Correct folding of an α-helix and a β-hairpin using a polarized 2D torsional potential
A new modification to the AMBER force field that incorporates the coupled two-dimensional main chain torsion energy has been evaluated for the balanced representation of secondary structures. In this modified AMBER force field (AMBER03 2D ), the main chain torsion energy is represented by 2-dimensio...
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| Published in | Scientific reports Vol. 5; no. 1; p. 10359 |
|---|---|
| Main Authors | , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
Nature Publishing Group UK
03.06.2015
Nature Publishing Group |
| Subjects | |
| Online Access | Get full text |
| ISSN | 2045-2322 2045-2322 |
| DOI | 10.1038/srep10359 |
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| Abstract | A new modification to the AMBER force field that incorporates the coupled two-dimensional main chain torsion energy has been evaluated for the balanced representation of secondary structures. In this modified AMBER force field (AMBER03
2D
), the main chain torsion energy is represented by 2-dimensional Fourier expansions with parameters fitted to the potential energy surface generated by high-level quantum mechanical calculations of small peptides in solution. Molecular dynamics simulations are performed to study the folding of two model peptides adopting either α-helix or β-hairpin structures. Both peptides are successfully folded into their native structures using an AMBER03
2D
force field with the implementation of a polarization scheme (AMBER03
2D
p). For comparison, simulations using a standard AMBER03 force field with and without polarization, as well as AMBER03
2D
without polarization, fail to fold both peptides successfully. The correction to secondary structure propensity in the AMBER03 force field and the polarization effect are critical to folding Trpzip2; without these factors, a helical structure is obtained. This study strongly suggests that this new force field is capable of providing a more balanced preference for helical and extended conformations. The electrostatic polarization effect is shown to be indispensable to the growth of secondary structures. |
|---|---|
| AbstractList | A new modification to the AMBER force field that incorporates the coupled two-dimensional main chain torsion energy has been evaluated for the balanced representation of secondary structures. In this modified AMBER force field (AMBER032D), the main chain torsion energy is represented by 2-dimensional Fourier expansions with parameters fitted to the potential energy surface generated by high-level quantum mechanical calculations of small peptides in solution. Molecular dynamics simulations are performed to study the folding of two model peptides adopting either α-helix or β-hairpin structures. Both peptides are successfully folded into their native structures using an AMBER032D force field with the implementation of a polarization scheme (AMBER032Dp). For comparison, simulations using a standard AMBER03 force field with and without polarization, as well as AMBER032D without polarization, fail to fold both peptides successfully. The correction to secondary structure propensity in the AMBER03 force field and the polarization effect are critical to folding Trpzip2; without these factors, a helical structure is obtained. This study strongly suggests that this new force field is capable of providing a more balanced preference for helical and extended conformations. The electrostatic polarization effect is shown to be indispensable to the growth of secondary structures. A new modification to the AMBER force field that incorporates the coupled two-dimensional main chain torsion energy has been evaluated for the balanced representation of secondary structures. In this modified AMBER force field (AMBER03(2D)), the main chain torsion energy is represented by 2-dimensional Fourier expansions with parameters fitted to the potential energy surface generated by high-level quantum mechanical calculations of small peptides in solution. Molecular dynamics simulations are performed to study the folding of two model peptides adopting either α-helix or β-hairpin structures. Both peptides are successfully folded into their native structures using an AMBER03(2D) force field with the implementation of a polarization scheme (AMBER03(2D)p). For comparison, simulations using a standard AMBER03 force field with and without polarization, as well as AMBER03(2D) without polarization, fail to fold both peptides successfully. The correction to secondary structure propensity in the AMBER03 force field and the polarization effect are critical to folding Trpzip2; without these factors, a helical structure is obtained. This study strongly suggests that this new force field is capable of providing a more balanced preference for helical and extended conformations. The electrostatic polarization effect is shown to be indispensable to the growth of secondary structures.A new modification to the AMBER force field that incorporates the coupled two-dimensional main chain torsion energy has been evaluated for the balanced representation of secondary structures. In this modified AMBER force field (AMBER03(2D)), the main chain torsion energy is represented by 2-dimensional Fourier expansions with parameters fitted to the potential energy surface generated by high-level quantum mechanical calculations of small peptides in solution. Molecular dynamics simulations are performed to study the folding of two model peptides adopting either α-helix or β-hairpin structures. Both peptides are successfully folded into their native structures using an AMBER03(2D) force field with the implementation of a polarization scheme (AMBER03(2D)p). For comparison, simulations using a standard AMBER03 force field with and without polarization, as well as AMBER03(2D) without polarization, fail to fold both peptides successfully. The correction to secondary structure propensity in the AMBER03 force field and the polarization effect are critical to folding Trpzip2; without these factors, a helical structure is obtained. This study strongly suggests that this new force field is capable of providing a more balanced preference for helical and extended conformations. The electrostatic polarization effect is shown to be indispensable to the growth of secondary structures. A new modification to the AMBER force field that incorporates the coupled two-dimensional main chain torsion energy has been evaluated for the balanced representation of secondary structures. In this modified AMBER force field (AMBER03(2D)), the main chain torsion energy is represented by 2-dimensional Fourier expansions with parameters fitted to the potential energy surface generated by high-level quantum mechanical calculations of small peptides in solution. Molecular dynamics simulations are performed to study the folding of two model peptides adopting either α-helix or β-hairpin structures. Both peptides are successfully folded into their native structures using an AMBER03(2D) force field with the implementation of a polarization scheme (AMBER03(2D)p). For comparison, simulations using a standard AMBER03 force field with and without polarization, as well as AMBER03(2D) without polarization, fail to fold both peptides successfully. The correction to secondary structure propensity in the AMBER03 force field and the polarization effect are critical to folding Trpzip2; without these factors, a helical structure is obtained. This study strongly suggests that this new force field is capable of providing a more balanced preference for helical and extended conformations. The electrostatic polarization effect is shown to be indispensable to the growth of secondary structures. A new modification to the AMBER force field that incorporates the coupled two-dimensional main chain torsion energy has been evaluated for the balanced representation of secondary structures. In this modified AMBER force field (AMBER03 2D ), the main chain torsion energy is represented by 2-dimensional Fourier expansions with parameters fitted to the potential energy surface generated by high-level quantum mechanical calculations of small peptides in solution. Molecular dynamics simulations are performed to study the folding of two model peptides adopting either α-helix or β-hairpin structures. Both peptides are successfully folded into their native structures using an AMBER03 2D force field with the implementation of a polarization scheme (AMBER03 2D p). For comparison, simulations using a standard AMBER03 force field with and without polarization, as well as AMBER03 2D without polarization, fail to fold both peptides successfully. The correction to secondary structure propensity in the AMBER03 force field and the polarization effect are critical to folding Trpzip2; without these factors, a helical structure is obtained. This study strongly suggests that this new force field is capable of providing a more balanced preference for helical and extended conformations. The electrostatic polarization effect is shown to be indispensable to the growth of secondary structures. |
| ArticleNumber | 10359 |
| Author | Gao, Ya Lin, Bingbing Mou, Lirong Li, Yongxiu Mei, Ye Zhang, John Z. H. |
| Author_xml | – sequence: 1 givenname: Ya surname: Gao fullname: Gao, Ya organization: Department of Physics and Institute of Theoretical and Computational Science, State Key Laboratory of Precision Spectroscopy, East China Normal University – sequence: 2 givenname: Yongxiu surname: Li fullname: Li, Yongxiu organization: Department of Physics and Institute of Theoretical and Computational Science, State Key Laboratory of Precision Spectroscopy, East China Normal University – sequence: 3 givenname: Lirong surname: Mou fullname: Mou, Lirong organization: Institutes for Advanced Interdisciplinary Research, East China Normal University – sequence: 4 givenname: Bingbing surname: Lin fullname: Lin, Bingbing organization: Department of Physics and Institute of Theoretical and Computational Science, State Key Laboratory of Precision Spectroscopy, East China Normal University – sequence: 5 givenname: John Z. H. surname: Zhang fullname: Zhang, John Z. H. organization: Department of Physics and Institute of Theoretical and Computational Science, State Key Laboratory of Precision Spectroscopy, East China Normal University, NYU-ECNU Center for Computational Chemistry at NYU Shanghai – sequence: 6 givenname: Ye surname: Mei fullname: Mei, Ye organization: Department of Physics and Institute of Theoretical and Computational Science, State Key Laboratory of Precision Spectroscopy, East China Normal University, NYU-ECNU Center for Computational Chemistry at NYU Shanghai |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/26039188$$D View this record in MEDLINE/PubMed |
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| Title | Correct folding of an α-helix and a β-hairpin using a polarized 2D torsional potential |
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