Sandbox Reserved 961
From Proteopedia
| Line 2: | Line 2: | ||
<Structure load='1WAP' size='350' frame='true' align='right' caption='Global structure of TRAP' scene='60/604480/Default1/4' /> | <Structure load='1WAP' size='350' frame='true' align='right' caption='Global structure of TRAP' scene='60/604480/Default1/4' /> | ||
| - | |||
| - | ==Your Heading Here (maybe something like 'Structure')== | ||
| - | 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. | ||
== Functions == | == Functions == | ||
| Line 15: | Line 11: | ||
== Structure == | == Structure == | ||
| - | The protein is formed by eleven identical chains, forming a doughnut-like structure called β-wheel. This structure contains an eleven fold symmetry axis between chains facing each-other, the total ring has a diameter of 23 Å and is 36 Å thick. | + | The protein is formed by eleven identical chains, forming a doughnut-like structure called β-wheel. This structure contains an eleven fold symmetry axis between chains facing each-other, the total ring has a diameter of 23 Å and is 36 Å thick. <ref name="one">DOI 10.1038/374693a0</ref> |
| - | Each subunit is 75 amino-acids long and consists of a three-stranded and a four stranded antiparallel β-sheet. The three-stranded sheet of a subunit interacts with the four-stranded one of the adjacent chain to form a seven-stranded sheet (3). This structure can be compared to structures found in immunoglobulins even if the connections between the beta-strands aren’t related. | + | Each subunit is 75 amino-acids long and consists of a three-stranded and a four stranded antiparallel β-sheet. The three-stranded sheet of a subunit interacts with the four-stranded one of the adjacent chain to form a seven-stranded sheet (3). This structure can be compared to structures found in immunoglobulins even if the connections between the beta-strands aren’t related. <ref name="one" /> |
| - | + | ||
=== Tryptophane binding === | === Tryptophane binding === | ||
| - | + | The protein can bind eleven L-tryptophane molecule, each one binds into an hydrophobic pocket formed between two adjacent subunits and it is covered by the histidines H33 and H34. The subunits are linked by hydrophobic interactions and the tryptophane binding reinforce the quaternary structure by adding new hydrophobic interactions and hydrogen bonds between the adjacent subunits. <ref name="one" /> | |
| - | The protein can bind eleven L-tryptophane molecule, each one binds into an hydrophobic pocket formed between two adjacent subunits and it is covered by the histidines H33 and H34. The subunits are linked by hydrophobic interactions and the tryptophane binding reinforce the quaternary structure by adding new hydrophobic interactions and hydrogen bonds between the adjacent subunits. | + | The amino and carboxy functions of tryptophane form 8 hydrogen bonds with the protein and its carboxyl oxygen interact with one water molecule. This is the only water molecule in the hydrophobic pocket, indeed tryptophane is totally isolated from solvent thanks to the conformation change induced its binding that allows the closing of the pocket. <ref name="one" /> |
| - | The amino and carboxy functions of tryptophane form 8 hydrogen bonds with the protein and its carboxyl oxygen interact with one water molecule. This is the only water molecule in the hydrophobic pocket, indeed tryptophane is totally isolated from solvent thanks to the conformation change induced its binding that allows the closing of the pocket. | + | The binding is highly cooperative, indeed the 46-54 loop is in contact with two consecutive tryptophane, thus the binding of a first molecule modifies the loop conformation and promotes the fixation of a second one. <ref name="one" /> |
| - | The binding is highly cooperative, indeed the 46-54 loop is in contact with two consecutive tryptophane, thus the binding of a first molecule modifies the loop conformation and promotes the fixation of a second one. | + | |
=== Interaction with RNA === | === Interaction with RNA === | ||
| - | When tryptophane binds to a subunit of the protein it induces a conformational change between residues 25-33 and 49-52. These conformational changes allow the binding of the target messenger RNA in circle around the wheel. The interaction is specific, indeed the protein recognizes two characteristic regions of ten nucleotides called DR1 and DR2 between positions +36 and +91 of the leader transcript. | + | When tryptophane binds to a subunit of the protein it induces a conformational change between residues 25-33 and 49-52. These conformational changes allow the binding of the target messenger RNA in circle around the wheel. The interaction is specific, indeed the protein recognizes two characteristic regions of ten nucleotides called DR1 and DR2 between positions +36 and +91 of the leader transcript. <ref name="one" /> |
| - | The recognition requires multiples (G/U)AG patterns spaced by two or three nucleotides. | + | The recognition requires multiples (G/U)AG patterns spaced by two or three nucleotides. <ref name="one" /> The adenine and the guanine at the third position of this pattern are packed against the Phe32 sidechain. These bases are also involved in an intricated network of interactions with the side chains of the aminoacids of TRAP: the adenosine forms a hydrogen bond with Lys 37 and the guanine with Lys56 and Arg58 (5). The first nucleotide (U or G) only forms a single hydrogen bond with the sidechain of an aspartate residue. (3) The backbone of the RNA points out of the circle, and even if it only interacts with the protein by a single hydrogen bond formed by the 2’-OH of the guanosine at the third position of each pattern, it allows the specific recognition of RNA. (4) However, if this interaction is conserved, it is possible to replace the others ribonucleotides by deoxyribonucleotides without altering the affinity of the binding. (2) These characteristics of RNA recognition and binding car be compared with the protein U1A of spliceosome in interaction with snRNA. (6) |
Footprint assays with different fragments of the leader region have shown that RNA binding to TRAP is oriented, indeed the bases triplets at the 5’ end of the RNA bind first and are then followed by those at the 3’ end. It is yet unclear why. (2) | Footprint assays with different fragments of the leader region have shown that RNA binding to TRAP is oriented, indeed the bases triplets at the 5’ end of the RNA bind first and are then followed by those at the 3’ end. It is yet unclear why. (2) | ||
| - | |||
| - | |||
| - | 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. | ||
| - | |||
| - | |||
== References == | == References == | ||
<references/> | <references/> | ||
Revision as of 17:10, 25 December 2014
| This Sandbox is Reserved from 15/11/2014, through 15/05/2015 for use in the course "Biomolecule" taught by Bruno Kieffer at the Strasbourg University. This reservation includes Sandbox Reserved 951 through Sandbox Reserved 975. |
To get started:
More help: Help:Editing |
|
Contents |
Functions
Mechanisms
Relevance
Structure
The protein is formed by eleven identical chains, forming a doughnut-like structure called β-wheel. This structure contains an eleven fold symmetry axis between chains facing each-other, the total ring has a diameter of 23 Å and is 36 Å thick. [1] Each subunit is 75 amino-acids long and consists of a three-stranded and a four stranded antiparallel β-sheet. The three-stranded sheet of a subunit interacts with the four-stranded one of the adjacent chain to form a seven-stranded sheet (3). This structure can be compared to structures found in immunoglobulins even if the connections between the beta-strands aren’t related. [1]
Tryptophane binding
The protein can bind eleven L-tryptophane molecule, each one binds into an hydrophobic pocket formed between two adjacent subunits and it is covered by the histidines H33 and H34. The subunits are linked by hydrophobic interactions and the tryptophane binding reinforce the quaternary structure by adding new hydrophobic interactions and hydrogen bonds between the adjacent subunits. [1] The amino and carboxy functions of tryptophane form 8 hydrogen bonds with the protein and its carboxyl oxygen interact with one water molecule. This is the only water molecule in the hydrophobic pocket, indeed tryptophane is totally isolated from solvent thanks to the conformation change induced its binding that allows the closing of the pocket. [1] The binding is highly cooperative, indeed the 46-54 loop is in contact with two consecutive tryptophane, thus the binding of a first molecule modifies the loop conformation and promotes the fixation of a second one. [1]
Interaction with RNA
When tryptophane binds to a subunit of the protein it induces a conformational change between residues 25-33 and 49-52. These conformational changes allow the binding of the target messenger RNA in circle around the wheel. The interaction is specific, indeed the protein recognizes two characteristic regions of ten nucleotides called DR1 and DR2 between positions +36 and +91 of the leader transcript. [1] The recognition requires multiples (G/U)AG patterns spaced by two or three nucleotides. [1] The adenine and the guanine at the third position of this pattern are packed against the Phe32 sidechain. These bases are also involved in an intricated network of interactions with the side chains of the aminoacids of TRAP: the adenosine forms a hydrogen bond with Lys 37 and the guanine with Lys56 and Arg58 (5). The first nucleotide (U or G) only forms a single hydrogen bond with the sidechain of an aspartate residue. (3) The backbone of the RNA points out of the circle, and even if it only interacts with the protein by a single hydrogen bond formed by the 2’-OH of the guanosine at the third position of each pattern, it allows the specific recognition of RNA. (4) However, if this interaction is conserved, it is possible to replace the others ribonucleotides by deoxyribonucleotides without altering the affinity of the binding. (2) These characteristics of RNA recognition and binding car be compared with the protein U1A of spliceosome in interaction with snRNA. (6) Footprint assays with different fragments of the leader region have shown that RNA binding to TRAP is oriented, indeed the bases triplets at the 5’ end of the RNA bind first and are then followed by those at the 3’ end. It is yet unclear why. (2)
