Talk:Cooperative binding

<mediawiki xmlns="http://www.mediawiki.org/xml/export-0.7/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.mediawiki.org/xml/export-0.7/ http://www.mediawiki.org/xml/export-0.7.xsd" version="0.7" xml:lang="en">
  <siteinfo>
    <sitename>PLoSWiki</sitename>
    <base>http://topicpages.ploscompbiol.org/wiki/Main_Page</base>
    <generator>MediaWiki 1.20.4</generator>
    <case>first-letter</case>
    <namespaces>
      <namespace key="-2" case="first-letter">Media</namespace>
      <namespace key="-1" case="first-letter">Special</namespace>
      <namespace key="0" case="first-letter" />
      <namespace key="1" case="first-letter">Talk</namespace>
      <namespace key="2" case="first-letter">User</namespace>
      <namespace key="3" case="first-letter">User talk</namespace>
      <namespace key="4" case="first-letter">PLoSWiki</namespace>
      <namespace key="5" case="first-letter">PLoSWiki talk</namespace>
      <namespace key="6" case="first-letter">File</namespace>
      <namespace key="7" case="first-letter">File talk</namespace>
      <namespace key="8" case="first-letter">MediaWiki</namespace>
      <namespace key="9" case="first-letter">MediaWiki talk</namespace>
      <namespace key="10" case="first-letter">Template</namespace>
      <namespace key="11" case="first-letter">Template talk</namespace>
      <namespace key="12" case="first-letter">Help</namespace>
      <namespace key="13" case="first-letter">Help talk</namespace>
      <namespace key="14" case="first-letter">Category</namespace>
      <namespace key="15" case="first-letter">Category talk</namespace>
    </namespaces>
  </siteinfo>
  <page>
    <title>Talk:Cooperative binding</title>
    <ns>1</ns>
    <id>204</id>
    <revision>
      <id>2248</id>
      <timestamp>2013-01-09T22:55:38Z</timestamp>
      <contributor>
        <username>Daniel Mietchen</username>
        <id>5</id>
      </contributor>
      <minor/>
      <comment>Wikification</comment>
      <sha1>eyai0oftli007vmgr7bxjmkfkhny75s</sha1>
      <text xml:space="preserve" bytes="367">== Wikification ==

The initial draft looks good in terms of wikification. What is missing is a proper [[wp:WP:LEAD|lead]] section (I left some comments in the source), and it would be preferable to have the illustrations in SVG. Will do another check once the review period is coming to a close. --[[User:Daniel Mietchen|Daniel Mietchen]] 14:55, 9 January 2013 (PST)</text>
    </revision>
    <revision>
      <id>2267</id>
      <parentid>2248</parentid>
      <timestamp>2013-01-31T06:20:44Z</timestamp>
      <contributor>
        <username>Edelstei</username>
        <id>39</id>
      </contributor>
      <comment>/* Suggested modifications */ new section</comment>
      <sha1>6b4w4xagj44daac5wzw9tusonzy53oy</sha1>
      <text xml:space="preserve" bytes="1925">== Wikification ==

The initial draft looks good in terms of wikification. What is missing is a proper [[wp:WP:LEAD|lead]] section (I left some comments in the source), and it would be preferable to have the illustrations in SVG. Will do another check once the review period is coming to a close. --[[User:Daniel Mietchen|Daniel Mietchen]] 14:55, 9 January 2013 (PST)

== Suggested modifications ==

This text provides an excellent overview of cooperative binding as it applies principally to multi-site proteins. However, for clarity and consistency a number of points could be clarified.
1. Concerning the Bohr effect, what is stated is correction, but more commonly the Bohr effect is associated directly with the pH dependence of oxygen binding curves for hemoglobin. 
2. The discussion of the Hill equation is fine, but concerning the Hill plot, the intercept at log [Y/(1-) = 0 gives log (Kd) directly, not - log (Kd), (as shown correctly in Figure 5). 
3.For th e Klotz equation the series that includes the statistical factors n, (n-1)/2 , …1/n provides enough information to interpolate the entire series, but for some readers unfamiliar with such series it would be help to note that each element is defined by : (n – i + 1)/i
4. For the KNF equation which reproduces equation 13 in the 1966 paper, the initial (1/4) does not appear in the original version and in fact the relationship to the Pauling equation would be clearer if the numerator were divided by 4. 
5. For general usage it is not necessary to capitalize Apartate for aspartate trans-carbamylase, nor Lambda for lambda phage.
6. The heading Ionic Channels would be more conventional if presented simply as Ion Channels. 
7. It was not obvious why some references include superscripted links a and b for returns to the text and other do not. I suspected they were for proper names cited in the text, but if so this rule is not applied consistently.</text>
    </revision>
    <revision>
      <id>2268</id>
      <parentid>2267</parentid>
      <timestamp>2013-01-31T06:22:31Z</timestamp>
      <contributor>
        <username>Edelstei</username>
        <id>39</id>
      </contributor>
      <comment>/* Suggested modifications */</comment>
      <sha1>d3uhw0dpd8l48z9i124jje3e7jmczqp</sha1>
      <text xml:space="preserve" bytes="1984">== Wikification ==

The initial draft looks good in terms of wikification. What is missing is a proper [[wp:WP:LEAD|lead]] section (I left some comments in the source), and it would be preferable to have the illustrations in SVG. Will do another check once the review period is coming to a close. --[[User:Daniel Mietchen|Daniel Mietchen]] 14:55, 9 January 2013 (PST)

== Suggested modifications ==

This text provides an excellent overview of cooperative binding as it applies principally to multi-site proteins. However, for clarity and consistency a number of points could be clarified.
1. Concerning the Bohr effect, what is stated is correction, but more commonly the Bohr effect is associated directly with the pH dependence of oxygen binding curves for hemoglobin. 
2. The discussion of the Hill equation is fine, but concerning the Hill plot, the intercept at log [Y/(1-) = 0 gives log (Kd) directly, not - log (Kd), (as shown correctly in Figure 5). 
3.For th e Klotz equation the series that includes the statistical factors n, (n-1)/2 , …1/n provides enough information to interpolate the entire series, but for some readers unfamiliar with such series it would be help to note that each element is defined by : (n – i + 1)/i
4. For the KNF equation which reproduces equation 13 in the 1966 paper, the initial (1/4) does not appear in the original version and in fact the relationship to the Pauling equation would be clearer if the numerator were divided by 4. 
5. For general usage it is not necessary to capitalize Apartate for aspartate trans-carbamylase, nor Lambda for lambda phage.
6. The heading Ionic Channels would be more conventional if presented simply as Ion Channels. 
7. It was not obvious why some references include superscripted links a and b for returns to the text and other do not. I suspected they were for proper names cited in the text, but if so this rule is not applied consistently.
                       -- Stuart Edelstein 30 January 2013</text>
    </revision>
    <revision>
      <id>2269</id>
      <parentid>2268</parentid>
      <timestamp>2013-02-01T09:37:22Z</timestamp>
      <contributor>
        <username>Nlenovere</username>
        <id>36</id>
      </contributor>
      <comment>/* Suggested modifications */ reformatting Edelsteins comments for lisibility</comment>
      <sha1>nn8ifcmpl53vvmemca1iy8ouqoidls7</sha1>
      <text xml:space="preserve" bytes="1991">== Wikification ==

The initial draft looks good in terms of wikification. What is missing is a proper [[wp:WP:LEAD|lead]] section (I left some comments in the source), and it would be preferable to have the illustrations in SVG. Will do another check once the review period is coming to a close. --[[User:Daniel Mietchen|Daniel Mietchen]] 14:55, 9 January 2013 (PST)

== Suggested modifications ==

This text provides an excellent overview of cooperative binding as it applies principally to multi-site proteins. However, for clarity and consistency a number of points could be clarified.

1. Concerning the Bohr effect, what is stated is correction, but more commonly the Bohr effect is associated directly with the pH dependence of oxygen binding curves for hemoglobin. 

2. The discussion of the Hill equation is fine, but concerning the Hill plot, the intercept at log [Y/(1-) = 0 gives log (Kd) directly, not - log (Kd), (as shown correctly in Figure 5). 

3.For the Klotz equation the series that includes the statistical factors n, (n-1)/2 , …1/n provides enough information to interpolate the entire series, but for some readers unfamiliar with such series it would be help to note that each element is 
defined by : (n – i + 1)/i

4. For the KNF equation which reproduces equation 13 in the 1966 paper, the initial (1/4) does not appear in the original version and in fact the relationship to the Pauling equation would be clearer if the numerator were divided by 4. 

5. For general usage it is not necessary to capitalize Apartate for aspartate trans-carbamylase, nor Lambda for lambda phage.

6. The heading Ionic Channels would be more conventional if presented simply as Ion Channels. 

7. It was not obvious why some references include superscripted links a and b for returns to the text and other do not. I suspected they were for proper names cited in the text, but if so this rule is not applied consistently.
                       -- Stuart Edelstein 30 January 2013</text>
    </revision>
    <revision>
      <id>2271</id>
      <parentid>2269</parentid>
      <timestamp>2013-02-01T11:30:20Z</timestamp>
      <contributor>
        <username>Nlenovere</username>
        <id>36</id>
      </contributor>
      <comment>/* Suggested modifications */</comment>
      <sha1>kxzutaja036fpq3ej49756axlupmkiv</sha1>
      <text xml:space="preserve" bytes="2137">== Wikification ==

The initial draft looks good in terms of wikification. What is missing is a proper [[wp:WP:LEAD|lead]] section (I left some comments in the source), and it would be preferable to have the illustrations in SVG. Will do another check once the review period is coming to a close. --[[User:Daniel Mietchen|Daniel Mietchen]] 14:55, 9 January 2013 (PST)

== Suggested modifications ==

This text provides an excellent overview of cooperative binding as it applies principally to multi-site proteins. However, for clarity and consistency a number of points could be clarified.

1. Concerning the Bohr effect, what is stated is correction, but more commonly the Bohr effect is associated directly with the pH dependence of oxygen binding curves for hemoglobin. 

2. The discussion of the Hill equation is fine, but concerning the Hill plot, the intercept at log [Y/(1-) = 0 gives log (Kd) directly, not - log (Kd), (as shown correctly in Figure 5). 

   Yes, of course. This was a fossil from a former figure and a different formulation. [[User:Nlenovere|Nlenovere]] 03:30, 1 February 2013 (PST)

3.For the Klotz equation the series that includes the statistical factors n, (n-1)/2 , …1/n provides enough information to interpolate the entire series, but for some readers unfamiliar with such series it would be help to note that each element is 
defined by : (n – i + 1)/i

4. For the KNF equation which reproduces equation 13 in the 1966 paper, the initial (1/4) does not appear in the original version and in fact the relationship to the Pauling equation would be clearer if the numerator were divided by 4. 

5. For general usage it is not necessary to capitalize Apartate for aspartate trans-carbamylase, nor Lambda for lambda phage.

6. The heading Ionic Channels would be more conventional if presented simply as Ion Channels. 

7. It was not obvious why some references include superscripted links a and b for returns to the text and other do not. I suspected they were for proper names cited in the text, but if so this rule is not applied consistently.
                       -- Stuart Edelstein 30 January 2013</text>
    </revision>
    <revision>
      <id>2277</id>
      <parentid>2271</parentid>
      <timestamp>2013-02-01T11:45:11Z</timestamp>
      <contributor>
        <username>Nlenovere</username>
        <id>36</id>
      </contributor>
      <comment>/* Suggested modifications */</comment>
      <sha1>c9r7qqtoh18focb8d09tqhfiso9hmrn</sha1>
      <text xml:space="preserve" bytes="2699">== Wikification ==

The initial draft looks good in terms of wikification. What is missing is a proper [[wp:WP:LEAD|lead]] section (I left some comments in the source), and it would be preferable to have the illustrations in SVG. Will do another check once the review period is coming to a close. --[[User:Daniel Mietchen|Daniel Mietchen]] 14:55, 9 January 2013 (PST)

== Suggested modifications ==

This text provides an excellent overview of cooperative binding as it applies principally to multi-site proteins. However, for clarity and consistency a number of points could be clarified.

1. Concerning the Bohr effect, what is stated is correction, but more commonly the Bohr effect is associated directly with the pH dependence of oxygen binding curves for hemoglobin. 

2. The discussion of the Hill equation is fine, but concerning the Hill plot, the intercept at log [Y/(1-) = 0 gives log (Kd) directly, not - log (Kd), (as shown correctly in Figure 5). 

   Yes, of course. This was a fossil from a former figure and a different formulation. [[User:Nlenovere|Nlenovere]] 03:30, 1 February 2013 (PST)

3.For the Klotz equation the series that includes the statistical factors n, (n-1)/2 , …1/n provides enough information to interpolate the entire series, but for some readers unfamiliar with such series it would be help to note that each element is 
defined by : (n – i + 1)/i

   We added an explanation in parenthesis. [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

4. For the KNF equation which reproduces equation 13 in the 1966 paper, the initial (1/4) does not appear in the original version and in fact the relationship to the Pauling equation would be clearer if the numerator were divided by 4. 

   We initially chose this form to relate Ybar the equation 13 of the 1966 paper, which presented Ns, the number of bound site, equals to 4 times Ybar. We agree that the simplification suggested by Prof Edelstein is better, and we changed the formula accordingly. [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

5. For general usage it is not necessary to capitalize Apartate for aspartate trans-carbamylase, nor Lambda for lambda phage.
 
   Fixed [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

6. The heading Ionic Channels would be more conventional if presented simply as Ion Channels. 

   Fixed [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

7. It was not obvious why some references include superscripted links a and b for returns to the text and other do not. I suspected they were for proper names cited in the text, but if so this rule is not applied consistently.
                       -- Stuart Edelstein 30 January 2013</text>
    </revision>
    <revision>
      <id>2278</id>
      <parentid>2277</parentid>
      <timestamp>2013-02-01T11:48:35Z</timestamp>
      <contributor>
        <username>Nlenovere</username>
        <id>36</id>
      </contributor>
      <comment>/* Suggested modifications */</comment>
      <sha1>8o99fajf0sg55q9106cbwj9hyo3d6kf</sha1>
      <text xml:space="preserve" bytes="2993">== Wikification ==

The initial draft looks good in terms of wikification. What is missing is a proper [[wp:WP:LEAD|lead]] section (I left some comments in the source), and it would be preferable to have the illustrations in SVG. Will do another check once the review period is coming to a close. --[[User:Daniel Mietchen|Daniel Mietchen]] 14:55, 9 January 2013 (PST)

== Suggested modifications ==

This text provides an excellent overview of cooperative binding as it applies principally to multi-site proteins. However, for clarity and consistency a number of points could be clarified.

1. Concerning the Bohr effect, what is stated is correction, but more commonly the Bohr effect is associated directly with the pH dependence of oxygen binding curves for hemoglobin. 

2. The discussion of the Hill equation is fine, but concerning the Hill plot, the intercept at log [Y/(1-) = 0 gives log (Kd) directly, not - log (Kd), (as shown correctly in Figure 5). 

   Yes, of course. This was a fossil from a former figure and a different formulation. [[User:Nlenovere|Nlenovere]] 03:30, 1 February 2013 (PST)

3.For the Klotz equation the series that includes the statistical factors n, (n-1)/2 , …1/n provides enough information to interpolate the entire series, but for some readers unfamiliar with such series it would be help to note that each element is 
defined by : (n – i + 1)/i

   We added an explanation in parenthesis. [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

4. For the KNF equation which reproduces equation 13 in the 1966 paper, the initial (1/4) does not appear in the original version and in fact the relationship to the Pauling equation would be clearer if the numerator were divided by 4. 

   We initially chose this form to relate Ybar the equation 13 of the 1966 paper, which presented Ns, the number of bound site, equals to 4 times Ybar. We agree that the simplification suggested by Prof Edelstein is better, and we changed the formula accordingly. [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

5. For general usage it is not necessary to capitalize Apartate for aspartate trans-carbamylase, nor Lambda for lambda phage.
 
   Fixed [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

6. The heading Ionic Channels would be more conventional if presented simply as Ion Channels. 

   Fixed [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

7. It was not obvious why some references include superscripted links a and b for returns to the text and other do not. I suspected they were for proper names cited in the text, but if so this rule is not applied consistently.

    These references are created automatically by mediawiki. When several citations are made to a given reference, this references links back to the citations though those superscripts (an advantage of webpages over classical papers). [[User:Nlenovere|Nlenovere]] 03:48, 1 February 2013 (PST)
                       -- Stuart Edelstein 30 January 2013</text>
    </revision>
    <revision>
      <id>2280</id>
      <parentid>2278</parentid>
      <timestamp>2013-02-01T22:22:48Z</timestamp>
      <contributor>
        <username>Mstefan</username>
        <id>25</id>
      </contributor>
      <comment>/* Suggested modifications */</comment>
      <sha1>o3py7vfyxho02q0q33nne89yjyg57np</sha1>
      <text xml:space="preserve" bytes="3378">== Wikification ==

The initial draft looks good in terms of wikification. What is missing is a proper [[wp:WP:LEAD|lead]] section (I left some comments in the source), and it would be preferable to have the illustrations in SVG. Will do another check once the review period is coming to a close. --[[User:Daniel Mietchen|Daniel Mietchen]] 14:55, 9 January 2013 (PST)

== Suggested modifications ==

This text provides an excellent overview of cooperative binding as it applies principally to multi-site proteins. However, for clarity and consistency a number of points could be clarified.

1. Concerning the Bohr effect, what is stated is correction, but more commonly the Bohr effect is associated directly with the pH dependence of oxygen binding curves for hemoglobin. 

   It is my understanding that the Bohr effect refers to the effect of both pH and CO2 concentration on oxygen binding. To reflect this, I have altered the sentence to read &quot;This latter phenomenon, together with the observation that hemoglobin's affinity for oxygen increases with increasing pH, is known as the Bohr effect.&quot; --[[User:Mstefan|Mstefan]] 14:22, 1 February 2013 (PST)


2. The discussion of the Hill equation is fine, but concerning the Hill plot, the intercept at log [Y/(1-) = 0 gives log (Kd) directly, not - log (Kd), (as shown correctly in Figure 5). 

   Yes, of course. This was a fossil from a former figure and a different formulation. [[User:Nlenovere|Nlenovere]] 03:30, 1 February 2013 (PST)

3.For the Klotz equation the series that includes the statistical factors n, (n-1)/2 , …1/n provides enough information to interpolate the entire series, but for some readers unfamiliar with such series it would be help to note that each element is 
defined by : (n – i + 1)/i

   We added an explanation in parenthesis. [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

4. For the KNF equation which reproduces equation 13 in the 1966 paper, the initial (1/4) does not appear in the original version and in fact the relationship to the Pauling equation would be clearer if the numerator were divided by 4. 

   We initially chose this form to relate Ybar the equation 13 of the 1966 paper, which presented Ns, the number of bound site, equals to 4 times Ybar. We agree that the simplification suggested by Prof Edelstein is better, and we changed the formula accordingly. [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

5. For general usage it is not necessary to capitalize Apartate for aspartate trans-carbamylase, nor Lambda for lambda phage.
 
   Fixed [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

6. The heading Ionic Channels would be more conventional if presented simply as Ion Channels. 

   Fixed [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

7. It was not obvious why some references include superscripted links a and b for returns to the text and other do not. I suspected they were for proper names cited in the text, but if so this rule is not applied consistently.

    These references are created automatically by mediawiki. When several citations are made to a given reference, this references links back to the citations though those superscripts (an advantage of webpages over classical papers). [[User:Nlenovere|Nlenovere]] 03:48, 1 February 2013 (PST)
                       -- Stuart Edelstein 30 January 2013</text>
    </revision>
    <revision>
      <id>2281</id>
      <parentid>2280</parentid>
      <timestamp>2013-02-01T22:24:17Z</timestamp>
      <contributor>
        <username>Mstefan</username>
        <id>25</id>
      </contributor>
      <comment>/* Suggested modifications */</comment>
      <sha1>ci1qecb7dx2ls0iuyt5kgzataa6rbhj</sha1>
      <text xml:space="preserve" bytes="3389">== Wikification ==

The initial draft looks good in terms of wikification. What is missing is a proper [[wp:WP:LEAD|lead]] section (I left some comments in the source), and it would be preferable to have the illustrations in SVG. Will do another check once the review period is coming to a close. --[[User:Daniel Mietchen|Daniel Mietchen]] 14:55, 9 January 2013 (PST)

== Suggested modifications ==

This text provides an excellent overview of cooperative binding as it applies principally to multi-site proteins. However, for clarity and consistency a number of points could be clarified.

1. Concerning the Bohr effect, what is stated is correction, but more commonly the Bohr effect is associated directly with the pH dependence of oxygen binding curves for hemoglobin. 

   It is my understanding that the Bohr effect refers to the effect of both pH and CO2 concentration on oxygen binding. 
   To reflect this, I have altered the sentence to read &quot;This latter phenomenon, together with the observation that 
   hemoglobin's affinity for oxygen increases with increasing pH, is known as the Bohr effect.&quot; 
   --[[User:Mstefan|Mstefan]] 14:22, 1 February 2013 (PST)


2. The discussion of the Hill equation is fine, but concerning the Hill plot, the intercept at log [Y/(1-) = 0 gives log (Kd) directly, not - log (Kd), (as shown correctly in Figure 5). 

   Yes, of course. This was a fossil from a former figure and a different formulation. [[User:Nlenovere|Nlenovere]] 03:30, 1 February 2013 (PST)

3.For the Klotz equation the series that includes the statistical factors n, (n-1)/2 , …1/n provides enough information to interpolate the entire series, but for some readers unfamiliar with such series it would be help to note that each element is 
defined by : (n – i + 1)/i

   We added an explanation in parenthesis. [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

4. For the KNF equation which reproduces equation 13 in the 1966 paper, the initial (1/4) does not appear in the original version and in fact the relationship to the Pauling equation would be clearer if the numerator were divided by 4. 

   We initially chose this form to relate Ybar the equation 13 of the 1966 paper, which presented Ns, the number of bound site, equals to 4 times Ybar. We agree that the simplification suggested by Prof Edelstein is better, and we changed the formula accordingly. [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

5. For general usage it is not necessary to capitalize Apartate for aspartate trans-carbamylase, nor Lambda for lambda phage.
 
   Fixed [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

6. The heading Ionic Channels would be more conventional if presented simply as Ion Channels. 

   Fixed [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

7. It was not obvious why some references include superscripted links a and b for returns to the text and other do not. I suspected they were for proper names cited in the text, but if so this rule is not applied consistently.

    These references are created automatically by mediawiki. When several citations are made to a given reference, this references links back to the citations though those superscripts (an advantage of webpages over classical papers). [[User:Nlenovere|Nlenovere]] 03:48, 1 February 2013 (PST)
                       -- Stuart Edelstein 30 January 2013</text>
    </revision>
    <revision>
      <id>2576</id>
      <parentid>2281</parentid>
      <timestamp>2013-03-25T13:19:46Z</timestamp>
      <contributor>
        <username>Daniel Mietchen</username>
        <id>5</id>
      </contributor>
      <comment>/* Wikification */</comment>
      <sha1>n6j2up42dq3jcwk2622cl6i6czdp371</sha1>
      <text xml:space="preserve" bytes="3778">== Wikification ==

The initial draft looks good in terms of wikification. What is missing is a proper [[wp:WP:LEAD|lead]] section (I left some comments in the source), and it would be preferable to have the illustrations in SVG. Will do another check once the review period is coming to a close. --[[User:Daniel Mietchen|Daniel Mietchen]] 14:55, 9 January 2013 (PST)
:I have now gone through the whole draft and adapted formatting and style to that of the English Wikipedia. Please provide references at the indicated positions, and keep in mind that while PLOS wants PNG or TIFF, Wikipedia prefers SVG versions because these can be more readily adapted to other languages or contexts. --[[User:Daniel Mietchen|Daniel Mietchen]] 06:19, 25 March 2013 (PDT)

== Suggested modifications ==

This text provides an excellent overview of cooperative binding as it applies principally to multi-site proteins. However, for clarity and consistency a number of points could be clarified.

1. Concerning the Bohr effect, what is stated is correction, but more commonly the Bohr effect is associated directly with the pH dependence of oxygen binding curves for hemoglobin. 

   It is my understanding that the Bohr effect refers to the effect of both pH and CO2 concentration on oxygen binding. 
   To reflect this, I have altered the sentence to read &quot;This latter phenomenon, together with the observation that 
   hemoglobin's affinity for oxygen increases with increasing pH, is known as the Bohr effect.&quot; 
   --[[User:Mstefan|Mstefan]] 14:22, 1 February 2013 (PST)


2. The discussion of the Hill equation is fine, but concerning the Hill plot, the intercept at log [Y/(1-) = 0 gives log (Kd) directly, not - log (Kd), (as shown correctly in Figure 5). 

   Yes, of course. This was a fossil from a former figure and a different formulation. [[User:Nlenovere|Nlenovere]] 03:30, 1 February 2013 (PST)

3.For the Klotz equation the series that includes the statistical factors n, (n-1)/2 , …1/n provides enough information to interpolate the entire series, but for some readers unfamiliar with such series it would be help to note that each element is 
defined by : (n – i + 1)/i

   We added an explanation in parenthesis. [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

4. For the KNF equation which reproduces equation 13 in the 1966 paper, the initial (1/4) does not appear in the original version and in fact the relationship to the Pauling equation would be clearer if the numerator were divided by 4. 

   We initially chose this form to relate Ybar the equation 13 of the 1966 paper, which presented Ns, the number of bound site, equals to 4 times Ybar. We agree that the simplification suggested by Prof Edelstein is better, and we changed the formula accordingly. [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

5. For general usage it is not necessary to capitalize Apartate for aspartate trans-carbamylase, nor Lambda for lambda phage.
 
   Fixed [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

6. The heading Ionic Channels would be more conventional if presented simply as Ion Channels. 

   Fixed [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

7. It was not obvious why some references include superscripted links a and b for returns to the text and other do not. I suspected they were for proper names cited in the text, but if so this rule is not applied consistently.

    These references are created automatically by mediawiki. When several citations are made to a given reference, this references links back to the citations though those superscripts (an advantage of webpages over classical papers). [[User:Nlenovere|Nlenovere]] 03:48, 1 February 2013 (PST)
                       -- Stuart Edelstein 30 January 2013</text>
    </revision>
    <revision>
      <id>2578</id>
      <parentid>2576</parentid>
      <timestamp>2013-03-26T16:12:21Z</timestamp>
      <contributor>
        <username>Nlenovere</username>
        <id>36</id>
      </contributor>
      <comment>/* Wikification */</comment>
      <sha1>l2vul3y13rsljtpduxl2rsndt8ydnwm</sha1>
      <text xml:space="preserve" bytes="4130">== Wikification ==

The initial draft looks good in terms of wikification. What is missing is a proper [[wp:WP:LEAD|lead]] section (I left some comments in the source), and it would be preferable to have the illustrations in SVG. Will do another check once the review period is coming to a close. --[[User:Daniel Mietchen|Daniel Mietchen]] 14:55, 9 January 2013 (PST)
:I have now gone through the whole draft and adapted formatting and style to that of the English Wikipedia. Please provide references at the indicated positions, and keep in mind that while PLOS wants PNG or TIFF, Wikipedia prefers SVG versions because these can be more readily adapted to other languages or contexts. --[[User:Daniel Mietchen|Daniel Mietchen]] 06:19, 25 March 2013 (PDT)

:: fantastic job, thanks. I added a reference in the Klotz section. However, we should not put citations in the lead section. The lead section is equivalent to an abstract, and must standalone. As far as I can see, it is not customary to put citations in the lead section of wikipedia articles. [[User:Nlenovere|Nlenovere]] 09:12, 26 March 2013 (PDT)

== Suggested modifications ==

This text provides an excellent overview of cooperative binding as it applies principally to multi-site proteins. However, for clarity and consistency a number of points could be clarified.

1. Concerning the Bohr effect, what is stated is correction, but more commonly the Bohr effect is associated directly with the pH dependence of oxygen binding curves for hemoglobin. 

   It is my understanding that the Bohr effect refers to the effect of both pH and CO2 concentration on oxygen binding. 
   To reflect this, I have altered the sentence to read &quot;This latter phenomenon, together with the observation that 
   hemoglobin's affinity for oxygen increases with increasing pH, is known as the Bohr effect.&quot; 
   --[[User:Mstefan|Mstefan]] 14:22, 1 February 2013 (PST)


2. The discussion of the Hill equation is fine, but concerning the Hill plot, the intercept at log [Y/(1-) = 0 gives log (Kd) directly, not - log (Kd), (as shown correctly in Figure 5). 

   Yes, of course. This was a fossil from a former figure and a different formulation. [[User:Nlenovere|Nlenovere]] 03:30, 1 February 2013 (PST)

3.For the Klotz equation the series that includes the statistical factors n, (n-1)/2 , …1/n provides enough information to interpolate the entire series, but for some readers unfamiliar with such series it would be help to note that each element is 
defined by : (n – i + 1)/i

   We added an explanation in parenthesis. [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

4. For the KNF equation which reproduces equation 13 in the 1966 paper, the initial (1/4) does not appear in the original version and in fact the relationship to the Pauling equation would be clearer if the numerator were divided by 4. 

   We initially chose this form to relate Ybar the equation 13 of the 1966 paper, which presented Ns, the number of bound site, equals to 4 times Ybar. We agree that the simplification suggested by Prof Edelstein is better, and we changed the formula accordingly. [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

5. For general usage it is not necessary to capitalize Apartate for aspartate trans-carbamylase, nor Lambda for lambda phage.
 
   Fixed [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

6. The heading Ionic Channels would be more conventional if presented simply as Ion Channels. 

   Fixed [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

7. It was not obvious why some references include superscripted links a and b for returns to the text and other do not. I suspected they were for proper names cited in the text, but if so this rule is not applied consistently.

    These references are created automatically by mediawiki. When several citations are made to a given reference, this references links back to the citations though those superscripts (an advantage of webpages over classical papers). [[User:Nlenovere|Nlenovere]] 03:48, 1 February 2013 (PST)
                       -- Stuart Edelstein 30 January 2013</text>
    </revision>
    <revision>
      <id>2581</id>
      <parentid>2578</parentid>
      <timestamp>2013-03-28T15:39:49Z</timestamp>
      <contributor>
        <username>Daniel Mietchen</username>
        <id>5</id>
      </contributor>
      <comment>/* Wikification */</comment>
      <sha1>eyh9bahy1zhoj6qxcvatg5mkifgx4pz</sha1>
      <text xml:space="preserve" bytes="4713">== Wikification ==

The initial draft looks good in terms of wikification. What is missing is a proper [[wp:WP:LEAD|lead]] section (I left some comments in the source), and it would be preferable to have the illustrations in SVG. Will do another check once the review period is coming to a close. --[[User:Daniel Mietchen|Daniel Mietchen]] 14:55, 9 January 2013 (PST)
:I have now gone through the whole draft and adapted formatting and style to that of the English Wikipedia. Please provide references at the indicated positions, and keep in mind that while PLOS wants PNG or TIFF, Wikipedia prefers SVG versions because these can be more readily adapted to other languages or contexts. --[[User:Daniel Mietchen|Daniel Mietchen]] 06:19, 25 March 2013 (PDT)

:: fantastic job, thanks. I added a reference in the Klotz section. However, we should not put citations in the lead section. The lead section is equivalent to an abstract, and must standalone. As far as I can see, it is not customary to put citations in the lead section of wikipedia articles. [[User:Nlenovere|Nlenovere]] 09:12, 26 March 2013 (PDT)

:::OK, no citations in the PLOS abstract, but I would prefer if you could provide some suitable references for those three claims in the lead. They can be put in once the article sits on Wikipedia.
[[wp:WP:LEADCITE|WP:LEADCITE]] states &quot;The presence of citations in the introduction is neither required in every article nor prohibited in any article.&quot;
:::Besides that, please think about an interesting fact from the article - along with a figure - that could serve in a [[wp:WP:DYK|Did you know]] item. Thanks! --[[User:Daniel Mietchen|Daniel Mietchen]] 08:39, 28 March 2013 (PDT)

== Suggested modifications ==

This text provides an excellent overview of cooperative binding as it applies principally to multi-site proteins. However, for clarity and consistency a number of points could be clarified.

1. Concerning the Bohr effect, what is stated is correction, but more commonly the Bohr effect is associated directly with the pH dependence of oxygen binding curves for hemoglobin. 

   It is my understanding that the Bohr effect refers to the effect of both pH and CO2 concentration on oxygen binding. 
   To reflect this, I have altered the sentence to read &quot;This latter phenomenon, together with the observation that 
   hemoglobin's affinity for oxygen increases with increasing pH, is known as the Bohr effect.&quot; 
   --[[User:Mstefan|Mstefan]] 14:22, 1 February 2013 (PST)


2. The discussion of the Hill equation is fine, but concerning the Hill plot, the intercept at log [Y/(1-) = 0 gives log (Kd) directly, not - log (Kd), (as shown correctly in Figure 5). 

   Yes, of course. This was a fossil from a former figure and a different formulation. [[User:Nlenovere|Nlenovere]] 03:30, 1 February 2013 (PST)

3.For the Klotz equation the series that includes the statistical factors n, (n-1)/2 , …1/n provides enough information to interpolate the entire series, but for some readers unfamiliar with such series it would be help to note that each element is 
defined by : (n – i + 1)/i

   We added an explanation in parenthesis. [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

4. For the KNF equation which reproduces equation 13 in the 1966 paper, the initial (1/4) does not appear in the original version and in fact the relationship to the Pauling equation would be clearer if the numerator were divided by 4. 

   We initially chose this form to relate Ybar the equation 13 of the 1966 paper, which presented Ns, the number of bound site, equals to 4 times Ybar. We agree that the simplification suggested by Prof Edelstein is better, and we changed the formula accordingly. [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

5. For general usage it is not necessary to capitalize Apartate for aspartate trans-carbamylase, nor Lambda for lambda phage.
 
   Fixed [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

6. The heading Ionic Channels would be more conventional if presented simply as Ion Channels. 

   Fixed [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

7. It was not obvious why some references include superscripted links a and b for returns to the text and other do not. I suspected they were for proper names cited in the text, but if so this rule is not applied consistently.

    These references are created automatically by mediawiki. When several citations are made to a given reference, this references links back to the citations though those superscripts (an advantage of webpages over classical papers). [[User:Nlenovere|Nlenovere]] 03:48, 1 February 2013 (PST)
                       -- Stuart Edelstein 30 January 2013</text>
    </revision>
    <revision>
      <id>2582</id>
      <parentid>2581</parentid>
      <timestamp>2013-03-28T15:40:10Z</timestamp>
      <contributor>
        <username>Daniel Mietchen</username>
        <id>5</id>
      </contributor>
      <minor/>
      <comment>/* Wikification */</comment>
      <sha1>729q8u83l43sxjcpjejtcmfzuhaz2s4</sha1>
      <text xml:space="preserve" bytes="4716">== Wikification ==

The initial draft looks good in terms of wikification. What is missing is a proper [[wp:WP:LEAD|lead]] section (I left some comments in the source), and it would be preferable to have the illustrations in SVG. Will do another check once the review period is coming to a close. --[[User:Daniel Mietchen|Daniel Mietchen]] 14:55, 9 January 2013 (PST)
:I have now gone through the whole draft and adapted formatting and style to that of the English Wikipedia. Please provide references at the indicated positions, and keep in mind that while PLOS wants PNG or TIFF, Wikipedia prefers SVG versions because these can be more readily adapted to other languages or contexts. --[[User:Daniel Mietchen|Daniel Mietchen]] 06:19, 25 March 2013 (PDT)

:: fantastic job, thanks. I added a reference in the Klotz section. However, we should not put citations in the lead section. The lead section is equivalent to an abstract, and must standalone. As far as I can see, it is not customary to put citations in the lead section of wikipedia articles. [[User:Nlenovere|Nlenovere]] 09:12, 26 March 2013 (PDT)

:::OK, no citations in the PLOS abstract, but I would prefer if you could provide some suitable references for those three claims in the lead. They can be put in once the article sits on Wikipedia.
:::[[wp:WP:LEADCITE|WP:LEADCITE]] states &quot;The presence of citations in the introduction is neither required in every article nor prohibited in any article.&quot;
:::Besides that, please think about an interesting fact from the article - along with a figure - that could serve in a [[wp:WP:DYK|Did you know]] item. Thanks! --[[User:Daniel Mietchen|Daniel Mietchen]] 08:39, 28 March 2013 (PDT)

== Suggested modifications ==

This text provides an excellent overview of cooperative binding as it applies principally to multi-site proteins. However, for clarity and consistency a number of points could be clarified.

1. Concerning the Bohr effect, what is stated is correction, but more commonly the Bohr effect is associated directly with the pH dependence of oxygen binding curves for hemoglobin. 

   It is my understanding that the Bohr effect refers to the effect of both pH and CO2 concentration on oxygen binding. 
   To reflect this, I have altered the sentence to read &quot;This latter phenomenon, together with the observation that 
   hemoglobin's affinity for oxygen increases with increasing pH, is known as the Bohr effect.&quot; 
   --[[User:Mstefan|Mstefan]] 14:22, 1 February 2013 (PST)


2. The discussion of the Hill equation is fine, but concerning the Hill plot, the intercept at log [Y/(1-) = 0 gives log (Kd) directly, not - log (Kd), (as shown correctly in Figure 5). 

   Yes, of course. This was a fossil from a former figure and a different formulation. [[User:Nlenovere|Nlenovere]] 03:30, 1 February 2013 (PST)

3.For the Klotz equation the series that includes the statistical factors n, (n-1)/2 , …1/n provides enough information to interpolate the entire series, but for some readers unfamiliar with such series it would be help to note that each element is 
defined by : (n – i + 1)/i

   We added an explanation in parenthesis. [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

4. For the KNF equation which reproduces equation 13 in the 1966 paper, the initial (1/4) does not appear in the original version and in fact the relationship to the Pauling equation would be clearer if the numerator were divided by 4. 

   We initially chose this form to relate Ybar the equation 13 of the 1966 paper, which presented Ns, the number of bound site, equals to 4 times Ybar. We agree that the simplification suggested by Prof Edelstein is better, and we changed the formula accordingly. [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

5. For general usage it is not necessary to capitalize Apartate for aspartate trans-carbamylase, nor Lambda for lambda phage.
 
   Fixed [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

6. The heading Ionic Channels would be more conventional if presented simply as Ion Channels. 

   Fixed [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

7. It was not obvious why some references include superscripted links a and b for returns to the text and other do not. I suspected they were for proper names cited in the text, but if so this rule is not applied consistently.

    These references are created automatically by mediawiki. When several citations are made to a given reference, this references links back to the citations though those superscripts (an advantage of webpages over classical papers). [[User:Nlenovere|Nlenovere]] 03:48, 1 February 2013 (PST)
                       -- Stuart Edelstein 30 January 2013</text>
    </revision>
    <revision>
      <id>2583</id>
      <parentid>2582</parentid>
      <timestamp>2013-03-28T15:40:48Z</timestamp>
      <contributor>
        <username>Daniel Mietchen</username>
        <id>5</id>
      </contributor>
      <minor/>
      <comment>/* Wikification */</comment>
      <sha1>eqrp75hbdw5rkhrm8mrfru0gqvwmqy1</sha1>
      <text xml:space="preserve" bytes="4713">== Wikification ==

The initial draft looks good in terms of wikification. What is missing is a proper [[wp:WP:LEAD|lead]] section (I left some comments in the source), and it would be preferable to have the illustrations in SVG. Will do another check once the review period is coming to a close. --[[User:Daniel Mietchen|Daniel Mietchen]] 14:55, 9 January 2013 (PST)
:I have now gone through the whole draft and adapted formatting and style to that of the English Wikipedia. Please provide references at the indicated positions, and keep in mind that while PLOS wants PNG or TIFF, Wikipedia prefers SVG versions because these can be more readily adapted to other languages or contexts. --[[User:Daniel Mietchen|Daniel Mietchen]] 06:19, 25 March 2013 (PDT)

:: fantastic job, thanks. I added a reference in the Klotz section. However, we should not put citations in the lead section. The lead section is equivalent to an abstract, and must standalone. As far as I can see, it is not customary to put citations in the lead section of wikipedia articles. [[User:Nlenovere|Nlenovere]] 09:12, 26 March 2013 (PDT)

:::OK, no citations in the PLOS abstract, but I would prefer if you could provide some suitable references for those three claims in the lead. They can be put in once the article sits on Wikipedia. [[wp:WP:LEADCITE|WP:LEADCITE]] states &quot;The presence of citations in the introduction is neither required in every article nor prohibited in any article.&quot;
:::Besides that, please think about an interesting fact from the article - along with a figure - that could serve in a [[wp:WP:DYK|Did you know]] item. Thanks! --[[User:Daniel Mietchen|Daniel Mietchen]] 08:39, 28 March 2013 (PDT)

== Suggested modifications ==

This text provides an excellent overview of cooperative binding as it applies principally to multi-site proteins. However, for clarity and consistency a number of points could be clarified.

1. Concerning the Bohr effect, what is stated is correction, but more commonly the Bohr effect is associated directly with the pH dependence of oxygen binding curves for hemoglobin. 

   It is my understanding that the Bohr effect refers to the effect of both pH and CO2 concentration on oxygen binding. 
   To reflect this, I have altered the sentence to read &quot;This latter phenomenon, together with the observation that 
   hemoglobin's affinity for oxygen increases with increasing pH, is known as the Bohr effect.&quot; 
   --[[User:Mstefan|Mstefan]] 14:22, 1 February 2013 (PST)


2. The discussion of the Hill equation is fine, but concerning the Hill plot, the intercept at log [Y/(1-) = 0 gives log (Kd) directly, not - log (Kd), (as shown correctly in Figure 5). 

   Yes, of course. This was a fossil from a former figure and a different formulation. [[User:Nlenovere|Nlenovere]] 03:30, 1 February 2013 (PST)

3.For the Klotz equation the series that includes the statistical factors n, (n-1)/2 , …1/n provides enough information to interpolate the entire series, but for some readers unfamiliar with such series it would be help to note that each element is 
defined by : (n – i + 1)/i

   We added an explanation in parenthesis. [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

4. For the KNF equation which reproduces equation 13 in the 1966 paper, the initial (1/4) does not appear in the original version and in fact the relationship to the Pauling equation would be clearer if the numerator were divided by 4. 

   We initially chose this form to relate Ybar the equation 13 of the 1966 paper, which presented Ns, the number of bound site, equals to 4 times Ybar. We agree that the simplification suggested by Prof Edelstein is better, and we changed the formula accordingly. [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

5. For general usage it is not necessary to capitalize Apartate for aspartate trans-carbamylase, nor Lambda for lambda phage.
 
   Fixed [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

6. The heading Ionic Channels would be more conventional if presented simply as Ion Channels. 

   Fixed [[User:Nlenovere|Nlenovere]] 03:45, 1 February 2013 (PST)

7. It was not obvious why some references include superscripted links a and b for returns to the text and other do not. I suspected they were for proper names cited in the text, but if so this rule is not applied consistently.

    These references are created automatically by mediawiki. When several citations are made to a given reference, this references links back to the citations though those superscripts (an advantage of webpages over classical papers). [[User:Nlenovere|Nlenovere]] 03:48, 1 February 2013 (PST)
                       -- Stuart Edelstein 30 January 2013</text>
    </revision>
  </page>
</mediawiki>