User:Karl Oberholser/Sandbox2
From Proteopedia
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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 (<scene name='User:Karl_Oberholser/Sandbox2/1b67_first/1' target='3'>Default dimer scene</scene>). (The HMfB dimer can be viewed by right clicking on the Jmol frank and selecting from the menu 1A7W|Biomolecule|load biomolecule 1.) Heterodimers of HNfA and HMfB can form as well | + | 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 (<scene name='User:Karl_Oberholser/Sandbox2/1b67_first/1' target='3'>Default dimer scene</scene>). (The HMfB dimer can be viewed by right clicking on the Jmol frank and selecting from the menu 1A7W|Biomolecule|load biomolecule 1.) Heterodimers of HNfA and HMfB can form as well. |
| - | <ref>Sandman, K., Grayling, R. A., Dobrinski, B., Lurz, R. & Reeve, J. N., Growth phase dependent synthesis of histones in the archaeon Methanothermus fervidus. Proc. Natl Acad. Sci. USA, '''91''', 12624-12628, 1994.</ref> | + | <ref>Sandman, K., Grayling, R. A., Dobrinski, B., Lurz, R. & Reeve, J. N., Growth phase dependent synthesis of histones in the archaeon Methanothermus fervidus. Proc. Natl Acad. Sci. USA, '''91''', 12624-12628, 1994.</ref> Displaying the <scene name='User:Karl_Oberholser/Sandbox2/Nonpolar_dimer/2' 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. |
| - | Some areas of nonpolar residues that remain exposed in the dimer would be involved in the tetrameric structure, and there is evidence for this higher level of structure | + | Some areas of nonpolar residues that remain exposed in the dimer would be involved in the tetrameric structure, and there is evidence for this higher level of structure. |
<ref>Luger, K., MaÈ der, A. W., Richmond, R. K., Sargent, D. F. & Richmond, T. J., Crystal structure of the nucleosome core particle at 2.8 AÊ resolution, Nature, '''389''', 251-260, 1997.</ref> | <ref>Luger, K., MaÈ der, A. W., Richmond, R. K., Sargent, D. F. & Richmond, T. J., Crystal structure of the nucleosome core particle at 2.8 AÊ resolution, Nature, '''389''', 251-260, 1997.</ref> | ||
<ref>Xie, X., Kokubo, T., Cohen, S. L., Mirza, U. A., Hoffmann, A., Chait, B. T., Roeder, R. G., Nakatani, Y. & Burley, S. K., Structural similarity between TAFs and the heterotetrameric core of the histone octamer. Nature, '''380''', 316-322, 1996.</ref> | <ref>Xie, X., Kokubo, T., Cohen, S. L., Mirza, U. A., Hoffmann, A., Chait, B. T., Roeder, R. G., Nakatani, Y. & Burley, S. K., Structural similarity between TAFs and the heterotetrameric core of the histone octamer. Nature, '''380''', 316-322, 1996.</ref> | ||
<ref>Birck, C., Poch, O., Romier, C., Ruff, M., Mengus, G., Lavigne, A.-C., Davidson, I. & Moras, D. | <ref>Birck, C., Poch, O., Romier, C., Ruff, M., Mengus, G., Lavigne, A.-C., Davidson, I. & Moras, D. | ||
| - | Human TAFII28 and TAFII18 interact through a histone fold encoded by atypical evolutionary conserved motifs also found in the SPT3 family, Cell, '''94''', 239-249, 1998.</ref> | + | Human TAFII28 and TAFII18 interact through a histone fold encoded by atypical evolutionary conserved motifs also found in the SPT3 family, Cell, '''94''', 239-249, 1998.</ref> The area of hydrophobic residues containing a <scene name='User:Karl_Oberholser/Sandbox2/P_tetrad/1'>proline tetrad</scene> would not be included in tetramer formation. The prolines which form the tetrad are present in the N terminus of each chain, and this tetrad structure is found in most archaeal homo- and heterodimeric histones but are not present in eukaryal histone dimers. |
<ref>Sandman, K., Pereira, S. L. & Reeve, J. N. Diversity of prokaryotic chromosomal proteins and the origin of the nucleosome. Cell. Mol. Life Sci. 54, 1350-1364, 1998.</ref> | <ref>Sandman, K., Pereira, S. L. & Reeve, J. N. Diversity of prokaryotic chromosomal proteins and the origin of the nucleosome. Cell. Mol. Life Sci. 54, 1350-1364, 1998.</ref> | ||
<ref>Higashibata, H., Fujiwara, S., Takagi, M. & Imanaka, T., Analysis of DNA compaction pro®le and | <ref>Higashibata, H., Fujiwara, S., Takagi, M. & Imanaka, T., Analysis of DNA compaction pro®le and | ||
intracellular contents of archaeal histones from Pyrococcus kodakaraensis KOD1. Biochem. Biophys. | intracellular contents of archaeal histones from Pyrococcus kodakaraensis KOD1. Biochem. Biophys. | ||
| - | Res. Commun. 258, 416-424, 1999</ref> | + | Res. Commun. 258, 416-424, 1999</ref> <scene name='User:Karl_Oberholser/Sandbox2/P_tetrad_spacefill/1'>Spacefill display</scene> shows that the rings are close enough to form attractive London forces, and these forces keep the peptide chain in position for <scene name='User:Karl_Oberholser/Sandbox2/Arg_pair/1'>two arginines</scene> with their positive charges to interact with DNA. There are <scene name='User:Karl_Oberholser/Sandbox2/Lys_thr_pairs/1'>lysine and threonine pairs</scene> that are involved in DNA binding. |
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Revision as of 20:26, 21 January 2010
Contents |
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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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 (). (The HMfB dimer can be viewed by right clicking on the Jmol frank and selecting from the menu 1A7W|Biomolecule|load biomolecule 1.) Heterodimers of HNfA and HMfB can form as well. [2] Displaying the reveals that many of the hydrophobic residues that were exposed in the monomeric structure are involved in the associative binding of the dimer.
Some areas of nonpolar residues that remain exposed in the dimer would be involved in the tetrameric structure, and there is evidence for this higher level of structure. [3] [4] [5] The area of hydrophobic residues containing a would not be included in tetramer formation. The prolines which form the tetrad are present in the N terminus of each chain, and this tetrad structure is found in most archaeal homo- and heterodimeric histones but are not present in eukaryal histone dimers. [6] [7] shows that the rings are close enough to form attractive London forces, and these forces keep the peptide chain in position for with their positive charges to interact with DNA. There are that are involved in DNA binding.
Notes and References
- ↑ From abstract of K. Decanniere, A. M. Babu, K. Sandman, J. N. Reeve, U. Heinemann Crystal Structure of Recombinant Histones HMfA and HMfB from the Hyperthermophilic Methanothermus fervidus. J. Mol. Biol., 303, 35-47, 2000
- ↑ Sandman, K., Grayling, R. A., Dobrinski, B., Lurz, R. & Reeve, J. N., Growth phase dependent synthesis of histones in the archaeon Methanothermus fervidus. Proc. Natl Acad. Sci. USA, 91, 12624-12628, 1994.
- ↑ Luger, K., MaÈ der, A. W., Richmond, R. K., Sargent, D. F. & Richmond, T. J., Crystal structure of the nucleosome core particle at 2.8 AÊ resolution, Nature, 389, 251-260, 1997.
- ↑ Xie, X., Kokubo, T., Cohen, S. L., Mirza, U. A., Hoffmann, A., Chait, B. T., Roeder, R. G., Nakatani, Y. & Burley, S. K., Structural similarity between TAFs and the heterotetrameric core of the histone octamer. Nature, 380, 316-322, 1996.
- ↑ Birck, C., Poch, O., Romier, C., Ruff, M., Mengus, G., Lavigne, A.-C., Davidson, I. & Moras, D. Human TAFII28 and TAFII18 interact through a histone fold encoded by atypical evolutionary conserved motifs also found in the SPT3 family, Cell, 94, 239-249, 1998.
- ↑ Sandman, K., Pereira, S. L. & Reeve, J. N. Diversity of prokaryotic chromosomal proteins and the origin of the nucleosome. Cell. Mol. Life Sci. 54, 1350-1364, 1998.
- ↑ Higashibata, H., Fujiwara, S., Takagi, M. & Imanaka, T., Analysis of DNA compaction pro®le and intracellular contents of archaeal histones from Pyrococcus kodakaraensis KOD1. Biochem. Biophys. Res. Commun. 258, 416-424, 1999
