Abstract
Formation of a specific contact between two residues of a polypeptide chain is an important elementary process in protein folding. Here we describe a method for studying contact formation between tryptophan and cysteine based on measurements of the lifetime of the tryptophan triplet state. With tryptophan at one end of a flexible peptide and cysteine at the other, the triplet decay rate is identical to the rate of quenching by cysteine. We show that this rate is also close to the diffusion-limited rate of contact formation. The length dependence of this end-to-end contact rate was studied in a series of Cys-(Ala-Gly-Gln) k -Trp peptides, with k varying from 1 to 6. The rate decreases from ∼1/(40 ns) for k = 1 to ∼1/(140 ns) for k = 6, approaching the length dependence expected for a random coil ( n −3/2 ) for the longest peptides.
Keywords
TryptophanChemistryCysteineQuenching (fluorescence)Folding (DSP implementation)Intramolecular forceRandom coilCrystallographyPeptideBiophysicsStereochemistryAmino acidFluorescenceBiochemistryBiologyCircular dichroismPhysics
Affiliated Institutions
Related Publications
Energy landscape of a peptide consisting of α‐helix, 3<sub>10</sub>‐helix, β‐turn, β‐hairpin, and other disordered conformations
Abstract The energy landscape of a peptide [Ace‐Lys‐Gln‐Cys‐Arg‐Glu‐Arg‐Ala‐Nme] in explicit water was studied with a multicanonical molecular dynamics simulation, and the AMBER...
Spin–orbit coupling and inelastic transitions in collisions of O(1<i>D</i>) with Ar, Kr, and Xe
Inelastic collisions of O(1D) with Ar, Kr, and Xe have been treated in the multistate Landau–Zener and the close-coupling approximations. The coupling mechanism is spin–orbit mi...
Optimization of high-sensitivity fluorescence detection
We present general expressions for the number of photons emitted by a fluorescent chromophore as a function of the intensity and the duration of illumination. The aim is to find...
α-Helical stabilization by side chain shielding of backbone hydrogen bonds
We study atomic models of the thermodynamics of the structural transition of peptides that form α-helices. The effect of sequence variation on α-helix formation for alanine-rich...
Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides
Obtaining the correct balance of secondary structure propensities is a central priority in protein force-field development. Given that current force fields differ significantly ...
Publication Info
- Year
- 2000
- Type
- article
- Volume
- 97
- Issue
- 13
- Pages
- 7220-7225
- Citations
- 412
- Access
- Closed
External Links
Social Impact
Altmetric
PlumX Metrics
Social media, news, blog, policy document mentions
Citation Metrics
412
OpenAlex
Cite This
Lisa J. Lapidus,
William A. Eaton,
James Hofrichter
(2000).
Measuring the rate of intramolecular contact formation in polypeptides.
Proceedings of the National Academy of Sciences
, 97
(13)
, 7220-7225.
https://doi.org/10.1073/pnas.97.13.7220
Identifiers
- DOI
- 10.1073/pnas.97.13.7220