User:Nikhil Malvankar/Cytochrome nanowires: Difference between revisions

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===Buried Cations===

~~In the [[6ef8]] structure for OmcS, the sidechains~~ of Arg333, Arg344, and Arg375 are buried~~, and none~~ have anions within 5 Å (not shown). The cationic sidechains of Arg333 and Arg344 touch each other (3.0 Å~~; not shown~~). These characteristics are confirmed in [[6nef]]. The presence of these cations deep within OmcS is reasonable, since proteins of this size have, on average, several buried charges<ref name="pace">PMID: 19164280</ref><ref name="kajander">PMID: 11080642</ref>. Moreover, on average from many proteins, more than half of all arginine guanidiniums are buried<ref name="pace" />. Burying charge seems to be an important factor in how evolution regulates protein stability<ref name="pace" /><ref name="kajander" />.

The <scene name='83/835223/Buried_cations/1'>sidechain nitrogens of Arg333, Arg344, and Arg375 are buried</scene>. None have anions within 5 Å (not shown). The cationic sidechains of Arg333 and Arg344 touch each other (3.0 Å). These characteristics are confirmed in [[6nef]]. The presence of these cations deep within OmcS is reasonable, since proteins of this size have, on average, several buried charges<ref name="pace">PMID: 19164280</ref><ref name="kajander">PMID: 11080642</ref>. Moreover, on average from many proteins, more than half of all arginine guanidiniums are buried<ref name="pace" />. Burying charge seems to be an important factor in how evolution regulates protein stability<ref name="pace" /><ref name="kajander" />.

The buried contact between two usually-cationic sidechains of Arg333 and Arg344 is also plausible because, when buried, the positive charge of the guanidinium group can be greatly diminished due to dehydration and nearby positive charges<ref name="pace" />. Although hydrated guanidinium retains more than half of its charge when the pH is below ~12 (its intrinsic pKa<ref name="pace" />), dehydration due to burial decreases the pKa. Furthermore, the samples for cryo-electron microscopy were prepared at pH 10.5<ref name="m3" /> (despite the pH being incorrectly stated as 7.0 in REMARK 245 of the PDB file).

@@ Line 82: / Line 82: @@
 ===Buried Cations===
-In the [[6ef8]] structure for OmcS, the sidechains of Arg333, Arg344, and Arg375 are buried, and none have anions within 5 Å (not shown). The cationic sidechains of Arg333 and Arg344 touch each other (3.0 Å; not shown). These characteristics are confirmed in [[6nef]]. The presence of these cations deep within OmcS is reasonable, since proteins of this size have, on average, several buried charges<ref name="pace">PMID: 19164280</ref><ref name="kajander">PMID: 11080642</ref>. Moreover, on average from many proteins, more than half of all arginine guanidiniums are buried<ref name="pace" />. Burying charge seems to be an important factor in how evolution regulates protein stability<ref name="pace" /><ref name="kajander" />.
+The <scene name='83/835223/Buried_cations/1'>sidechain nitrogens of Arg333, Arg344, and Arg375 are buried</scene>. None have anions within 5 Å (not shown). The cationic sidechains of Arg333 and Arg344 touch each other (3.0 Å). These characteristics are confirmed in [[6nef]]. The presence of these cations deep within OmcS is reasonable, since proteins of this size have, on average, several buried charges<ref name="pace">PMID: 19164280</ref><ref name="kajander">PMID: 11080642</ref>. Moreover, on average from many proteins, more than half of all arginine guanidiniums are buried<ref name="pace" />. Burying charge seems to be an important factor in how evolution regulates protein stability<ref name="pace" /><ref name="kajander" />.
 The buried contact between two usually-cationic sidechains of Arg333 and Arg344 is also plausible because, when buried, the positive charge of the guanidinium group can be greatly diminished due to dehydration and nearby positive charges<ref name="pace" />. Although hydrated guanidinium retains more than half of its charge when the pH is below ~12 (its intrinsic pKa<ref name="pace" />), dehydration due to burial decreases the pKa. Furthermore, the samples for cryo-electron microscopy were prepared at pH 10.5<ref name="m3" /> (despite the pH being incorrectly stated as 7.0 in REMARK 245 of the PDB file).