Sampling of states for estimating the folding funnel entropy and energy landscape of a model alpha-helical hairpin peptide

Chapagain, Prem P.; Parra, J. L.; Gerstman, Bernard S.; Liu, Yanxin

doi:10.1063/1.2757172

Cited by 13 publications

(9 citation statements)

References 42 publications

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“…On the other hand, apparently the nucleation-condensation process of at least some of the six previously and nine here investigated proteins also involves early funneling in the sense of multiple pathways as suggested by the funnel model (Wolynes et al, 1995(Wolynes et al, , 1996Onuchic et al, 1996;Shoemaker et al, 1997Shoemaker et al, , 1999Nymeyer et al 1998;Wolynes, 2001;Simler et al, 2006;Kameda & Takada, 2006;Chapagain et al, 2007;Kamiya et al, 2007;Kim et al, 2007;Lindberg & Oliveberg, 2007;MacCallum et al, 2007) and a decrease in molecular volume (see, e.g., Nölting et al, 1997;Kataoka et al, 1997;Pollack et al, 1999) as suggested by the hydrophobic collapse model (Rackovsky & Scheraga, 1977;Dill, 1985Dill, , 1990aDill, , 1990bDill et al, 1995;Akiyama et al, 2000;Hausrath, 2006;Arai et al, 2007).…”

Section: Nucleation-condensation Mechanism Of Foldingmentioning

confidence: 67%

“…The native elements of secondary structure are then thought to form in the collapsed state by structural rearrangement. Two further important models, the zipper model (Dill et al, 1993;Thompson et al, 1997) and funnel model (Wolynes et al, 1995(Wolynes et al, , 1996Onuchic et al, 1996;Shoemaker et al, 1997Shoemaker et al, , 1999Nymeyer et al 1998;Wolynes, 2001;Simler et al, 2006;Kameda & Takada, 2006;Chapagain et al, 2007;Kamiya et al, 2007;Kim et al, 2007;Lindberg & Oliveberg, 2007;MacCallum et al, 2007) emphasize zipper-like folding processes and parallel pathways of folding, respectively.…”

Section: Introductionmentioning

confidence: 99%

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How general is the nucleation–condensation mechanism?

Nölting¹,

Agard²

2008

Proteins

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We investigate the structures of the major folding transition states of nine proteins by correlation of published Phi-values with inter-residue contact maps. Combined with previous studies on six proteins, the analysis suggests that at least 10 of the 15 small globular proteins fold via a nucleation-condensation mechanism with a concurrent build-up of secondary and tertiary structure contacts, but a structural consolidation that is clearly nonuniformly distributed over the molecule and most intense in a single structural region suggesting the occurrence of a single folding nucleus. However, on average helix- and sheet-forming residues show somewhat larger Phi-values in the major transition state, suggesting that secondary structure formation is one important driving force in the nucleation-condensation in many proteins and that secondary-structure forming residues tend to be more prominent in folding nuclei. We synthesize the combined information on these 10 of 15 proteins into a unified nucleation-condensation mechanism which also accounts for effects described by the framework, hydrophobic collapse, zipper, and funnel models.

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Section: Nucleation-condensation Mechanism Of Foldingmentioning

confidence: 67%

Section: Introductionmentioning

confidence: 99%

How general is the nucleation–condensation mechanism?

Nölting¹,

Agard²

2008

Proteins

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“…Nevertheless, fine-scale details such as sharp barriers (as above) or local roughness in the landscape [38,39] typically cannot be recovered. We note that the problem of resolving fine details in the landscapes of biomolecules is ubiquitous across different reconstruction approaches, whether due to Gaussian filtering by a probe as above, coarse binning [8], or inadequate sampling [40].…”

mentioning

confidence: 99%

Reconstructing Folding Energy Landscape Profiles from Nonequilibrium Pulling Curves with an Inverse Weierstrass Integral Transform

et al. 2014

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The energy landscapes that drive structure formation in biopolymers are difficult to measure. Here we validate experimentally a novel method to reconstruct landscape profiles from single-molecule pulling curves using an inverse Weierstrass transform (IWT) of the Jarzysnki free-energy integral. The method was applied to unfolding measurements of a DNA hairpin, replicating the results found by the more-established weighted histogram (WHAM) and inverse Boltzmann methods. Applying both WHAM and IWT methods to reconstruct the folding landscape for a RNA pseudoknot having a stiff energy barrier, we found that landscape features with sharper curvature than the force probe stiffness could not be recovered with the IWT method. The IWT method is thus best for analyzing data from stiff force probes such as atomic force microscopes.

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“…This can be taken as an indication that the transition state possesses a restricted degree of freedom compared to both the relaxed and the quenched LHCII conformers. A relatively wide landscape of possible transition state conformers is typically discussed for protein folding, and computational investigation have been performed for small globular polypeptides (e.g., (48)(49)(50)). The negative value of DS q y points toward the existence of a defined intermediate in the transition between the unquenched and quenched form of the complex, rather than a pure transition state, which is unresolved due to temporal resolution of the measurement (see (32,38,50) for discussions relating to intermediate in protein folding).…”

Section: Thermodynamic Characterization Of the Transition Statementioning

confidence: 99%

Comparison of the Thermodynamic Landscapes of Unfolding and Formation of the Energy Dissipative State in the Isolated Light Harvesting Complex II

Santabarbara

Horton

Ruban

2009

Biophysical Journal

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In biochemistry and cell biology, understanding the molecular mechanisms by which physiological processes are regulated is regarded as an ultimate goal. In higher plants, one of the most widely investigated regulatory processes occurs in the light harvesting complexes (LHCII) of the chloroplast thylakoid membranes. Under limiting photon flux densities, LHCII harvests sunlight with high efficiency. When the intensity of incident radiation reaches levels close to the saturation of the photosynthesis, the efficiency of light harvesting is decreased by a process referred to as nonphotochemical quenching (NPQ), which enhances the singlet-excited state deactivation via nonradiative dissipative processes. Conformational rearrangements in LHCII are known to be crucial in promoting and controlling NPQ in vitro and in vivo. In this article, we address the thermodynamic nature of the conformational rearrangements promoting and controlling NPQ in isolated LHCII. A combined, linear reaction scheme in which the folded, quenched state represents a stable intermediate on the unfolding pathway was employed to describe the temperature dependence of the spectroscopic signatures associated with the chlorophyll fluorescence quenching and the loss of secondary structure motifs in LHCII. The thermodynamic model requires considering the temperature dependence of Gibbs free energy difference between the quenched and the unquenched states, as well as the unfolded and quenched states, of LHCII. Even though the same reaction scheme is adequate to describe the quenching and the unfolding processes in LHCII monomers and trimers, their thermodynamic characteristics were found to be markedly different. The results of the thermodynamic analysis shed light on the physiological importance of the trimeric state of LHCII in stabilizing the efficient light harvesting mode as well as preventing the quenched conformation of the protein from unfolding. Moreover, the transition to the quenched conformation in trimers reveals a larger degree of cooperativity than in monomers, explained by a small characteristic entropy (DeltaH(q) = 85 +/- 3 kJ mol(-1) compared to 125 +/- 5 kJ mol(-1) in monomers), which enables the fine-tuning of nonphotochemical quenching in vivo.

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Sampling of states for estimating the folding funnel entropy and energy landscape of a model alpha-helical hairpin peptide

Cited by 13 publications

References 42 publications

How general is the nucleation–condensation mechanism?

How general is the nucleation–condensation mechanism?

Reconstructing Folding Energy Landscape Profiles from Nonequilibrium Pulling Curves with an Inverse Weierstrass Integral Transform

Comparison of the Thermodynamic Landscapes of Unfolding and Formation of the Energy Dissipative State in the Isolated Light Harvesting Complex II

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