Structural interpretations of a flexible cold-active AMS8 lipase by combining small-angle X-ray scattering and molecular dynamics simulation (SAXS-MD)
Determining structure of highly flexible protein with multiple conformations can be challenging. This paper aims to combine molecular dynamics (MD) and small angle X-ray diffraction (SAX) techniques as a solution to overcome issues related to protein conformation in hardly crystallized protein. Base...
| Main Authors: | , , , , , |
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| Format: | Article |
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Elsevier
2022
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| _version_ | 1825938830946992128 |
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| author | Yaacob, Norhayati Kamonsutthipaijit, Nuntaporn Soontaranon, Siriwat Thean, Adam Chor Leow Raja Abd Rahman, Raja Noor Zaliha Mohamad Ali, Mohd Shukuri |
| author_facet | Yaacob, Norhayati Kamonsutthipaijit, Nuntaporn Soontaranon, Siriwat Thean, Adam Chor Leow Raja Abd Rahman, Raja Noor Zaliha Mohamad Ali, Mohd Shukuri |
| author_sort | Yaacob, Norhayati |
| collection | UPM |
| description | Determining structure of highly flexible protein with multiple conformations can be challenging. This paper aims to combine molecular dynamics (MD) and small angle X-ray diffraction (SAX) techniques as a solution to overcome issues related to protein conformation in hardly crystallized protein. Based on prior studies, a cold-active lipase AMS8 was simulated in solvents showing stability in its N-terminal and high flexibility in its C-terminal. However, MD in its own algorithm could not explain the basis of macromolecule conformational transitions or changes related to protein through folding. Hence, by combining SAXS with MD, it is possible to understand the structure of flexible AMS8 lipase in natural space. Based on the findings, SAXS ab-initio model of AMS8 lipase was identified as a monomeric protein in which the optimized model of cold-active lipase AMS8 derived from SAXS data was found to be aligned with AMS8 homology model under series of MD timeframe. |
| first_indexed | 2024-03-06T11:18:10Z |
| format | Article |
| id | upm.eprints-103319 |
| institution | Universiti Putra Malaysia |
| last_indexed | 2024-03-06T11:18:10Z |
| publishDate | 2022 |
| publisher | Elsevier |
| record_format | dspace |
| spelling | upm.eprints-1033192023-11-01T03:53:10Z http://psasir.upm.edu.my/id/eprint/103319/ Structural interpretations of a flexible cold-active AMS8 lipase by combining small-angle X-ray scattering and molecular dynamics simulation (SAXS-MD) Yaacob, Norhayati Kamonsutthipaijit, Nuntaporn Soontaranon, Siriwat Thean, Adam Chor Leow Raja Abd Rahman, Raja Noor Zaliha Mohamad Ali, Mohd Shukuri Determining structure of highly flexible protein with multiple conformations can be challenging. This paper aims to combine molecular dynamics (MD) and small angle X-ray diffraction (SAX) techniques as a solution to overcome issues related to protein conformation in hardly crystallized protein. Based on prior studies, a cold-active lipase AMS8 was simulated in solvents showing stability in its N-terminal and high flexibility in its C-terminal. However, MD in its own algorithm could not explain the basis of macromolecule conformational transitions or changes related to protein through folding. Hence, by combining SAXS with MD, it is possible to understand the structure of flexible AMS8 lipase in natural space. Based on the findings, SAXS ab-initio model of AMS8 lipase was identified as a monomeric protein in which the optimized model of cold-active lipase AMS8 derived from SAXS data was found to be aligned with AMS8 homology model under series of MD timeframe. Elsevier 2022 Article PeerReviewed Yaacob, Norhayati and Kamonsutthipaijit, Nuntaporn and Soontaranon, Siriwat and Thean, Adam Chor Leow and Raja Abd Rahman, Raja Noor Zaliha and Mohamad Ali, Mohd Shukuri (2022) Structural interpretations of a flexible cold-active AMS8 lipase by combining small-angle X-ray scattering and molecular dynamics simulation (SAXS-MD). International Journal of Biological Macromolecules, 220. 1095 - 1103. ISSN 0141-8130; ESSN: 1879-0003 https://www.sciencedirect.com/science/article/pii/S0141813022018487 10.1016/j.ijbiomac.2022.08.145 |
| spellingShingle | Yaacob, Norhayati Kamonsutthipaijit, Nuntaporn Soontaranon, Siriwat Thean, Adam Chor Leow Raja Abd Rahman, Raja Noor Zaliha Mohamad Ali, Mohd Shukuri Structural interpretations of a flexible cold-active AMS8 lipase by combining small-angle X-ray scattering and molecular dynamics simulation (SAXS-MD) |
| title | Structural interpretations of a flexible cold-active AMS8 lipase by combining small-angle X-ray scattering and molecular dynamics simulation (SAXS-MD) |
| title_full | Structural interpretations of a flexible cold-active AMS8 lipase by combining small-angle X-ray scattering and molecular dynamics simulation (SAXS-MD) |
| title_fullStr | Structural interpretations of a flexible cold-active AMS8 lipase by combining small-angle X-ray scattering and molecular dynamics simulation (SAXS-MD) |
| title_full_unstemmed | Structural interpretations of a flexible cold-active AMS8 lipase by combining small-angle X-ray scattering and molecular dynamics simulation (SAXS-MD) |
| title_short | Structural interpretations of a flexible cold-active AMS8 lipase by combining small-angle X-ray scattering and molecular dynamics simulation (SAXS-MD) |
| title_sort | structural interpretations of a flexible cold active ams8 lipase by combining small angle x ray scattering and molecular dynamics simulation saxs md |
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