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Crowning proteins: modulating the protein surface properties using crown ethers.

Lee CC, Maestre-Reyna M, Hsu KC, Wang HC, Liu CI, Jeng WY, Lin LL, Wood R, Chou CC, Yang JM, Wang AH - Angew. Chem. Int. Ed. Engl. (2014)

Bottom Line: We elucidated the crystal structures of several protein-crown ether co-crystals grown in the presence of 18-crown-6.We then employed biophysical methods and molecular dynamics simulations to compare these complexes with the corresponding apoproteins and with similar complexes with ring-shaped low-molecular-weight polyethylene glycols.Consequently, we propose that crown ethers can be used to modulate a wide variety of protein surface behaviors, such as oligomerization, domain-domain interactions, stabilization in organic solvents, and crystallization.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529 (Taiwan); Core Facilities for Protein Structural Analysis, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529 (Taiwan).

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18-Crown-6 binding modes in DMP19 and Pin1-R14A. a) Structure of the DMP19⋅CR dimeric complex. Four C-crowns (C-crowna-d) and two K-crowns (K-crowna and K-crownb), in purple, bind each DMP19 dimer (green and blue). The Fo−Fc omit maps of the CRs (orange) were calculated for each CR and contoured at a 1.5 σ level. α1 and α2 stand for α-helices 1 and 2. b) Comparison of the monomers of the published DMP19 structure (3VJZ, in blue) and the DMP19⋅CR complex (cyan). While 73.6 % of the structure remains practically unchanged (rmsd 0.95 over 108 common Cα atoms), the region between the N-terminus and α-helix 2 changes dramatically, rotating by 179 degrees. The rotated elements are shown as cylinder diagrams, with α1, α2, and Y26 corresponding to 3VJZ, and α1′, α2′, and Y26′ to the DMP19⋅CR complex. c) Ribbon diagram of Pin1R14A⋅CR complex. Two CRs (K- and C-crown) and protein residues interacting with them are shown as stick models (purple, and yellow, respectively). Symmetry related CRs (K- and C-crown*) are shown in green. e) Crystal packing of Pin1R14A and CRs. Six Pin1R14A molecules are shown in different colors in the unit cell. The CRs are presented as sphere diagrams with carbon atoms in purple.
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fig02: 18-Crown-6 binding modes in DMP19 and Pin1-R14A. a) Structure of the DMP19⋅CR dimeric complex. Four C-crowns (C-crowna-d) and two K-crowns (K-crowna and K-crownb), in purple, bind each DMP19 dimer (green and blue). The Fo−Fc omit maps of the CRs (orange) were calculated for each CR and contoured at a 1.5 σ level. α1 and α2 stand for α-helices 1 and 2. b) Comparison of the monomers of the published DMP19 structure (3VJZ, in blue) and the DMP19⋅CR complex (cyan). While 73.6 % of the structure remains practically unchanged (rmsd 0.95 over 108 common Cα atoms), the region between the N-terminus and α-helix 2 changes dramatically, rotating by 179 degrees. The rotated elements are shown as cylinder diagrams, with α1, α2, and Y26 corresponding to 3VJZ, and α1′, α2′, and Y26′ to the DMP19⋅CR complex. c) Ribbon diagram of Pin1R14A⋅CR complex. Two CRs (K- and C-crown) and protein residues interacting with them are shown as stick models (purple, and yellow, respectively). Symmetry related CRs (K- and C-crown*) are shown in green. e) Crystal packing of Pin1R14A and CRs. Six Pin1R14A molecules are shown in different colors in the unit cell. The CRs are presented as sphere diagrams with carbon atoms in purple.

Mentions: To elucidate the diverse effects of CRs on protein crystallization, we solved the structures of all crystals obtained in the presence of CRs. Direct interactions with CR were revealed only in hemoglobin, DMP19, RbmA, and Pin1R14A crystals (Figure 2; Supporting Information, Figure S5, Tables S2–S4). Lysozyme, SARS-CoV 3CL protease, hemoglobin, and Pin1R14A yielded crystals belonging to known space groups, whereas the addition of CR resulted in a new space group for DMP19. Addition of CR improved RbmA crystal quality and resolution, making it possible to solve the complex structure.16 On the other hand, the DMP19, Pin1R14A, and hemoglobin structures presented novel CR interactions with common characteristics (Figure 2 and 3; Supporting Information, Figure S5).


Crowning proteins: modulating the protein surface properties using crown ethers.

Lee CC, Maestre-Reyna M, Hsu KC, Wang HC, Liu CI, Jeng WY, Lin LL, Wood R, Chou CC, Yang JM, Wang AH - Angew. Chem. Int. Ed. Engl. (2014)

18-Crown-6 binding modes in DMP19 and Pin1-R14A. a) Structure of the DMP19⋅CR dimeric complex. Four C-crowns (C-crowna-d) and two K-crowns (K-crowna and K-crownb), in purple, bind each DMP19 dimer (green and blue). The Fo−Fc omit maps of the CRs (orange) were calculated for each CR and contoured at a 1.5 σ level. α1 and α2 stand for α-helices 1 and 2. b) Comparison of the monomers of the published DMP19 structure (3VJZ, in blue) and the DMP19⋅CR complex (cyan). While 73.6 % of the structure remains practically unchanged (rmsd 0.95 over 108 common Cα atoms), the region between the N-terminus and α-helix 2 changes dramatically, rotating by 179 degrees. The rotated elements are shown as cylinder diagrams, with α1, α2, and Y26 corresponding to 3VJZ, and α1′, α2′, and Y26′ to the DMP19⋅CR complex. c) Ribbon diagram of Pin1R14A⋅CR complex. Two CRs (K- and C-crown) and protein residues interacting with them are shown as stick models (purple, and yellow, respectively). Symmetry related CRs (K- and C-crown*) are shown in green. e) Crystal packing of Pin1R14A and CRs. Six Pin1R14A molecules are shown in different colors in the unit cell. The CRs are presented as sphere diagrams with carbon atoms in purple.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
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fig02: 18-Crown-6 binding modes in DMP19 and Pin1-R14A. a) Structure of the DMP19⋅CR dimeric complex. Four C-crowns (C-crowna-d) and two K-crowns (K-crowna and K-crownb), in purple, bind each DMP19 dimer (green and blue). The Fo−Fc omit maps of the CRs (orange) were calculated for each CR and contoured at a 1.5 σ level. α1 and α2 stand for α-helices 1 and 2. b) Comparison of the monomers of the published DMP19 structure (3VJZ, in blue) and the DMP19⋅CR complex (cyan). While 73.6 % of the structure remains practically unchanged (rmsd 0.95 over 108 common Cα atoms), the region between the N-terminus and α-helix 2 changes dramatically, rotating by 179 degrees. The rotated elements are shown as cylinder diagrams, with α1, α2, and Y26 corresponding to 3VJZ, and α1′, α2′, and Y26′ to the DMP19⋅CR complex. c) Ribbon diagram of Pin1R14A⋅CR complex. Two CRs (K- and C-crown) and protein residues interacting with them are shown as stick models (purple, and yellow, respectively). Symmetry related CRs (K- and C-crown*) are shown in green. e) Crystal packing of Pin1R14A and CRs. Six Pin1R14A molecules are shown in different colors in the unit cell. The CRs are presented as sphere diagrams with carbon atoms in purple.
Mentions: To elucidate the diverse effects of CRs on protein crystallization, we solved the structures of all crystals obtained in the presence of CRs. Direct interactions with CR were revealed only in hemoglobin, DMP19, RbmA, and Pin1R14A crystals (Figure 2; Supporting Information, Figure S5, Tables S2–S4). Lysozyme, SARS-CoV 3CL protease, hemoglobin, and Pin1R14A yielded crystals belonging to known space groups, whereas the addition of CR resulted in a new space group for DMP19. Addition of CR improved RbmA crystal quality and resolution, making it possible to solve the complex structure.16 On the other hand, the DMP19, Pin1R14A, and hemoglobin structures presented novel CR interactions with common characteristics (Figure 2 and 3; Supporting Information, Figure S5).

Bottom Line: We elucidated the crystal structures of several protein-crown ether co-crystals grown in the presence of 18-crown-6.We then employed biophysical methods and molecular dynamics simulations to compare these complexes with the corresponding apoproteins and with similar complexes with ring-shaped low-molecular-weight polyethylene glycols.Consequently, we propose that crown ethers can be used to modulate a wide variety of protein surface behaviors, such as oligomerization, domain-domain interactions, stabilization in organic solvents, and crystallization.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529 (Taiwan); Core Facilities for Protein Structural Analysis, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529 (Taiwan).

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