1
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Das D, Ainavarapu SRK. Protein engineering using circular permutation - structure, function, stability, and applications. FEBS J 2024. [PMID: 38676939 DOI: 10.1111/febs.17146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 03/13/2024] [Accepted: 04/12/2024] [Indexed: 04/29/2024]
Abstract
Protein engineering is important for creating novel variants from natural proteins, enabling a wide range of applications. Approaches such as rational design and directed evolution are routinely used to make new protein variants. Computational tools like de novo design can introduce new protein folds. Expanding the amino acid repertoire to include unnatural amino acids with non-canonical side chains in vitro by native chemical ligation and in vivo via codon expansion methods broadens sequence and structural possibilities. Circular permutation (CP) is an invaluable approach to redesigning a protein by rearranging the amino acid sequence, where the connectivity of the secondary structural elements is altered without changing the overall structure of the protein. Artificial CP proteins (CPs) are employed in various applications such as biocatalysis, sensing of small molecules by fluorescence, genome editing, ligand-binding protein switches, and optogenetic engineering. Many studies have shown that CP can lead to either reduced or enhanced stability or catalytic efficiency. The effects of CP on a protein's energy landscape cannot be predicted a priori. Thus, it is important to understand how CP can affect the thermodynamic and kinetic stability of a protein. In this review, we discuss the discovery and advancement of techniques to create protein CP, and existing reviews on CP. We delve into the plethora of biological applications for designed CP proteins. We subsequently discuss the experimental and computational reports on the effects of CP on the thermodynamic and kinetic stabilities of proteins of various topologies. An understanding of the various aspects of CP will allow the reader to design robust CP proteins for their specific purposes.
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Affiliation(s)
- Debanjana Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
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2
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Coleman T, Shin J, Silberg JJ, Shamoo Y, Atkinson JT. The Biochemical Impact of Extracting an Embedded Adenylate Kinase Domain Using Circular Permutation. Biochemistry 2024; 63:599-609. [PMID: 38357768 DOI: 10.1021/acs.biochem.3c00605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Adenylate kinases (AKs) have evolved AMP-binding and lid domains that are encoded as continuous polypeptides embedded at different locations within the discontinuous polypeptide encoding the core domain. A prior study showed that AK homologues of different stabilities consistently retain cellular activity following circular permutation that splits a region with high energetic frustration within the AMP-binding domain into discontinuous fragments. Herein, we show that mesophilic and thermophilic AKs having this topological restructuring retain activity and substrate-binding characteristics of the parental AK. While permutation decreased the activity of both AK homologues at physiological temperatures, the catalytic activity of the thermophilic AK increased upon permutation when assayed >30 °C below the melting temperature of the native AK. The thermostabilities of the permuted AKs were uniformly lower than those of native AKs, and they exhibited multiphasic unfolding transitions, unlike the native AKs, which presented cooperative thermal unfolding. In addition, proteolytic digestion revealed that permutation destabilized each AK in differing manners, and mass spectrometry suggested that the new termini within the AMP-binding domain were responsible for the increased proteolysis sensitivity. These findings illustrate how changes in contact order can be used to tune enzyme activity and alter folding dynamics in multidomain enzymes.
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Affiliation(s)
- Tom Coleman
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
| | - John Shin
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
| | - Jonathan J Silberg
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
- Department of Chemical and Biomolecular Engineering, Rice University, MS-362, 6100 Main Street, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, MS-142, 6100 Main Street, Houston, Texas 77005, United States
| | - Yousif Shamoo
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
| | - Joshua T Atkinson
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90007, United States
- Department of Civil and Environmental Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton, New Jersey 08544, United States
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3
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Leonard AC, Weinstein JJ, Steiner PJ, Erbse AH, Fleishman SJ, Whitehead TA. Stabilization of the SARS-CoV-2 receptor binding domain by protein core redesign and deep mutational scanning. Protein Eng Des Sel 2022; 35:6553331. [PMID: 35325236 PMCID: PMC9077414 DOI: 10.1093/protein/gzac002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/21/2022] [Accepted: 02/16/2022] [Indexed: 11/12/2022] Open
Abstract
Stabilizing antigenic proteins as vaccine immunogens or diagnostic reagents is a stringent case of protein engineering and design as the exterior surface must maintain recognition by receptor(s) and antigen-specific antibodies at multiple distinct epitopes. This is a challenge, as stability enhancing mutations must be focused on the protein core, whereas successful computational stabilization algorithms typically select mutations at solvent-facing positions. In this study, we report the stabilization of SARS-CoV-2 Wuhan Hu-1 Spike receptor binding domain using a combination of deep mutational scanning and computational design, including the FuncLib algorithm. Our most successful design encodes I358F, Y365W, T430I, and I513L receptor binding domain mutations, maintains recognition by the receptor ACE2 and a panel of different anti-receptor binding domain monoclonal antibodies, is between 1 and 2°C more thermally stable than the original receptor binding domain using a thermal shift assay, and is less proteolytically sensitive to chymotrypsin and thermolysin than the original receptor binding domain. Our approach could be applied to the computational stabilization of a wide range of proteins without requiring detailed knowledge of active sites or binding epitopes. We envision that this strategy may be particularly powerful for cases when there are multiple or unknown binding sites.
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Affiliation(s)
- Alison C Leonard
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80303, USA
| | - Jonathan J Weinstein
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Paul J Steiner
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80303, USA
| | - Annette H Erbse
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
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4
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Yurkova MS, Zenin VA, Nagibina GS, Melnik BS, Fedorov AN. Physico-Chemical Characterization of Permutated Variants of Chaperone GroEL Apical Domain. APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683819130027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Yurkova MS, Sharapova OA, Zenin VA, Fedorov AN. Versatile format of minichaperone-based protein fusion system. Sci Rep 2019; 9:15063. [PMID: 31636289 PMCID: PMC6803692 DOI: 10.1038/s41598-019-51015-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/17/2019] [Indexed: 11/23/2022] Open
Abstract
Hydrophobic recombinant proteins often tend to aggregate upon expression into inclusion bodies and are difficult to refold. Producing them in soluble forms constitutes a common bottleneck problem. A fusion system for production of insoluble hydrophobic proteins in soluble stable forms with thermophilic minichaperone, GroEL apical domain (GrAD) as a carrier, has recently been developed. To provide the utmost flexibility of the system for interactions between the carrier and various target protein moieties a strategy of making permutated protein variants by gene engineering has been applied: the original N- and C-termini of the minichaperone were linked together by a polypeptide linker and new N- and C-termini were made at desired parts of the protein surface. Two permutated GrAD forms were created and analyzed. Constructs of GrAD and both of its permutated forms fused with the initially insoluble N-terminal fragment of hepatitis C virus' E2 protein were tested. Expressed fusions formed inclusion bodies. After denaturation, all fusions were completely renatured in stable soluble forms. A variety of permutated GrAD variants can be created. The versatile format of the system provides opportunities for choosing an optimal pair between particular target protein moiety and the best-suited original or specific permutated carrier.
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Affiliation(s)
- Maria S Yurkova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russian Federation
- Tropogen Inc, Moscow, Russia
| | - Olga A Sharapova
- Alder BioPharmaceuticals, Inc., 11804 N Creek Pkwy S, Bothell, WA, 98011, USA
| | - Vladimir A Zenin
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russian Federation
| | - Alexey N Fedorov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russian Federation.
- Tropogen Inc, Moscow, Russia.
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6
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Oakes BL, Fellmann C, Rishi H, Taylor KL, Ren SM, Nadler DC, Yokoo R, Arkin AP, Doudna JA, Savage DF. CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification. Cell 2019; 176:254-267.e16. [PMID: 30633905 PMCID: PMC6414052 DOI: 10.1016/j.cell.2018.11.052] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/21/2018] [Accepted: 11/28/2018] [Indexed: 12/20/2022]
Abstract
The ability to engineer natural proteins is pivotal to a future, pragmatic biology. CRISPR proteins have revolutionized genome modification, yet the CRISPR-Cas9 scaffold is not ideal for fusions or activation by cellular triggers. Here, we show that a topological rearrangement of Cas9 using circular permutation provides an advanced platform for RNA-guided genome modification and protection. Through systematic interrogation, we find that protein termini can be positioned adjacent to bound DNA, offering a straightforward mechanism for strategically fusing functional domains. Additionally, circular permutation enabled protease-sensing Cas9s (ProCas9s), a unique class of single-molecule effectors possessing programmable inputs and outputs. ProCas9s can sense a wide range of proteases, and we demonstrate that ProCas9 can orchestrate a cellular response to pathogen-associated protease activity. Together, these results provide a toolkit of safer and more efficient genome-modifying enzymes and molecular recorders for the advancement of precision genome engineering in research, agriculture, and biomedicine.
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Affiliation(s)
- Benjamin L Oakes
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christof Fellmann
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Gladstone Institutes, San Francisco, CA 94158, USA
| | - Harneet Rishi
- Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kian L Taylor
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Shawn M Ren
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Dana C Nadler
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rayka Yokoo
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Adam P Arkin
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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7
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Herrera-Morande A, Castro-Fernández V, Merino F, Ramírez-Sarmiento CA, Fernández FJ, Vega MC, Guixé V. Protein topology determines substrate-binding mechanism in homologous enzymes. Biochim Biophys Acta Gen Subj 2018; 1862:2869-2878. [PMID: 30251675 DOI: 10.1016/j.bbagen.2018.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/21/2018] [Accepted: 09/11/2018] [Indexed: 10/28/2022]
Abstract
During evolution, some homologs proteins appear with different connectivity between secondary structures (different topology) but conserving the tridimensional arrangement of them (same architecture). These events can produce two types of arrangements; circular permutation or non-cyclic permutations. The first one results in the N and C terminus transferring to a different position on a protein sequence while the second refers to a more complex arrangement of the structural elements. In ribokinase superfamily, two different topologies can be identified, which are related to each other as a non-cyclic permutation occurred during the evolution. Interestingly, this change in topology is correlated with the nucleotide specificity of its members. Thereby, the connectivity of the secondary elements allows us to distinguish an ATP-dependent and an ADP-dependent topology. Here we address the impact of introducing the topology of a homologous ATP-dependent kinase in an ADP-dependent kinase (Thermococcus litoralis glucokinase) in the structure, nucleotide specificity, and substrate binding order of the engineered enzyme. Structural evidence demonstrates that rewiring the topology of TlGK leads to an active and soluble enzyme without modifications on its three-dimensional architecture. The permuted enzyme (PerGK) retains the nucleotide preference of the parent TlGK enzyme but shows a change in the substrate binding order. Our results illustrate how the rearrangement of the protein folding topology during the evolution of the ribokinase superfamily enzymes may have dictated the substrate-binding order in homologous enzymes of this superfamily.
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Affiliation(s)
| | | | - Felipe Merino
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | | | - Francisco J Fernández
- Centro de Investigaciones Biológicas (CIB-CSIC), Structural and Chemical Biology Dep., Madrid, Spain
| | - M Cristina Vega
- Centro de Investigaciones Biológicas (CIB-CSIC), Structural and Chemical Biology Dep., Madrid, Spain.
| | - Victoria Guixé
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
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8
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Rathore U, Purwar M, Vignesh VS, Das R, Kumar AA, Bhattacharyya S, Arendt H, DeStefano J, Wilson A, Parks C, La Branche CC, Montefiori DC, Varadarajan R. Bacterially expressed HIV-1 gp120 outer-domain fragment immunogens with improved stability and affinity for CD4-binding site neutralizing antibodies. J Biol Chem 2018; 293:15002-15020. [PMID: 30093409 DOI: 10.1074/jbc.ra118.005006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/20/2022] Open
Abstract
Protein minimization is an attractive approach for designing vaccines against rapidly evolving pathogens such as human immunodeficiency virus, type 1 (HIV-1), because it can help in focusing the immune response toward conserved conformational epitopes present on complex targets. The outer domain (OD) of HIV-1 gp120 contains epitopes for a large number of neutralizing antibodies and therefore is a primary target for structure-based vaccine design. We have previously designed a bacterially expressed outer-domain immunogen (ODEC) that bound CD4-binding site (CD4bs) ligands with 3-12 μm affinity and elicited a modest neutralizing antibody response in rabbits. In this study, we have optimized ODEC using consensus sequence design, cyclic permutation, and structure-guided mutations to generate a number of variants with improved yields, biophysical properties, stabilities, and affinities (KD of 10-50 nm) for various CD4bs targeting broadly neutralizing antibodies, including the germline-reverted version of the broadly neutralizing antibody VRC01. In contrast to ODEC, the optimized immunogens elicited high anti-gp120 titers in rabbits as early as 6 weeks post-immunization, before any gp120 boost was given. Following two gp120 boosts, sera collected at week 22 showed cross-clade neutralization of tier 1 HIV-1 viruses. Using a number of different prime/boost combinations, we have identified a cyclically permuted OD fragment as the best priming immunogen, and a trimeric, cyclically permuted gp120 as the most suitable boosting molecule among the tested immunogens. This study also provides insights into some of the biophysical correlates of improved immunogenicity.
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Affiliation(s)
- Ujjwal Rathore
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | - Mansi Purwar
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | | | - Raksha Das
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | - Aditya Arun Kumar
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | - Sanchari Bhattacharyya
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | - Heather Arendt
- the International AIDS Vaccine Initiative, Brooklyn, New York 11226, and
| | - Joanne DeStefano
- the International AIDS Vaccine Initiative, Brooklyn, New York 11226, and
| | - Aaron Wilson
- the International AIDS Vaccine Initiative, Brooklyn, New York 11226, and
| | - Christopher Parks
- the International AIDS Vaccine Initiative, Brooklyn, New York 11226, and
| | - Celia C La Branche
- the Department of Surgery, Duke University Medical Center, Durham, North Carolina 27707
| | - David C Montefiori
- the Department of Surgery, Duke University Medical Center, Durham, North Carolina 27707
| | - Raghavan Varadarajan
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012,
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9
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Gaytán P, Roldán-Salgado A, Yáñez JA, Morales-Arrieta S, Juárez-González VR. CiPerGenesis, A Mutagenesis Approach that Produces Small Libraries of Circularly Permuted Proteins Randomly Opened at a Focused Region: Testing on the Green Fluorescent Protein. ACS COMBINATORIAL SCIENCE 2018; 20:400-413. [PMID: 29812897 DOI: 10.1021/acscombsci.7b00152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Circularly permuted proteins (cpPs) represent a novel type of mutant proteins with original termini that are covalently linked through a peptide connector and opened at any other place of the polypeptide backbone to create new ends. cpPs are finding wide applications in biotechnology because their properties may be quite different from those of the parental protein. However, the actual challenge for the creation of successful cpPs is to identify those peptide bonds that can be broken to create new termini and ensure functional and well-folded cpPs. Herein, we describe CiPerGenesis, a combinatorial mutagenesis approach that uses two oligonucleotide libraries to amplify a circularized gene by PCR, starting and ending from a focused target region. This approach creates small libraries of circularly permuted genes that are easily cloned in the correct direction and frame using two different restriction sites encoded in the oligonucleotides. Once expressed, the protein libraries exhibit a unique sequence diversity, comprising cpPs that exhibit ordinary breakpoints between adjacent amino acids localized at the target region as well as cpPs with new termini containing user-defined truncations and repeats of some amino acids. CiPerGenesis was tested at the lid region G134-H148 of green fluorescent protein (GFP), revealing that the most fluorescent variants were those starting at Leu141 and ending at amino acids Tyr145, Tyr143, Glu142, Leu141, Lys140, and H139. Purification and biochemical characterization of some variants suggested a differential expression, solubility and maturation extent of the mutant proteins as the likely cause for the variability in fluorescence intensity observed in colonies.
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Affiliation(s)
- Paul Gaytán
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Abigail Roldán-Salgado
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Jorge A. Yáñez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Sandra Morales-Arrieta
- Departamento de Ingeniería en Biotecnología, Universidad Politécnica del Estado de Morelos, Boulevard Cuauhnáhuac No. 566, Col. Lomas del Texcal, Jiutepec, Morelos 62550, México
| | - Víctor R. Juárez-González
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, México
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10
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Yachnin BJ, Khare SD. Engineering carboxypeptidase G2 circular permutations for the design of an autoinhibited enzyme. Protein Eng Des Sel 2017; 30:321-331. [PMID: 28160000 PMCID: PMC6283397 DOI: 10.1093/protein/gzx005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 01/11/2017] [Accepted: 01/18/2017] [Indexed: 11/14/2022] Open
Abstract
Carboxypeptidase G2 (CPG2) is an Food and Drug Administration (FDA)-approved enzyme drug used to treat methotrexate (MTX) toxicity in cancer patients receiving MTX treatment. It has also been used in directed enzyme-prodrug chemotherapy, but this strategy has been hampered by off-site activation of the prodrug by the circulating enzyme. The development of a tumor protease activatable CPG2, which could be achieved using a circular permutation of CPG2 fused to an inactivating 'prodomain', would aid in these applications. We report the development of a protease accessibility-based screen to identify candidate sites for circular permutation in proximity of the CPG2 active site. The resulting six circular permutants showed similar expression, structure, thermal stability, and, in four cases, activity levels compared to the wild-type enzyme. We rationalize these results based on structural models of the permutants obtained using the Rosetta software. We developed a cell growth-based selection system, and demonstrated that when fused to periplasm-directing signal peptides, one of our circular permutants confers MTX resistance in Escherichia coli with equal efficiency as the wild-type enzyme. As the permutants have similar properties to wild-type CPG2, these enzymes are promising starting points for the development of autoinhibited, protease-activatable zymogen forms of CPG2 for use in therapeutic contexts.
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Affiliation(s)
- Brahm J. Yachnin
- Department of Chemistry & Chemical Biology and the Center for Integrative Proteomics, Rutgers University, Piscataway, NJ 08854, USA
| | - Sagar D. Khare
- Department of Chemistry & Chemical Biology and the Center for Integrative Proteomics, Rutgers University, Piscataway, NJ 08854, USA
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11
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Structure prediction and functional analysis of a non-permutated lectin from Dioclea grandiflora. Biochimie 2016; 131:54-67. [DOI: 10.1016/j.biochi.2016.09.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 09/19/2016] [Indexed: 01/22/2023]
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12
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Shah V, Kim JR. Transposon for protein engineering. Mob Genet Elements 2016; 6:e1239601. [PMID: 28090378 DOI: 10.1080/2159256x.2016.1239601] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 09/14/2016] [Indexed: 12/21/2022] Open
Abstract
Protein insertional fusion and circular permutation are 2 promising protein engineering techniques for creating integrated functionalities and sequence diversity of a protein, respectively. Finding insertion locations for protein insertional fusion and new termini for circular permutation through a rational approach is not always straightforward, especially, for proteins without detailed structural knowledge. On the contrary, a combinatorial approach facilitates a comprehensive search to evaluate all potential insertion sites and new termini locations. Conventional methods used to create random insertional fusion libraries generate sub-optimal inter-domain linker length and composition between fused proteins. There are also methods available for construction of random circular permutation libraries. However, these methods too, impose many drawbacks, such as significant sequence modification at the new termini of circular permutants and additionally, require re-design of transposons for tailored expression of circular permutants. Furthermore, these conventional methods employ relatively inefficient blunt-end ligation during library construction. In this commentary, we present a concise overview and key findings of engineered Mu transposons, which have recently been developed in our group as a facile and efficient tool to alleviate limitations realized from conventional methods and to construct high quality libraries for random insertional fusion and random circular permutation.
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Affiliation(s)
- Vandan Shah
- Othmer-Jacobs Department of Chemical and Biomolecular Engineering, New York University , Brooklyn, NY, USA
| | - Jin Ryoun Kim
- Othmer-Jacobs Department of Chemical and Biomolecular Engineering, New York University , Brooklyn, NY, USA
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13
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Pandey N, Kuypers BE, Nassif B, Thomas EE, Alnahhas RN, Segatori L, Silberg JJ. Tolerance of a Knotted Near-Infrared Fluorescent Protein to Random Circular Permutation. Biochemistry 2016; 55:3763-73. [PMID: 27304983 DOI: 10.1021/acs.biochem.6b00258] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacteriophytochrome photoreceptors (BphP) are knotted proteins that have been developed as near-infrared fluorescent protein (iRFP) reporters of gene expression. To explore how rearrangements in the peptides that interlace into the knot within the BphP photosensory core affect folding, we subjected iRFPs to random circular permutation using an improved transposase mutagenesis strategy and screened for variants that fluoresce. We identified 27 circularly permuted iRFPs that display biliverdin-dependent fluorescence in Escherichia coli. The variants with the brightest whole cell fluorescence initiated translation at residues near the domain linker and knot tails, although fluorescent variants that initiated translation within the PAS and GAF domains were discovered. Circularly permuted iRFPs retained sufficient cofactor affinity to fluoresce in tissue culture without the addition of biliverdin, and one variant displayed enhanced fluorescence when expressed in bacteria and tissue culture. This variant displayed a quantum yield similar to that of iRFPs but exhibited increased resistance to chemical denaturation, suggesting that the observed increase in the magnitude of the signal arose from more efficient protein maturation. These results show how the contact order of a knotted BphP can be altered without disrupting chromophore binding and fluorescence, an important step toward the creation of near-infrared biosensors with expanded chemical sensing functions for in vivo imaging.
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Affiliation(s)
- Naresh Pandey
- Department of Biosciences, Rice University , Houston, Texas 77005, United States.,Biochemistry and Cell Biology Graduate Program, Rice University , Houston, Texas 77005, United States
| | - Brianna E Kuypers
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University , Houston, Texas 77005, United States.,Department of Chemical and Biomolecular Engineering, Rice University , Houston, Texas 77005, United States
| | - Barbara Nassif
- Department of Biosciences, Rice University , Houston, Texas 77005, United States
| | - Emily E Thomas
- Department of Biosciences, Rice University , Houston, Texas 77005, United States.,Biochemistry and Cell Biology Graduate Program, Rice University , Houston, Texas 77005, United States
| | - Razan N Alnahhas
- Department of Biosciences, Rice University , Houston, Texas 77005, United States.,Biochemistry and Cell Biology Graduate Program, Rice University , Houston, Texas 77005, United States
| | - Laura Segatori
- Department of Biosciences, Rice University , Houston, Texas 77005, United States.,Department of Chemical and Biomolecular Engineering, Rice University , Houston, Texas 77005, United States.,Department of Bioengineering, Rice University , Houston, Texas 77005, United States
| | - Jonathan J Silberg
- Department of Biosciences, Rice University , Houston, Texas 77005, United States.,Department of Bioengineering, Rice University , Houston, Texas 77005, United States
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14
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Protein rethreading: A novel approach to protein design. Sci Rep 2016; 6:26847. [PMID: 27229326 PMCID: PMC4882587 DOI: 10.1038/srep26847] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 05/04/2016] [Indexed: 12/29/2022] Open
Abstract
Protein engineering is an important tool for the design of proteins with novel and desirable features. Templates from the protein databank (PDB) are often used as initial models that can be modified to introduce new properties. We examine whether it is possible to reconnect a protein in a manner that generates a new topology yet preserves its structural integrity. Here, we describe the rethreading of dihydrofolate reductase (DHFR) from E. coli (wtDHFR). The rethreading process involved the removal of three native loops, and the introduction of three new loops with alternate connections. The structure of the rethreaded DHFR (rDHFR-1) was determined to 1.6 Å, demonstrating the success of the rethreading process. Both wtDHFR and rDHFR-1 exhibited similar affinities towards methotrexate. However, rDHFR-1 showed no reducing activity towards dihydrofolate, and exhibited about ~6-fold lower affinity towards NADPH than wtDHFR. This work demonstrates that protein rethreading can be a powerful tool for the design of a large array of proteins with novel structures and topologies, and that by careful rearrangement of a protein sequence, the sequence to structure relationship can be expanded substantially.
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15
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Pierre B, Shah V, Xiao J, Kim JR. Construction of a random circular permutation library using an engineered transposon. Anal Biochem 2015; 474:16-24. [DOI: 10.1016/j.ab.2014.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 12/12/2014] [Accepted: 12/16/2014] [Indexed: 02/01/2023]
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16
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Daugherty AB, Horton JR, Cheng X, Lutz S. STRUCTURAL AND FUNCTIONAL CONSEQUENCES OF CIRCULAR PERMUTATION ON THE ACTIVE SITE OF OLD YELLOW ENZYME. ACS Catal 2015; 5:892-899. [PMID: 25692074 PMCID: PMC4327928 DOI: 10.1021/cs501702k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Circular
permutation of the NADPH-dependent oxidoreductase
Old Yellow Enzyme from Saccharomyces pastorianus (OYE1) can significantly enhance the enzyme’s catalytic performance.
Termini relocation into four regions of the protein (sectors I–IV)
near the active site has proven effective in altering enzyme function.
To better understand the structural consequences and rationalize the
observed functional gains in these OYE1 variants, we selected representatives
from sectors I–III for further characterization by biophysical
methods and X-ray crystallography. These investigations not only show
trends in enzyme stability and quaternary structure as a function
of termini location but also provide a possible explanation for the
catalytic gains in our top-performing OYE variant (new N-terminus
at residue 303; sector III). Crystallographic analysis indicates that
termini relocation into sector III affects the loop β6 region
(amino acid positions: 290–310) of OYE1, which forms a lid
over the active site. Peptide backbone cleavage greatly enhances local
flexibility, effectively converting the loop into a tether and consequently
increasing the environmental exposure of the active site. Interestingly,
such an active site remodeling does not negatively impact the enzyme’s
activity and stereoselectivity; neither does it perturb the conformation
of other key active site residues with the exception of Y375. These
observations were confirmed in truncation experiments, deleting all
residues of the loop β6 region in our OYE variant. Intrigued
by the finding that circular permutation leaves most of the key catalytic
residues unchanged, we also tested OYE permutants for possible additive
or synergistic effects of amino acid substitutions. Distinct functional
changes in these OYE variants were detected upon mutations at W116,
known in native OYE1 to cause inversion of diastereoselectivity for
(S)-carvone reduction. Our findings demonstrate the
contribution of loop β6 toward determining the stereoselectivity
of OYE1, an important insight for future OYE engineering efforts.
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Affiliation(s)
- Ashley B. Daugherty
- Department
of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322. United States
| | - John R. Horton
- Department
of Biochemistry, Emory University, 1510 Clifton Rd., Atlanta, Georgia 30322, United States
| | - Xiaodong Cheng
- Department
of Biochemistry, Emory University, 1510 Clifton Rd., Atlanta, Georgia 30322, United States
| | - Stefan Lutz
- Department
of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322. United States
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17
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Bliven SE, Bourne PE, Prlić A. Detection of circular permutations within protein structures using CE-CP. Bioinformatics 2014; 31:1316-8. [PMID: 25505094 DOI: 10.1093/bioinformatics/btu823] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 12/08/2014] [Indexed: 12/19/2022] Open
Abstract
MOTIVATION Circular permutation is an important type of protein rearrangement. Natural circular permutations have implications for protein function, stability and evolution. Artificial circular permutations have also been used for protein studies. However, such relationships are difficult to detect for many sequence and structure comparison algorithms and require special consideration. RESULTS We developed a new algorithm, called Combinatorial Extension for Circular Permutations (CE-CP), which allows the structural comparison of circularly permuted proteins. CE-CP was designed to be user friendly and is integrated into the RCSB Protein Data Bank. It was tested on two collections of circularly permuted proteins. Pairwise alignments can be visualized both in a desktop application or on the web using Jmol and exported to other programs in a variety of formats. AVAILABILITY AND IMPLEMENTATION The CE-CP algorithm can be accessed through the RCSB website at http://www.rcsb.org/pdb/workbench/workbench.do. Source code is available under the LGPL 2.1 as part of BioJava 3 (http://biojava.org; http://github.com/biojava/biojava). CONTACT sbliven@ucsd.edu or info@rcsb.org.
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Affiliation(s)
- Spencer E Bliven
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Philip E Bourne
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Andreas Prlić
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
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18
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Engineering strictosidine synthase: Rational design of a small, focused circular permutation library of the β-propeller fold enzyme. Bioorg Med Chem 2014; 22:5633-7. [DOI: 10.1016/j.bmc.2014.06.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 06/09/2014] [Accepted: 06/11/2014] [Indexed: 12/23/2022]
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19
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Dai X, Zhu M, Wang YP. Circular permutation of E. coli EPSP synthase: increased inhibitor resistance, improved catalytic activity, and an indicator for protein fragment complementation. Chem Commun (Camb) 2014; 50:1830-2. [PMID: 24402609 DOI: 10.1039/c3cc48722a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We performed the first circular permutation analysis for E. coli 5-enolpyruvylshikimate-3-phosphate synthase, and identified one circular permutant with notably increased resistance to its specific inhibitor and several others with moderately improved catalytic activity. Valid circular permutation sites can be used as effective split sites of protein fragment complementation.
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Affiliation(s)
- Xiongfeng Dai
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.
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20
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Daugherty AB, Govindarajan S, Lutz S. Improved biocatalysts from a synthetic circular permutation library of the flavin-dependent oxidoreductase old yellow enzyme. J Am Chem Soc 2013; 135:14425-32. [PMID: 23987134 DOI: 10.1021/ja4074886] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Members of the old yellow enzyme (OYE) family are widely used, effective biocatalysts for the stereoselective trans-hydrogenation of activated alkenes. To further expand their substrate scope and improve catalytic performance, we have applied a protein engineering strategy called circular permutation (CP) to enhance the function of OYE1 from Saccharomyces pastorianus. CP can influence a biocatalyst's function by altering protein backbone flexibility and active site accessibility, both critical performance features because the catalytic cycle for OYE1 is thought to involve rate-limiting conformational changes. To explore the impact of CP throughout the OYE1 protein sequence, we implemented a highly efficient approach for cell-free cpOYE library preparation by combining whole-gene synthesis with in vitro transcription/translation. The versatility of such an ex vivo system was further demonstrated by the rapid and reliable functional evaluation of library members under variable environmental conditions with three reference substrates ketoisophorone, cinnamaldehyde, and (S)-carvone. Library analysis identified over 70 functional OYE1 variants with several biocatalysts exhibiting over an order of magnitude improved catalytic activity. Although catalytic gains of individual cpOYE library members vary by substrate, the locations of new protein termini in functional variants for all tested substates fall within the same four distinct loop/lid regions near the active site. Our findings demonstrate the importance of these structural elements in enzyme function and support the hypothesis of conformational flexibility as a limiting factor for catalysis in wild type OYE.
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Affiliation(s)
- Ashley B Daugherty
- Department of Chemistry, Emory University , 1515 Dickey Drive, Atlanta, Georgia 30084, United States
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21
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Ryan BJ, Henehan GT. Overview of approaches to preventing and avoiding proteolysis during expression and purification of proteins. ACTA ACUST UNITED AC 2013; Chapter 5:Unit5.25. [PMID: 23377852 DOI: 10.1002/0471140864.ps0525s71] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Proteases are enzymes that cleave proteins. They occur widely in nature and play a fundamental role in cellular homeostasis; however, their presence can result in unwanted protein degradation during recombinant protein expression and purification. This unit introduces proteases, specifically focusing on the types commonly encountered during production of recombinant proteins. The strategies used to avoid and to prevent proteolysis are also described, with extensive consideration of the molecular, technical, and logistic methodologies involved.
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Affiliation(s)
- Barry J Ryan
- Food Science and Environmental Health, Dublin Institute of Technology, Dublin, Ireland
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22
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Circular permutation prediction reveals a viable backbone disconnection for split proteins: an approach in identifying a new functional split intein. PLoS One 2012; 7:e43820. [PMID: 22937103 PMCID: PMC3427171 DOI: 10.1371/journal.pone.0043820] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 07/26/2012] [Indexed: 01/30/2023] Open
Abstract
Split-protein systems have emerged as a powerful tool for detecting biomolecular interactions and reporting biological reactions. However, reliable methods for identifying viable split sites are still unavailable. In this study, we demonstrated the feasibility that valid circular permutation (CP) sites in proteins have the potential to act as split sites and that CP prediction can be used to search for internal permissive sites for creating new split proteins. Using a protein ligase, intein, as a model, CP predictor facilitated the creation of circular permutants in which backbone opening imposes the least detrimental effects on intein folding. We screened a series of predicted intein CPs and identified stable and native-fold CPs. When the valid CP sites were introduced as split sites, there was a reduction in folding enthalpy caused by the new backbone opening; however, the coincident loss in entropy was sufficient to be compensated, yielding a favorable free energy for self-association. Since split intein is exploited in protein semi-synthesis, we tested the related protein trans-splicing (PTS) activities of the corresponding split inteins. Notably, a novel functional split intein composed of the N-terminal 36 residues combined with the remaining C-terminal fragment was identified. Its PTS activity was shown to be better than current reported two-piece intein with a short N-terminal segment. Thus, the incorporation of in silico CP prediction facilitated the design of split intein as well as circular permutants.
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23
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Redesigning the single-chain variant of the restriction endonuclease PvuII by circular permutation. FEBS Lett 2012; 586:1736-41. [PMID: 22613569 DOI: 10.1016/j.febslet.2012.05.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 05/08/2012] [Accepted: 05/09/2012] [Indexed: 12/24/2022]
Abstract
The restriction endonuclease PvuII has been introduced as a sequence-specific cleavage module in highly-specific nucleases for gene targeting. Here, a structural reorganization of the single-chain variant of PvuII (scPvuII) was performed by circular permutation as a proof-of-concept in order to find out whether the relocated, new termini next to structural elements important for DNA recognition and catalysis could be used for the fusion with other regulatory protein domains. Three circularly permuted variants of scPvuII were obtained that all maintain the specific endonucleolytic activity of scPvuII.
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24
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Affiliation(s)
- Spencer Bliven
- Bioinformatics Program, University of California, San Diego, La Jolla, California, United States of America
- * E-mail: (SB); (AP)
| | - Andreas Prlić
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California, United States of America
- * E-mail: (SB); (AP)
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25
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Mehta MM, Liu S, Silberg JJ. A transposase strategy for creating libraries of circularly permuted proteins. Nucleic Acids Res 2012; 40:e71. [PMID: 22319214 PMCID: PMC3351165 DOI: 10.1093/nar/gks060] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A simple approach for creating libraries of circularly permuted proteins is described that is called PERMutation Using Transposase Engineering (PERMUTE). In PERMUTE, the transposase MuA is used to randomly insert a minitransposon that can function as a protein expression vector into a plasmid that contains the open reading frame (ORF) being permuted. A library of vectors that express different permuted variants of the ORF-encoded protein is created by: (i) using bacteria to select for target vectors that acquire an integrated minitransposon; (ii) excising the ensemble of ORFs that contain an integrated minitransposon from the selected vectors; and (iii) circularizing the ensemble of ORFs containing integrated minitransposons using intramolecular ligation. Construction of a Thermotoga neapolitana adenylate kinase (AK) library using PERMUTE revealed that this approach produces vectors that express circularly permuted proteins with distinct sequence diversity from existing methods. In addition, selection of this library for variants that complement the growth of Escherichia coli with a temperature-sensitive AK identified functional proteins with novel architectures, suggesting that PERMUTE will be useful for the directed evolution of proteins with new functions.
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Affiliation(s)
- Manan M Mehta
- Department of Biochemistry and Cell Biology Rice University, Houston, TX 77251, USA
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26
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Correia BE, Holmes MA, Huang PS, Strong RK, Schief WR. High-resolution structure prediction of a circular permutation loop. Protein Sci 2011; 20:1929-34. [PMID: 21898647 DOI: 10.1002/pro.725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 08/10/2011] [Accepted: 08/12/2011] [Indexed: 01/12/2023]
Abstract
Methods for rapid and reliable design and structure prediction of linker loops would facilitate a variety of protein engineering applications. Circular permutation, in which the existing termini of a protein are linked by the polypeptide chain and new termini are created, is one such application that has been employed for decreasing proteolytic susceptibility and other functional purposes. The length and sequence of the linker can impact the expression level, solubility, structure and function of the permuted variants. Hence it is desirable to achieve atomic-level accuracy in linker design. Here, we describe the use of RosettaRemodel for design and structure prediction of circular permutation linkers on a model protein. A crystal structure of one of the permuted variants confirmed the accuracy of the computational prediction, where the all-atom rmsd of the linker region was 0.89 Å between the model and the crystal structure. This result suggests that RosettaRemodel may be generally useful for the design and structure prediction of protein loop regions for circular permutations or other structure-function manipulations.
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Affiliation(s)
- Bruno E Correia
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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27
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Yu Y, Lutz S. Circular permutation: a different way to engineer enzyme structure and function. Trends Biotechnol 2011; 29:18-25. [DOI: 10.1016/j.tibtech.2010.10.004] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 10/11/2010] [Accepted: 10/18/2010] [Indexed: 12/15/2022]
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28
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Montalbán-López M, Martínez-Bueno M, Valdivia E, Maqueda M. Expression of linear permutated variants from circular enterocin AS-48. Biochimie 2010; 93:549-55. [PMID: 21130135 DOI: 10.1016/j.biochi.2010.11.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 11/24/2010] [Indexed: 10/18/2022]
Abstract
To confirm whether the head-to-tail circularization could be involved in the stability and activity of the circular bacteriocin AS-48, two permutated linear structural as-48A genes have been constructed by circular permutation. The absence of the leaderless linear AS(23/24) and AS(48/49) proteins in Escherichia coli, under all the conditions investigated, supports the idea that the circular backbone is important to stabilize their structure and also indicates the significance of a leader peptide. In fact, the approach taken in this study to generate linear permutated proteins fused to an appropriate partner was sufficient to prevent cellular proteolysis. In this case, the high expression levels found favour their intracellular accumulations as inclusion bodies, which after solubilization showed a propensity to aggregate, thus hindering the specific EK cleavage. This could explain the presence of active hybrid tagged proteins identified in this work. The conserved distribution of hydrophobic and hydrophilic surfaces in the hybrid proteins is responsible for the antibacterial activity. In addition, the opening of the AS-48 molecule between the residues G(23) W(24) connecting the α1/α2 helices, confers greater stability, suggesting that the sequence and/or the free amino acid in the polypeptide chain are critical aspects in the design of new variants.
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Affiliation(s)
- Manuel Montalbán-López
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, C/Fuentenueva s/n, Granada, Spain
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29
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Eisenbeis S, Höcker B. Evolutionary mechanism as a template for protein engineering. J Pept Sci 2010; 16:538-44. [DOI: 10.1002/psc.1233] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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