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Hober S, Lindbo S, Nilvebrant J. Bispecific applications of non-immunoglobulin scaffold binders. Methods 2019; 154:143-152. [DOI: 10.1016/j.ymeth.2018.09.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/24/2018] [Accepted: 09/28/2018] [Indexed: 12/13/2022] Open
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2
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Abstract
Synthetic protein switches with tailored response functions are finding increasing applications as tools in basic research and biotechnology. With a number of successful design strategies emerging, the construction of synthetic protein switches still frequently necessitates an integrated approach that combines detailed biochemical and biophysical characterization in combination with high-throughput screening to construct tailored synthetic protein switches. This is increasingly complemented by computational strategies that aim to reduce the need for costly empirical optimization and thus facilitate the protein design process. Successful computational design approaches range from analyzing phylogenetic data to infer useful structural, biophysical, and biochemical information to modeling the structure and function of proteins ab initio. The following chapter provides an overview over the theoretical considerations and experimental approaches that have been successful applied in the construction of synthetic protein switches.
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Affiliation(s)
- Viktor Stein
- Fachbereich Biologie, Technische Universität Darmstadt, 64287, Darmstadt, Germany.
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3
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Moar WJ, Evans AJ, Kessenich CR, Baum JA, Bowen DJ, Edrington TC, Haas JA, Kouadio JLK, Roberts JK, Silvanovich A, Yin Y, Weiner BE, Glenn KC, Odegaard ML. The sequence, structural, and functional diversity within a protein family and implications for specificity and safety: The case for ETX_MTX2 insecticidal proteins. J Invertebr Pathol 2017; 142:50-59. [DOI: 10.1016/j.jip.2016.05.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 05/20/2016] [Accepted: 05/24/2016] [Indexed: 11/26/2022]
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4
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Aper SJ, Merkx M. Rewiring Multidomain Protein Switches: Transforming a Fluorescent Zn(2+) Sensor into a Light-Responsive Zn(2+) Binding Protein. ACS Synth Biol 2016; 5:698-709. [PMID: 27031076 DOI: 10.1021/acssynbio.6b00027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein-based sensors and switches provide attractive tools for the real-time monitoring and control of molecular processes in complex biological environments. Fluorescent sensor proteins have been developed for a wide variety of small molecules, but the construction of genetically encoded light-responsive ligand binding proteins remains mostly unexplored. Here we present a generic approach to reengineer a previously developed FRET-based Zn(2+) sensor into a light-activatable Zn(2+) binding protein using a design strategy based on mutually exclusive domain interactions. These so-called VividZn proteins consist of two light-responsive Vivid domains that homodimerize upon illumination with blue light, thus preventing the binding of Zn(2+) between two Zn(2+) binding domains, Atox1 and WD4. Following optimization of the linker between WD4 and the N-terminus of one of the Vivid domains, VividZn variants were obtained that show a 9- to 55-fold decrease in Zn(2+) affinity upon illumination, which is fully reversible following dark adaptation. The Zn(2+) affinities of the switch could be rationally tuned between 1 pM and 2 nM by systematic variation of linker length and mutation of one of the Zn(2+) binding residues. Similarly, introduction of mutations in the Vivid domains allowed tuning of the switching kinetics between 10 min and 7 h. Low expression levels in mammalian cells precluded the demonstration of light-induced perturbation of cytosolic Zn(2+) levels. Nonetheless, our results firmly establish the use of intramolecular Vivid dimerization as an attractive light-sensitive input module to rationally engineer light-responsive protein switches based on mutually exclusive domain interactions.
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Affiliation(s)
- Stijn J.A. Aper
- Laboratory
of Chemical Biology
and Institute for Complex Molecular Systems (ICMS), Department of
Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory
of Chemical Biology
and Institute for Complex Molecular Systems (ICMS), Department of
Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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5
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Jacobs TM, Williams B, Williams T, Xu X, Eletsky A, Federizon JF, Szyperski T, Kuhlman B. Design of structurally distinct proteins using strategies inspired by evolution. Science 2016; 352:687-90. [PMID: 27151863 DOI: 10.1126/science.aad8036] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 03/14/2016] [Indexed: 12/25/2022]
Abstract
Natural recombination combines pieces of preexisting proteins to create new tertiary structures and functions. We describe a computational protocol, called SEWING, which is inspired by this process and builds new proteins from connected or disconnected pieces of existing structures. Helical proteins designed with SEWING contain structural features absent from other de novo designed proteins and, in some cases, remain folded at more than 100°C. High-resolution structures of the designed proteins CA01 and DA05R1 were solved by x-ray crystallography (2.2 angstrom resolution) and nuclear magnetic resonance, respectively, and there was excellent agreement with the design models. This method provides a new strategy to rapidly create large numbers of diverse and designable protein scaffolds.
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Affiliation(s)
- T M Jacobs
- Program in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - B Williams
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - T Williams
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - X Xu
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260, USA. Northeast Structural Genomics Consortium
| | - A Eletsky
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260, USA. Northeast Structural Genomics Consortium
| | - J F Federizon
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260, USA
| | - T Szyperski
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260, USA
| | - B Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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6
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Design of catalytically amplified sensors for small molecules. Biomolecules 2014; 4:402-18. [PMID: 24970222 PMCID: PMC4101489 DOI: 10.3390/biom4020402] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 03/21/2014] [Accepted: 03/26/2014] [Indexed: 01/15/2023] Open
Abstract
Catalytically amplified sensors link an allosteric analyte binding site with a reactive site to catalytically convert substrate into colored or fluorescent product that can be easily measured. Such an arrangement greatly improves a sensor’s detection limit as illustrated by successful application of ELISA-based approaches. The ability to engineer synthetic catalytic sites into non-enzymatic proteins expands the repertoire of analytes as well as readout reactions. Here we review recent examples of small molecule sensors based on allosterically controlled enzymes and organometallic catalysts. The focus of this paper is on biocompatible, switchable enzymes regulated by small molecules to track analytes both in vivo and in the environment.
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7
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Jones DD, Arpino JAJ, Baldwin AJ, Edmundson MC. Transposon-based approaches for generating novel molecular diversity during directed evolution. Methods Mol Biol 2014; 1179:159-172. [PMID: 25055777 DOI: 10.1007/978-1-4939-1053-3_11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This chapter introduces a set of transposon-based methods that were developed to sample trinucleotide deletion, trinucleotide replacement, and domain insertion. Each approach has a common initial step that utilizes an engineered version of the Mu transposon called MuDel. The inherent low sequence specificity of MuDel results in its random insertion into target DNA during in vitro transposition. Removal of the transposon using a type IIS restriction endonuclease generates blunt-end random breaks at a frequency of one per target gene and the concomitant loss of 3 bp. Self-ligation or insertion of another DNA cassette results in the sampling of trinucleotide deletion or trinucleotide substitution/domain insertion, respectively.
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Affiliation(s)
- D Dafydd Jones
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AT, UK,
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8
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Idili A, Plaxco KW, Vallée-Bélisle A, Ricci F. Thermodynamic basis for engineering high-affinity, high-specificity binding-induced DNA clamp nanoswitches. ACS NANO 2013; 7:10863-9. [PMID: 24219761 PMCID: PMC4281346 DOI: 10.1021/nn404305e] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Naturally occurring chemoreceptors almost invariably employ structure-switching mechanisms, an observation that has inspired the use of biomolecular switches in a wide range of artificial technologies in the areas of diagnostics, imaging, and synthetic biology. In one mechanism for generating such behavior, clamp-based switching, binding occurs via the clamplike embrace of two recognition elements onto a single target molecule. In addition to coupling recognition with a large conformational change, this mechanism offers a second advantage: it improves both affinity and specificity simultaneously. To explore the physics of such switches we have dissected here the thermodynamics of a clamp-switch that recognizes a target DNA sequence through both Watson-Crick base pairing and triplex-forming Hoogsteen interactions. When compared to the equivalent linear DNA probe (which relies solely on Watson-Crick interactions), the extra Hoogsteen interactions in the DNA clamp-switch increase the probe's affinity for its target by ∼0.29 ± 0.02 kcal/mol/base. The Hoogsteen interactions of the clamp-switch likewise provide an additional specificity check that increases the discrimination efficiency toward a single-base mismatch by 1.2 ± 0.2 kcal/mol. This, in turn, leads to a 10-fold improvement in the width of the "specificity window" of this probe relative to that of the equivalent linear probe. Given these attributes, clamp-switches should be of utility not only for sensing applications but also, in the specific field of DNA nanotechnology, for applications calling for a better control over the building of nanostructures and nanomachines.
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Affiliation(s)
- Andrea Idili
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
- Consorzio Interuniversitario Biostrutture e Biosistemi “INBB”, Rome, Italy
| | - Kevin W. Plaxco
- Center for Bioengineering & Department of Chemistry and Biochemistry, University of California, Santa Barbara CA 93106 USA
- Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara CA 93106 USA
| | - Alexis Vallée-Bélisle
- Laboratory of Biosensors and Nanomachines, Département de Chimie, Université de Montréal, Québec, Canada
| | - Francesco Ricci
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
- Consorzio Interuniversitario Biostrutture e Biosistemi “INBB”, Rome, Italy
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9
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Guellouz A, Valerio-Lepiniec M, Urvoas A, Chevrel A, Graille M, Fourati-Kammoun Z, Desmadril M, van Tilbeurgh H, Minard P. Selection of specific protein binders for pre-defined targets from an optimized library of artificial helicoidal repeat proteins (alphaRep). PLoS One 2013; 8:e71512. [PMID: 24014183 PMCID: PMC3754942 DOI: 10.1371/journal.pone.0071512] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 07/01/2013] [Indexed: 12/16/2022] Open
Abstract
We previously designed a new family of artificial proteins named αRep based on a subgroup of thermostable helicoidal HEAT-like repeats. We have now assembled a large optimized αRep library. In this library, the side chains at each variable position are not fully randomized but instead encoded by a distribution of codons based on the natural frequency of side chains of the natural repeats family. The library construction is based on a polymerization of micro-genes and therefore results in a distribution of proteins with a variable number of repeats. We improved the library construction process using a “filtration” procedure to retain only fully coding modules that were recombined to recreate sequence diversity. The final library named Lib2.1 contains 1.7×109 independent clones. Here, we used phage display to select, from the previously described library or from the new library, new specific αRep proteins binding to four different non-related predefined protein targets. Specific binders were selected in each case. The results show that binders with various sizes are selected including relatively long sequences, with up to 7 repeats. ITC-measured affinities vary with Kd values ranging from micromolar to nanomolar ranges. The formation of complexes is associated with a significant thermal stabilization of the bound target protein. The crystal structures of two complexes between αRep and their cognate targets were solved and show that the new interfaces are established by the variable surfaces of the repeated modules, as well by the variable N-cap residues. These results suggest that αRep library is a new and versatile source of tight and specific binding proteins with favorable biophysical properties.
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Affiliation(s)
- Asma Guellouz
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris-Sud, Orsay, France
- Unité Mixte de Recherche 8619, Centre National de Recherche Scientifique, Orsay, France
| | - Marie Valerio-Lepiniec
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris-Sud, Orsay, France
- Unité Mixte de Recherche 8619, Centre National de Recherche Scientifique, Orsay, France
| | - Agathe Urvoas
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris-Sud, Orsay, France
- Unité Mixte de Recherche 8619, Centre National de Recherche Scientifique, Orsay, France
| | - Anne Chevrel
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris-Sud, Orsay, France
- Unité Mixte de Recherche 8619, Centre National de Recherche Scientifique, Orsay, France
| | - Marc Graille
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris-Sud, Orsay, France
- Unité Mixte de Recherche 8619, Centre National de Recherche Scientifique, Orsay, France
| | - Zaineb Fourati-Kammoun
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris-Sud, Orsay, France
- Unité Mixte de Recherche 8619, Centre National de Recherche Scientifique, Orsay, France
| | - Michel Desmadril
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris-Sud, Orsay, France
- Unité Mixte de Recherche 8619, Centre National de Recherche Scientifique, Orsay, France
| | - Herman van Tilbeurgh
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris-Sud, Orsay, France
- Unité Mixte de Recherche 8619, Centre National de Recherche Scientifique, Orsay, France
| | - Philippe Minard
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris-Sud, Orsay, France
- Unité Mixte de Recherche 8619, Centre National de Recherche Scientifique, Orsay, France
- * E-mail:
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10
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Choi EJ, Jacak R, Kuhlman B. A structural bioinformatics approach for identifying proteins predisposed to bind linear epitopes on pre-selected target proteins. Protein Eng Des Sel 2013; 26:283-9. [PMID: 23341643 DOI: 10.1093/protein/gzs108] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We have developed a protocol for identifying proteins that are predisposed to bind linear epitopes on target proteins of interest. The protocol searches through the protein database for proteins (scaffolds) that are bound to peptides with sequences similar to accessible, linear epitopes on the target protein. The sequence match is considered more significant if residues calculated to be important in the scaffold-peptide interaction are present in the target epitope. The crystal structure of the scaffold-peptide complex is then used as a template for creating a model of the scaffold bound to the target epitope. This model can then be used in conjunction with sequence optimization algorithms or directed evolution methods to search for scaffold mutations that further increase affinity for the target protein. To test the applicability of this approach we targeted three disease-causing proteins: a tuberculosis virulence factor (TVF), the apical membrane antigen (AMA) from malaria, and hemagglutinin from influenza. In each case the best scoring scaffold was tested, and binders with Kds equal to 37 μM and 50 nM for TVF and AMA, respectively, were identified. A web server (http://rosettadesign.med.unc.edu/scaffold/) has been created for performing the scaffold search process with user-defined target sequences.
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Affiliation(s)
- Eun Jung Choi
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
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11
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Koide S, Huang J. Generation of high-performance binding proteins for peptide motifs by affinity clamping. Methods Enzymol 2013; 523:285-302. [PMID: 23422435 DOI: 10.1016/b978-0-12-394292-0.00013-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
We describe concepts and methodologies for generating "Affinity Clamps," a new class of recombinant binding proteins that achieve high affinity and high specificity toward short peptide motifs of biological importance, which is a major challenge in protein engineering. The Affinity Clamping concept exploits the potential of nonhomologous recombination of protein domains in generating large changes in protein function and the inherent binding affinity and specificity of the so-called modular interaction domains toward short peptide motifs. Affinity Clamping creates a clamshell architecture that clamps onto a target peptide. The design processes involve (i) choosing a starting modular interaction domain appropriate for the target and applying structure-guided modifications; (ii) attaching a second domain, termed "enhancer domain"; and (iii) optimizing the peptide-binding site located between the domains by directed evolution. The two connected domains work synergistically to achieve high levels of affinity and specificity that are unattainable with either domain alone. Because of the simple and modular architecture, Affinity Clamps are particularly well suited as building blocks for designing more complex functionalities. Affinity Clamping represents a major advance in protein design that is broadly applicable to the recognition of peptide motifs.
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Affiliation(s)
- Shohei Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, USA.
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12
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Protein Engineering as an Enabling Tool for Synthetic Biology. Synth Biol (Oxf) 2013. [DOI: 10.1016/b978-0-12-394430-6.00002-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] Open
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13
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Zhou X, Wang H, Zhang Y, Gao L, Feng Y. Alteration of substrate specificities of thermophilic α/β hydrolases through domain swapping and domain interface optimization. Acta Biochim Biophys Sin (Shanghai) 2012; 44:965-73. [PMID: 23099882 DOI: 10.1093/abbs/gms086] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Protein domain swapping is an efficient way in protein functional evolution in vivo and also has been proved to be an effective strategy to modify the function of the multi-domain proteins in vitro. To explore the potentials of domain swapping for alteration of the enzyme substrate specificities and the structure-function relationship of the homologous proteins, here we constructed two chimeras from a pair of thermophilic members of the α/β hydrolase superfamily by grafting their functional domains to the conserved α/β hydrolase fold domain: a carboxylesterase from Archaeoglobus fulgidus (AFEST) and an acylpeptide hydrolase from Aeropyrum pernix K1 (apAPH) and explored their activities on hydrolyze p-nitrophenyl esters (pNP) with different acyl chain lengths. We took two approaches to reduce the crossover disruptions when creating the chimeras: chose the residue which involved in the least contacts as the splicing site and optimized the newly formed domain interfaces of the chimeras by site-directed mutations. Characterizations of AAM7 and PAR showed that these chimeras inherited the thermophilic property of both parents. In the aspect of substrate specificity, AAM7 and PAR showed highest activity towards short chain length substrate pNPC4 and middle chain length substrate pNPC8, similar to parent AFEST and apAPH, respectively. These results suggested that the substrate-binding domain is the dominant factor on enzyme substrate specificity, and the optimization of the newly formed domain interface is an important guarantee for successful domain swapping of proteins with low-sequence homology.
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Affiliation(s)
- Xiaoli Zhou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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14
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Peng Q, Kong N, Wang HCE, Li H. Designing redox potential-controlled protein switches based on mutually exclusive proteins. Protein Sci 2012; 21:1222-30. [PMID: 22733630 DOI: 10.1002/pro.2109] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Synthetic/artificial protein switches provide an efficient means of controlling protein functions using chemical signals and stimuli. Mutually exclusive proteins, in which only the host or guest domain can remain folded at a given time owing to conformational strain, have been used to engineer novel protein switches that can switch enzymatic functions on and off in response to ligand binding. To further explore the potential of mutually exclusive proteins as protein switches and sensors, we report here a new redox-based approach to engineer a mutually exclusive folding-based protein switch. By introducing a disulfide bond into the host domain of a mutually exclusive protein, we demonstrate that it is feasible to use redox potential to switch the host domain between its folded and unfolded conformations via the mutually exclusive folding mechanism, and thus switching the functionality of the host domain on and off. Our study opens a new and potentially general avenue that uses mutually exclusive proteins to design novel switches able to control the function of a variety of proteins.
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Affiliation(s)
- Qing Peng
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
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15
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Messih MA, Chitale M, Bajic VB, Kihara D, Gao X. Protein domain recurrence and order can enhance prediction of protein functions. Bioinformatics 2012; 28:i444-i450. [PMID: 22962465 PMCID: PMC3436825 DOI: 10.1093/bioinformatics/bts398] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
MOTIVATION Burgeoning sequencing technologies have generated massive amounts of genomic and proteomic data. Annotating the functions of proteins identified in this data has become a big and crucial problem. Various computational methods have been developed to infer the protein functions based on either the sequences or domains of proteins. The existing methods, however, ignore the recurrence and the order of the protein domains in this function inference. RESULTS We developed two new methods to infer protein functions based on protein domain recurrence and domain order. Our first method, DRDO, calculates the posterior probability of the Gene Ontology terms based on domain recurrence and domain order information, whereas our second method, DRDO-NB, relies on the naïve Bayes methodology using the same domain architecture information. Our large-scale benchmark comparisons show strong improvements in the accuracy of the protein function inference achieved by our new methods, demonstrating that domain recurrence and order can provide important information for inference of protein functions. AVAILABILITY The new models are provided as open source programs at http://sfb.kaust.edu.sa/Pages/Software.aspx. CONTACT dkihara@cs.purdue.edu, xin.gao@kaust.edu.sa SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics Online.
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Affiliation(s)
- Mario Abdel Messih
- Mathematical and Computer Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
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16
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Arpino JAJ, Czapinska H, Piasecka A, Edwards WR, Barker P, Gajda MJ, Bochtler M, Jones DD. Structural basis for efficient chromophore communication and energy transfer in a constructed didomain protein scaffold. J Am Chem Soc 2012; 134:13632-40. [PMID: 22822710 DOI: 10.1021/ja301987h] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The construction of useful functional biomolecular components not currently part of the natural repertoire is central to synthetic biology. A new light-capturing ultra-high-efficiency energy transfer protein scaffold has been constructed by coupling the chromophore centers of two normally unrelated proteins: the autofluorescent protein enhanced green fluorescent protein (EGFP) and the heme-binding electron transfer protein cytochrome b(562) (cyt b(562)). Using a combinatorial domain insertion strategy, a variant was isolated in which resonance energy transfer from the donor EGFP to the acceptor cyt b(562) was close to 100% as evident by virtually full fluorescence quenching on heme binding. The fluorescence signal of the variant was also sensitive to the reactive oxygen species H(2)O(2), with high signal gain observed due to the release of heme. The structure of oxidized holoprotein, determined to 2.75 Å resolution, revealed that the two domains were arranged side-by-side in a V-shape conformation, generating an interchromophore distance of ~17 Å (14 Å edge-to-edge). Critical to domain arrangement is the formation of a molecular pivot point between the two domains as a result of different linker sequence lengths at each domain junction and formation of a predominantly polar interdomain interaction surface. The retrospective structural analysis has provided an explanation for the basis of the observed highly efficient energy transfer through chromophore arrangement in the directly evolved protein scaffold and provides an insight into the molecular principles by which to design new proteins with coupled functions.
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Affiliation(s)
- James A J Arpino
- School of Biosciences, Main Building, Park Place, Cardiff University, Cardiff CF10 3AT, United Kingdom
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17
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Abstract
Protein conformational switches alter their shape upon receiving an input signal, such as ligand binding, chemical modification, or change in environment. The apparent simplicity of this transformation--which can be carried out by a molecule as small as a thousand atoms or so--belies its critical importance to the life of the cell as well as its capacity for engineering by humans. In the realm of molecular switches, proteins are unique because they are capable of performing a variety of biological functions. Switchable proteins are therefore of high interest to the fields of biology, biotechnology, and medicine. These molecules are beginning to be exploited as the core machinery behind a new generation of biosensors, functionally regulated enzymes, and "smart" biomaterials that react to their surroundings. As inspirations for these designs, researchers continue to analyze existing examples of allosteric proteins. Recent years have also witnessed the development of new methodologies for introducing conformational change into proteins that previously had none. Herein we review examples of both natural and engineered protein switches in the context of four basic modes of conformational change: rigid-body domain movement, limited structural rearrangement, global fold switching, and folding-unfolding. Our purpose is to highlight examples that can potentially serve as platforms for the design of custom switches. Accordingly, we focus on inducible conformational changes that are substantial enough to produce a functional response (e.g., in a second protein to which it is fused), yet are relatively simple, structurally well-characterized, and amenable to protein engineering efforts.
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Affiliation(s)
| | - Stewart N. Loh
- Department of Biochemistry & Molecular Biology, State University of New York Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210 (USA), Tel: (315)464-8731, Fax: (315)464-8750
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18
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Structure of an engineered β-lactamase maltose binding protein fusion protein: insights into heterotropic allosteric regulation. PLoS One 2012; 7:e39168. [PMID: 22720063 PMCID: PMC3375305 DOI: 10.1371/journal.pone.0039168] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 05/16/2012] [Indexed: 11/21/2022] Open
Abstract
Engineering novel allostery into existing proteins is a challenging endeavor to obtain novel sensors, therapeutic proteins, or modulate metabolic and cellular processes. The RG13 protein achieves such allostery by inserting a circularly permuted TEM-1 β-lactamase gene into the maltose binding protein (MBP). RG13 is positively regulated by maltose yet is, serendipitously, inhibited by Zn2+ at low µM concentration. To probe the structure and allostery of RG13, we crystallized RG13 in the presence of mM Zn2+ concentration and determined its structure. The structure reveals that the MBP and TEM-1 domains are in close proximity connected via two linkers and a zinc ion bridging both domains. By bridging both TEM-1 and MBP, Zn2+ acts to “twist tie” the linkers thereby partially dislodging a linker between the two domains from its original catalytically productive position in TEM-1. This linker 1 contains residues normally part of the TEM-1 active site including the critical β3 and β4 strands important for activity. Mutagenesis of residues comprising the crystallographically observed Zn2+ site only slightly affected Zn2+ inhibition 2- to 4-fold. Combined with previous mutagenesis results we therefore hypothesize the presence of two or more inter-domain mutually exclusive inhibitory Zn2+ sites. Mutagenesis and molecular modeling of an intact TEM-1 domain near MBP within the RG13 framework indicated a close surface proximity of the two domains with maltose switching being critically dependent on MBP linker anchoring residues and linker length. Structural analysis indicated that the linker attachment sites on MBP are at a site that, upon maltose binding, harbors both the largest local Cα distance changes and displays surface curvature changes, from concave to relatively flat becoming thus less sterically intrusive. Maltose activation and zinc inhibition of RG13 are hypothesized to have opposite effects on productive relaxation of the TEM-1 β3 linker region via steric and/or linker juxtapositioning mechanisms.
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Moore AD, Bornberg-Bauer E. The dynamics and evolutionary potential of domain loss and emergence. Mol Biol Evol 2011; 29:787-96. [PMID: 22016574 PMCID: PMC3258042 DOI: 10.1093/molbev/msr250] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The wealth of available genomic data presents an unrivaled opportunity to study the molecular basis of evolution. Studies on gene family expansions and site-dependent analyses have already helped establish important insights into how proteins facilitate adaptation. However, efforts to conduct full-scale cross-genomic comparisons between species are challenged by both growing amounts of data and the inherent difficulty in accurately inferring homology between deeply rooted species. Proteins, in comparison, evolve by means of domain rearrangements, a process more amenable to study given the strength of profile-based homology inference and the lower rates with which rearrangements occur. However, adapting to a constantly changing environment can require molecular modulations beyond reach of rearrangement alone. Here, we explore rates and functional implications of novel domain emergence in contrast to domain gain and loss in 20 arthropod species of the pancrustacean clade. Emerging domains are more likely disordered in structure and spread more rapidly within their genomes than established domains. Furthermore, although domain turnover occurs at lower rates than gene family turnover, we find strong evidence that the emergence of novel domains is foremost associated with environmental adaptation such as abiotic stress response. The results presented here illustrate the simplicity with which domain-based analyses can unravel key players of nature's adaptational machinery, complementing the classical site-based analyses of adaptation.
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Affiliation(s)
- Andrew D Moore
- Evolutionary Bioinformatics Group, Institute for Evolution and Biodiversity, University of Muenster, Germany
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20
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Bonsor DA, Postel S, Pierce BG, Wang N, Zhu P, Buonpane RA, Weng Z, Kranz DM, Sundberg EJ. Molecular basis of a million-fold affinity maturation process in a protein-protein interaction. J Mol Biol 2011; 411:321-8. [PMID: 21689661 DOI: 10.1016/j.jmb.2011.06.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 06/02/2011] [Accepted: 06/04/2011] [Indexed: 11/30/2022]
Abstract
Protein engineering is becoming increasingly important for pharmaceutical applications where controlling the specificity and affinity of engineered proteins is required to create targeted protein therapeutics. Affinity increases of several thousand-fold are now routine for a variety of protein engineering approaches, and the structural and energetic bases of affinity maturation have been investigated in a number of such cases. Previously, a 3-million-fold affinity maturation process was achieved in a protein-protein interaction composed of a variant T-cell receptor fragment and a bacterial superantigen. Here, we present the molecular basis of this affinity increase. Using X-ray crystallography, shotgun reversion/replacement scanning mutagenesis, and computational analysis, we describe, in molecular detail, a process by which extrainterfacial regions of a protein complex can be rationally manipulated to significantly improve protein engineering outcomes.
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Affiliation(s)
- Daniel A Bonsor
- Boston Biomedical Research Institute, 64 Grove Street, Watertown, MA 02472, USA
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21
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Camsund D, Lindblad P, Jaramillo A. Genetically engineered light sensors for control of bacterial gene expression. Biotechnol J 2011; 6:826-36. [PMID: 21648094 DOI: 10.1002/biot.201100091] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2011] [Revised: 04/11/2011] [Accepted: 04/18/2011] [Indexed: 12/28/2022]
Abstract
Light of different wavelengths can serve as a transient, noninvasive means of regulating gene expression for biotechnological purposes. Implementation of advanced gene regulatory circuits will require orthogonal transcriptional systems that can be simultaneously controlled and that can produce several different control states. Fully genetically encoded light sensors take advantage of the favorable characteristics of light, do not need the supplementation of any chemical inducers or co-factors, and have been demonstrated to control gene expression in Escherichia coli. Herein, we review engineered light-sensor systems with potential for in vivo regulation of gene expression in bacteria, and highlight different means of extending the range of available light input and transcriptional output signals. Furthermore, we discuss advances in multiplexing different light sensors for achieving multichromatic control of gene expression and indicate developments that could facilitate the construction of efficient systems for light-regulated, multistate control of gene expression.
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Affiliation(s)
- Daniel Camsund
- Department of Photochemistry and Molecular Science, Uppsala University, Ångström Laboratories, Uppsala, Sweden
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22
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Mills BM, Chong LT. Molecular simulations of mutually exclusive folding in a two-domain protein switch. Biophys J 2011; 100:756-764. [PMID: 21281591 DOI: 10.1016/j.bpj.2010.12.3710] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 12/13/2010] [Accepted: 12/17/2010] [Indexed: 01/11/2023] Open
Abstract
A major challenge with testing designs of protein conformational switches is the need for experimental probes that can independently monitor their individual protein domains. One way to circumvent this issue is to use a molecular simulation approach in which each domain can be directly observed. Here we report what we believe to be the first molecular simulations of mutually exclusive folding in an engineered two-domain protein switch, providing a direct view of how folding of one protein drives unfolding of the other in a barnase-ubiquitin fusion protein. These simulations successfully capture the experimental effects of interdomain linker length and ligand binding on the extent of unfolding in the less stable domain. In addition, the effect of linker length on the potential for oligomerization, which eliminates switch activity, is in qualitative agreement with analytical ultracentrifugation experiments. We also perform what we believe to be the first study of protein unfolding via progressive localized compression. Finally, we are able to explore the kinetics of mutually exclusive folding by determining the effect of linker length on rates of unfolding and refolding of each protein domain. Our results demonstrate that molecular simulations can provide seemingly novel biological insights on the behavior of individual protein domains, thereby aiding in the rational design of bifunctional switches.
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Affiliation(s)
- Brandon M Mills
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Lillian T Chong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania.
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23
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Stratton MM, Loh SN. Converting a protein into a switch for biosensing and functional regulation. Protein Sci 2011; 20:19-29. [PMID: 21064163 DOI: 10.1002/pro.541] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Proteins that switch conformations in response to a signaling event (e.g., ligand binding or chemical modification) present a unique solution to the design of reagent-free biosensors as well as molecules whose biological functions are regulated in useful ways. The principal roadblock in the path to develop such molecules is that the majority of natural proteins do not change conformation upon binding their cognate ligands or becoming chemically modified. Herein, we review recent protein engineering efforts to introduce switching properties into binding proteins. By co-opting natural allosteric coupling, joining proteins in creative ways and formulating altogether new switching mechanisms, researchers are learning how to coax conformational changes from proteins that previously had none. These studies are providing some answers to the challenging question: how can one convert a lock-and-key binding protein into a molecular switch?
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Affiliation(s)
- Margaret M Stratton
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 750 East Adams Street, Syracuse, New York 13210, USA
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Kojima M, Iwai H, Dong J, Lim SL, Ito S, Okumura K, Ihara M, Ueda H. Activation of Circularly Permutated β-Lactamase Tethered to Antibody Domains by Specific Small Molecules. Bioconjug Chem 2011; 22:633-41. [DOI: 10.1021/bc1004125] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | - Shigekazu Ito
- Horiba Ltd., 2 Miyanohigashi, Kisshoin, Minami-ku Kyoto 601-8510, Japan
| | - Koichi Okumura
- Horiba Ltd., 2 Miyanohigashi, Kisshoin, Minami-ku Kyoto 601-8510, Japan
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Golynskiy MV, Koay MS, Vinkenborg JL, Merkx M. Engineering Protein Switches: Sensors, Regulators, and Spare Parts for Biology and Biotechnology. Chembiochem 2011; 12:353-61. [DOI: 10.1002/cbic.201000642] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Indexed: 12/31/2022]
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26
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Yadid I, Tawfik DS. Functional β-propeller lectins by tandem duplications of repetitive units. Protein Eng Des Sel 2010; 24:185-95. [DOI: 10.1093/protein/gzq053] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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27
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Edwards WR, Williams AJ, Morris JL, Baldwin AJ, Allemann RK, Jones DD. Regulation of β-Lactamase Activity by Remote Binding of Heme: Functional Coupling of Unrelated Proteins through Domain Insertion. Biochemistry 2010; 49:6541-9. [DOI: 10.1021/bi100793y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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28
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Dübel S, Stoevesandt O, Taussig MJ, Hust M. Generating recombinant antibodies to the complete human proteome. Trends Biotechnol 2010; 28:333-9. [PMID: 20538360 DOI: 10.1016/j.tibtech.2010.05.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Revised: 04/29/2010] [Accepted: 05/03/2010] [Indexed: 10/19/2022]
Abstract
In vitro antibody generation technologies have now been available for two decades. Research reagents prepared via phage display are becoming available and several recent studies have demonstrated that these technologies are now sufficiently advanced to facilitate generation of a comprehensive renewable resource of antibodies for any protein encoded by the approximately 22,500 human protein-coding genes. Antibody selection in vitro offers properties not available in animal-based antibody generation methods. By adjusting the biochemical milieu during selection, it is possible to control the antigen conformation recognized, the antibody affinity or unwanted cross-reactivity. For larger-scale antibody generation projects, the handling, transport and storage logistics and bacterial production offer cost benefits. Because the DNA sequence encoding the antibody is available, modifications, such as site-specific in vivo biotinylation and multimerization, are only a cloning step away. This opinion article summarizes opportunities for the generation of antibodies for proteome research using in vitro technologies.
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Affiliation(s)
- Stefan Dübel
- Technische Universität Braunschweig, Institute of Biochemistry and Biotechnology, D-38106 Braunschweig, Germany.
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