Guiding the search for a protein's maximum rate of folding

Zhu, Yili; Fu, Xiaoran; Wang, Ting; Tamura, Atsuo; Takada, Shoji; Saven, Jeffery G.; Gai, Feng

doi:10.1016/j.chemphys.2004.05.008

Cited by 50 publications

(57 citation statements)

References 51 publications

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“…Loss of the charge is not expected to have any global effect on the structure, because previous thermodynamic studies showed minimal change in stability upon changing the ionization state of H27 (22). Stabilizing effects, attributed to the increased hydrophobicity and increased folding rate upon removal of partially buried changed groups, have also been observed for another ultrafast folding helical protein, the albumin binding domain 1prb (41,42). Kubelka et al (18) have used both empirical and theoretical arguments to suggest that a protein's folding ''speed limit'' (43) is approximately (N͞100 s) Ϫ1 , where N is the number of residues, (0.4 s) Ϫ1 for HP35.…”

Section: Discussionmentioning

confidence: 88%

High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein

Chiu

Kubelka

Herbst‐Irmer

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

215

290

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The 35-residue subdomain of the villin headpiece (HP35) is a small ultrafast folding protein that is being intensely studied by experiments, theory, and simulations. We have solved the x-ray structures of HP35 and its fastest folding mutant [K24 norleucine (nL)] to atomic resolution and compared their experimentally measured folding kinetics by using laser temperature jump. The structures, which are in different space groups, are almost identical to each other but differ significantly from previously solved NMR structures. Hence, the differences between the x-ray and NMR structures are probably not caused by lattice contacts or crystal͞solution differences, but reflect the higher accuracy of the x-ray structures. The x-ray structures reveal important details of packing of the hydrophobic core and some additional features, such as crosshelical H bonds. Comparison of the x-ray structures indicates that the nL substitution produces only local perturbations. Consequently, the finding that the small stabilization by the mutation is completely reflected in an increased folding rate suggests that this region of the protein is as structured in the transition state as in the folded structure. It is therefore a target for engineering to increase the folding rate of the subdomain from Ϸ0.5 s ؊1 for the nL mutant to the estimated theoretical speed limit of Ϸ3 s ؊1 .kinetics ͉ temperature jump ͉ NMR R ecent developments in both experimental and computational methods have opened exciting new possibilities for combining experiments with all-atom molecular dynamics (MD) simulations of protein folding. The dramatic improvement in time resolution in protein folding kinetic studies brought about by the introduction of nanosecond optical triggering methods (1-4), together with the use of distributed computing, now make it possible to directly compare MD simulations with experiments on ultrafast folding proteins (5). Such simulations are important because, if accurate, they contain a complete atomic description of the folding mechanism. The computational cost of folding simulations demands small size and ultrafast folding. HP35 is a subdomain of the headpiece of actinbinding protein villin and is the smallest naturally occurring polypeptide that folds autonomously without any cofactor or disulfide bond (6). Unlike other ''miniproteins'' (7), HP35 is highly thermostable (6) and, as revealed by the NMR structure, globular with a well packed hydrophobic core (8). These properties resemble much larger single-domain helical proteins and have made HP36 (HP35 plus an N-terminal Met) the focus of several all-atom folding simulations (9-17), which have thus far been based on the NMR structure.Because of the delicate balance of stabilization forces involved in protein folding an accurate structure for the folded state is essential for MD simulations of folding and protein redesign calculations. We have previously shown that HP35 is one of the fastest folding proteins, with a folding rate (Ϸ0.2 s Ϫ1 ) approaching its theoretical limit (3 s Ϫ1 ...

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Section: Discussionmentioning

confidence: 88%

High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein

Chiu

Kubelka

Herbst‐Irmer

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

215

290

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“…This pursuit has produced many notable examples of microsecond and submicrosecond folders whose kinetics have been characterized both experimentally [1][2][3][4][5][6][7][8][9] and computationally. 4,[10][11][12][13][14][15][16][17] These studies attempt to address such issues as the existence of a "speed limit" to folding 3,6,8 and the proposition of barrierless folding.…”

Section: Introductionmentioning

confidence: 99%

Heterogeneity Even at the Speed Limit of Folding: Large-scale Molecular Dynamics Study of a Fast-folding Variant of the Villin Headpiece

Ensign

Kasson

Pande

2007

Journal of Molecular Biology

179

183

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We have performed molecular dynamics simulations on a set of nine unfolded conformations of the fastest-folding protein yet discovered, a variant of the villin headpiece subdomain (HP-35 NleNle). The simulations were generated using a new distributed computing method, yielding hundreds of trajectories each on a time scale comparable to the experimental folding time, despite the large (10,000 atom) size of the simulation system. This strategy eliminates the need to assume a two-state kinetic model or to build a Markov state model. The relaxation to the folded state at 300 K from the unfolded configurations (generated by simulation at 373 K) was monitored by a method intended to reflect the experimental observable (quenching of tryptophan by histidine). We also monitored the relaxation to the native state by directly comparing structural snapshots with the native state. The rate of relaxation to the native state and the number of resolvable kinetic time scales both depend upon starting structure. Moreover, starting structures with folding rates most similar to experiment show some native-like structure in the N-terminal helix (helix 1) and the phenylalanine residues constituting the hydrophobic core, suggesting that these elements may exist in the experimentally relevant unfolded state. Our large-scale simulation data reveal kinetic complexity not resolved in the experimental data. Based on these findings, we propose additional experiments to further probe the kinetics of villin folding.

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“…For related reasons, some proteins of the ∼40 size range 84 are useful for probing the general "speed limit" of folding as well. 85,86 In the present study, we compare the folding cooperativity of NTL9 and two homologous peripheral subunitbinding domain (PSBD) proteins (PDB IDs: 1W4E and 2BTH), for which experimental structural and folding data are available. 30,32,73,87 Among these three proteins, each of the two PSBD proteins has a clearly different native topology from that of NTL9, whereas the two PSBD homologs have essentially identical folds with only subtle differences in packing.…”

Section: Introductionmentioning

confidence: 99%

Probing Possible Downhill Folding: Native Contact Topology Likely Places a Significant Constraint on the Folding Cooperativity of Proteins with ∼40 Residues

Badasyan

Liu

Chan

2008

Journal of Molecular Biology

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Guiding the search for a protein's maximum rate of folding

Cited by 50 publications

References 51 publications

High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein

High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein

Heterogeneity Even at the Speed Limit of Folding: Large-scale Molecular Dynamics Study of a Fast-folding Variant of the Villin Headpiece

Probing Possible Downhill Folding: Native Contact Topology Likely Places a Significant Constraint on the Folding Cooperativity of Proteins with ∼40 Residues

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