A computational approach to targeted amino acid mutagenesis for enhancing enzyme efficiency through improved enzyme-substrate dynamics and thermostability Article Swipe
Suryasarathi Kumar
,
A. R. GHOSH
,
Bornali Dutta
,
Sharda Sambhakar
,
S. N. MUKHERJEE
,
Chhanda Dutta
,
Indrakshi Dey
,
Nirupam Roy Choudhury
,
Sneha Sarkar
,
Naibedya Chattopadhyay
,
Anuraj Kar
,
Priyanka Talukdar
,
Somnath Das
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1007/s44371-025-00349-y
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1007/s44371-025-00349-y
Advancements in computational protein engineering have enabled the precise optimisation of enzyme stability and catalytic efficiency. This study employs site-directed amino acid-specific mutagenesis to enhance protein-ligand binding affinity while preserving structural integrity. Molecular docking analysis showed significant binding free energy (ΔG) improvements, with 1FCE_Thr226Leu_Cellulose (-7.2160 kcal/mol → -8.1532 kcal/mol, + 13.0%), 1FCE_Pro174Ala_AVICEL (-7.2160 kcal/mol → -8.8992 kcal/mol, + 23.3%), and 1AVA_Asp126Arg_Starch (-5.2035 kcal/mol → -7.5767 kcal/mol, + 45.6%). Ramachandran plot analysis confirmed minimal deviations (≤ 0.6%) in structural stability. RMSF analysis indicated increased flexibility at key residues, with peak shifts of 0.2–0.5 Å, supporting enhanced adaptability. Molecular Dynamics Simulations (MDS) verified stability, with wild-type 1FCE stabilising at 0.25 nm RMSD and mutants at 0.26 nm. Thermodynamic analysis showed Tm variations within ± 1.3 °C, ensuring mutation resilience (1FCE: 74.7 °C → 75.1 °C, 1AVA: 67.9 °C → 67.8 °C, 6M4K: 62.4 °C → 62.1 °C). pH-dependent aggregation analysis confirmed broader enzyme stability across pH 5.0–8.5, enhancing industrial applicability. Integrating MEME, SWOTein, SIAS Analysis, CABS-Flex 2.0, and WebGRO, this study offers a comprehensive approach to enzyme optimisation. The results demonstrate that computational mutagenesis significantly improves enzyme efficiency, making this a promising strategy for industrial biocatalysts in biotechnology, pharmaceuticals, and biofuels. Graphical abstract
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- Language
- en
- Landing Page
- https://doi.org/10.1007/s44371-025-00349-y
- https://link.springer.com/content/pdf/10.1007/s44371-025-00349-y.pdf
- OA Status
- diamond
- References
- 63
- OpenAlex ID
- https://openalex.org/W4415783976
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https://openalex.org/W4415783976Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1007/s44371-025-00349-yDigital Object Identifier
- Title
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A computational approach to targeted amino acid mutagenesis for enhancing enzyme efficiency through improved enzyme-substrate dynamics and thermostabilityWork title
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articleOpenAlex work type
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enPrimary language
- Publication year
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2025Year of publication
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-
2025-11-03Full publication date if available
- Authors
-
Suryasarathi Kumar, A. R. GHOSH, Bornali Dutta, Sharda Sambhakar, S. N. MUKHERJEE, Chhanda Dutta, Indrakshi Dey, Nirupam Roy Choudhury, Sneha Sarkar, Naibedya Chattopadhyay, Anuraj Kar, Priyanka Talukdar, Somnath DasList of authors in order
- Landing page
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https://doi.org/10.1007/s44371-025-00349-yPublisher landing page
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https://link.springer.com/content/pdf/10.1007/s44371-025-00349-y.pdfDirect link to full text PDF
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diamondOpen access status per OpenAlex
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https://link.springer.com/content/pdf/10.1007/s44371-025-00349-y.pdfDirect OA link when available
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63Number of works referenced by this work
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| abstract_inverted_index.biocatalysts | 194 |
| abstract_inverted_index.optimisation | 10 |
| abstract_inverted_index.pH-dependent | 146 |
| abstract_inverted_index.Thermodynamic | 116 |
| abstract_inverted_index.acid-specific | 22 |
| abstract_inverted_index.adaptability. | 96 |
| abstract_inverted_index.comprehensive | 172 |
| abstract_inverted_index.computational | 3, 181 |
| abstract_inverted_index.improvements, | 42 |
| abstract_inverted_index.optimisation. | 176 |
| abstract_inverted_index.significantly | 183 |
| abstract_inverted_index.site-directed | 20 |
| abstract_inverted_index.applicability. | 158 |
| abstract_inverted_index.biotechnology, | 196 |
| abstract_inverted_index.protein-ligand | 26 |
| abstract_inverted_index.pharmaceuticals, | 197 |
| abstract_inverted_index.1AVA_Asp126Arg_Starch | 61 |
| abstract_inverted_index.1FCE_Pro174Ala_AVICEL | 52 |
| abstract_inverted_index.1FCE_Thr226Leu_Cellulose | 44 |
| cited_by_percentile_year | |
| countries_distinct_count | 0 |
| institutions_distinct_count | 13 |
| citation_normalized_percentile |