Proteopedia - User contributions [en]

A-RNA tour

2025-05-19T19:14:39Z

James Nolan:

==A-form RNA==
<StructureSection load='1rna' size='350' side='right' caption='A-RNA [[1rna]]' scene='72/725869/A-rna_overview/1'>
Source <ref>PMID:7071593</ref>
== Structural highlights ==
<UL>
<LI> Most RNA and RNA-DNA duplex in this form
<LI> Shorter, wider helix than B.
<LI> Deep, narrow major groove not easily accessible to proteins
<LI> Wide, shallow minor groove accessible to proteins, but lower information content than major groove.
<LI> Favored conformation at low water concentrations
<LI> Base pairs tilted to helix axis and displaced from axis
<LI> Sugar pucker C3'-''endo'' (in RNA 2'-OH inhibits C2'-''endo'' conformation)
</UL>

== Take the Tour ==

The tour starts with the <scene name='72/725869/A-rna_overview/1'>Default</scene> view. Now look at this <scene name='72/725869/Rna_space_filling_view/2'>space filling view</scene>.The backbone is yellow and the bases are magenta. Note that the major groove (at the top, when you have just clicked the button) is very deep.

Now change the display to make the show the <scene name='72/725869/Rna_space_filling_bbone/1'>sugar-phosphate backbone as pseudo-bonds</scene> connecting the phosphate atoms. Now the bases are easier to see. Notice how they are stacked upon each other but not perpendicular to the axis of the double helix. They are also displaced to the side of the axis. The result is a wide, short helix. Note also that the backbone forms a smooth, continuous curve.

You can <scene name='72/725869/Zoom_pairs/1'>look at just four of the base pairs.</scene>.You are looking into the major groove and the colors of the base pairs alternate. You can also <scene name='72/725869/Zoom_pairs_only/1'>look at just the bases</scene>.
Each base pair stacks on the next similarly, as shown from <scene name='72/725869/Zoom_pairs_top/1'>this top view</scene>. This is the <scene name='72/725869/Zoom_pairs_only_top/1'>same top view of just the bases</scene>.
B-DNA stacks similarly, but compare this with Z-DNA, which behaves much differently. Essentially all helical RNA is in A form, but DNA can also be found in A form under certain conditions (particularly in RNA-DNA hybrids). The 2'-OH of ribose favors the C3'-''endo'' sugar pucker necessary for A-form geometry. The O2' is easily seen as white spheres in <scene name='72/725869/Rna_space_filling_o2prime/1'>this space fill view</scene>.

You can compare it with the DNA forms by looking at this [[Media:JnABZ3d.gif|3D red-blue stereo picture of A, B, and Z DNA]]
</StructureSection>
==See Also==
* My [[Z-DNA model tour]]
* My [[B-DNA tour]]
* My [[Transfer RNA tour]]
* [[Z-DNA]]
* A more general overview will be found at [[DNA]].
* [[Forms of DNA]] shows a side-by-side comparison of A, B, and Z forms of DNA.
* An interactive tutorial on [http://dna.molviz.org DNA Structure], ''disponible también en español'' and eight other languages.
== References ==

JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

<references />

Z-DNA model tour

2025-05-19T19:12:50Z

James Nolan:

==Z-form DNA model==
Source <ref>PMID:7071593</ref>
<StructureSection load='5zna' size='400' side='right' caption='Z-DNA [[5zna]]' scene='72/725870/Z-dna_overview/1'>
== Structural highlights ==
<UL>
<LI> Helix has left-handed sense
<LI> Can be formed in vivo, given proper sequence and superhelical tension, but function remains obscure.
<LI> Narrower, more elongated helix than A or B.
<LI> Major "groove" not really groove
<LI> Narrow minor groove
<LI> Conformation favored by high salt concentrations, some base substitutions, but requires alternating purine-pyrimidine sequence.
<LI> Base pairs nearly perpendicular to helix axis
<LI> GpC repeat, not single base-pair
<UL>
<LI> P-P distances: vary for GpC and CpG
<LI> GpC stack: good base overlap
<LI> CpG: less overlap.
</UL>
<LI> Zigzag backbone due to C sugar conformation compensating for G glycosidic bond conformation
<LI> Conformations:
<UL>
<LI>G; ''syn'', C2'-''endo''
<LI>C; ''anti'', C3'-''endo''
</UL>
</UL>

== Take the Tour ==

The tour starts with the <scene name='72/725870/Z-dna_overview/1'>Default</scene> view. Now look at this <scene name='72/725870/Space_filling_view/1'>space filling view</scene>.The backbone is yellow and the bases are magenta. Note that the major groove (at the top, when you have just clicked the button) is so wide that it is not really a groove any more.

Now change the display to make it show the <scene name='72/725870/Space_filling_bbone/1'>sugar-phosphate backbone as pseudo-bonds</scene> connecting the phosphate atoms. Now the bases are easier to see. Now the bases are easier to see. Notice how they are stacked upon each other and are nearly perpendicular to the axis of the double helix. But notice that the base pairs do not stack upon each other equivalently. The backbone also is not a continuous curve, it "zig-zags" back and forth (hence "Z"-DNA).

<scene name='72/725870/Zoom_pair/2'>In this view</scene>, the molecule is shown in stick representation, with the backbone in yellow and sets of base pairs in red and blue. Notice how the blue bases stack well on the adjacent blue ones, but not on adjacent red ones, and vice versa. So it is the dinucleotide unit, rather than mononucleotide that is the repeating unit of the structure. This explains the need for alternating purines and pyrimidines to form Z-DNA.

You can see <scene name='72/725870/Zoom_pairs_only/2'>the same view without the backbone</scene> here.Going 5' to 3', there is good stacking within the GpC dinucleotide, but not between them (CpG).
A <scene name='72/725870/Zoom_pair_top/1'>top view</scene> also illustrates the stacking arrangement. You can also see this <scene name='72/725870/Zoom_pairs_only_top/1'>top view of just the bases.</scene>. Note the stacking of red base pairs on each other is much different than the stacking of red on blue.

You can compare it with the other DNA forms by looking at this [http://proteopedia.org/wiki/images/d/d3/JnABZ3d.gif 3D red-blue stereo picture of A, B, and Z DNA]
</StructureSection>
==See Also==
* My [[B-DNA tour]]
* My [[A-RNA tour]]
* [[Z-DNA]]
* A more general overview will be found at [[DNA]].
* [[Forms of DNA]] shows a side-by-side comparison of A, B, and Z forms of DNA.
* An interactive tutorial on [http://dna.molviz.org DNA Structure], ''disponible también en español'' and eight other languages.
== References ==

JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

<references />

B-DNA tour

2025-05-19T19:11:06Z

James Nolan:

==B-form DNA==
<StructureSection load='1bna' size='400' side='right' caption='B-DNA [[1bna]]' scene='72/725442/B-dna_overview/2'>
Source <ref>PMID:7071593</ref>
== Structural highlights ==
<UL>
<LI> Most common DNA conformation ''in vivo''
<LI> Narrower, more elongated helix than A-form
<LI> Wide major groove easily accessible to proteins
<LI> Narrow minor groove
<LI> Favored conformation at high water concentrations (hydration of minor groove seems to favor B-form)
<LI> Base pairs nearly perpendicular to helix axis
<LI> Sugar pucker C2'-''endo''
</UL>

== Take the Tour ==

The tour starts with the <scene name='72/725442/B-dna_overview/2'>Default</scene> view. Now look at this <scene name='72/725442/Space_filling_view/2'>space filling view</scene>.The backbone is yellow and the bases are magenta. Note that the major groove (in the middle, when you have just clicked the button) is wide and easily accessible.

Now change the display to make it show the <scene name='72/725442/Space_filling_bbone/2'>sugar-phosphate backbone as pseudo-bonds</scene> connecting the phosphate atoms. Now the bases are easier to see. Notice how they are stacked upon each other and are nearly perpendicular to the axis of the double helix. Note also that the backbone forms a smooth, continuous curve.

You can <scene name='72/725442/Zoom_pairs/1'>look at just four of the base pairs.</scene>.You are looking into the major groove and the colors of the base pairs alternate. You can also <scene name='72/725442/Zoom_pairs_only/1'>look at just the bases</scene>.
Each base pair stacks on the next similarly, as shown from <scene name='72/725442/Zoom_pairs_top/1'>this top view</scene>. This is the <scene name='72/725442/Zoom_pairs_only_top/1'>same top view of just the bases</scene>. A-form DNA also stacks in this way, but compare this with Z-DNA, which behaves much differently.

DNA is usually found in the B form under physiological conditions. The B-form conformation is stabilized by water molecules bound to the minor groove. You can see them as red dots <scene name='72/725442/Water_spine/1'>in this view</scene>. Sometimes kinks are found in the B helix at transcriptional control regions. These kinks can either be intrinsic to the DNA sequence or caused by transcription factor binding.

You can compare it with the DNA forms by looking at this [http://proteopedia.org/wiki/images/d/d3/JnABZ3d.gif 3D red-blue stereo picture of A, B, and Z DNA]
</StructureSection>
==See Also==
* My [[Z-DNA model tour]]
* My [[A-RNA tour]]
* A more general overview will be found at [[DNA]].
* [[Z-DNA]]
* [[Forms of DNA]] shows a side-by-side comparison of A, B, and Z forms of DNA.
* An interactive tutorial on [http://dna.molviz.org DNA Structure], ''disponible también en español'' and eight other languages.
== References ==

JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

<references />

Sandbox GGC12

2021-04-28T17:58:19Z

James Nolan:

== Human Serum Albumin==
<StructureSection load='1AO6' size='340' side='right' caption='Serum Albumin Protein' scene='78/781196/00_green_cartoon/1'>
Human serum albumin or HSA is one of the major types of proteins that are present in the plasma composition. It is such abundant that its concentration on a common blood sample is 5 grams per 100 milliliters. Due to its high concentration in plasma as well as its physiological and pharmaceutical features, it has been subjected to several studies to determine its 3D structure, function, domains, important binding sites, and diseases. The primary structure of HSA describes a single polypeptide with 585 amino acids with the characteristics of having 17 pairs of disulfide bridges, one free cysteine <ref>PMID: 6275391</ref>. It has been discovered that there are highly conserved sequences between bovine, human and rat albumins such as Trp-212, 143-155 and 244-263 sequence <ref>PMID: 6192439</ref>. It is composed of three domains at positions 19-210, 211-403, and 404-601 with two subdomains each (Ia&b, IIa&b, and IIIa&b). The subcellular location of these protein is the extracellular region on the outside of the cell membrane or secreted. There are 11 metal binding sites, including 1 copper site, 7 calcium sites, 3 zinc sites, additionally, 1 binding site for bilirubin and 1 site for aspirin-acetylated lysine <ref>PMID: 10388840</ref>.

== Function ==
HSA functions as the essential protein for the circulatory system, however, it has been discovered that possesses a high affinity an extensive range of amino acids, ligands, fatty acids, metals like copper and zinc, and metabolites such as bilirubin and drugs ingredients <ref>PMID: 10388840</ref>.Its fundamental role is to transport these varied types of solutes through the bloodstream to specific organs, control the level of pH and osmotic pressure of the plasma, and interaction with the cell membrane exchange of molecules at binding sites <ref>PMID: 3548415</ref>. It is considered to be the vital carrier of zinc in the plasma as well as the calcium and magnesium. In terms of affinity, the order from higher to lower affinity follows this pattern: zinc, calcium and magnesium <ref>PMID:19021548</ref>. Pharmaceutically, it has been used to target certain organs with some drugs by HSA being the carrier. By performing experiments on E.coli, it was discovered that it inhibits enterobactin-mediated iron absorption from ferric transferrin due to its binding to the bacterial siderophore limiting the uptake of iron, and consequently, blocking the growth of E.coli <ref>PMID: 6234017</ref>.

== Disease ==
HSA is involved in two important diseases, Hyperthyroxinemia, familial dysalbuminemic (FDAH) and Analbuminemia (ANALBA).

First, FDAH is a condition based on the genetic composition of the individual. It is caused by a mutation in the ALB gene, which corresponds to an increased affinity of the protein HSA for thyroxine. In detail, this autosomal dominant genetic disorder is characterized by the mutation of HSA causing the assembly of thyroxine in a higher proportion. There are two positions with three natural variants identified on the HSA that mutate to cause this disorder. The first position is at 90 amino acid, where leucine is replaced by a proline. The second position at 242 amino acid, where arginine is substituted by histidine or proline. This disorder could lead to confusion and several misdiagnoses of hyperthyroidism because it is difficult to detect it due to the normal TSH and free thyroxine levels but with an elevated total of thyroxine <ref>PMID: 32665066</ref>.

Second, ANALBA is an uncommon autosomal recessive genetic mutation characterized by the identification of very low levels of HSA circulating in the bloodstream <ref>PMID: 8134387</ref>. The affected individuals have symptoms corresponding to mild edema, hypotension, fatigue, and lower body lipodystrophy in females. The mutagenesis is located in the position 91 where histidine is replaced by alanine impairing metal binding <ref>PMID: 28567254</ref>. The complications of this disorder could lead to early atherosclerosis and heart problems.

== Relevance ==
The relevance of this protein, HSA, relies on the its capacity to transports molecules through out the bloodstream. It helps move substances such as metals, amino acids, drugs, fatty acids to every part of the body because it is a protein present in the blood that flows around the body. It is a significant protein because it allows us to use it pharmaceutically to target certain organs with specific drugs. Additionally, it is essential for the control of the levels of pH and the osmotic pressure in the plasma. And finally, it is a protein that allows the cell membrane interact with the outer space of the cell by the help of HSA in the targeting of binding sites.

== Structural highlights ==
The structural highlights of this protein are four: the six subdomains that compose the protein, the binding site in domain II for salicylates, sulfonamides and several drug ingredients, the bilirubin binding site at position 264, and the free cysteine in the structure of the protein <ref> PMID: 32162429</ref>.

This is the structural view of <scene name='78/781196/Six_subdomains/1'>HSA six subdomains</scene> by different colors. nd another to make <scene name="/12/3456/Sample/2"> by different colors. a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Sandbox GGC20

2021-04-07T21:11:51Z

James Nolan:

==RNAse P==
<StructureSection load='1a6f' size='340' side='right' caption='RNAse P Protein' scene='87/874954/00green_ribbon/1'>
This is a default text for your page '''Sandbox GGC20'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
This is the <scene name='87/874954/00green_ribbon/1'>RNAse P protein</scene>.
== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes. Here are <scene name='87/874954/00helix1_res/1'>some random residues on a helix</scene> The basic residues are important. <scene name='87/874954/00basic_side_chains/1'>Here are two important basic residues.</scene>. Here's a <scene name='87/874954/00basic_side_chains-zoom/1'>closer look</scene>.

</StructureSection>
== References ==
<references/>

Sandbox GGC20

2021-02-24T20:15:14Z

James Nolan:

==RNAse P==
<StructureSection load='1a6f' size='340' side='right' caption='RNAse P Protein' scene='87/874954/00green_ribbon/1'>
This is a default text for your page '''Sandbox GGC20'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
This is the <scene name='87/874954/00green_ribbon/1'>RNAse P protein</scene>.
== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes. Here are <scene name='87/874954/00helix1_res/1'>some random residues on a helix</scene>

</StructureSection>
== References ==
<references/>

Sandbox GGC20

2021-02-10T20:01:13Z

James Nolan:

==RNAse P==
<StructureSection load='1a6f' size='340' side='right' caption='RNAse P Protein' scene='87/874954/00green_ribbon/1'>
This is a default text for your page '''Sandbox GGC20'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
This is the <scene name='87/874954/00green_ribbon/1'>RNAse P protein</scene>.
== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Sandbox GGC20

2021-02-10T19:59:13Z

James Nolan:

==RNAse P==
<StructureSection load='1a6f' size='340' side='right' caption='RNAse P Protein' scene=''>
This is a default text for your page '''Sandbox GGC20'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
This is the <scene name='87/874954/00green_ribbon/1'>RNAse P protein</scene>.
== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Sandbox GGC20

2021-02-10T19:21:09Z

James Nolan:

==RNAse P==
<StructureSection load='1a6f' size='340' side='right' caption='RNAse P Protein' scene=''>
This is a default text for your page '''Sandbox GGC20'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Sandbox GGC20

2021-02-10T19:17:23Z

James Nolan:

==RNAse P==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox GGC20'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Sandbox GGC20

2021-02-10T18:50:32Z

James Nolan: New page: ==Your Heading Here (maybe something like 'Structure')== <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> This is a default text for you...

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox GGC20'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Sandbox GGC14

2021-02-10T15:46:50Z

James Nolan:

==Name of your Protein==
<StructureSection load='3VEV' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Sandbox GGC13

2021-02-10T15:46:15Z

James Nolan:

Sandbox GGC12

2021-02-10T15:45:44Z

James Nolan:

Sandbox GGC1

2021-02-10T15:45:11Z

James Nolan:

Sandbox GGC2

2021-02-10T15:44:27Z

James Nolan:

Sandbox GGC3

2021-02-10T15:43:06Z

James Nolan:

Sandbox GGC4

2021-02-10T15:42:19Z

James Nolan:

Sandbox GGC5

2021-02-10T15:41:32Z

James Nolan:

Sandbox GGC6

2021-02-10T15:40:48Z

James Nolan:

Sandbox GGC7

2021-02-10T15:37:40Z

James Nolan:

Sandbox GGC8

2021-02-10T15:36:27Z

James Nolan:

Sandbox GGC9

2021-02-10T15:35:38Z

James Nolan:

Sandbox GGC10

2021-02-10T15:34:56Z

James Nolan:

Sandbox GGC11

2021-02-10T15:31:22Z

James Nolan:

Sandbox GGC18

2021-02-10T15:28:54Z

James Nolan: New page: ==Name of your Protein== <StructureSection load='3VEV' size='340' side='right' caption='Caption for this structure' scene=''> This is a default text for your page. Click above on '''edit t...

Sandbox GGC17

2021-02-10T15:28:10Z

Sandbox GGC16

2021-02-10T15:23:18Z

Sandbox GGC15

2021-02-10T15:22:41Z

James Nolan:

Sandbox GGC15

2021-02-10T15:21:27Z

James Nolan:

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='3VEV' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Sandbox GGC14

2021-02-10T15:20:27Z

James Nolan:

Sandbox GGC13

2021-02-10T15:19:40Z

James Nolan:

Sandbox GGC12

2021-02-10T15:17:50Z

James Nolan:

B-DNA tour

2021-01-25T21:36:28Z

James Nolan:

==B-form DNA==
<StructureSection load='1bna' size='400' side='right' caption='B-DNA [[1bna]]' scene='72/725442/B-dna_overview/2'>
Source <ref>PMID:7071593</ref>
== Structural highlights ==
<UL>
<LI> Most common DNA conformation ''in vivo''
<LI> Narrower, more elongated helix than A-form
<LI> Wide major groove easily accessible to proteins
<LI> Narrow minor groove
<LI> Favored conformation at high water concentrations (hydration of minor groove seems to favor B-form)
<LI> Base pairs nearly perpendicular to helix axis
<LI> Sugar pucker C2'-''endo''
</UL>

== Take the Tour ==

The tour starts with the <scene name='72/725442/B-dna_overview/2'>Default</scene> view. Now look at this <scene name='72/725442/Space_filling_view/2'>space filling view</scene>.The backbone is yellow and the bases are magenta. Note that the major groove (in the middle, when you have just clicked the button) is wide and easily accessible.

Now change the display to make it show the <scene name='72/725442/Space_filling_bbone/2'>sugar-phosphate backbone as pseudo-bonds</scene> connecting the phosphate atoms. Now the bases are easier to see. Notice how they are stacked upon each other and are nearly perpendicular to the axis of the double helix. Note also that the backbone forms a smooth, continuous curve.

You can <scene name='72/725442/Zoom_pairs/1'>look at just four of the base pairs.</scene>.You are looking into the major groove and the colors of the base pairs alternate. You can also <scene name='72/725442/Zoom_pairs_only/1'>look at just the bases</scene>.
Each base pair stacks on the next similarly, as shown from <scene name='72/725442/Zoom_pairs_top/1'>this top view</scene>. This is the <scene name='72/725442/Zoom_pairs_only_top/1'>same top view of just the bases</scene>. A-form DNA also stacks in this way, but compare this with Z-DNA, which behaves much differently.

DNA is usually found in the B form under physiological conditions. The B-form conformation is stabilized by water molecules bound to the minor groove. You can see them as red dots <scene name='72/725442/Water_spine/1'>in this view</scene>. Sometimes kinks are found in the B helix at transcriptional control regions. These kinks can either be intrinsic to the DNA sequence or caused by transcription factor binding.

You can compare it with the DNA forms by looking at this [http://proteopedia.org/wiki/images/d/d3/JnABZ3d.gif 3D red-blue stereo picture of A, B, and Z DNA]
</StructureSection>
==See Also==
* [[Z-DNA model tour]] and [[Z-DNA]]
* [[A-RNA tour]]
* A more general overview will be found at [[DNA]].
* [[Forms of DNA]] shows a side-by-side comparison of A, B, and Z forms of DNA.
* An interactive tutorial on [http://dna.molviz.org DNA Structure], ''disponible también en español'' and eight other languages.
== References ==

JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

<references />

Sandbox GGC4

2020-11-14T02:05:20Z

James Nolan:

==Apolipoprotein==

'''Apolipoprotein A1'''
<StructureSection load='1av1' size='340' side='right' caption='Caption for this structure' scene=''>This is a default text for your page Sandbox GGC1. Click above on edit this page to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia [1] or to the article describing Jmol [2] to the rescue
== Function ==

Apolipoproteins are proteins that coat lipoprotein surface that binds lipids such as cholesterol, low-density lipoprotein (LDL), or high-density lipoproteins (HDL) in lipid metabolism. They function in the transport of such lipids in their structure that acts as a ligand to cell receptors and lipid transport proteins. <scene name='75/752268/Polar/1'>Amphipathic</scene> structural behavior are what allows the interaction between hydrophobic properties of water, such as in the blood stream and hydrophobic lipids.

Apolipoprotein A-I is a protein APOA1 gene in humans that is a component of HDL, which a form of good cholesterol in human's diet, used in the transport of cholesterol and phospholipids in the body through the bloodstream in the reverse transport of cholesterol from the tissues to the liver of hepatocytes. They promote cholesterol efflux, a pathway in transferring intracellular cholesterol to extracellular acceptors, from tissues and act as a cofactor for the lecithin cholesterol acyltransferase (LCAT).

== Disease ==

== Clinical Significance ==

== Structural highlights ==

Apolipoprotein a-1 (apoA-I) is a fairly small molecule that consists of a total of 243 residues and is 29-kD polypeptide in size. Structure in <scene name='75/752268/Color/9'>color</scene> is shown in rainbow, in arrangement from N-terminus (red) of amine group to C-terminus (dark blue) end of carboxyl group.

Apolipoprotein a-1 in the monomer form truncated (lacking 1-43 residues) consists of unique pseudo-continuous alpha helix highlighted by kinks at <scene name='75/752268/Truncated/3'>Pro residues</scene>, spaced approximately every 22 residues.

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="apoliporproetin">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

<scene name='75/752268/Color/8'>color</scene>

</StructureSection>

== References ==
1. Voet, D., Voet, J. G., & Pratt, C. W. (2016). Fundamentals of Biochemistry (5th ed.). Hoboken, NJ: John Wiley & Sons.<references/>

2. APOA1 gene: MedlinePlus Genetics. (2020, August 18). Retrieved October 26, 2020, from https://medlineplus.gov/genetics/gene/apoa1/<references/>

3. Mangaraj, M., Nanda, R., & Panda, S. (2016, July). Apolipoprotein A-I: A Molecule of Diverse Function. Retrieved November 04, 2020, from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4910842<references/>

Sandbox GGC6

2020-11-13T21:07:19Z

James Nolan:

==Fibrinogen alpha chain==
<StructureSection load='3VEV' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox GGC6'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==
protease thrombin cleaves fibrinogen into monomers. The formation of monomers, fibrinogen beta, and fibrinogen alpha is insoluble fibrin matrix. fibrin works as a binding or trapping agent in the coagulation process, which creates blood clot.

For small wounds, the polymerized fibrin with platelets forms a hemostatic plug over the wounds site. Fibrin is also anti inflammatory which it protects against IFNG- mediated hemorrhage.

Afibrinogenemic pregnant patients will result in spontaneous miscarriage. Fibrinogen supplemental will allow the patients to sustain the pregnancy, therefore, maternal fibrinogen plays a important role for successful pregnancy.<ref>PMID: 16026273</ref>

== Disease ==
'''Congenital afibrinogenemia (CAFBN)'''

This is an inherited blood disorder where the blood does not clot normally. This disease is caused by truncating mutations. Changing in position Arg-35 when Thrombin cleaves the site of Fibrinopeptide leads to alpha- Dysfibrinogenemias. <ref>doi: 10.1160/TH14-07-0629</ref>

Nosebleeds, bleeding from the gums and tongue are commons after a minor trauma for people with this disease. bleedings in the brain and internal organs can occur for affected individuals which can lead to be fatal. However, it's rare. Women with this disease can experience an abnormal heavy menstrual bleeding, they could also have a difficult time carrying a pregnancy, and could result in miscarriages. Newborn with this disease can experience bleeding from the umbilical cord stump after birth. The treatment for this disease includes cryoprecipitate, fibrinogen, and plasma (contains clotting factors). <ref>PMID: 19598064</ref>

'''Amyloidosis 8 (AMYL8)'''

This is hereditary disease which insoluble amyloid proteins deposits in body tissues and organs. This tends to abnormal protein build-up and leads to damaged organs and deaths. The disease is caused by a mutation fibrinogen alpha chain.<ref>PMID: 23227278</ref>

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes. <scene name='78/781192/Hydrophobic_and_polar/2'>this shows polar and unpolar structure of 1XKT </scene>

</StructureSection>
== References ==
<references/>

Sandbox GGC13

2020-09-16T13:51:16Z

James Nolan:

=Factor IX=
==Structure==
<StructureSection load='6MV4' size='340' side='right' caption='Factor IX structure' scene=''>
This is a default text for your page '''Sandbox GGC13'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==
This is my function.
== Disease ==
This causes hemophilia.
== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes. <scene name='78/781197/Sec_structure/2'>This shows the secondary structure</scene> of Factor IX. Here is a <scene name='78/781197/Ile212/3'>Zoomed out view</scene> This is <scene name='78/781197/Ile212/2'>This is Ile212</scene> which is important.

</StructureSection>
== References ==
<references/>

Sandbox GGC13

2020-09-14T14:12:20Z

James Nolan:

=Factor IX=
==Structure==
<StructureSection load='6MV4' size='340' side='right' caption='Factor IX structuree' scene=''>
This is a default text for your page '''Sandbox GGC13'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==
This is my function.
== Disease ==
This causes hemophilia.
== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes. <scene name='78/781197/Sec_structure/2'>This shows the secondary structure</scene> of Factor IX. Here is a <scene name='78/781197/Ile212/3'>Zoomed out view</scene> This is <scene name='78/781197/Ile212/2'>This is Ile212</scene> which is important.

</StructureSection>
== References ==
<references/>

Sandbox GGC13

2020-09-14T14:06:44Z

James Nolan:

=Factor IX=
==Structure==
<StructureSection load='6MV4' size='340' side='right' caption='Factor IX structuree' scene=''>
This is a default text for your page '''Sandbox GGC13'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==
This is my function.
== Disease ==
This causes hemophilia.
== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes. <scene name='78/781197/Sec_structure/2'>This shows the secondary structure</scene> of Factor IX.<scene name='78/781197/Ile212/2'>This is Ile212</scene> which is important.

</StructureSection>
== References ==
<references/>

Sandbox GGC13

2020-09-14T13:39:59Z

James Nolan:

=Factor IX=
==Structure==
<StructureSection load='6MV4' size='340' side='right' caption='Factor IX structuree' scene=''>
This is a default text for your page '''Sandbox GGC13'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==
This is my function.
== Disease ==
This causes hemophilia.
== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes. <scene name='78/781197/Sec_structure/1'>This shows the secondary structure</scene> of Factor IX.

</StructureSection>
== References ==
<references/>

Sandbox GGC13

2020-09-14T13:16:58Z

James Nolan:

=Factor IX=
==Structure==
<StructureSection load='6MV4' size='340' side='right' caption='Factor IX structuree' scene=''>
This is a default text for your page '''Sandbox GGC13'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==
This is my function.
== Disease ==
This causes hemophilia.
== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Sandbox GGC13

2020-09-14T12:20:40Z

James Nolan:

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='3VEV' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox GGC13'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Sandbox GGC11

2020-09-14T10:13:17Z

James Nolan:

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='3VEV' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox GGC11'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Sandbox GGC12

2020-09-14T10:11:35Z

James Nolan:

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='3VEV' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox GGC12'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Sandbox GGC10

2020-09-14T10:09:27Z

James Nolan:

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='3VEV' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox GGC10'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Sandbox GGC9

2020-09-14T10:07:41Z

James Nolan:

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='3VEV' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox GGC9'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Sandbox GGC8

2020-09-14T10:05:46Z

James Nolan:

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='3VEV' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox GGC8'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Sandbox GGC7

2020-09-14T10:04:03Z

James Nolan:

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='3VEV' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox GGC7'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Sandbox GGC6

2020-09-14T10:02:09Z

James Nolan:

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='3VEV' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox GGC6'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Sandbox GGC5

2020-09-14T10:00:08Z

James Nolan:

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='3VEV' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox GGC5'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>