Molecular dynamics simulation studies of novel marine psychrophilic adenylate kinase with mesophilic and thermophilic homologous
Also available in printed version
| المؤلف الرئيسي: | |
|---|---|
| مؤلفون آخرون: | |
| التنسيق: | Bachelor thesis |
| اللغة: | الإنجليزية |
| منشور في: |
Universiti Teknologi Malaysia
2025
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| الموضوعات: | |
| الوصول للمادة أونلاين: | https://utmik.utm.my/handle/123456789/55930 |
| Abstract | Abstract here |
| _version_ | 1854975040247824384 |
|---|---|
| author | Yusra Nazira Mohd. Yusop |
| author2 | Mohd. Shahir Shamsir, supervisor |
| author_facet | Mohd. Shahir Shamsir, supervisor Yusra Nazira Mohd. Yusop |
| author_sort | Yusra Nazira Mohd. Yusop |
| description | Also available in printed version |
| format | Bachelor thesis |
| id | utm-123456789-55930 |
| institution | Universiti Teknologi Malaysia |
| language | English |
| publishDate | 2025 |
| publisher | Universiti Teknologi Malaysia |
| record_format | dspace |
| record_pdf | Abstract |
| spelling | utm-123456789-559302025-08-20T15:45:35Z Molecular dynamics simulation studies of novel marine psychrophilic adenylate kinase with mesophilic and thermophilic homologous Yusra Nazira Mohd. Yusop Mohd. Shahir Shamsir, supervisor Biosciences and medical engineering Also available in printed version J. marinus adenylate kinase (AKjm) is a novel psychrophilic adenylate kinase that was originally isolated from sediment in the North East Atlantic Ocean. The structure and biochemical characteristic of AKjm were performed in previous studies. However the dynamics of marine psychrophilic adenylate kinase is still limited. The dynamic signature and conformational behaviour under different temperatures has yet to be studied using molecular dynamic (MD) simulation. In this study, MD comparative structural analysis between AKjm, AKbs and AKgs were performed to identify the amino acids that contribute towards the temperature adaptation of these adenylate kinases. 40 ns of MD simulations were performed for all proteins using the GROMACS 4.6.3 software package and GROMOS96 force field, each at temperatures of 298 K, 318 K and 338 K to assess the structural stability of the AKs. The trajectories were analyzed in terms of factors such as RMSD, RMSF, the secondary structure of the protein and hydrogen bonds which indicate distinct differences between AKjm and its counterparts. The results showed differences in stability and dynamics between AKjm, AKbs and AKgs at different temperatures. Psychrophilic AKjm demonstrated increased flexibility compared to mesophilic and thermophilic adenylate kinase counterparts were observed. However, the secondary structure elements were mainly preserved in all AKs structures in the simulation timescale fazli UTM 59 p. Project Paper (Sarjana Muda Sains (Biologi)) - Universiti Teknologi Malaysia, 2014 2025-03-17T04:06:46Z 2025-03-17T04:06:46Z 2014 Bachelor thesis https://utmik.utm.my/handle/123456789/55930 valet-20170212-145935 vital:95117 ENG Closed Access UTM Complete Unpublished application/pdf Universiti Teknologi Malaysia |
| spellingShingle | Biosciences and medical engineering Yusra Nazira Mohd. Yusop Molecular dynamics simulation studies of novel marine psychrophilic adenylate kinase with mesophilic and thermophilic homologous |
| thesis_level | Other |
| title | Molecular dynamics simulation studies of novel marine psychrophilic adenylate kinase with mesophilic and thermophilic homologous |
| title_full | Molecular dynamics simulation studies of novel marine psychrophilic adenylate kinase with mesophilic and thermophilic homologous |
| title_fullStr | Molecular dynamics simulation studies of novel marine psychrophilic adenylate kinase with mesophilic and thermophilic homologous |
| title_full_unstemmed | Molecular dynamics simulation studies of novel marine psychrophilic adenylate kinase with mesophilic and thermophilic homologous |
| title_short | Molecular dynamics simulation studies of novel marine psychrophilic adenylate kinase with mesophilic and thermophilic homologous |
| title_sort | molecular dynamics simulation studies of novel marine psychrophilic adenylate kinase with mesophilic and thermophilic homologous |
| topic | Biosciences and medical engineering |
| url | https://utmik.utm.my/handle/123456789/55930 |
| work_keys_str_mv | AT yusranaziramohdyusop moleculardynamicssimulationstudiesofnovelmarinepsychrophilicadenylatekinasewithmesophilicandthermophilichomologous |