24
123. Hanes J, Pluckthun A (1997) In vitro
selection and evolution of functional proteins by using ribosome display. Proc Natl
Acad Sci 94:4937–4942. doi:10.1073/
pnas.94.10.4937
124. Zahnd C, Amstutz P, Plückthun A (2007)
Ribosome display: selecting and evolving proteins in vitro that specifically bind to a target.
Nat Methods 4:269–279. doi:10.1038/
nmeth1003
125. Odegrip R, Coomber D, Eldridge B et al
(2004) CIS display: in vitro selection
of peptides from libraries of proteinDNA complexes. Proc Natl Acad Sci
U S A 101:2806–2810. doi:10.1073/pnas.
0400219101
126. Bertschinger J, Neri D (2004) Covalent DNA
display as a novel tool for directed evolution
of proteins in vitro. Protein Eng Des Sel
17:699–707. doi:10.1093/protein/gzh082
127. Stein V, Sielaff I, Johnsson K, Hollfelder F
(2007) A covalent chemical genotypephenotype linkage for in vitro protein evolution.
Chembiochem
8:2191–2194.
doi:10.1002/cbic.200700459
128. Kaltenbach M, Stein V, Hollfelder F (2011)
SNAP dendrimers: multivalent protein display on dendrimer-like DNA for directed evolution.
Chembiochem
12:2208–2216.
doi:10.1002/cbic.201100240
129. Diamante L, Gatti-Lafranconi P, Schaerli Y,
Hollfelder F (2013) In vitro affinity screening
of protein and peptide binders by megavalent
bead surface display. Protein Eng Des Sel
26:713–724. doi:10.1093/protein/gzt039
130. Gebauer M, Skerra A (2009) Engineered protein scaffolds as next-generation antibody
therapeutics. Curr Opin Chem Biol 13:245–
255. doi:10.1016/j.cbpa.2009.04.627
131. Binz HK, Amstutz P, Plückthun A (2005)
Engineering novel binding proteins from
nonimmunoglobulin
domains.
Nat
Biotechnol 23:1257–1268. doi:10.1038/
nbt1127
132. Gilbreth RN, Koide S (2012) Structural
insights for engineering binding proteins
based on non-antibody scaffolds. Curr Opin
Struct Biol 22:413–420. doi:10.1016/j.
sbi.2012.06.001
133. Kalko EKV, Dukas R, Ratcliffe JM et al
(2011) An expanded palette of genetically
encoded Ca2+ indicators. Science 333:1888–
1891. doi:10.1126/science.1208592
134. Litzlbauer J, Schifferer M, Ng D et al (2015)
Large Scale Bacterial Colony Screening
of Diversified FRET Biosensors. PLoS
One 10:e0119860. doi:10.1371/journal.
pone.0119860
135. Tian L, Hires SA, Mao T et al (2009) Imaging
neural activity in worms, flies and mice with
improved GCaMP calcium indicators. Nat
Methods 6:875–881. doi:10.1038/nmeth.1398
136. Wright RC, Khakhar A, Eshleman JR,
Ostermeier M (2014) Advancements in the
development of hif-1a-activated protein
switches for use in enzyme prodrug therapy
e114032. PLoS One 9:1–19. doi:10.1371/
journal.pone.0114032
137. Nadler DC, Morgan S-A, Flamholz A et al
(2016) CIS display: in vitro selection of peptides from libraries of protein-DNA complexes. Nat Commun 7:12266. doi:10.1038/
ncomms12266
138. Feng J, Jester BW, Tinberg CE et al (2015) A
general strategy to construct small molecule
biosensors in eukaryotes. Elife. doi:10.7554/
eLife.10606
139. Yi L, Gebhard MC, Li Q et al (2013)
Engineering of TEV protease variants by
yeast ER sequestration screening (YESS)
of combinatorial libraries. Proc Natl Acad
Sci U S A 110:7229–7234. doi:10.1073/
pnas.1215994110
140. Kaminski TS, Scheler O, Garstecki P (2016)
Droplet microfluidics for microbiology: techniques, applications and challenges. Lab Chip
16:2168–2187. doi:10.1039/C6LC00367B
141. Colin P-Y, Zinchenko A, Hollfelder F (2015)
Enzyme engineering in biomimetic compartments. Curr Opin Struct Biol 33:42–51.
doi:10.1016/j.sbi.2015.06.001
142. Vyawahare S, Griffiths AD, Merten CA
(2010) Miniaturization and parallelization of
biological and chemical assays in microfluidic
devices.
Chem
Biol
17:1052–1065.
doi:10.1016/j.chembiol.2010.09.007
143. Kintses B, Hein C, Mohamed MF et al (2012)
Picoliter cell lysate assays in microfluidic
droplet compartments for directed enzyme
evolution. Chem Biol 19:1001–1009.
doi:10.1016/j.chembiol.2012.06.009
144. Colin P-Y, Kintses B, Gielen F et al (2015)
Ultrahigh-throughput discovery of promiscuous enzymes by picodroplet functional
metagenomics. Nat Commun 6:10008.
doi:10.1038/ncomms10008
145. Agresti JJ, Antipov E, Abate AR et al (2010)
Ultrahigh-throughput screening in dropbased microfluidics for directed evolution.
Proc Natl Acad Sci 107:4004–4009.
doi:10.1073/pnas.0910781107
146. Wang BL, Ghaderi A, Zhou H et al (2014)
Microfluidic high-throughput culturing of
single cells for selection based on extracellular metabolite production or consumption.
Nat
Biotechnol
32:473–478.
Viktor Stein
123. Hanes J, Pluckthun A (1997) In vitro
selection and evolution of functional proteins by using ribosome display. Proc Natl
Acad Sci 94:4937–4942. doi:10.1073/
pnas.94.10.4937
124. Zahnd C, Amstutz P, Plückthun A (2007)
Ribosome display: selecting and evolving proteins in vitro that specifically bind to a target.
Nat Methods 4:269–279. doi:10.1038/
nmeth1003
125. Odegrip R, Coomber D, Eldridge B et al
(2004) CIS display: in vitro selection
of peptides from libraries of proteinDNA complexes. Proc Natl Acad Sci
U S A 101:2806–2810. doi:10.1073/pnas.
0400219101
126. Bertschinger J, Neri D (2004) Covalent DNA
display as a novel tool for directed evolution
of proteins in vitro. Protein Eng Des Sel
17:699–707. doi:10.1093/protein/gzh082
127. Stein V, Sielaff I, Johnsson K, Hollfelder F
(2007) A covalent chemical genotypephenotype linkage for in vitro protein evolution.
Chembiochem
8:2191–2194.
doi:10.1002/cbic.200700459
128. Kaltenbach M, Stein V, Hollfelder F (2011)
SNAP dendrimers: multivalent protein display on dendrimer-like DNA for directed evolution.
Chembiochem
12:2208–2216.
doi:10.1002/cbic.201100240
129. Diamante L, Gatti-Lafranconi P, Schaerli Y,
Hollfelder F (2013) In vitro affinity screening
of protein and peptide binders by megavalent
bead surface display. Protein Eng Des Sel
26:713–724. doi:10.1093/protein/gzt039
130. Gebauer M, Skerra A (2009) Engineered protein scaffolds as next-generation antibody
therapeutics. Curr Opin Chem Biol 13:245–
255. doi:10.1016/j.cbpa.2009.04.627
131. Binz HK, Amstutz P, Plückthun A (2005)
Engineering novel binding proteins from
nonimmunoglobulin
domains.
Nat
Biotechnol 23:1257–1268. doi:10.1038/
nbt1127
132. Gilbreth RN, Koide S (2012) Structural
insights for engineering binding proteins
based on non-antibody scaffolds. Curr Opin
Struct Biol 22:413–420. doi:10.1016/j.
sbi.2012.06.001
133. Kalko EKV, Dukas R, Ratcliffe JM et al
(2011) An expanded palette of genetically
encoded Ca2+ indicators. Science 333:1888–
1891. doi:10.1126/science.1208592
134. Litzlbauer J, Schifferer M, Ng D et al (2015)
Large Scale Bacterial Colony Screening
of Diversified FRET Biosensors. PLoS
One 10:e0119860. doi:10.1371/journal.
pone.0119860
135. Tian L, Hires SA, Mao T et al (2009) Imaging
neural activity in worms, flies and mice with
improved GCaMP calcium indicators. Nat
Methods 6:875–881. doi:10.1038/nmeth.1398
136. Wright RC, Khakhar A, Eshleman JR,
Ostermeier M (2014) Advancements in the
development of hif-1a-activated protein
switches for use in enzyme prodrug therapy
e114032. PLoS One 9:1–19. doi:10.1371/
journal.pone.0114032
137. Nadler DC, Morgan S-A, Flamholz A et al
(2016) CIS display: in vitro selection of peptides from libraries of protein-DNA complexes. Nat Commun 7:12266. doi:10.1038/
ncomms12266
138. Feng J, Jester BW, Tinberg CE et al (2015) A
general strategy to construct small molecule
biosensors in eukaryotes. Elife. doi:10.7554/
eLife.10606
139. Yi L, Gebhard MC, Li Q et al (2013)
Engineering of TEV protease variants by
yeast ER sequestration screening (YESS)
of combinatorial libraries. Proc Natl Acad
Sci U S A 110:7229–7234. doi:10.1073/
pnas.1215994110
140. Kaminski TS, Scheler O, Garstecki P (2016)
Droplet microfluidics for microbiology: techniques, applications and challenges. Lab Chip
16:2168–2187. doi:10.1039/C6LC00367B
141. Colin P-Y, Zinchenko A, Hollfelder F (2015)
Enzyme engineering in biomimetic compartments. Curr Opin Struct Biol 33:42–51.
doi:10.1016/j.sbi.2015.06.001
142. Vyawahare S, Griffiths AD, Merten CA
(2010) Miniaturization and parallelization of
biological and chemical assays in microfluidic
devices.
Chem
Biol
17:1052–1065.
doi:10.1016/j.chembiol.2010.09.007
143. Kintses B, Hein C, Mohamed MF et al (2012)
Picoliter cell lysate assays in microfluidic
droplet compartments for directed enzyme
evolution. Chem Biol 19:1001–1009.
doi:10.1016/j.chembiol.2012.06.009
144. Colin P-Y, Kintses B, Gielen F et al (2015)
Ultrahigh-throughput discovery of promiscuous enzymes by picodroplet functional
metagenomics. Nat Commun 6:10008.
doi:10.1038/ncomms10008
145. Agresti JJ, Antipov E, Abate AR et al (2010)
Ultrahigh-throughput screening in dropbased microfluidics for directed evolution.
Proc Natl Acad Sci 107:4004–4009.
doi:10.1073/pnas.0910781107
146. Wang BL, Ghaderi A, Zhou H et al (2014)
Microfluidic high-throughput culturing of
single cells for selection based on extracellular metabolite production or consumption.
Nat
Biotechnol
32:473–478.
Viktor Stein