References
1. Spence MA, Kaczmarski JA, Saunders JW, Jackson CJ. Ancestral sequence reconstruction for protein engineers. Current Opinion in Structural Biology. 2021 AUG 2021;69:131-141.
2. Thomson RES, Carrera-Pacheco SE, Gillam EMJ. Engineering functional thermostable proteins using ancestral sequence reconstruction. The Journal of Biological Chemistry. 2022 Aug 27 (Epub 2022 Aug 27) 2022;298(10):102435-102435.
3. Johansson KE, Lindorff-Larsen K. Structural heterogeneity and dynamics in protein evolution and design. Current Opinion in Structural Biology. 2018 FEB 2018;48:157-163.
4. Hayashi J, Seto T, Akita H, et al. Structure-based engineering of an artificially generated NADP(+)-dependent d-amino acid dehydrogenase. Applied and Environmental Microbiology. 2017 JUN 2017;83(11).
5. Pollegioni L, Rosini E, Molla G. Advances in enzymatic synthesis of d-amino acids. Internatoinal Journal of Molecular Sciences. 2020 MAY 2020;21(9).
6. Prier CK. Enzymes for amino acid synthesis by design. Nature Catalysis. 2021 MAY 2021;4(5):348-349.
7. Akita H, Hayashi J, Sakuraba H, Ohshima T. Artificial thermostable d-amino acid dehydrogenase: creation and application. Frontiers in Microbiology. 2018 AUG 3 2018;9.
8. Cheng X, Chen X, Feng J, Wu Q, Zhu D. Structure-guided engineering of meso-diaminopimelate dehydrogenase for enantioselective reductive amination of sterically bulky 2-keto acids. Catalysis Science & Technology. 2018 OCT 7 2018;8(19):4994-5002.
9. Wilding M, Scott C, Warden AC. Computer-guided surface engineering for enzyme improvement. Scientific Reports. 2018 AUG 10 2018;8.
10. Zhu L, Song Y, Chang C, et al. Engineering leifsonia alcohol dehydrogenase for thermostability and catalytic efficiency by enhancing subunit interactions. Chembiochem. 2021 NOV 16 2021;22(22):3178-3183.
11. Boucher L, Somani S, Negron C, et al. Surface salt bridges contribute to the extreme thermal stability of an FN3-like domain from a thermophilic bacterium. Proteins- Structure Function and Bionformatics. 2022 JAN 2022;90(1):270-281.
12. Arcus VL, van der Kamp MW, Pudney CR, Mulholland AJ. Enzyme evolution and the temperature dependence of enzyme catalysis. Current Opinion in Structural Biology. 2020 DEC 2020;65:96-101.
13. Hockenberry AJ, Wilke CO. Evolutionary couplings detect side-chain interactions. Peerj. 2019 JUL 8 2019;7.
14. Sun Z, Liu Q, Qu G, Feng Y, Reetz MT. Utility of B-Factors in Protein Science: Interpreting rigidity, flexibility, and internal motion and engineering thermostability. Chemical Reviews. 2019 FEB 13 2019;119(3):1626-1665.
15. Zhang Y, Ren H, Wang Y, Chen K, Fang B, Wang S. Bioinspired immobilization of glycerol dehydrogenase by metal ion-chelated polyethyleneimines as artificial polypeptides. Scientific Reports. 2016 APR 7 2016;6.
16. Kleiner D, Shmulevich F, Zarivach R, et al. The interdimeric interface controls function and stability of ureaplasma urealiticum methionine s-adenosyltransferase. Journal of Molecular Biology. 2019 DEC 6 2019;431(24):4796-4816.
17. Huang L, Ma J, Sang J, et al. Enhancing the thermostability of phospholipase d from Streptomyces halstedii by directed evolution and elucidating the mechanism of a key amino acid residue using molecular dynamics simulation. International Journal of Biological Macromolecules. 2020/12/01/ 2020;164:3065-3074.
18. Copley SD. Setting the stage for evolution of a new enzyme. Current Opinion in Structural Biology. 2021 AUG 2021;69:41-49.
19. Kayikci M, Venkatakrishnan AJ, Scott-Brown J, Ravarani CNJ, Flock T, Babu MM. Visualization and analysis of non-covalent contacts using the protein contacts atlas. Nature Structural & Molecular Biology. 2018 FEB 2018;25(2):185-+.
20. Oteri F, Nadalin F, Champeimont R, Carbone A. Bis2analyzer: a server for co-evolution analysis of conserved protein families. Nucleic Acids Research. 2017 JUL 3 2017;45(W1):W307-W314.
21. Ashkenazy H, Abadi S, Martz E, et al. Consurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucleic Acids Research. 2016 JUL 8 2016;44(W1):W344-W350.
22. Wang S, Duan L, Jiang L, Liu K, Wang S. Assembly of peptide linker to amino acid dehydrogenase and immobilized with metal-organic framework. Journal of Chemical Technology and Biotechnology. 2022 MAR 2022;97(3):741-748.
23. Tajik S. Topological analysis of high temperature enzyme activity. Biophysical Journal. 2022/02/11/ 2022;121(3, Supplement 1):320a.
24. Sfriso P, Duran-Frigola M, Mosca R, Emperador A, Aloy P, Orozco M. Residues coevolution guides the systematic identification of alternative functional conformations in proteins. Structure. 2016 JAN 5 2016;24(1):116-126.
25. Pucci F, Kwasigroch JM, Rooman M. Scoop: an accurate and fast predictor of protein stability curves as a function of temperature. Bioinformatics. 2017 NOV 1 2017;33(21):3415-3422.
26. Van der Kamp MW, Prentice EJ, Kraakman KL, Connolly M, Mulholland AJ, Arcus VL. Dynamical origins of heat capacity changes in enzyme-catalysed reactions. Nature Communications. 2018 MAR 21 2018;9.
27. Vijayabaskar MS, Vishveshwara S. Interaction energy based protein structure networks. Biophysical Journal. 2010 DEC 1 2010;99(11):3704-3715.
28. Agarwal PK, Bernard DN, Bafna K, Doucet N. Enzyme dynamics: looking beyond a single structure. Chemcatchem. 2020 OCT 6 2020;12(19):4704-4720.
29. Zhang W, Zhang Y, Huang J, et al. Thermostability improvement of the d-allulose 3-epimerase from dorea sp CAG317 by site-directed mutagenesis at the interface regions. Journal of Agricultural and Food Chemistry. 2018 JUN 6 2018;66(22):5593-5601.
30. Liu Y, Luo G, Huu Hao N, Guo W, Zhang S. Advances in thermostable laccase and its current application in lignin-first biorefinery: A review. Bioresource Technology. 2020 FEB 2020;298.
31. Chan C-H, Yu T-H, Wong K-B. Stabilizing salt-bridge enhances protein thermostability by reducing the heat capacity change of unfolding. Plos one. 2011 JUN 24 2011;6(6).
32. Yu H, Dalby PA. Exploiting correlated molecular-dynamics networks to counteract enzyme activity-stability trade-off. Proceedings of the National Academy of Sciences of the United States of America. 2018 DEC 26 2018;115(52):E12192-E12200.
33. Cui H, Stadtmüller THJ, Jiang Q, Jaeger K-E, Schwaneberg U, Davari MD. How to engineer organic solvent resistant enzymes: insights from combined molecular dynamics and directed evolution study. Chemcatchem. 2020;12(16):4073-4083.
34. Badgujar KC, Badgujar VC, Bhanage BM. Recent update on use of ionic liquids for enzyme immobilization, activation, and catalysis: a partnership for sustainability. Current Opinion in Green and Sustainable Chemistry. 2022 AUG 2022;36.