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The mechanism of folding of Im7 reveals competition between functional and kinetic evolutionary constraints.

Friel CT, Smith DA, Vendruscolo M, Gsponer J, Radford SE - Nat. Struct. Mol. Biol. (2009)

Bottom Line: It is not clear whether this type of folding landscape results from insufficient evolutionary pressure to optimize folding efficiency, or arises from a conflict between functional and folding constraints.The results provide a comprehensive view of the folding process of this small protein.An analysis of the contributions of native and non-native interactions at different stages of folding reveals how the complexity of the folding landscape arises from concomitant evolutionary pressures for function and folding efficiency.

View Article: PubMed Central - PubMed

Affiliation: Astbury Centre for Structural Molecular Biology, University of Leeds, Mount Preston Street, Leeds LS2 9JT, UK.

ABSTRACT
Many proteins reach their native state through pathways involving the presence of folding intermediates. It is not clear whether this type of folding landscape results from insufficient evolutionary pressure to optimize folding efficiency, or arises from a conflict between functional and folding constraints. Here, using protein-engineering, ultra-rapid mixing and stopped-flow experiments combined with restrained molecular dynamics simulations, we characterize the transition state for the formation of the intermediate populated during the folding of the bacterial immunity protein, Im7, and the subsequent molecular steps leading to the native state. The results provide a comprehensive view of the folding process of this small protein. An analysis of the contributions of native and non-native interactions at different stages of folding reveals how the complexity of the folding landscape arises from concomitant evolutionary pressures for function and folding efficiency.

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Schematic illustration of the folding landscape of Im7. Ribbon diagram representations of selected cluster centers of TS1, I, TS2 and N are shown. The helix forming segments are coloured red (helix I), green (helix II), purple (helix III) and yellow (helix IV). Water molecules within a 12Å sphere around the centre of masses of TS1, I, TS2 and N are shown in ball and stick representation. Lower plots: the average interaction energy maps of TS1, I and TS2 (below the diagonal) are compared with that of N (above the diagonal). The scale is in kcal mol−1.
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Figure 6: Schematic illustration of the folding landscape of Im7. Ribbon diagram representations of selected cluster centers of TS1, I, TS2 and N are shown. The helix forming segments are coloured red (helix I), green (helix II), purple (helix III) and yellow (helix IV). Water molecules within a 12Å sphere around the centre of masses of TS1, I, TS2 and N are shown in ball and stick representation. Lower plots: the average interaction energy maps of TS1, I and TS2 (below the diagonal) are compared with that of N (above the diagonal). The scale is in kcal mol−1.

Mentions: Analysis of the ensemble of structures representing TS1 showed that this species is almost devoid of ordered secondary structure, a characteristic common to all the members of this ensemble (Fig. 4a,b). The large majority of residues remain solvent exposed in TS1 (Supplementary Fig. S4a), consistent with its expanded nature (βT), large radius of gyration (Fig. 4c) and lack of a stable hydrophobic core (Fig. 5). This conclusion is supported by the large radius of gyration of residues that comprise the native hydrophobic core of TS1 (Fig. 4c). Moreover, the helix-forming regions of the protein sequence are more than 20Å apart in TS1, except for the nascent helices I and II which contact each other via long-range side chain interactions between residues 16-20 and 37-42 (Figs. 4d and 5). The presence of these side chain contacts in TS1 is consistent with the high Φ-values experimentally determined for residues 18, 19 and 37 (Fig. 3b). Although these residues form some native-like contacts in this early transition state, many interactions are non-native (Fig. 5).


The mechanism of folding of Im7 reveals competition between functional and kinetic evolutionary constraints.

Friel CT, Smith DA, Vendruscolo M, Gsponer J, Radford SE - Nat. Struct. Mol. Biol. (2009)

Schematic illustration of the folding landscape of Im7. Ribbon diagram representations of selected cluster centers of TS1, I, TS2 and N are shown. The helix forming segments are coloured red (helix I), green (helix II), purple (helix III) and yellow (helix IV). Water molecules within a 12Å sphere around the centre of masses of TS1, I, TS2 and N are shown in ball and stick representation. Lower plots: the average interaction energy maps of TS1, I and TS2 (below the diagonal) are compared with that of N (above the diagonal). The scale is in kcal mol−1.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2651959&req=5

Figure 6: Schematic illustration of the folding landscape of Im7. Ribbon diagram representations of selected cluster centers of TS1, I, TS2 and N are shown. The helix forming segments are coloured red (helix I), green (helix II), purple (helix III) and yellow (helix IV). Water molecules within a 12Å sphere around the centre of masses of TS1, I, TS2 and N are shown in ball and stick representation. Lower plots: the average interaction energy maps of TS1, I and TS2 (below the diagonal) are compared with that of N (above the diagonal). The scale is in kcal mol−1.
Mentions: Analysis of the ensemble of structures representing TS1 showed that this species is almost devoid of ordered secondary structure, a characteristic common to all the members of this ensemble (Fig. 4a,b). The large majority of residues remain solvent exposed in TS1 (Supplementary Fig. S4a), consistent with its expanded nature (βT), large radius of gyration (Fig. 4c) and lack of a stable hydrophobic core (Fig. 5). This conclusion is supported by the large radius of gyration of residues that comprise the native hydrophobic core of TS1 (Fig. 4c). Moreover, the helix-forming regions of the protein sequence are more than 20Å apart in TS1, except for the nascent helices I and II which contact each other via long-range side chain interactions between residues 16-20 and 37-42 (Figs. 4d and 5). The presence of these side chain contacts in TS1 is consistent with the high Φ-values experimentally determined for residues 18, 19 and 37 (Fig. 3b). Although these residues form some native-like contacts in this early transition state, many interactions are non-native (Fig. 5).

Bottom Line: It is not clear whether this type of folding landscape results from insufficient evolutionary pressure to optimize folding efficiency, or arises from a conflict between functional and folding constraints.The results provide a comprehensive view of the folding process of this small protein.An analysis of the contributions of native and non-native interactions at different stages of folding reveals how the complexity of the folding landscape arises from concomitant evolutionary pressures for function and folding efficiency.

View Article: PubMed Central - PubMed

Affiliation: Astbury Centre for Structural Molecular Biology, University of Leeds, Mount Preston Street, Leeds LS2 9JT, UK.

ABSTRACT
Many proteins reach their native state through pathways involving the presence of folding intermediates. It is not clear whether this type of folding landscape results from insufficient evolutionary pressure to optimize folding efficiency, or arises from a conflict between functional and folding constraints. Here, using protein-engineering, ultra-rapid mixing and stopped-flow experiments combined with restrained molecular dynamics simulations, we characterize the transition state for the formation of the intermediate populated during the folding of the bacterial immunity protein, Im7, and the subsequent molecular steps leading to the native state. The results provide a comprehensive view of the folding process of this small protein. An analysis of the contributions of native and non-native interactions at different stages of folding reveals how the complexity of the folding landscape arises from concomitant evolutionary pressures for function and folding efficiency.

Show MeSH
Related in: MedlinePlus