Sandbox Reserved 195: Difference between revisions

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<Structure load='1RNU' size='500' frame='true' align='right' caption='RNase S (PDB: 1RNU) is a protein composed of 2 fragments:  S Peptide (residues 1-20) and S Protein (residues 21-124).  It is a result of cleavage of RNase A between residues 20 and 21.' scene='Insert optional scene name here' target='0' />


[[Image:surface view of rnase s.png|200px|left|thumb|  The image above depicts the surface interaction between the S peptide and S protein fragments; S peptide is blue, S protein is yellow.]]






RNase A and RNase S have very similar structures except for a few key areas, one being the cleavage site (residues 16-23)<ref name="Raines"> PMID:11848924</ref>.  Decreased order in these amino acids is seen in RNase S.  The <scene name='Sandbox_Reserved_195/Clevage_site/1' target='1'>cleavage site</scene> on RNase A is located between residues Ala 20 and Ser 21.  Upon cleavage, the fragments S peptide and S protein are created, giving RNase S its unique structure.  <scene name='Sandbox_Reserved_195/S_peptide/1' target='0'>S Peptide</scene> consists of residues 1-20, and is largely responsible for proper folding. S protein is comprised of residues 21-124.  Additionally, RNase A and RNase S have many conserved structural components, as they are essentially the same protein.  Glutamine 60 is a highly conserved amino acid throughout many different species, showing its importance in both <scene name='Sandbox_Reserved_195/Gln_60/2' target='0'>RNase S</scene> and <scene name='Sandbox_Reserved_195/Glutamine_60_rnase_a/1' target='1'>RNase A</scene>.  Glu 60 is also interesting, because it is the only residue in an unfavorable position (Φ= -100, ψ= -130) as defined in the Ramachandran plot <ref name="Kim">PMID:1463719</ref>.   
RNase A and RNase S have very similar structures except for a few key areas, one being the cleavage site (residues 16-23)<ref name="Raines"> PMID:11848924</ref>.  Decreased order in these amino acids is seen in RNase S.  The <scene name='Sandbox_Reserved_195/Clevage_site/4' target='1'>cleavage site</scene> on RNase A is located between residues Ala 20 and Ser 21.  Upon cleavage, the fragments S peptide and S protein are created, giving RNase S its unique structure.  <scene name='Sandbox_Reserved_195/S_peptide/8' target='0'>S Peptide</scene> consists of residues 1-20, and is largely responsible for proper folding.   <scene name='Sandbox_Reserved_195/S_protein/2'>S protein</scene> is comprised of residues 21-124.  Additionally, RNase A and RNase S have many conserved structural components, as they are essentially the same protein.  Glutamine 60 is highly conserved structurally between  <scene name='Sandbox_Reserved_195/Gln_60/3' target='0'>RNase S</scene> and <scene name='Sandbox_Reserved_195/Glutamine_60_rnase_a/5' target='1'>RNase A</scene>, as well as in many different species, demonstrating its importance.  Glu 60 is also interesting, because it is the only residue in an unfavorable position (Φ= -100, ψ= -130) as defined in the Ramachandran plot <ref name="Kim">PMID:1463719</ref>.   






The <scene name='Sandbox_Reserved_195/Active_site/1' target='0'>active site</scene> of RNase S consists of residues His 12, Lys 41, Val 43, Asn 44, Thr 45, His 119, Phe 120, Asp 121, and Ser 123.  Residues 1, 15-20, 21-23, and 124 could be removed without serious consequence to the structure or activity of RNase S.  Residue 124 could also be removed from RNase A without compromising the structure. <ref name="Wyckoff et al">PMID:6037556</ref>


<scene name='Sandbox_Reserved_195/Asp_14/2'>Asp 14</scene>
<Structure load='1RNU' size='500' frame='true' align='right' caption='RNase S (PDB: 1RNU) is a protein composed of 2 fragments:  S Peptide (residues 1-20) and S Protein (residues 21-124).  It is a result of cleavage of RNase A between residues 20 and 21.' scene='Sandbox_Reserved_195/Ribonuclese_s_basic/3' target='0' />


<Structure load='7rsa' size='500' frame='true' align='left' caption='RNase A (PDB: 7rsa), also known as bovine pancreatic ribonuclease A, has been studied for years to learn about protein structure, stability, and folding.' scene='Insert optional scene name here' target='1' />


The <scene name='Sandbox_Reserved_195/Active_site/2' target='0'>active site</scene> of RNase S consists of <scene name='Sandbox_Reserved_195/Active_site/3'>residues</scene> His 12, Lys 41, Val 43, Asn 44, Thr 45, His 119, Phe 120, Asp 121, and Ser 123. <scene name='Sandbox_Reserved_195/His_12/1'>His 12</scene> is the only residue in the active site that is located on the S peptide fragment. <scene name='Sandbox_Reserved_195/Lys_41_and_his_119/1'>Lys 41 and His 119</scene> are also crucial to the functioning of RNase S.  Interestingly, both catalytic Histidines perform the same function, even though they are located on <scene name='Sandbox_Reserved_195/Histines_and_lysines/2'>different fragments</scene>.  Residues 1, 15-20, 21-23, and 124 could be removed without serious consequence to the structure or activity of RNase S.  Residue 124 could also be removed from RNase A without compromising the structure. <ref name="Wyckoff et al">PMID:6037556</ref>






<Structure load='7rsa' size='500' frame='true' align='left' caption='RNase A (PDB: 7rsa), also known as bovine pancreatic ribonuclease A, has been studied for years to learn about protein structure, stability, and folding.' scene='Sandbox_Reserved_195/Ribonuclease_a_basic/3' target='1' />




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Hydrogen bonding and hydrophobic interactions play a major role in the structure of RNase S. <ref name="Kim" /> There are 84 water molecules present, with 8 of these specifically connecting S peptide and S protein.  Some of these water molecules are also conserved throughout all RNase derivatives.  Hydrophobic interactions between residues Phe 8, Met 13, His 12, Ala 4 are essential in holding the S Peptide in place.  In addition to these residues, Asp 14 is also important in peptide-protein binding, as represented in the 2D picture.  In the picture, it appears that the protein and peptide are not connected; this is because the bond cleavage between residues 20 and 21 of RNase A has already occurred.  Additionally RNase S has a rigid hydrophobic core; one-third of the surface of the core is made up of the S peptide.  The surrounding loops have more flexibility. 




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[[Image:surface view of rnase s.png]]
                                                                                                                        {{Quote box
| quote  = The image above depicts the surface interaction between the S peptide and S protein fragments; S peptide is blue, S protein is yellow.
| source =
| width  =10
| align  =Left
}}








Conclusion??
 
Hydrogen bonding and hydrophobic interactions play a major role in the structure of RNase S. <ref name="Kim" /> There are 84 water molecules present, with 8 of these specifically connecting S peptide and S protein.  Some of these water molecules are also conserved throughout all RNase derivatives.  Hydrophobic interactions between residues Phe 8, Met 13, His 12, Ala 4 are essential in holding the S Peptide in place.  In addition to these residues, <scene name='Sandbox_Reserved_195/Asp_14/4'>Asp 14</scene> is also important in peptide-protein binding.  In the picture, it appears that the protein and peptide are not connected; this is because the bond cleavage between residues 20 and 21 of RNase A has already occurred.  Additionally RNase S has a rigid hydrophobic core; one-third of the surface of the core is made up of the S peptide.  The surrounding loops have more flexibility. 
 
 
 
 
 
 
 


[[References ]]
[[References ]]

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA, Melanie Clark, Ashton Chaffee, R. Jeremy Johnson
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