References
Abrahmsen L, Tom J, Burnier J, et al. (1991) Engineering subtilisin and its substrates for efficient ligation of peptide bonds in aqueous solution. Biochemistry 30 (17): 4151–4159.
Bale JB, Gonen S, Liu Y, et al. (2016) Accurate design of megadalton‐scale two‐component icosahedral protein complexes. Science 353 (6297): 389–394.
Ballister ER, Lai AH, Zuckermann RN, et al. (2008) In vitro self‐assembly of tailorable nanotubes from a simple protein building block. Proceedings of the National Academy of Sciences of the United States of America 105 (10): 3733–3738.
Bhardwaj G, Mulligan VK, Bahl CD, et al. (2016) Accurate de novo design of hyperstable constrained peptides. Nature 538 (7625): 329–335.
Buchko GW, Pulavarti S, Ovchinnikov V, et al. (2018) Cytosolic expression, solution structures, and molecular dynamics simulation of genetically encodable disulfide‐rich de novo designed peptides. Protein Science 27 (9): 1611–1623.
Chen KQ and Arnold FH (1991) Enzyme engineering for nonaqueous solvents: random mutagenesis to enhance activity of subtilisin E in polar organic media. Biotechnology (N Y) 9 (11): 1073–1077.
Coelho PS, Brustad EM, Kannan A, et al. (2013) Olefin cyclopropanation via carbene transfer catalyzed by engineered cytochrome P450 enzymes. Science 339 (6117): 307–310.
Doyle L, Hallinan J, Bolduc J, et al. (2015) Rational design of alpha‐helical tandem repeat proteins with closed architectures. Nature 528 (7583): 585–588.
Garcia‐Seisdedos H, Empereur‐Mot C, Elad N, et al. (2017) Proteins evolve on the edge of supramolecular self‐assembly. Nature 548 (7666): 244–247.
Giver L, Gershenson A, Freskgard PO, et al. (1998) Directed evolution of a thermostable esterase. Proceedings of the National Academy of Sciences of the United States of America 95 (22): 12809–12813.
Graycar T, Knapp M, Ganshaw G, et al. (1999) Engineered Bacillus lentus subtilisins having altered flexibility. Journal of Molecular Biology 292 (1): 97–109.
Grayson KJ and Anderson JLR (2018) Designed for life: biocompatible de novo designed proteins and components. Journal of the Royal Society Interface 15 (145).
Grueninger D, Treiber N, Ziegler MO, et al. (2008) Designed protein‐protein association. Science 319 (5860): 206–209.
Hamley IW (2019) Protein assemblies: nature‐inspired and designed nanostructures. Biomacromolecules 20 (5): 1829–1848.
Hill CM, Li WS, Thoden JB, et al. (2003) Enhanced degradation of chemical warfare agents through molecular engineering of the phosphotriesterase active site. Journal of the American Chemical Society 125 (30): 8990–8991.
Hollingsworth SA and Dror RO (2018) Molecular dynamics simulation for all. Neuron 99 (6): 1129–1143.
Huang PS, Oberdorfer G, Xu C, et al. (2014) High thermodynamic stability of parametrically designed helical bundles. Science 346 (6208): 481–485.
Huang PS, Boyken SE and Baker D (2016a) The coming of age of de novo protein design. Nature 537 (7620): 320–327.
Huang PS, Feldmeier K, Parmeggiani F, et al. (2016b) De novo design of a four‐fold symmetric TIM‐barrel protein with atomic‐level accuracy. Nature Chemical Biology 12 (1): 29–34.
Huard DJ, Kane KM and Tezcan FA (2013) Re‐engineering protein interfaces yields copper‐inducible ferritin cage assembly. Nature Chemical Biology 9 (3): 169–176.
Jemli S, Ayadi‐Zouari D, Hlima HB, et al. (2016) Biocatalysts: application and engineering for industrial purposes. Critical Reviews in Biotechnology 36 (2): 246–258.
King NP, Bale JB, Sheffler W, et al. (2014) Accurate design of co‐assembling multi‐component protein nanomaterials. Nature 510 (7503): 103–108.
Kiss G, Celebi‐Olcum N, Moretti R, et al. (2013) Computational enzyme design. Angewandte Chemie (International Ed. in English) 52 (22): 5700–5725.
Koga N, Tatsumi‐Koga R, Liu G, et al. (2012) Principles for designing ideal protein structures. Nature 491 (7423): 222–227.
Lai YT, Cascio D and Yeates TO (2012) Structure of a 16‐nm cage designed by using protein oligomers. Science 336 (6085): 1129.
Lai YT, Reading E, Hura GL, et al. (2014) Structure of a designed protein cage that self‐assembles into a highly porous cube. Nature Chemistry 6 (12): 1065–1071.
Lehmann M, Loch C, Middendorf A, et al. (2002) The consensus concept for thermostability engineering of proteins: further proof of concept. Protein Engineering 15 (5): 403–411.
Lindorff‐Larsen K, Piana S, Dror RO, et al. (2011) How fast‐folding proteins fold. Science 334 (6055): 517–520.
Liu J, Zheng Q, Deng Y, et al. (2006) A seven‐helix coiled coil. Proceedings of the National Academy of Sciences of the United States of America 103 (42): 15457–15462.
Ljubetic A, Gradisar H and Jerala R (2017) Advances in design of protein folds and assemblies. Current Opinion in Chemical Biology 40: 65–71.
Lombardi A, Summa CM, Geremia S, et al. (2000) Retrostructural analysis of metalloproteins: application to the design of a minimal model for diiron proteins. Proceedings of the National Academy of Sciences of the United States of America 97 (12): 6298–6305.
Marcos E, Basanta B, Chidyausiku TM, et al. (2017) Principles for designing proteins with cavities formed by curved beta sheets. Science 355 (6321): 201–206.
Matthews JM and Sunde M (2012) Dimers, oligomers, everywhere. Advances in Experimental Medicine and Biology 747: 1–18.
Mignon D and Simonson T (2016) Comparing three stochastic search algorithms for computational protein design: Monte Carlo, replica exchange Monte Carlo, and a multistart, steepest‐descent heuristic. Journal of Computational Chemistry 37 (19): 1781–1793.
Packer MS and Liu DR (2015) Methods for the directed evolution of proteins. Nature Reviews. Genetics 16 (7): 379–394.
Peacock AF (2013) Incorporating metals into de novo proteins. Current Opinion in Chemical Biology 17 (6): 934–939.
Penning TM and Jez JM (2001) Enzyme redesign. Chemical Reviews 101 (10): 3027–3046.
Pica A, Merlino A, Buell AK, et al. (2013) Three‐dimensional domain swapping and supramolecular protein assembly: insights from the X‐ray structure of a dimeric swapped variant of human pancreatic RNase. Acta Crystallographica. Section D, Biological Crystallography 69 (Pt 10): 2116–2123.
Porter JL, Rusli RA and Ollis DL (2016) Directed evolution of enzymes for industrial biocatalysis. Chembiochem 17 (3): 197–203.
Reetz MT, Puls M, Carballeira JD, et al. (2007) Learning from directed evolution: further lessons from theoretical investigations into cooperative mutations in lipase enantioselectivity. Chembiochem 8 (1): 106–112.
Rosenfeld L, Heyne M, Shifman JM, et al. (2016) Protein engineering by combined computational and in vitro evolution approaches. Trends in Biochemical Sciences 41 (5): 421–433.
Rothlisberger D, Khersonsky O, Wollacott AM, et al. (2008) Kemp elimination catalysts by computational enzyme design. Nature 453 (7192): 190–195.
Samish I (2017) Achievements and challenges in computational protein design. Methods in Molecular Biology 1529: 21–94.
Stranges PB, Machius M, Miley MJ, et al. (2011) Computational design of a symmetric homodimer using beta‐strand assembly. Proceedings of the National Academy of Sciences of the United States of America 108 (51): 20562–20567.
Swint‐Kruse L (2016) Using evolution to guide protein engineering: The Devil IS in the Details. Biophysical Journal 111 (1): 10–18.
Toscano MD, Woycechowsky KJ and Hilvert D (2007) Minimalist active‐site redesign: teaching old enzymes new tricks. Angewandte Chemie (International Ed. in English) 46 (18): 3212–3236.
Voelz VA, Bowman GR, Beauchamp K, et al. (2010) Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1‐39). Journal of the American Chemical Society 132 (5): 1526–1528.
Voet AR, Noguchi H, Addy C, et al. (2014) Computational design of a self‐assembling symmetrical beta‐propeller protein. Proceedings of the National Academy of Sciences of the United States of America 111 (42): 15102–15107.
Votteler J, Ogohara C, Yi S, et al. (2016) Designed proteins induce the formation of nanocage‐containing extracellular vesicles. Nature 540 (7632): 292–295.
Walsh ST, Cheng H, Bryson JW, et al. (1999) Solution structure and dynamics of a de novo designed three‐helix bundle protein. Proceedings of the National Academy of Sciences of the United States of America 96 (10): 5486–5491.
Further Reading
Alberghina L (ed.) (2003) Protein Engineering for Industrial Biotechnology, vol. 388. CRC Press: Boca Raton, FL.
Arnold FH and Georgiou G (eds) (2003) Directed enzyme evolution: screening and selection methods. In: Methods in Molecular Biology, vol. 230, p 370. Humana Press Inc: Totowa, NJ.
Bornscheuer UT and Höhne M (eds) (2018) Protein engineering: methods and protocols. In: Methods in Molecular Biology, vol. 1685, p 350. Humana Press Inc: New York, NY.
Keating AE (ed.) (2013) Methods in protein design. In: Methods in Enzymology, vol. 523, p 520. Academic Press: Cambridge, MA.
Park SJ and Cochran JR (eds) (2009) Protein Engineering and Design, p 416. CRC Press: Boca Raton, FL.
Reetz MT (ed.) (2017) Directed Evolution of Selective Enzymes: Catalysts for Organic Chemistry and Biotechnology, vol. 320. Wiley‐VCH Verlag GmbH & Co. KGaA: Weinheim, Germany.
Samish I (ed.) (2018) Computational protein design. In: Methods in Molecular Biology, vol. 1529, p 450. Humana Press Inc: New York, NY.
Sheehan MN (ed.) (2013) Protein Engineering: Design, Selection and Applications, p 221. Nova Science Publishers: Hauppauge, NY.
Stoddard BL (ed.) (2018) Computational design of ligand‐binding proteins. In: Methods in Molecular Biology, vol. 1414, p 375. Humana Press Inc: New York, NY.
Voynov V and Caravella JA (eds) (2016) Therapeutic proteins: methods and protocols. In: Methods in Molecular Biology, vol. 899, p 502. Humana Press Inc: New York, NY.