Folding of the Villin Headpiece Subdomain from Random Structures. Analysis of the Charge Distribution as a Function of pH

Ripoll, Daniel R.; Vila, Jorge A.; Scheraga, Harold A.

doi:10.1016/j.jmb.2004.04.002

Cited by 72 publications

(36 citation statements)

References 47 publications

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“…At this resolution it is possible to describe in atomic detail a number of structural features that contribute to the stabilization of the folded state. Although helices ␣1 (residues 2-11) and ␣2 (residues [13][14][15][16][17][18][19][20] are much shorter than ␣3 (residues 21-33), peptide fragments from which ␣3 has been removed still have considerable structure as judged by NMR and CD (30), suggesting these two helices together play a more important role in establishing the proper fold.…”

Section: Resultsmentioning

confidence: 99%

“…These accurate atomic-resolution x-ray structures are important for the current effort to simulate folding by all-atom MD methods (9)(10)(11)(12)(13)(14)(15)(16)(17), which up to now have used the NMR structure 1VII (8).…”

Section: Discussionmentioning

confidence: 99%

“…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)(10)(11)(12)(13)(14)(15)(16)(17), which have thus far been based on the NMR structure.…”

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confidence: 99%

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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.

220

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: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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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.

220

290

View full text Add to dashboard Cite

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“…The helical subdomain is probably the smallest occurring natural sequence that has been shown to fold cooperatively. Its small size and very rapid folding have made it the focus of a large number of theoretical and computational studies (4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18).…”

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confidence: 99%

Effect of modulating unfolded state structure on the folding kinetics of the villin headpiece subdomain

Brewer

Tang

et al. 2005

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

148

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Equilibrium Fourier transform infrared (FTIR) and temperaturejump (T-jump) IR spectroscopic techniques were used to study the thermodynamics and kinetics of the unfolding and folding of the villin headpiece helical subdomain (HP36), a small three-helix protein. A double phenylalanine mutant (HP36 F47L, F51L) that destabilizes the hydrophobic core of this protein also was studied. The double mutant is less stable than wild type (WT) and has been shown to contain less residual secondary structure and tertiary contacts in its unfolded state. The relaxation kinetics after a T-jump perturbation were studied for both HP36 and HP36 F47L, F51L. Both proteins exhibited biphasic relaxation kinetics in response to a T-jump. The folding times for the WT (3.23 s at 60.2°C) and double phenylalanine mutant (3.01 s at 49.9°C) at the approximate midpoints of their thermal unfolding transitions were found to be similar. The folding time for the WT was determined to be 3.34 s at 49.9°C, similar to the folding time of the double phenylalanine mutant at that temperature. The double phenylalanine mutant, however, unfolds faster with an unfolding time of 3.01 s compared with 6.97 s for the WT at 49.9°C.protein folding ͉ Fourier transform IR ͉ temperature jump ͉ diffusion collision T he mechanism by which an unfolded polypeptide chain folds into its final native structure is still not fully understood, despite the obvious importance of the protein folding problem. In recent years there has been considerable interest in small single-domain proteins that fold quickly. These proteins provide attractive systems for computational and theoretical studies, and they are useful experimental models of the early steps in the assembly of more complicated folds. The helical subdomain derived from the villin headpiece, HP36, is a small three-helix structure found in the extreme C terminus of villin ( Fig. 1). Its modest size and helical structure suggest that it should fold rapidly, and this hypothesis has been independently confirmed by fluorescence-detected temperature-jump (T-jump) studies and NMR lineshape analysis (1-3). The helical subdomain is probably the smallest occurring natural sequence that has been shown to fold cooperatively. Its small size and very rapid folding have made it the focus of a large number of theoretical and computational studies (4-18).Residual structure and interactions in the unfolded state may play an important role in determining the rate of protein folding. Unfolded state structure might contribute to rapid folding by constraining and limiting the initial conformational search in the unfolded basin. Some models of folding postulate an important role for residual unfolded state structure. The diffusion collision model, for example, has been applied to rapidly folding helical proteins, and a key parameter in the model is the intrinsic stability of the individual microdomains (11,19,20). Although there have been a number of experimental studies of fast folding proteins, surprisingly little work has been reported that ...

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“…However, such test can be misleading as the physics (and therefore also the complexity of the problem) is different for larger molecules. For this reason, we have chosen already for our initial tests a much larger molecule, the 36-residue villin headpiece sub-domain HP-36, which has recently raised considerable interest in computational protein studies [6][7][8][9]. With its well-defined secondary and tertiary structure [10] it is sufficiently complex and with 596 atoms large enough that numerical simulations become indeed a challenge [11].…”

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confidence: 99%

Efficient Sampling of Protein Structures by Model Hopping

Kwak

Hansmann

2005

Phys. Rev. Lett.

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We introduce a novel simulation method, model hopping, that enhances sampling of low-energy configurations in complex systems. The approach is illustrated for a protein folding problem. Thermodynamic quantities of proteins with up to 46 residues are evaluated from all-atom simulations with this method.The solution of many pharmacological and medical problems, such as rational drug design or the pathology of diseases associated with the mis-folding of proteins, requires a detailed understanding of the relation between chemical composition and structure of proteins. However, despite more than two decades of research, this so-called protein-folding problem has remained a hard computational task. This is because proteins in an all-atom representation are characterized by a rough energy landscape with a huge number of local minima separated by high energy barriers. Various numerical techniques exist that can alleviate this multiple minima problem. One popular example is parallel tempering (also known as replica exchange method) [1], a technique that was first introduced to protein studies in Ref. [2]. In its most common form, one considers an artificial system built up of N non-interacting copies of a molecule, each at a different temperature T i . In addition to standard Monte Carlo or molecular dynamics moves that affect only one copy, parallel tempering allows also the exchange of conformations between two copies i and j = i + 1 with probability w(C old → C new ) = min(1, exp(ΔβΔE)). The resulting random walk in temperature enables configurations to cross energy barriers and move out of local minima leading in this way to an enhanced sampling of lowenergy structures. Variants of parallel tempering introducing non-canonical weights have been proposed [2,3].Here, we introduce another variant of this idea, dubbed by us "model hopping" (MH), where as in the Hamilton Exchange method [4] or the Multi-Self-Overlap-Ensemble [5] the random walk in temperatures is replaced by one through an ensemble of models with slightly altered energy functions. For this we assume that the energy function can be separated in two terms: E = E A + aE B . As in parallel tempering, MH considers N non-interacting copies of the molecule, but copies are now exchanged according toHere, Δa = a j − a i and ΔE B = E B (C j ) − E B (C i ). Due to this exchange move configurations perform a random walk on a ladder of models with a 1 = 1 > a 2 > a 3 > …. > a N that differ by the relative contributions of E B to the total energy E of the molecule. For instance, barriers in the energy landscape of proteins often arise from van der Waals repulsion between atoms that come too close. Generalized-ensemble techniques circumvent the problem by performing a random walk in energy that allows crossing of these barriers. On the other hand, in MH the protein walks randomly up and down on a ladder of models with successively smaller contributions from the van der Waals energy. While the "physical" system is on one side of the ladder (at a 1 = 1), the (non-p...

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Folding of the Villin Headpiece Subdomain from Random Structures. Analysis of the Charge Distribution as a Function of pH

Cited by 72 publications

References 47 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

Effect of modulating unfolded state structure on the folding kinetics of the villin headpiece subdomain

Efficient Sampling of Protein Structures by Model Hopping

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