news & views most pragmatic approach is to introduce simulation constraints. By fixing the chemical composition, novel polytypes can be explored through crystal structure prediction, with many successes for microporous materials4. Alternatively, by fixing the crystal structure, the screening of different combinations of elements can be used to identify previously overlooked stable compositions5,6. As search algorithms are improving, such constraints are gradually being overcome7,8. In the work of Poeppelmeier, Zunger and co-workers1, a valiant route was taken. They chose to fix the valence state of their target compounds to satisfy the 18-electron rule, and screen both the chemical composition and crystal structure. From 483 chemically plausible ternary compounds with 18 valence electrons, 83 have been previously reported, leaving 400 ‘missing’ compounds. A rigorous multi-step selection process was implemented (Fig. 1 shows one such process), and validated by ‘searching’ known compounds — the method did correctly predict their stability and structures. A crystal structure search was carried out to ensure a global minimum configuration was identified, and the vibrational spectrum of each candidate material was investigated to confirm its dynamic stability. Finally, thermodynamic calculations were performed to ensure stability with respect to each competing phase. This screening procedure ensures that fanciful predictions of hypothetical compounds with exotic properties are avoided. In the end only 54 candidates
survived — that is, were predicted to be stable — and of these, 15 new materials were successfully synthesized. One of the roles of materials prediction in this study is to reduce the possible phase space and direct synthetic efforts to the most realistic and important targets. The simulations also provide valuable information to expedite the characterization of the novel compounds, ranging from predicted crystal structure parameters to vibrational and electronic spectral signatures. For all 15 materials predicted then synthesized in the study, the simulated and measured X-ray and electron diffraction patterns are in very good agreement. Although in the past materials modelling has been largely responsive to experiment, the predictive power of modern simulation techniques is becoming increasingly apparent. The 18-electron compounds predicted to be stable are distributed amongst eight structure types. Phenomenologically, compounds with one transition metal (such as MgPdTe) are found to be metallic; those with two transition metals (such as TaIrSn) have a gap between their valence and conduction bands. The potential applications of these new materials with unconventional chemical bonding are wide ranging. For example, HfIrAs is a topological semimetal of interest in quantum electronics, ZrNiPb is a small-gap semiconductor with a large Seebeck coefficient suitable for thermoelectric applications, and ZrIrSb is a rare example of a transparent p-type conductor with high conductivity of holes.
It is an exciting time for materials chemistry. The ability to synthesize materials of increasing complexity continues to astound. Even fundamental thermodynamic limits can be overcome, as metastable structures and kinetically stable compositions are accessible through non-equilibrium growth techniques. The challenge now is not simply to make new compounds, but to enable new functionality. The combination of theory and simulation has adopted a new role in the field, as a quantitative tool that can direct and inform experimental synthesis and characterization. When used appropriately, it can help to navigate the immense structural and compositional landscape at a fraction of the time and cost of an empirical search. The googol of possible materials may contain a room-temperature superconductor, the next high-voltage battery, or indeed, a viable photocatalyst for splitting H2O or converting CO2 into a chemical feedstock. The quest is to find them. ❐ Aron Walsh is in the Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK. e-mail: [email protected]; Twitter: @lonepair References 1. 2. 3. 4. 5. 6.
Gautier, R. et al. Nature Chem. 7, 308–316 (2015). Curtarolo, S. et al. Nature Mater. 12, 191–201 (2013). Jain, A. et al. APL Mater. 1, 011002 (2013). Woodley, S. M. & Catlow, R. Nature Mater. 7, 937–946 (2008). Castelli, I. E. et al. Energy Environ. Sci. 5, 9034 (2012). Chen, S., Gong, X. G., Walsh, A. & Wei, S.-H. Phys. Rev. B 79, 165211 (2009). 7. Meredig, B. et al. Phys. Rev. B 89, 094104 (2014). 8. Zhang, W. et al. Science 342, 1502–1505 (2013).
SUPRAMOLECULAR SENSING
Enzyme activity with a twist
A supramolecular polymer comprising stacked artificial chromophores to which zinc(ii) complexes are appended is able to respond to enzymatic hydrolysis in aqueous solution. The assembly of molecules can twist reversibly and quickly in response to changes in the type of adenosine phosphate present.
David B. Amabilino
M
onitoring the activity of chemical processes in biological systems can lead to a greater understanding of how they function and also provides an opportunity find out when they go wrong. Particularly interesting targets are the adenosine phosphates (APs) because of the integral part they play in various processes in living cells. A great number of chemicalsensing approaches relevant to APs have been demonstrated with small-molecule probes1,2,3,
but genetically encoded indicators composed of fluorescent proteins have also been used to measure their levels inside single cells4. Now, writing in Nature Communications, a team led by Subi George has shown that entirely synthetic supramolecular polymers — a series of monomeric molecular units held together by non-covalent bonds — can also act as useful reporter groups for enzyme activity through their interaction with adenosine triphosphate (ATP)5. Up to
NATURE CHEMISTRY | VOL 7 | APRIL 2015 | www.nature.com/naturechemistry
© 2015 Macmillan Publishers Limited. All rights reserved
now, such supramolecular polymers have been primarily of interest for their mimicry of biological self-assembly processes as well as for the preparation of synthetic materials with novel properties6,7. This present work show how the non-destructive and dynamic response of supramolecular polymers to the presence of APs can be used to monitor biochemical activity and is a fascinating development with regard to potential new applications. 275
news & views a
b
N N
Zn N
O
O
N
N
O
O
N Zn
N N
NH2 O n = 1: AMP n = 2: ADP n = 3: ATP
O
P O
N O n
O
N
N N
OH OH
Right-handed ATP–polymer helix
Left-handed ADP–polymer helix
Left-handed Left handed AMP–polymer helix
c
+ve CD signal
–ve CD signal
–ve CD signal
No CD signal sig
Figure 1 | An NDI monomer bearing two zinc(ii) complexes can form helical supramolecular polymers with adenosine phosphates. a, The structures of AMP, ADP and ATP and the NDI-based monomer with a flat aromatic core (red), and two zinc(ii)-based complexes (green metal ion, blue ligands). The colour-coding in the chemical structure is maintained in the helical structures in b and c. b, The binding of ATP to the supramolecular polymer induces a right-handed helical twist, whereas the binding of either AMP or ADP leads to a left-handed helical structure. c, When the ATP–supramolecular polymer complex is treated with calf intestinal alkaline phosphatase (purple structure shown above the arrows), the ATP is hydrolysed to ADP, then AMP, and finally inorganic phosphate. This process can be monitored by recording the CD signal, which initially changes from positive to negative as the ATP is consumed and the supramolecular polymer undergoes a helix reversal as it subsequently binds ADP and then AMP. Once all of the APs have been converted into inorganic phosphate, the ribose groups no longer bind to the supramolecular polymer and so a racemic mixture of left- and right-handed helices is formed and the CD signal disappears. The images in b and c are reproduced from ref. 5, NPG.
The approach taken by George and co-workers is based on the recognition of the anionic phosphate moieties in adenosine monophosphate (AMP), adenosine diphosphate (ADP) and ATP by two identical zinc(ii) complexes appended to a naphthalenediimide (NDI) unit (Fig. 1). This bis-zinc(ii) complex undergoes supramolecular polymerization in aqueous solution with the NDI units stacking on top of one another. Because there is no source of chirality in the monomer, the supramolecular polymer is not optically active (that is, it does not produce a chiroptical signal). The stacks may exist as a racemic mixture of left- and right-handed helices as well as other achiral structures. But when the assembly binds to an AP, the intrinsic chirality of the ribose ring induces a handedness in the supramolecular polymer and this change is observed by circular dichroism (CD) spectroscopy. Each of the APs induces a different CD spectrum for the supramolecular polymers. At 400 nm, AMP induces a weak negative 276
signal, ADP a stronger negative signal, and ATP a positive signal. The reason for this effect was elucidated by molecular modelling which showed that both AMP and ADP form complexes in which the hydroxyl groups of the ribose ring interact directly with the oxygen atoms in the chromophore through hydrogen bonding and favour a left-handed structure for the helical arrangement of the NDI units. For ATP, many supramolecular complexes are theoretically possible with the phosphates bonding to the zinc(ii) ions in a multivalent manner, and perhaps because of these strong interactions the conformation of the complex is completely different to that formed with ADP or AMP. The hydrogen bonds present in the latter cases are apparently not favoured when ATP binds with the stack, rather the hydroxyl groups of the ribose point away from the NDI units and this orientation (completely different to that of the other complexes) induces a right-handed helicity in the supramolecular polymer, the reverse of what happens with the other two APs.
This induction of helical structure is reversible; the addition of ATP to aqueous solutions of either AMP or ADP bound to the supramolecular polymer resulted in an instantaneous reversal of the CD signal. Therefore, somewhat surprisingly, a rapid helical reversal takes place and this means that the system could potentially be useful as a probe for the APs. Also, unlike other supramolecular polymers of this ilk (where chiral twist is transferred over long distances6), no amplification of chirality was observed (pointing to short-range induction of chirality where only local preference in orientation is affected) and therefore the optical response is linear with respect to the AP concentration, which is an important feature for quantitative detection. The supramolecular polymer was then used in situ to study the kinetics of enzymatic hydrolysis of APs. Calf intestinal alkaline phosphatase was used to cleave the phosphate groups from the ribose moiety in the ATP–supramolecular polymer complex. This action of the enzyme causes
NATURE CHEMISTRY | VOL 7 | APRIL 2015 | www.nature.com/naturechemistry
© 2015 Macmillan Publishers Limited. All rights reserved
news & views a gradual inversion of the CD signal, from positive to negative, indicative of the formation of either ADP or AMP (this firstgeneration supramolecular polymer cannot distinguish between them). Increasing the concentration of enzyme or the temperature of the experiment (up to 40 °C) resulted in faster inversion kinetics as a direct result of ATP hydrolysis; in the fastest case a steady negative CD signal was reached in approximately 10 minutes. Further hydrolysis resulted in a disappearance of optical activity, highlighting that the phosphate groups are essential to the observation of a CD signal induced by the chirality of the ribose unit. The present strategy based on the observation of CD absorption spectroscopy is not the most sensitive that one could envisage. Indeed, synthetic molecular systems that monitor fluorescence are more sensitive2,3, and supramolecular pores have also been
used to sense enzyme activity 8. Nevertheless, the inversion of chirality could be monitored in fluorescence mode, and the promise of using either spectroscopy or even microscopy based on this kind of system is an attractive prospect when it comes to the observation of processes at the single-cell level. Sensing molecular species in biological systems based on responses of selfassembled synthetic systems is a compelling paradigm. It begs important questions. Could entirely man-made supramolecular constructs be used to monitor and regulate functions within living cells? What might be the consequences of this intrusion on the living matter? Given the success of the modelling in defining the chirality in this particular system, could modelling help predict new supramolecular systems capable of specifically detecting all three APs? Whatever the answers, using the
chemistry of aggregates to probe biological function has taken an intriguing step forward that promises to lead to exciting new knowledge that may not be accessible through other routes. ❐ David B. Amabilino is in the School of Chemistry at the University of Nottingham, Nottingham NG7 2RD, UK. e-mail: [email protected] References
1. Moro, A. J., Cywinski, P. J., Körsten, S. & Mohr, G. J. Chem. Commun. 46, 1085–1087 (2010). 2. Butler, S. J. Chem. Eur. J. 20, 15768–15774 (2014). 3. Tang, J. L., Li, C. Y., Li, Y. F. & Zou, C. X. Chem. Commun. 50, 15411–15414 (2014). 4. Imamura, H. et al. Proc. Natl Acad. Sci. USA 106, 15651–15656 (2009). 5. Kumar, M. et al. Nature Commun. 5, 5793 (2014). 6. Palmans, A. R. A. & Meijer, E. W. Angew. Chem. Int. Ed. 46, 8948–8968 (2007). 7. Aida, T., Meijer, E. W. & Stupp, S. I. Science 335, 813–817 (2012). 8. Das, G., Talukdar, P. & Matile, S. Science 298, 1600–1602 (2002).
PROTEIN ENGINEERING
The power of four
Supramolecular assembly has been used to design and create new proteins capable of performing biomimetic functions in complex environments such as membranes and inside living cells.
Arnold J. Boersma and Gerard Roelfes
T
he high activity and accuracy demonstrated by proteins in processes such as catalysis and transport relies on the precise positioning of residues in three dimensions for every chemical step. This requires the folding of the peptide chain using a myriad of non-covalent interactions; a process that, despite decades of research and undeniable progress, is still not understood to a level that allows the de novo design of functional proteins. The
fact that even nature simplifies the folding problem as much as possible illustrates the challenges involved. For example, nature often recycles successful protein folds and equips them with a repurposed active site1. Also, instead of using a single large peptide chain, complex protein structures are frequently created by supramolecular assembly of two or more proteins, which is a relatively simple and economical way to achieve complexity 2,3. Indeed, many
proteins even have active sites that comprise residues from multiple subunits. Similar strategies, combining the use of existing proteins and protein fragments and supramolecular assembly, are also applied in the laboratory for the design of new proteins. For many years, the workhorse for protein design has been the coiled coil, which is a supramolecular assembly of α-helical peptides4. These are relatively simple structures that can be designed by
Zn
H
α-helices H H
H H
Zn Zn Zn
Ampicillin
Zn Zn Metal-induced self assembly in vivo
Tetramer in a lipid bilayer H
H
H
H
Cyt cb562
H
Zn Structural Zinc
Hydrolysed ampicillin
Zn Catalytic Zinc
Figure 1 | Supramolecular assembly of four components can be used to design proteins with a diverse range of biomimetic functions. Left, the assembly of four α-helices to create a membrane channel that is capable of transporting Zn2+ across a membrane whilst antiporting protons. Right, the assembly of a tetramer that can hydrolyse the antibiotic ampicillin in E. coli. NATURE CHEMISTRY | VOL 7 | APRIL 2015 | www.nature.com/naturechemistry
© 2015 Macmillan Publishers Limited. All rights reserved
277
survived — that is, were predicted to be stable — and of these, 15 new materials were successfully synthesized. One of the roles of materials prediction in this study is to reduce the possible phase space and direct synthetic efforts to the most realistic and important targets. The simulations also provide valuable information to expedite the characterization of the novel compounds, ranging from predicted crystal structure parameters to vibrational and electronic spectral signatures. For all 15 materials predicted then synthesized in the study, the simulated and measured X-ray and electron diffraction patterns are in very good agreement. Although in the past materials modelling has been largely responsive to experiment, the predictive power of modern simulation techniques is becoming increasingly apparent. The 18-electron compounds predicted to be stable are distributed amongst eight structure types. Phenomenologically, compounds with one transition metal (such as MgPdTe) are found to be metallic; those with two transition metals (such as TaIrSn) have a gap between their valence and conduction bands. The potential applications of these new materials with unconventional chemical bonding are wide ranging. For example, HfIrAs is a topological semimetal of interest in quantum electronics, ZrNiPb is a small-gap semiconductor with a large Seebeck coefficient suitable for thermoelectric applications, and ZrIrSb is a rare example of a transparent p-type conductor with high conductivity of holes.
It is an exciting time for materials chemistry. The ability to synthesize materials of increasing complexity continues to astound. Even fundamental thermodynamic limits can be overcome, as metastable structures and kinetically stable compositions are accessible through non-equilibrium growth techniques. The challenge now is not simply to make new compounds, but to enable new functionality. The combination of theory and simulation has adopted a new role in the field, as a quantitative tool that can direct and inform experimental synthesis and characterization. When used appropriately, it can help to navigate the immense structural and compositional landscape at a fraction of the time and cost of an empirical search. The googol of possible materials may contain a room-temperature superconductor, the next high-voltage battery, or indeed, a viable photocatalyst for splitting H2O or converting CO2 into a chemical feedstock. The quest is to find them. ❐ Aron Walsh is in the Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK. e-mail: [email protected]; Twitter: @lonepair References 1. 2. 3. 4. 5. 6.
Gautier, R. et al. Nature Chem. 7, 308–316 (2015). Curtarolo, S. et al. Nature Mater. 12, 191–201 (2013). Jain, A. et al. APL Mater. 1, 011002 (2013). Woodley, S. M. & Catlow, R. Nature Mater. 7, 937–946 (2008). Castelli, I. E. et al. Energy Environ. Sci. 5, 9034 (2012). Chen, S., Gong, X. G., Walsh, A. & Wei, S.-H. Phys. Rev. B 79, 165211 (2009). 7. Meredig, B. et al. Phys. Rev. B 89, 094104 (2014). 8. Zhang, W. et al. Science 342, 1502–1505 (2013).
SUPRAMOLECULAR SENSING
Enzyme activity with a twist
A supramolecular polymer comprising stacked artificial chromophores to which zinc(ii) complexes are appended is able to respond to enzymatic hydrolysis in aqueous solution. The assembly of molecules can twist reversibly and quickly in response to changes in the type of adenosine phosphate present.
David B. Amabilino
M
onitoring the activity of chemical processes in biological systems can lead to a greater understanding of how they function and also provides an opportunity find out when they go wrong. Particularly interesting targets are the adenosine phosphates (APs) because of the integral part they play in various processes in living cells. A great number of chemicalsensing approaches relevant to APs have been demonstrated with small-molecule probes1,2,3,
but genetically encoded indicators composed of fluorescent proteins have also been used to measure their levels inside single cells4. Now, writing in Nature Communications, a team led by Subi George has shown that entirely synthetic supramolecular polymers — a series of monomeric molecular units held together by non-covalent bonds — can also act as useful reporter groups for enzyme activity through their interaction with adenosine triphosphate (ATP)5. Up to
NATURE CHEMISTRY | VOL 7 | APRIL 2015 | www.nature.com/naturechemistry
© 2015 Macmillan Publishers Limited. All rights reserved
now, such supramolecular polymers have been primarily of interest for their mimicry of biological self-assembly processes as well as for the preparation of synthetic materials with novel properties6,7. This present work show how the non-destructive and dynamic response of supramolecular polymers to the presence of APs can be used to monitor biochemical activity and is a fascinating development with regard to potential new applications. 275
news & views a
b
N N
Zn N
O
O
N
N
O
O
N Zn
N N
NH2 O n = 1: AMP n = 2: ADP n = 3: ATP
O
P O
N O n
O
N
N N
OH OH
Right-handed ATP–polymer helix
Left-handed ADP–polymer helix
Left-handed Left handed AMP–polymer helix
c
+ve CD signal
–ve CD signal
–ve CD signal
No CD signal sig
Figure 1 | An NDI monomer bearing two zinc(ii) complexes can form helical supramolecular polymers with adenosine phosphates. a, The structures of AMP, ADP and ATP and the NDI-based monomer with a flat aromatic core (red), and two zinc(ii)-based complexes (green metal ion, blue ligands). The colour-coding in the chemical structure is maintained in the helical structures in b and c. b, The binding of ATP to the supramolecular polymer induces a right-handed helical twist, whereas the binding of either AMP or ADP leads to a left-handed helical structure. c, When the ATP–supramolecular polymer complex is treated with calf intestinal alkaline phosphatase (purple structure shown above the arrows), the ATP is hydrolysed to ADP, then AMP, and finally inorganic phosphate. This process can be monitored by recording the CD signal, which initially changes from positive to negative as the ATP is consumed and the supramolecular polymer undergoes a helix reversal as it subsequently binds ADP and then AMP. Once all of the APs have been converted into inorganic phosphate, the ribose groups no longer bind to the supramolecular polymer and so a racemic mixture of left- and right-handed helices is formed and the CD signal disappears. The images in b and c are reproduced from ref. 5, NPG.
The approach taken by George and co-workers is based on the recognition of the anionic phosphate moieties in adenosine monophosphate (AMP), adenosine diphosphate (ADP) and ATP by two identical zinc(ii) complexes appended to a naphthalenediimide (NDI) unit (Fig. 1). This bis-zinc(ii) complex undergoes supramolecular polymerization in aqueous solution with the NDI units stacking on top of one another. Because there is no source of chirality in the monomer, the supramolecular polymer is not optically active (that is, it does not produce a chiroptical signal). The stacks may exist as a racemic mixture of left- and right-handed helices as well as other achiral structures. But when the assembly binds to an AP, the intrinsic chirality of the ribose ring induces a handedness in the supramolecular polymer and this change is observed by circular dichroism (CD) spectroscopy. Each of the APs induces a different CD spectrum for the supramolecular polymers. At 400 nm, AMP induces a weak negative 276
signal, ADP a stronger negative signal, and ATP a positive signal. The reason for this effect was elucidated by molecular modelling which showed that both AMP and ADP form complexes in which the hydroxyl groups of the ribose ring interact directly with the oxygen atoms in the chromophore through hydrogen bonding and favour a left-handed structure for the helical arrangement of the NDI units. For ATP, many supramolecular complexes are theoretically possible with the phosphates bonding to the zinc(ii) ions in a multivalent manner, and perhaps because of these strong interactions the conformation of the complex is completely different to that formed with ADP or AMP. The hydrogen bonds present in the latter cases are apparently not favoured when ATP binds with the stack, rather the hydroxyl groups of the ribose point away from the NDI units and this orientation (completely different to that of the other complexes) induces a right-handed helicity in the supramolecular polymer, the reverse of what happens with the other two APs.
This induction of helical structure is reversible; the addition of ATP to aqueous solutions of either AMP or ADP bound to the supramolecular polymer resulted in an instantaneous reversal of the CD signal. Therefore, somewhat surprisingly, a rapid helical reversal takes place and this means that the system could potentially be useful as a probe for the APs. Also, unlike other supramolecular polymers of this ilk (where chiral twist is transferred over long distances6), no amplification of chirality was observed (pointing to short-range induction of chirality where only local preference in orientation is affected) and therefore the optical response is linear with respect to the AP concentration, which is an important feature for quantitative detection. The supramolecular polymer was then used in situ to study the kinetics of enzymatic hydrolysis of APs. Calf intestinal alkaline phosphatase was used to cleave the phosphate groups from the ribose moiety in the ATP–supramolecular polymer complex. This action of the enzyme causes
NATURE CHEMISTRY | VOL 7 | APRIL 2015 | www.nature.com/naturechemistry
© 2015 Macmillan Publishers Limited. All rights reserved
news & views a gradual inversion of the CD signal, from positive to negative, indicative of the formation of either ADP or AMP (this firstgeneration supramolecular polymer cannot distinguish between them). Increasing the concentration of enzyme or the temperature of the experiment (up to 40 °C) resulted in faster inversion kinetics as a direct result of ATP hydrolysis; in the fastest case a steady negative CD signal was reached in approximately 10 minutes. Further hydrolysis resulted in a disappearance of optical activity, highlighting that the phosphate groups are essential to the observation of a CD signal induced by the chirality of the ribose unit. The present strategy based on the observation of CD absorption spectroscopy is not the most sensitive that one could envisage. Indeed, synthetic molecular systems that monitor fluorescence are more sensitive2,3, and supramolecular pores have also been
used to sense enzyme activity 8. Nevertheless, the inversion of chirality could be monitored in fluorescence mode, and the promise of using either spectroscopy or even microscopy based on this kind of system is an attractive prospect when it comes to the observation of processes at the single-cell level. Sensing molecular species in biological systems based on responses of selfassembled synthetic systems is a compelling paradigm. It begs important questions. Could entirely man-made supramolecular constructs be used to monitor and regulate functions within living cells? What might be the consequences of this intrusion on the living matter? Given the success of the modelling in defining the chirality in this particular system, could modelling help predict new supramolecular systems capable of specifically detecting all three APs? Whatever the answers, using the
chemistry of aggregates to probe biological function has taken an intriguing step forward that promises to lead to exciting new knowledge that may not be accessible through other routes. ❐ David B. Amabilino is in the School of Chemistry at the University of Nottingham, Nottingham NG7 2RD, UK. e-mail: [email protected] References
1. Moro, A. J., Cywinski, P. J., Körsten, S. & Mohr, G. J. Chem. Commun. 46, 1085–1087 (2010). 2. Butler, S. J. Chem. Eur. J. 20, 15768–15774 (2014). 3. Tang, J. L., Li, C. Y., Li, Y. F. & Zou, C. X. Chem. Commun. 50, 15411–15414 (2014). 4. Imamura, H. et al. Proc. Natl Acad. Sci. USA 106, 15651–15656 (2009). 5. Kumar, M. et al. Nature Commun. 5, 5793 (2014). 6. Palmans, A. R. A. & Meijer, E. W. Angew. Chem. Int. Ed. 46, 8948–8968 (2007). 7. Aida, T., Meijer, E. W. & Stupp, S. I. Science 335, 813–817 (2012). 8. Das, G., Talukdar, P. & Matile, S. Science 298, 1600–1602 (2002).
PROTEIN ENGINEERING
The power of four
Supramolecular assembly has been used to design and create new proteins capable of performing biomimetic functions in complex environments such as membranes and inside living cells.
Arnold J. Boersma and Gerard Roelfes
T
he high activity and accuracy demonstrated by proteins in processes such as catalysis and transport relies on the precise positioning of residues in three dimensions for every chemical step. This requires the folding of the peptide chain using a myriad of non-covalent interactions; a process that, despite decades of research and undeniable progress, is still not understood to a level that allows the de novo design of functional proteins. The
fact that even nature simplifies the folding problem as much as possible illustrates the challenges involved. For example, nature often recycles successful protein folds and equips them with a repurposed active site1. Also, instead of using a single large peptide chain, complex protein structures are frequently created by supramolecular assembly of two or more proteins, which is a relatively simple and economical way to achieve complexity 2,3. Indeed, many
proteins even have active sites that comprise residues from multiple subunits. Similar strategies, combining the use of existing proteins and protein fragments and supramolecular assembly, are also applied in the laboratory for the design of new proteins. For many years, the workhorse for protein design has been the coiled coil, which is a supramolecular assembly of α-helical peptides4. These are relatively simple structures that can be designed by
Zn
H
α-helices H H
H H
Zn Zn Zn
Ampicillin
Zn Zn Metal-induced self assembly in vivo
Tetramer in a lipid bilayer H
H
H
H
Cyt cb562
H
Zn Structural Zinc
Hydrolysed ampicillin
Zn Catalytic Zinc
Figure 1 | Supramolecular assembly of four components can be used to design proteins with a diverse range of biomimetic functions. Left, the assembly of four α-helices to create a membrane channel that is capable of transporting Zn2+ across a membrane whilst antiporting protons. Right, the assembly of a tetramer that can hydrolyse the antibiotic ampicillin in E. coli. NATURE CHEMISTRY | VOL 7 | APRIL 2015 | www.nature.com/naturechemistry
© 2015 Macmillan Publishers Limited. All rights reserved
277
