User:Karl Oberholser/Sandbox2
From Proteopedia
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HMfB Seq: MELPIAPIGR IIKDAGAERV SDDARITLAK ILEEMGRDIA SEAIKLARHA GRKTIKAEDI ELAVRRFKK <br> | HMfB Seq: MELPIAPIGR IIKDAGAERV SDDARITLAK ILEEMGRDIA SEAIKLARHA GRKTIKAEDI ELAVRRFKK <br> | ||
| - | Comparing the above sequences one can see that an important difference is that A has a glycine at position 2 which is lacking in B. In addition to that deletion, there are a number of substitutions which creates differences in the sequence of the two peptides. As a consequence of this similarity of primary structure, as shown in the two applets below, the tertiary structures of both peptides are quite similar. Also the location of the nonpolar residues within the tertiary structure are similarly located <scene name='User:Karl_Oberholser/Sandbox2/Nonpolar_1hta/1' target='1'>HMfA</scene>, <scene name='User:Karl_Oberholser/Sandbox2/Nonpolar_1a7w/2' target='2'>HMfB</scene>. | + | Comparing the above sequences one can see that an important difference is that A has a glycine at position 2 which is lacking in B. In addition to that deletion, there are a number of substitutions which creates differences in the sequence of the two peptides. As a consequence of this similarity of primary structure, as shown in the two applets below, the tertiary structures of both peptides are quite similar (<scene name='User:Karl_Oberholser/Sandbox2/1hta_first/1' target='1'>Default scene HMfA</scene>, <scene name='User:Karl_Oberholser/Sandbox2/1a7w_first/2' target='2'>Default scene HMfB</scene>). Also the location of the nonpolar residues within the tertiary structure are similarly located <scene name='User:Karl_Oberholser/Sandbox2/Nonpolar_1hta/1' target='1'>HMfA</scene>, <scene name='User:Karl_Oberholser/Sandbox2/Nonpolar_1a7w/2' target='2'>HMfB</scene>. |
| - | <applet load='1hta' size='400' frame='true' align='left' caption='HMfA, PDB ID:1hta' name='1' /> | + | <applet load='1hta' size='400' frame='true' align='left' caption='HMfA, PDB ID:1hta' name='1' scene='User:Karl_Oberholser/Sandbox2/1hta_first/1'> /> |
| - | <applet load='1a7w' size='400' frame='true' align='right' caption='HMfB, PDB ID: 1a7w' name='2' scene='User:Karl_Oberholser/Sandbox2/1a7w_first/ | + | <applet load='1a7w' size='400' frame='true' align='right' caption='HMfB, PDB ID: 1a7w' name='2' scene='User:Karl_Oberholser/Sandbox2/1a7w_first/2' /> |
<applet load='1b67' size='400' frame='true' align='right' caption='Dimer of HMfA, PDB ID:1b67' name='3' scene='User:Karl_Oberholser/Sandbox2/1b67_first/1' /> | <applet load='1b67' size='400' frame='true' align='right' caption='Dimer of HMfA, PDB ID:1b67' name='3' scene='User:Karl_Oberholser/Sandbox2/1b67_first/1' /> | ||
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== Dimer Structure == | == Dimer Structure == | ||
The significance of exposed areas of hydrophobic side chains are that they are potential sites of monomeric interaction to form dimers. In the applet to the right the orthorombic form of HMfA (PDB:1B67) is shown as a dimer structure. Displaying the <scene name='User:Karl_Oberholser/Sandbox2/Nonpolar_dimer/1' target='3'>hydrophobic residues</scene> reveals that many of the hydrophobic residues that were exposed in the monomeric structure are involved in the associative binding of the dimer. The nonpolar residues that remain exposed would be involved in the tetrameric structure, and there is evidence for this higher level of structure | The significance of exposed areas of hydrophobic side chains are that they are potential sites of monomeric interaction to form dimers. In the applet to the right the orthorombic form of HMfA (PDB:1B67) is shown as a dimer structure. Displaying the <scene name='User:Karl_Oberholser/Sandbox2/Nonpolar_dimer/1' target='3'>hydrophobic residues</scene> reveals that many of the hydrophobic residues that were exposed in the monomeric structure are involved in the associative binding of the dimer. The nonpolar residues that remain exposed would be involved in the tetrameric structure, and there is evidence for this higher level of structure | ||
Revision as of 16:17, 21 January 2010
Histones HMfA and HMfB from Methanothermus fervidus
"The hyperthermophilic archaeon Methanothermus fervidus contains two small basic proteins, HMfA (68 amino acid residues) and HMfB (69 residues)that share a common ancestry with the eukaryal nucleosome core histones H2A, H2B, H3, and H4. HMfA and HMfB have sequences that differ at 11 locations, they have different structural stabilities, and the complexes that they form with DNA have different electrophoretic mobilities." [1]
Comparison of Structures
HMfA Seq: MGELPIAPIG RIIKNAGAER VSDDARIALA KVLEEMGEEI ASEAVKLAKH AGRKTIKAED IELARKMFK
HMfB Seq: MELPIAPIGR IIKDAGAERV SDDARITLAK ILEEMGRDIA SEAIKLARHA GRKTIKAEDI ELAVRRFKK
Comparing the above sequences one can see that an important difference is that A has a glycine at position 2 which is lacking in B. In addition to that deletion, there are a number of substitutions which creates differences in the sequence of the two peptides. As a consequence of this similarity of primary structure, as shown in the two applets below, the tertiary structures of both peptides are quite similar (, ). Also the location of the nonpolar residues within the tertiary structure are similarly located , .
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