Protein folding using fragment assembly and physical energy function

Seung Yeon Kim; Weontae Lee; Julian Lee

doi:10.1063/1.2364500

Protein folding using fragment assembly and physical energy function

Seung Yeon Kim, Weontae Lee, Julian Lee

Research output: Contribution to journal › Article › peer-review

15 Citations (Scopus)

Abstract

We perform a systematic study of the effects of sequence-independent backbone interactions and sequence-dependent side-chain interactions on protein folding using fragment assembly and physical energy function. Structures for ten proteins belonging to various structural classes are predicted only with Lennard-Jones interaction between backbone atoms. We find nativelike structures for Β proteins, suggesting that for proteins in this class, the global tertiary structures can be determined mainly by sequence-independent backbone interactions. On the other hand, for α proteins, nonlocal hydrophobic side-chain interaction is also required to obtain nativelike structures.

Original language	English
Article number	194908
Journal	Journal of Chemical Physics
Volume	125
Issue number	19
DOIs	https://doi.org/10.1063/1.2364500
Publication status	Published - 2006

Bibliographical note

Funding Information:
This work was supported by the NRL program of MOST NRDP (M1–0203–00–0020). The authors thank Kyoungrim Lee for useful discussions.

All Science Journal Classification (ASJC) codes

Physics and Astronomy(all)
Physical and Theoretical Chemistry

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10.1063/1.2364500

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AU - Lee, Weontae

AU - Lee, Julian

N1 - Funding Information: This work was supported by the NRL program of MOST NRDP (M1–0203–00–0020). The authors thank Kyoungrim Lee for useful discussions.

PY - 2006

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AB - We perform a systematic study of the effects of sequence-independent backbone interactions and sequence-dependent side-chain interactions on protein folding using fragment assembly and physical energy function. Structures for ten proteins belonging to various structural classes are predicted only with Lennard-Jones interaction between backbone atoms. We find nativelike structures for Β proteins, suggesting that for proteins in this class, the global tertiary structures can be determined mainly by sequence-independent backbone interactions. On the other hand, for α proteins, nonlocal hydrophobic side-chain interaction is also required to obtain nativelike structures.

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ER -

Protein folding using fragment assembly and physical energy function

Abstract

Bibliographical note

All Science Journal Classification (ASJC) codes

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