TY - JOUR
T1 - Structural distributions from single-molecule measurements as a tool for molecular mechanics
AU - Hanson, Jeffrey A.
AU - Brokaw, Jason
AU - Hayden, Carl C.
AU - Chu, Jhih Wei
AU - Yang, Haw
N1 - Funding Information:
We thank David King for synthesis of poly- l -proline peptides, Susan Marqusee for the use of a steady-state fluorimeter, and Bill Eaton for helpful discussions and NMR results. This work was supported by grants from the National Institutes of Health, the Camille and Henry Dreyfus Foundation, the Princeton University (HY), the American Chemical Society Petroleum Research Fund (ACS-PRF-49727-DNI6), University of California, Berkeley (JWC), and from the Division of Chemical Sciences, Geosciences and Biosciences, the Office of Basic Energy Sciences, the U.S. Department of Energy (CCH & HY). Sandia is a multi-program laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy’s National Nuclear Security Administration under Contract No. DE-AC04-94AL85000.
PY - 2012/3/2
Y1 - 2012/3/2
N2 - A mechanical view provides an attractive alternative for predicting the behavior of complex systems since it circumvents the resource-intensive requirements of atomistic models; however, it remains extremely challenging to characterize the mechanical responses of a system at the molecular level. Here, the structural distribution is proposed to be an effective means to extracting the molecular mechanical properties. End-to-end distance distributions for a series of short poly-l-proline peptides with the sequence P nCG 3K-biotin (n = 8, 12, 15 and 24) were used to experimentally illustrate this new approach. High-resolution single-molecule Förster-type resonance energy transfer (FRET) experiments were carried out and the conformation-resolving power was characterized and discussed in the context of the conventional constant-time binning procedure for FRET data analysis. It was shown that the commonly adopted theoretical polymer models - including the worm-like chain, the freely jointed chain, and the self-avoiding chain - could not be distinguished by the averaged end-to-end distances, but could be ruled out using the molecular details gained by conformational distribution analysis because similar polymers of different sizes could respond to external forces differently. Specifically, by fitting the molecular conformational distribution to a semi-flexible polymer model, the effective persistence lengths for the series of short poly-l-proline peptides were found to be size-dependent with values of ∼190 , ∼67 , ∼51 , and ∼76 for n = 8, 12, 15, and 24, respectively. A comprehensive computational modeling was carried out to gain further insights for this surprising discovery. It was found that P 8 exists as the extended all-trans isomaer whereas P 12 and P 15 predominantly contained one proline residue in the cis conformation. P 24 exists as a mixture of one-cis (75%) and two-cis (25%) isomers where each isomer contributes to an experimentally resolvable conformational mode. This work demonstrates the resolving power of the distribution-based approach, and the capacity of integrating high-resolution single-molecule FRET experiments with molecular modeling to reveal detailed structural information about the conformation of molecules on the length scales relevant to the study of biological molecules.
AB - A mechanical view provides an attractive alternative for predicting the behavior of complex systems since it circumvents the resource-intensive requirements of atomistic models; however, it remains extremely challenging to characterize the mechanical responses of a system at the molecular level. Here, the structural distribution is proposed to be an effective means to extracting the molecular mechanical properties. End-to-end distance distributions for a series of short poly-l-proline peptides with the sequence P nCG 3K-biotin (n = 8, 12, 15 and 24) were used to experimentally illustrate this new approach. High-resolution single-molecule Förster-type resonance energy transfer (FRET) experiments were carried out and the conformation-resolving power was characterized and discussed in the context of the conventional constant-time binning procedure for FRET data analysis. It was shown that the commonly adopted theoretical polymer models - including the worm-like chain, the freely jointed chain, and the self-avoiding chain - could not be distinguished by the averaged end-to-end distances, but could be ruled out using the molecular details gained by conformational distribution analysis because similar polymers of different sizes could respond to external forces differently. Specifically, by fitting the molecular conformational distribution to a semi-flexible polymer model, the effective persistence lengths for the series of short poly-l-proline peptides were found to be size-dependent with values of ∼190 , ∼67 , ∼51 , and ∼76 for n = 8, 12, 15, and 24, respectively. A comprehensive computational modeling was carried out to gain further insights for this surprising discovery. It was found that P 8 exists as the extended all-trans isomaer whereas P 12 and P 15 predominantly contained one proline residue in the cis conformation. P 24 exists as a mixture of one-cis (75%) and two-cis (25%) isomers where each isomer contributes to an experimentally resolvable conformational mode. This work demonstrates the resolving power of the distribution-based approach, and the capacity of integrating high-resolution single-molecule FRET experiments with molecular modeling to reveal detailed structural information about the conformation of molecules on the length scales relevant to the study of biological molecules.
KW - FRET
KW - Polyproline
KW - Single-molecule
KW - Worm-like chain
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U2 - 10.1016/j.chemphys.2011.06.014
DO - 10.1016/j.chemphys.2011.06.014
M3 - Article
C2 - 22661822
AN - SCOPUS:84859522695
SN - 0301-0104
VL - 396
SP - 61
EP - 71
JO - Chemical Physics
JF - Chemical Physics
IS - 1
ER -