Effect of electronic polarization on alanine-based peptides' alpha helices.
It is a general belief that the electrostatic field arising from the electrostatic polarization of an alpha helix is important in protein folding and its stability. In this experiment, polarized protein-specific charges update are employ to introduce this effect into conventional molecular dynamic s...
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| Format: | Final Year Project (FYP) |
| Language: | English |
| Published: |
2010
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| Online Access: | http://hdl.handle.net/10356/39921 |
| _version_ | 1811697151168741376 |
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| author | Tung, Dickson. |
| author2 | School of Physical and Mathematical Sciences |
| author_facet | School of Physical and Mathematical Sciences Tung, Dickson. |
| author_sort | Tung, Dickson. |
| collection | NTU |
| description | It is a general belief that the electrostatic field arising from the electrostatic polarization of an alpha helix is important in protein folding and its stability. In this experiment, polarized protein-specific charges update are employ to introduce this effect into conventional molecular dynamic simulation. Simulation for 3 alanine-based peptides, Ac-AAQAAAAQAAGY-NH2, Ac-AAKAAAAKAAGY-NH2,and Ac-AADAAAADAAGY-NH2 in 40% trifluoroethanol are done. As a comparison, simulation was also done using conventional force fields. Without proper inclusion of electronic polarization effect, the structure generated from the simulation are fairly similar with each other which suggest the system is unable to distinguish the substitution of amino acid. However, helix content calculated and detailed analysis of data produced from PPC update system matches experimental values thus suggesting that PPC update provides a better representation of electronic density on peptide atoms. Hydrogen bonds on alpha helix backbone are also more stable with the implementation of electronic polarization which is critcal to the stability of secondary structures on protein. |
| first_indexed | 2024-10-01T07:50:42Z |
| format | Final Year Project (FYP) |
| id | ntu-10356/39921 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T07:50:42Z |
| publishDate | 2010 |
| record_format | dspace |
| spelling | ntu-10356/399212023-02-28T23:18:06Z Effect of electronic polarization on alanine-based peptides' alpha helices. Tung, Dickson. School of Physical and Mathematical Sciences Zhang Dawei DRNTU::Science::Chemistry::Physical chemistry::Electrochemistry It is a general belief that the electrostatic field arising from the electrostatic polarization of an alpha helix is important in protein folding and its stability. In this experiment, polarized protein-specific charges update are employ to introduce this effect into conventional molecular dynamic simulation. Simulation for 3 alanine-based peptides, Ac-AAQAAAAQAAGY-NH2, Ac-AAKAAAAKAAGY-NH2,and Ac-AADAAAADAAGY-NH2 in 40% trifluoroethanol are done. As a comparison, simulation was also done using conventional force fields. Without proper inclusion of electronic polarization effect, the structure generated from the simulation are fairly similar with each other which suggest the system is unable to distinguish the substitution of amino acid. However, helix content calculated and detailed analysis of data produced from PPC update system matches experimental values thus suggesting that PPC update provides a better representation of electronic density on peptide atoms. Hydrogen bonds on alpha helix backbone are also more stable with the implementation of electronic polarization which is critcal to the stability of secondary structures on protein. Bachelor of Science in Chemistry and Biological Chemistry 2010-06-08T02:38:09Z 2010-06-08T02:38:09Z 2010 2010 Final Year Project (FYP) http://hdl.handle.net/10356/39921 en 18 p. application/pdf |
| spellingShingle | DRNTU::Science::Chemistry::Physical chemistry::Electrochemistry Tung, Dickson. Effect of electronic polarization on alanine-based peptides' alpha helices. |
| title | Effect of electronic polarization on alanine-based peptides' alpha helices. |
| title_full | Effect of electronic polarization on alanine-based peptides' alpha helices. |
| title_fullStr | Effect of electronic polarization on alanine-based peptides' alpha helices. |
| title_full_unstemmed | Effect of electronic polarization on alanine-based peptides' alpha helices. |
| title_short | Effect of electronic polarization on alanine-based peptides' alpha helices. |
| title_sort | effect of electronic polarization on alanine based peptides alpha helices |
| topic | DRNTU::Science::Chemistry::Physical chemistry::Electrochemistry |
| url | http://hdl.handle.net/10356/39921 |
| work_keys_str_mv | AT tungdickson effectofelectronicpolarizationonalaninebasedpeptidesalphahelices |