An insight in the mechanism of beta sheet formation via CSAW.
Protein folding problem is an emerging eld in biophysics and great progress has been seen in experiments, theories and computations for the last 40 years. Approaching the problem with theoretical and computational studies, Conditioned Self-Avoiding Walk (CSAW) model is developed in the aim of st...
| Main Author: | |
|---|---|
| Other Authors: | |
| Format: | Final Year Project (FYP) |
| Language: | English |
| Published: |
2011
|
| Subjects: | |
| Online Access: | http://hdl.handle.net/10356/45172 |
| _version_ | 1826110722098069504 |
|---|---|
| author | Goh, Boon Chong. |
| author2 | Chew Lock Yue |
| author_facet | Chew Lock Yue Goh, Boon Chong. |
| author_sort | Goh, Boon Chong. |
| collection | NTU |
| description | Protein folding problem is an emerging eld in biophysics and great progress has been seen
in experiments, theories and computations for the last 40 years. Approaching the problem
with theoretical and computational studies, Conditioned Self-Avoiding Walk (CSAW) model
is developed in the aim of studying the key interactions resulted in folding of a protein.
The earlier versions of CSAW model consider hydrophobic interaction and hydrogen bonding
while neglecting all other interactions. Though simple, these models have successfully formed
hydrophobic core and alpha helix. However, none of them has consistently folded a beta
sheet, the complementary secondary structure of alpha helix.
In my Final Year Project, I consolidated various ideas in our research group and introduced
the neighboring hydrogen bond interaction, also named as the 4-body interaction. After
incorporating the 4-body interaction into CSAW, beta sheets are consistently formed. We
continued to investigate the folding of polyalanine of di erent lengths and attempt to fold two
real proteins in CSAW. At low temperatures, the polypeptides were folded into alpha helix
while they formed beta sheet at higher temperatures. We observed as the length of protein
increases, the transition temperature from alpha helix to beta sheet increases. |
| first_indexed | 2024-10-01T02:39:07Z |
| format | Final Year Project (FYP) |
| id | ntu-10356/45172 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T02:39:07Z |
| publishDate | 2011 |
| record_format | dspace |
| spelling | ntu-10356/451722023-02-28T23:11:17Z An insight in the mechanism of beta sheet formation via CSAW. Goh, Boon Chong. Chew Lock Yue School of Physical and Mathematical Sciences DRNTU::Science::Physics::Atomic physics::Statistical physics DRNTU::Science::Biological sciences::Biophysics Protein folding problem is an emerging eld in biophysics and great progress has been seen in experiments, theories and computations for the last 40 years. Approaching the problem with theoretical and computational studies, Conditioned Self-Avoiding Walk (CSAW) model is developed in the aim of studying the key interactions resulted in folding of a protein. The earlier versions of CSAW model consider hydrophobic interaction and hydrogen bonding while neglecting all other interactions. Though simple, these models have successfully formed hydrophobic core and alpha helix. However, none of them has consistently folded a beta sheet, the complementary secondary structure of alpha helix. In my Final Year Project, I consolidated various ideas in our research group and introduced the neighboring hydrogen bond interaction, also named as the 4-body interaction. After incorporating the 4-body interaction into CSAW, beta sheets are consistently formed. We continued to investigate the folding of polyalanine of di erent lengths and attempt to fold two real proteins in CSAW. At low temperatures, the polypeptides were folded into alpha helix while they formed beta sheet at higher temperatures. We observed as the length of protein increases, the transition temperature from alpha helix to beta sheet increases. Bachelor of Science in Physics 2011-06-09T07:41:46Z 2011-06-09T07:41:46Z 2011 2011 Final Year Project (FYP) http://hdl.handle.net/10356/45172 en 112 p. application/pdf |
| spellingShingle | DRNTU::Science::Physics::Atomic physics::Statistical physics DRNTU::Science::Biological sciences::Biophysics Goh, Boon Chong. An insight in the mechanism of beta sheet formation via CSAW. |
| title | An insight in the mechanism of beta sheet formation via CSAW. |
| title_full | An insight in the mechanism of beta sheet formation via CSAW. |
| title_fullStr | An insight in the mechanism of beta sheet formation via CSAW. |
| title_full_unstemmed | An insight in the mechanism of beta sheet formation via CSAW. |
| title_short | An insight in the mechanism of beta sheet formation via CSAW. |
| title_sort | insight in the mechanism of beta sheet formation via csaw |
| topic | DRNTU::Science::Physics::Atomic physics::Statistical physics DRNTU::Science::Biological sciences::Biophysics |
| url | http://hdl.handle.net/10356/45172 |
| work_keys_str_mv | AT gohboonchong aninsightinthemechanismofbetasheetformationviacsaw AT gohboonchong insightinthemechanismofbetasheetformationviacsaw |