Dynamics of Unfolded Polypeptide Chains

Fierz, Beat; Kiefhaber, Thomas

doi:10.1002/9783527619498.ch22

Cited by 16 publications

(27 citation statements)

References 113 publications

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“…Because local chain motions and chain stiffness are affected by the intramolecular interactions, their breakage must be slower than local chain motions, which are on the 10-ps time scale for bond rotations. On the other hand, single-exponential kinetics are observed for loop formation, which indicates rapid conformational equilibration of the ensemble of unfolded states (18,19,37,42,43). These considerations set an upper limit of a few hundred picoseconds on the interconversion of the peptide conformations.…”

Section: Properties Of Polypeptide Chains In Watermentioning

confidence: 99%

“…The use of parameters for the dimensions of polypeptide chains reported by Flory and coworkers (35,36) yields ͗r 0 2 ͘ 1/2 ϭ 37.6 Å for a (Gly-Ser) 16 chain when the properties of serine are approximated by alanine (36,37). Although the validity of the underlying ''isolated-pair hypothesis'' has recently been shown to be oversimplified (16), this number still provides a useful estimate, which should, however, only apply to ⌰ conditions where a real polymer chain behaves like an ideal chain and repulsive steric interactions (excluded volume) are exactly compensated by intramolecular attractive forces.…”

Section: Effect Of Gdmcl On Polypeptide Chain Propertiesmentioning

confidence: 99%

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End-to-end distance distributions and intrachain diffusion constants in unfolded polypeptide chains indicate intramolecular hydrogen bond formation

Möglich

Joder

Kiefhaber

2006

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

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234

335

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Characterization of the unfolded state is essential for the understanding of the protein folding reaction. We performed time-resolved FRET measurements to gain information on the dimensions and the internal dynamics of unfolded polypeptide chains. Using an approach based on global analysis of data obtained from two different donor–acceptor pairs allowed for the determination of distance distribution functions and diffusion constants between the chromophores. Results on a polypeptide chain consisting of 16 Gly-Ser repeats between the FRET chromophores reveal an increase in the average end-to-end distance from 18.9 to 39.2 Å between 0 and 8 M GdmCl. The increase in chain dimensions is accompanied by an increase in the end-to-end diffusion constant from (3.6 ± 1.0) × 10 −7 cm 2 s −1 in water to (14.8 ± 2.5) × 10 −7 cm 2 s −1 in 8 M GdmCl. This finding suggests that intrachain interactions in water exist even in very flexible chains lacking hydrophobic groups, which indicates intramolecular hydrogen bond formation. The interactions are broken upon denaturant binding, which leads to increased chain flexibility and longer average end-to-end distances. This finding implies that rapid collapse of polypeptide chains during refolding of denaturant-unfolded proteins is an intrinsic property of polypeptide chains and can, at least in part, be ascribed to nonspecific intramolecular hydrogen bonding. Despite decreased intrachain diffusion constants, the conformational search is accelerated in the collapsed state because of shorter diffusion distances. The measured distance distribution functions and diffusion constants in combination with Szabo–Schulten–Schulten theory were able to reproduce experimentally determined rate constants for end-to-end loop formation.

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Section: Properties Of Polypeptide Chains In Watermentioning

confidence: 99%

Section: Effect Of Gdmcl On Polypeptide Chain Propertiesmentioning

confidence: 99%

End-to-end distance distributions and intrachain diffusion constants in unfolded polypeptide chains indicate intramolecular hydrogen bond formation

Möglich

Joder

Kiefhaber

2006

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

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234

335

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“…The experiments were initiated by a 4-ns laserflash at 355 nm, which produces the xanthone triplet state that can be detected by its strong absorbance band at 590 nm (24,26). TTET to naphthylalanine leads to a decay in xanthone triplet absorbance band ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Transition state and ground state properties of the helix–coil transition in peptides deduced from high-pressure studies

Neumaier

Büttner

Bachmann

et al. 2013

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

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Volume changes associated with protein folding reactions contain valuable information about the folding mechanism and the nature of the transition state. However, meaningful interpretation of such data requires that overall volume changes be deconvoluted into individual contributions from different structural components. Here we focus on one type of structural element, the α-helix, and measure triplet-triplet energy transfer at high pressure to determine volume changes associated with the helix-coil transition. Our results reveal that the volume of a 21-amino-acid alanine-based peptide shrinks upon helix formation. Thus, helices, in contrast with native proteins, become more stable with increasing pressure, explaining the frequently observed helical structures in pressureunfolded proteins. Both helix folding and unfolding become slower with increasing pressure. per molecule) for removing one residue. Thus, addition or removal of a helical residue proceeds through a transitory high-energy state with a large volume, possibly due to the presence of unsatisfied hydrogen bonds, although steric effects may also contribute.protein stability | helix dynamics | protein dynamics U nderstanding the effect of pressure on protein stability and dynamics provides insight into fundamental principles and mechanisms of protein folding (1). For most proteins, increasing pressure shifts the folding equilibrium toward the unfolded state, which, according to Le Chatelier's principle, shows that the native state has a larger volume than the unfolded state (2-4). The origin of the volume increase upon folding has been discussed controversially for a long time. The major obstacle in the interpretation of volume changes is opposing contributions from different effects. Analysis of high-resolution X-ray structures suggested that formation of intramolecular hydrogen bonds and van der Waals interactions in the native state lead to a decrease in atomic volumes and thus to a decrease in protein volume upon folding (5). Further, water around hydrophobic groups has a larger volume than bulk water, which also leads to a decrease in volume upon burial of hydrophobic groups in the native protein (6). On the other hand, formation of ordered water structures around charged groups (7) and solvation of the peptide backbone decrease the water volume (6), which leads to a volume increase upon folding. Recent experimental results suggested that volume changes associated with transfer of groups from solvent to the protein interior upon folding are small and that the formation of void volumes in native proteins is the major origin of the volume increase upon folding (8).Volume changes associated with the formation of protein folding transition states are only poorly characterized. Highpressure stopped-flow experiments on tendamistat (9) and cold shock protein (10), as well as pressure-jump experiments on coldshock protein (10) and an ankyrin repeat domain (11), revealed that volumes of protein folding transition states are close to the volume of the native...

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“…For different polypeptide-solvent systems, the scaling relations have been found to be 1.05 ± 0.06, 8 1.5 3,12 and 1.7 ± 0.1 6,13 (good solvent). The scaling exponent of 1.5 has been rationalized using the SSS description of the diffusion-controlled contact formation dynamics in a theta solvent, which yields τ sss ∼ N 3/2 .…”

Section: Comparison With Experimentsmentioning

confidence: 99%

“…The typical values of α for different protein-solvent systems are 1.05 ± 0.06, 8 1.5 3,12 and 1.7 ± 0.1 6,13 for N ≃ 10 − 20.…”

Section: Introductionmentioning

confidence: 98%

Solvent-quality-dependent contact formation dynamics in proteins

Kundu¹,

Dua²

2016

J. Stat. Mech.

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Dynamics of Unfolded Polypeptide Chains

Cited by 16 publications

References 113 publications

End-to-end distance distributions and intrachain diffusion constants in unfolded polypeptide chains indicate intramolecular hydrogen bond formation

End-to-end distance distributions and intrachain diffusion constants in unfolded polypeptide chains indicate intramolecular hydrogen bond formation

Transition state and ground state properties of the helix–coil transition in peptides deduced from high-pressure studies

Solvent-quality-dependent contact formation dynamics in proteins

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