==
In order to discover key functional residues, it is important to inspect multiple ConSurf Server jobs for highly conserved residues, including multiple jobs with [[#Average Pairwise Distance]]s (APD) in the range 0.25-0.5 using the [[#Limiting ConSurf Analysis to Proteins of a Single Function|above methods]]. Jobs with APD higher than 0.5 may obscure conservation of residues crucial for the function of the query protein. Residues conserved in the broader family of more distantly related proteins with different functions will typically be revealed with default ConSurf Server settings (APD ~ 1.0), or even in the ConSurf'''DB''' result.


==The ConSurf-DB Mechanism==
==The ConSurf-DB Mechanism==
:{{Yelspan| In January 2018: ConSurfDB had not been updated with new entries in the [[Protein Data Bank]] since January, 2013. }}
:{{Yelspan| In January 2018: ConSurfDB had not been updated with new entries in the [[Protein Data Bank]] since January, 2013. }}


Because results from the ConSurf DataBase server, [http://consurfdb.tau.ac.il ConSurf-DB]<ref name="consurfdb">PMID: 18971256</ref> are displayed within Proteopedia as ''Evolutionary Conservation'', an overview of its methods is provided here. ConSurf-DB pre-calculates conservation levels for each amino acid in every protein chain in the [[Protein Data Bank]]. It went into service in 2008. It uses state-of-the-art methods, all published in peer-reviewed journals<ref name="consurfdb" />.  
Because results from the ConSurf DataBase server, [http://consurfdb.tau.ac.il ConSurf-DB]<ref name="consurfdb">PMID: 18971256</ref> are displayed within Proteopedia as ''Evolutionary Conservation'', an overview of its methods is provided here. ConSurf-DB '''pre-calculates''' conservation levels for each amino acid in every protein chain in the [[Protein Data Bank]]. It went into service in 2008. It uses state-of-the-art methods, all published in peer-reviewed journals<ref name="consurfdb" />.  


===ConSurf-DB Process===
===ConSurf-DB Process===
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==The ConSurf Server==
==The ConSurf Server==


The [http://consurf.tau.ac.il ConSurf Server], first available in 2001<ref>PMID: 11243830</ref><ref>PMID: 12499312</ref><ref>PMID: 15980475</ref> with many subsequent enhancements, can calculate and display the conservation pattern for 3D structures '''completely automatically'''. It should be used whenever the pre-calculated result at the [[#The ConSurf-DB Mechanism|ConSurf-DB]] needs improvement (for example, see [[#Limiting ConSurf Analysis to Proteins of a Single Function|above]]), or if you have your own multiple sequence alignment (MSA) that you wish to use. The default settings of ConSurf may need to be adjusted in order to get an optimally informative result. The main adjustment needed is to gather an adequate number of sequences for proteins of the same function as your protein of interest (see  [[#Limiting ConSurf Analysis to Proteins of a Single Function|above]]).
The [http://consurf.tau.ac.il ConSurf Server], first available in 2001<ref>PMID: 11243830</ref><ref>PMID: 12499312</ref><ref>PMID: 15980475</ref> with many subsequent enhancements, can calculate and display the conservation pattern for 3D structures '''completely automatically'''. It should be used whenever the pre-calculated result at the [[#The ConSurf-DB Mechanism|ConSurf-DB]] is unavailable, or does not meet your needs (for example, see [[#Limiting ConSurf Analysis to Proteins of a Single Function|above]]), or if you have your own multiple sequence alignment (MSA) that you wish to use. The default settings of ConSurf may need to be adjusted in order to get an optimally informative result. The main adjustment needed is to gather an adequate number of sequences for proteins of the same function as your protein of interest (see  [[#Limiting ConSurf Analysis to Proteins of a Single Function|above]]).
 
[[ConSurf Quick Analysis Procedure|ConSurf Server job submission instructions]].


Like ConSurf-DB, the ConSurf Server uses the same state-of-the-art methods, all of which are published in peer-reviewed journal articles. Unlike ConSurf-DB's pre-calculated results the ConSurf Server permits considerable customization. For example, the user may specify the number of sequences to use, choose the database from which sequences are obtained, set the Expectation cutoff<ref name="evalue" />, set the number of HMMER iterations, or submit their own multiple sequence alignment, or phylogenetic tree. Also you can upload your own PDB file, which enables you to process unpublished data, theoretical models, or "trimmed" chains, e.g. a [[domain]] of interest from a multiple-domain chain.
Like ConSurf-DB, the ConSurf Server uses the same state-of-the-art methods, all of which are published in peer-reviewed journal articles. Unlike ConSurf-DB's pre-calculated results the ConSurf Server permits considerable customization. For example, the user may specify the number of sequences to use, choose the database from which sequences are obtained, set the Expectation cutoff<ref name="evalue" />, set the number of HMMER iterations, or submit their own multiple sequence alignment, or phylogenetic tree. Also you can upload your own PDB file, which enables you to process unpublished data, theoretical models, or "trimmed" chains, e.g. a [[domain]] of interest from a multiple-domain chain.
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# Displays the protein, colored by conservation, in interactive 3D, using the NGL Viewer, [[FirstGlance in Jmol]], [[Chimera]], or [[PyMOL]].
# Displays the protein, colored by conservation, in interactive 3D, using the NGL Viewer, [[FirstGlance in Jmol]], [[Chimera]], or [[PyMOL]].


==Examples==
==See Also==
<StructureSection load='' size='350' side='right' caption='' scene='39/399854/2vaa_consurf_halos_w274_y159/4'>
*[[ConSurf/Index]] provides links to all pages about evolutionary conservation and ConSurf in Proteopedia.
With default parameters, the ConSurf Server results have an average [[#Average Pairwise Distance]] (APD) of 1.00<ref name="APD">Tested with 20 arbitrarily selected proteins, mostly enzymes. Average of the average pairwise distance (APD) values: 1.00; range 0.82-1.42.</ref>, and an average of only a few "yellow" residues with insufficient data.<ref name="ISD">Tested with 20 arbitrarily selected proteins, mostly enzymes. Average number of amino acids with insufficient data ("yellow" in ConSurf): 3.5; range 0 to 16.</ref>
==Notes & References==
 
===Case #1: MHC===
The alpha chain of [https://www.youtube.com/watch?v=2ZakngfbHSo Major Histocompatibility Complex (MHC)] Class I protein has a groove that binds a wide range of peptides, and a small loop that binds CD8. Our example is [[2vaa]] (mouse H-2Kb).
<span style="float:right;">{{Template:ColorKey_ConSurf}}</span>
[[2vaa]] contains three chains. Here, (<scene name='39/399854/2vaa_consurf_halos_w274_y159/4'>restore initial scene, ConSurf Server default settings, APD 1.1</scene>) ConSurf colors are applied only to the alpha chain (chain A), while the beta chain (chain B = &beta;-2 microglobulin) and the peptide (chain P) are shown as gray backbone traces.
 
Conservation of important residues in the groove is obscured by inclusion in the MSA of proteins with different functions ([[#Example With Multiple Functions|see analysis above]]). The sides of the groove are variable, as expected (enabling it to bind a wide range of peptide sequences). The only groove residue that is conserved at greater than level 6 is '''Tyr159''' (level 8), whose sidechain hydrogen bonds the main-chain oxygen of the amino-terminal peptide residue. Only a handful of surface residues are highly conserved (level 9), including '''Trp274''' involved in binding CD8.
 
See also [[Help:How to Insert a ConSurf Result Into a Proteopedia Green Link|How to Insert a ConSurf Result Into a Proteopedia Green Link]].
 
====ConSurfDB====
ConSurfDB has a result (NOT SHOWN) with an '''APD of 1.63'''.
 
<font color="red">UPDATE IN PROGRESS:</FONT> [[User:Eric Martz|Eric Martz]] 21:24, 23 July 2024 (UTC)
 
Examples of conserved patches on other proteins, revealed by ConSurf, will be found in the articles on
*[[Lac repressor]]
*[[Avian Influenza Neuraminidase, Tamiflu and Relenza]]
*[[Mechanosensitive channels: opening and closing]]
 
</StructureSection>
 
==References==
  {{Reflist}}
  {{Reflist}}

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Eric Martz, Timothy Gregory, Joel L. Sussman
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