22
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501:212–216. doi:10.1038/nature12443
74. Schreier B, Stumpp C, Wiesner S, Höcker B
(2009) Computational design of ligand binding is not a solved problem. Proc Natl Acad
Sci U S A 106:18491–18496. doi:10.1073/
pnas.0907950106
75. Röthlisberger D, Khersonsky O, Wollacott
AM et al (2008) Kemp elimination catalysts
by computational enzyme design. Nature
453:190–195. doi:10.1038/nature06879
76. Jiang L, Althoff EA, Clemente FR et al
(2008) De novo computational design of
retro-aldol enzymes. Science 319:1387–
1391. doi:10.1126/science.1152692
77. Korendovych IV, Kulp DW, Wu Y et al (2011)
Design of a switchable eliminase. Proc Natl
Acad Sci U S A 108:6823–6827.
doi:10.1073/pnas.1018191108
78. Taylor ND, Garruss AS, Moretti R et al
(2016) Engineering an allosteric transcription
factor to respond to new ligands. Nat
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79. Van Dongen EMWM, Evers TH, Dekkers
LM et al (2007) Variation of linker length in
ratiometric fluorescent sensor proteins allows
rational tuning of Zn(II) affinity in the picomolar to femtomolar range. J Am Chem Soc
129:3494–3495. doi:10.1021/ja069105d
80. Porebski BT, Buckle AM (2016) Consensus
protein design. 29:1–7. doi: 10.1093/protein/gzw015
81. Steipe B, Schiller B, Plückthun A, Steinbacher
S (1994) Sequence statistics reliably predict
stabilizing mutations in a protein domain.
J Mol Biol 240:188–192. doi:10.1006/
jmbi.1994.1434
82. Jacobs SA, Diem MD, Luo J et al (2012)
Design of novel FN3 domains with high stability by a consensus sequence approach.
Protein Eng Des Sel 25:107–117.
doi:10.1093/protein/gzr064
83. Binz HK, Stumpp MT, Forrer P et al (2003)
Designing repeat proteins: well-expressed,
soluble and stable proteins from combinatorial libraries of consensus ankyrin repeat proteins. J Mol Biol 332:489–503. doi:10.1016/
S0022-2836(03)00896-9
84. Lehmann M, Pasamontes L, Lassen SF, Wyss
M (2000) The consensus concept for thermostability engineering of proteins. Biochim
Biophys Acta 1543:408–415. doi:10.1016/
S0167-4838(00)00238-7
85. Lehmann M, Kostrewa D, Wyss M et al
(2000) From DNA sequence to improved
functionality: using protein sequence comparisons to rapidly design a thermostable consensus phytase. Protein Eng Des Sel 13:49–57.
doi:10.1093/protein/13.1.49
86. Starr T (2015) Epistasis in protein evolution.
Protein Sci 00:1–8. doi:10.1002/pro
87. Harms MJ, Thornton JW (2010) Analyzing
protein structure and function using ancestral
gene reconstruction. Curr Opin Struct Biol
20:360–366. doi:10.1016/j.sbi.2010.03.005
88. Thornton JW (2004) Resurrecting ancient
genes: experimental analysis of extinct molecules.
Nat
Rev
Genet
5:366–375.
doi:10.1038/nrg1324
89. Risso VA, Gavira JA, Mejia-Carmona DF et al
(2013) Hyperstability and substrate promiscuity in laboratory resurrections of precambrian β-lactamases. J Am Chem Soc
135:2899–2902. doi:10.1021/ja311630a
90. Whitfield JH, Zhang WH, Herde MK et al
(2015) Construction of a robust and sensitive
arginine biosensor through ancestral protein
reconstruction. Protein Sci 24:1412–1422.
doi:10.1002/pro.2721
91. Gaucher EA, Thomson JM, Burgan MF,
Benner SA (2003) Inferring the palaeoenvironment of ancient bacteria on the basis of
resurrected proteins. Nature 425:285–288.
doi:10.1038/nature01977
92. Clifton BE, Jackson CJ (2016) Ancestral protein reconstruction yields insights into adaptive
evolution of binding specificity in solute-binding proteins. Cell Chem Biol 23:236–245.
doi:10.1016/j.chembiol.2015.12.010
93. Süel GM, Lockless SW, Wall MA, Ranganathan
R (2003) Evolutionarily conserved networks
of residues mediate allosteric communication
in proteins. Nat Struct Biol 10:59–69.
doi:10.1038/nsb881
94. Reynolds KA, McLaughlin RN, Ranganathan
R (2011) Hot spots for allosteric regulation
on protein surfaces. Cell 147:1564–1575.
doi:10.1016/j.cell.2011.10.049
95. Lee J, Natarajan M, Nashine VC et al (2008)
Surface sites for engineering allosteric control
in
proteins.
Science
322:438–442.
doi:10.1126/science.1159052
96. Yu Y, Lutz S (2011) Circular permutation: a
different way to engineer enzyme structure
and function. Trends Biotechnol 29:18–25.
doi:10.1016/j.tibtech.2010.10.004
97. Guntas G, Mansell TJ, Kim JR, Ostermeier M
(2005) Directed evolution of protein
switches and their application to the creation
of ligand- binding proteins. Proc Natl Acad
Sci U S A 102:11224–11229. doi:10.1073/
pnas.0502673102
Viktor Stein
73. Tinberg CE, Khare SD, Dou J et al (2013)
Computational design of ligand-binding proteins with high affinity and selectivity. Nature
501:212–216. doi:10.1038/nature12443
74. Schreier B, Stumpp C, Wiesner S, Höcker B
(2009) Computational design of ligand binding is not a solved problem. Proc Natl Acad
Sci U S A 106:18491–18496. doi:10.1073/
pnas.0907950106
75. Röthlisberger D, Khersonsky O, Wollacott
AM et al (2008) Kemp elimination catalysts
by computational enzyme design. Nature
453:190–195. doi:10.1038/nature06879
76. Jiang L, Althoff EA, Clemente FR et al
(2008) De novo computational design of
retro-aldol enzymes. Science 319:1387–
1391. doi:10.1126/science.1152692
77. Korendovych IV, Kulp DW, Wu Y et al (2011)
Design of a switchable eliminase. Proc Natl
Acad Sci U S A 108:6823–6827.
doi:10.1073/pnas.1018191108
78. Taylor ND, Garruss AS, Moretti R et al
(2016) Engineering an allosteric transcription
factor to respond to new ligands. Nat
Methods 1–11. doi: 10.1038/nmeth.3696
79. Van Dongen EMWM, Evers TH, Dekkers
LM et al (2007) Variation of linker length in
ratiometric fluorescent sensor proteins allows
rational tuning of Zn(II) affinity in the picomolar to femtomolar range. J Am Chem Soc
129:3494–3495. doi:10.1021/ja069105d
80. Porebski BT, Buckle AM (2016) Consensus
protein design. 29:1–7. doi: 10.1093/protein/gzw015
81. Steipe B, Schiller B, Plückthun A, Steinbacher
S (1994) Sequence statistics reliably predict
stabilizing mutations in a protein domain.
J Mol Biol 240:188–192. doi:10.1006/
jmbi.1994.1434
82. Jacobs SA, Diem MD, Luo J et al (2012)
Design of novel FN3 domains with high stability by a consensus sequence approach.
Protein Eng Des Sel 25:107–117.
doi:10.1093/protein/gzr064
83. Binz HK, Stumpp MT, Forrer P et al (2003)
Designing repeat proteins: well-expressed,
soluble and stable proteins from combinatorial libraries of consensus ankyrin repeat proteins. J Mol Biol 332:489–503. doi:10.1016/
S0022-2836(03)00896-9
84. Lehmann M, Pasamontes L, Lassen SF, Wyss
M (2000) The consensus concept for thermostability engineering of proteins. Biochim
Biophys Acta 1543:408–415. doi:10.1016/
S0167-4838(00)00238-7
85. Lehmann M, Kostrewa D, Wyss M et al
(2000) From DNA sequence to improved
functionality: using protein sequence comparisons to rapidly design a thermostable consensus phytase. Protein Eng Des Sel 13:49–57.
doi:10.1093/protein/13.1.49
86. Starr T (2015) Epistasis in protein evolution.
Protein Sci 00:1–8. doi:10.1002/pro
87. Harms MJ, Thornton JW (2010) Analyzing
protein structure and function using ancestral
gene reconstruction. Curr Opin Struct Biol
20:360–366. doi:10.1016/j.sbi.2010.03.005
88. Thornton JW (2004) Resurrecting ancient
genes: experimental analysis of extinct molecules.
Nat
Rev
Genet
5:366–375.
doi:10.1038/nrg1324
89. Risso VA, Gavira JA, Mejia-Carmona DF et al
(2013) Hyperstability and substrate promiscuity in laboratory resurrections of precambrian β-lactamases. J Am Chem Soc
135:2899–2902. doi:10.1021/ja311630a
90. Whitfield JH, Zhang WH, Herde MK et al
(2015) Construction of a robust and sensitive
arginine biosensor through ancestral protein
reconstruction. Protein Sci 24:1412–1422.
doi:10.1002/pro.2721
91. Gaucher EA, Thomson JM, Burgan MF,
Benner SA (2003) Inferring the palaeoenvironment of ancient bacteria on the basis of
resurrected proteins. Nature 425:285–288.
doi:10.1038/nature01977
92. Clifton BE, Jackson CJ (2016) Ancestral protein reconstruction yields insights into adaptive
evolution of binding specificity in solute-binding proteins. Cell Chem Biol 23:236–245.
doi:10.1016/j.chembiol.2015.12.010
93. Süel GM, Lockless SW, Wall MA, Ranganathan
R (2003) Evolutionarily conserved networks
of residues mediate allosteric communication
in proteins. Nat Struct Biol 10:59–69.
doi:10.1038/nsb881
94. Reynolds KA, McLaughlin RN, Ranganathan
R (2011) Hot spots for allosteric regulation
on protein surfaces. Cell 147:1564–1575.
doi:10.1016/j.cell.2011.10.049
95. Lee J, Natarajan M, Nashine VC et al (2008)
Surface sites for engineering allosteric control
in
proteins.
Science
322:438–442.
doi:10.1126/science.1159052
96. Yu Y, Lutz S (2011) Circular permutation: a
different way to engineer enzyme structure
and function. Trends Biotechnol 29:18–25.
doi:10.1016/j.tibtech.2010.10.004
97. Guntas G, Mansell TJ, Kim JR, Ostermeier M
(2005) Directed evolution of protein
switches and their application to the creation
of ligand- binding proteins. Proc Natl Acad
Sci U S A 102:11224–11229. doi:10.1073/
pnas.0502673102
Viktor Stein