Simplified Protein Models: Predicting Folding Pathways and Structure Using Amino Acid Sequences

Adhikari, Aashish N.; Freed, Karl F.; Sosnick, Tobin R.

doi:10.1103/physrevlett.111.028103

Cited by 34 publications

(48 citation statements)

References 36 publications

(37 reference statements)

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“…Recent progress in computer simulations of the course of native structure formation now finds similar folding pathways for a number of small proteins (79)(80)(81).…”

Section: Discussionmentioning

confidence: 99%

Folding of a large protein at high structural resolution

Walters

Mayne²,

Hinshaw³

et al. 2013

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

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107

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Kinetic folding of the large two-domain maltose binding protein (MBP; 370 residues) was studied at high structural resolution by an advanced hydrogen-exchange pulse-labeling mass-spectrometry method (HX MS). Dilution into folding conditions initiates a fast molecular collapse into a polyglobular conformation (<20 ms), determined by various methods including small angle X-ray scattering. The compaction produces a structurally heterogeneous state with widespread low-level HX protection and spectroscopic signals that match the equilibrium melting posttransition-state baseline. In a much slower step (7-s time constant), all of the MBP molecules, although initially heterogeneously structured, form the same distinct helix plus sheet folding intermediate with the same time constant. The intermediate is composed of segments that are distant in the MBP sequence but adjacent in the native protein where they close the longest residue-to-residue contact. Segments that are most HX protected in the early molecular collapse do not contribute to the initial intermediate, whereas the segments that do participate are among the less protected. The 7-s intermediate persists through the rest of the folding process. It contains the sites of three previously reported destabilizing mutations that greatly slow folding. These results indicate that the intermediate is an obligatory step on the MBP folding pathway. MBP then folds to the native state on a longer time scale (∼100 s), suggestively in more than one step, the first of which forms structure adjacent to the 7-s intermediate. These results add a large protein to the list of proteins known to fold through distinct native-like intermediates in distinct pathways.SAXS | HDX | protein collapse | denatured state ensemble F ifty years after Anfinsen's seminal demonstration that an unfolded protein can refold spontaneously when placed under native conditions, major questions concerning the folding process remain unanswered (1, 2). What is the unfolded state like, its degree of compaction, the reality and character of residual structure before folding begins, and its possible role in guiding the folding process (3-7)? Analogous questions relate to folding intermediates and the folding pathway itself. Do proteins fold through many alternative independent pathways as earlier theoretical investigations have suggested (8-12), or do they fold through necessary intermediates in a distinct pathway (13), as a growing list of experimental observations indicate (14, 15)? To answer these questions, it will be necessary to define experimentally the intermediate forms that proteins move through on their way to the native state. The problem has been that these transient states are beyond the reach of the usual high-resolution crystallographic and NMR structural methods. Most experimental folding studies have therefore relied on low-resolution optical methods that can follow folding in real time but rarely provide the structural information necessary to resolve the basic mechanistic questions.Recent work...

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“…Recent progress in computer simulations of the course of native structure formation now finds similar folding pathways for a number of small proteins (79)(80)(81).…”

Section: Discussionmentioning

confidence: 99%

Folding of a large protein at high structural resolution

Walters

Mayne²,

Hinshaw³

et al. 2013

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

Self Cite

107

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“…Previous simulations on λ repressor and variants used a variety of methodologies from all-atom molecular dynamics (MD) simulations to coarse-grain models (13)(14)(15)(16)(17)(18)(19)62) (Fig. S4 and Table S4).…”

Section: Discussionmentioning

confidence: 99%

“…The 80-residue subdomain of the λ-repressor transcription factor, λ (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11), is an appealing system as it contains five α-helices arranged in a nonsymmetric pattern, folds in microseconds, and is nearly a downhill folder (12), a condition where a continuous series of folding events may be characterized. These characteristics along with a folding time that nears the upper limit for current all-atom simulations (13)(14)(15)(16)(17)(18)(19) make this protein appropriate for detailed comparisons between experiment and simulations.…”

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confidence: 99%

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confidence: 99%

“…Lapidus and coworkers proposed that the λ D14A variant folds in a downhill manner based on a combination of microfluidic mixing measurements and probe-dependent melting temperatures (10). Various computational methods, ranging from Gō models to all-atom simulations, have been applied to study the folding of λ 6-85 and its variants, yielding mixed agreement with experiment and each other (13)(14)(15)(16)(17)(18)(19).Here, a high-resolution characterization of the landscape and of the TSE of the λ YA variant is obtained from a combination of equilibrium native state hydrogen exchange (NSHX) data, along with kinetic studies using both ψ analysis with bi-Histidine (biHis) metal ion binding sites and ϕ analysis at 298 K. The hydrogen exchange (HX) rates and their denaturant dependence provide information on individual H-bond stabilities and the structural fluctuations that lead to their breakage. Another advantage of HX is that measurements can be carried out without denaturant at room temperature, thereby enabling the characterization of folding behavior under highly stabilizing conditions where downhill folding is most likely to occur (7).…”

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confidence: 99%

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Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange

Baxa

Gagnon

et al. 2016

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

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The relationship between folding cooperativity and downhill, or barrier-free, folding of proteins under highly stabilizing conditions remains an unresolved topic, especially for proteins such as λ-repressor that fold on the microsecond timescale. Under aqueous conditions where downhill folding is most likely to occur, we measure the stability of multiple H bonds, using hydrogen exchange (HX) in a λ YA variant that is suggested to be an incipient downhill folder having an extrapolated folding rate constant of 2 × 10 5 s −1 and a stability of 7.4 kcal·mol −1 at 298 K. At least one H bond on each of the three largest helices (α1, α3, and α4) breaks during a common unfolding event that reflects global denaturation. The use of HX enables us to both examine folding under highly stabilizing, native-like conditions and probe the pretransition state region for stable species without the need to initiate the folding reaction. The equivalence of the stability determined at zero and high denaturant indicates that any residual denatured state structure minimally affects the stability even under native conditions. Using our ψ analysis method along with mutational ϕ analysis, we find that the three aforementioned helices are all present in the folding transition state. Hence, the free energy surface has a sufficiently high barrier separating the denatured and native states that folding appears cooperative even under extremely stable and fast folding conditions. T he nature of the energy landscape when folding occurs on the microsecond timescale continues to be investigated using both experimental and computational approaches. The 80-residue subdomain of the λ-repressor transcription factor, λ 6-85 (1-11), is an appealing system as it contains five α-helices arranged in a nonsymmetric pattern, folds in microseconds, and is nearly a downhill folder (12), a condition where a continuous series of folding events may be characterized. These characteristics along with a folding time that nears the upper limit for current all-atom simulations (13-19) make this protein appropriate for detailed comparisons between experiment and simulations.The energy landscape of λ 6-85 is significantly influenced by its sequence. Oas and coworkers found that the wild type and a fasterfolding mutant with two helix-promoting substitutions (λ AA with G46A/G48A, Fig. S1A) fold cooperatively (1-4). The transition state ensemble (TSE) characterized using ϕ analysis minimally contains α1 and α4 (3). Kinetic H/D isotope effect measurements in the Sosnick laboratory found that both λ 6-85 and λ AA fold cooperatively with ∼70% of the H bonds being formed in the TSE, matching the degree of surface buried in the TSE [beta Tanford value (β Tanford )] (5).Using nanosecond T-jump and other methods, Gruebele and coworkers proposed that faster-folding and stabilized variants, such as λ YA (λ AA + Q33Y) and λ D14A (λ YA + D14A), fold in an incipient or fully downhill manner, especially under highly stable conditions at lower temperatures (6-9). Key signatures of downhi...

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Protein Structure Prediction: Assembly of Secondary Structure Elements by Basin‐Hopping

et al. 2014

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The prediction of protein tertiary structure from primary structure remains a challenging task. A possible approach to this problem is the application of basin-hopping global optimization combined with an all-atom force field. In this work, we further improve the efficiency of basin-hopping by introducing an approach that derives tertiary structures from the secondary structure assignments of individual residues. We term this approach secondary-to-tertiary basin-hopping and benchmark it for three miniproteins, trpzip, trp-cage and ER-10. For each of the the three miniproteins the secondaryto-tertiary basin-hopping approach successfully and reliably predicts the three-dimensional structure.When it is applied to larger proteins we also obtain correctly folded structures. We thus conclude that the assembly of secondary structure elements using basin-hopping is a promising tool for de novo protein structure prediction.1 These authors contributed equally to this work.

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Simplified Protein Models: Predicting Folding Pathways and Structure Using Amino Acid Sequences

Cited by 34 publications

References 36 publications

Folding of a large protein at high structural resolution

Folding of a large protein at high structural resolution

Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange

Protein Structure Prediction: Assembly of Secondary Structure Elements by Basin‐Hopping

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