Alternate locations of backbones: Difference between revisions

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Eric Martz

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-At sufficiently high [[resolution]], [[Empirical models|empirical methods]] for determining macromolecular structure may detect multiple locations for some atoms, termed [[alternate locations]]. When alternate locations for backbones (main chains) deviate substantially, the backbone may separate into two pathways ("fork") and then rejoin into a single pathway.
+<table align="right" border="0" width="550" style="margin:0px 0px 0px 10px;"><tr><td>
+</td>
+<td rowspan="2">
+[[Image:Altloc-anim-cartoon-5sop.gif]]
+</td></tr><tr><td>
+Animation of the alternate location 3 backbone [http://firstglance.jmol.org/conformations.htm conformations] of [[5sop]]:
+<br><big>
+<font color="red"><b>1</b></font>
+<font color="orange"><b>2</b></font>
+<font color="#00b000"><b>3</b></font>.</big><br>
+[http://firstglance.jmol.org/videocapture.htm Captured] from [[FirstGlance in Jmol]].
+<span style="background-color:black;padding:3px 3px 0px 3px;font-weight:bold;">
+<span style="color:white;">Common to all conformations.&nbsp;</span>
+<br>
+<span style="color:Pink;">&nbsp;Pink</span></span>: [http://firstglance.jmol.org/notes.htm#singletons Singletons].
+<br><br>
+This is a major oversimplification of [http://firstglance.jmol.org/notes.htm#conformations all possible conformations].
+</td></tr></table>
+At sufficiently high [[resolution]], [[Empirical models|empirical methods]] for determining macromolecular structure may detect multiple locations for some atoms, termed [[alternate locations]]. When alternate locations for backbones (main chains) deviate substantially, the backbone may separate into two pathways ("fork") and then rejoin into a single pathway. [[FirstGlance in Jmol]] can color each [http://firstglance.jmol.org/conformations.htm conformation] distinctly, animate them, and isolate each. [http://firstglance.jmol.org/fg.htm?mol=5sop Explore 5sop in FirstGlance in Jmol].
 ==Alternate location server==
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   ID    Method            Res   Dep Date
 ins  X-ray diffraction 1.70  1991-10-23  min=-1.0  ave=-1.0  max=-1.0  A=48  B=48
 dgd  X-ray diffraction 1.4   2012-01-25  min=0.03  ave=4.78  max=15.87 A=84  B=84  A.CA=13  B.CA=13
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 <!--However, not quite ~500 entries (<1%) have "substantial" separations of some AltLoc backbone atoms, namely separations averaging >2.5 &Aring;.-->
 (The [[van der Waals radii|van der Waals diameter]] of a carbon atom is 3.4 &Aring;.
-The '''average''' separations for those 1,035 with maximum separations >5.0 &Aring; range from 0.14 to 91 &Aring;, with 184 entries having average separations >5.0 &Aring;.)
+The '''average''' separations for those 1,035 with maximum separations >5.0 &Aring; range from 0.14 to 91 &Aring;, with 184 entries having average separations >5.0 &Aring;.) 3,560 entries have maximum separations &ge;2.0 &Aring;, and 6,125 &ge; 1.0 &Aring;.
 {| class="wikitable"
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 |-
-| [https://www.uniprot.org/uniprotkb/B0LJC8/entry TRIMCyp protein] mediates innate immunity to HIV by inhibiting post-entry retrovirus replication. Evidence suggests that TRIMCyp has evolved through mutations to broaden the range of retroviruses it can inhibit<ref name="4dgd">PMID: 22407016</ref>. These mutations render the active site able to assume multiple conformations. In particular, the cyclophilin-binding loop 64-74 (GGNFT HCNGT GG), flanked by double glycine pivots, exhibited flexibility<ref name="4dgd" />. A crystal structure, [[4dgd]], resolved two alternate location conformations for the loop residues 66-74, shown at right in red (AltLoc A) and orange (AltLoc B), each at about 50% occupancy.
+| [https://www.uniprot.org/uniprotkb/B0LJC8/entry TRIMCyp protein] mediates innate immunity to HIV by inhibiting post-entry retrovirus replication. Evidence suggests that TRIMCyp has evolved through mutations to broaden the range of retroviruses it can inhibit<ref name="4dgd">PMID: 22407016</ref>. These mutations render the active site able to assume multiple conformations. In particular, the cyclophilin-binding loop 64-74 (GGNFT HCNGT GG), flanked by double glycine pivots, exhibited flexibility<ref name="4dgd" />. A crystal structure, [[4dgd]], resolved two alternate location conformations for the loop residues 66-74, shown at right in '''{{Font color|red|red (AltLoc A)}}''' and '''{{Font color|orange|orange (AltLoc B)}}''', each at about 50% occupancy.
 Explore [http://firstglance.jmol.org/fg.htm?mol=4dgd 4DGD in FirstGlance in Jmol], which has [[Alternate_locations#Visualizing_alternate_locations|AltLoc visualization/animation capabilities]].
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 ====Additional Cases====
+* [http://firstglance.jmol.org/fg.htm?mol=3pga 3PGA], a glutaminase-asparaginase, has a 20-residue flexible loop that is thought to orient substrate and help to transport substrate and product from the active site.
+* [http://firstglance.jmol.org/fg.htm?mol=3kqu 3KQU] illustrates a helicase ratchet translocation mechanism with its single-stranded DNA in four positions (conformations).
+* The [http://firstglance.jmol.org/fg.htm?mol=4myd&au=1 asymmetric unit of 4MYD] is a trimeric enzyme, in which "two [chains] bind one or both small molecule ligands and the third in the middle is present in two C2-symmetric conformations in a 1:1 ratio without any ligands." Here you will see alternate locations representing the entire middle chain rotated close to 180 degrees.
+* [http://firstglance.jmol.org/fg.htm?mol=6xkc 6XKC] is a hexamer. Two of the chains are modeled at two different angles relative to the other 4. In animation, these chains wave back and forth.
 ==References==
 <references />