51
|
Wang S, Blois A, El Rayes T, Liu JF, Hirsch MS, Gravdal K, Palakurthi S, Bielenberg DR, Akslen LA, Drapkin R, Mittal V, Watnick RS. Development of a prosaposin-derived therapeutic cyclic peptide that targets ovarian cancer via the tumor microenvironment. Sci Transl Med 2016; 8:329ra34. [PMID: 26962158 DOI: 10.1126/scitranslmed.aad5653] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The vast majority of ovarian cancer-related deaths are caused by metastatic dissemination of tumor cells, resulting in subsequent organ failure. However, despite our increased understanding of the physiological processes involved in tumor metastasis, there are no clinically approved drugs that have made a major impact in increasing the overall survival of patients with advanced, metastatic ovarian cancer. We identified prosaposin (psap) as a potent inhibitor of tumor metastasis, which acts via stimulation of p53 and the antitumorigenic protein thrombospondin-1 (TSP-1) in bone marrow-derived cells that are recruited to metastatic sites. We report that more than 97% of human serous ovarian tumors tested express CD36, the receptor that mediates the proapoptotic activity of TSP-1. Accordingly, we sought to determine whether a peptide derived from psap would be effective in treating this form of ovarian cancer. To that end, we developed a cyclic peptide with drug-like properties derived from the active sequence in psap. The cyclic psap peptide promoted tumor regression in a patient-derived tumor xenograft model of metastatic ovarian cancer. Thus, we hypothesize that a therapeutic agent based on this psap peptide would have efficacy in treating patients with metastatic ovarian cancer.
Collapse
Affiliation(s)
- Suming Wang
- Vascular Biology Program, Boston Children's Hospital, Boston, MA 02115, USA. Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Anna Blois
- Vascular Biology Program, Boston Children's Hospital, Boston, MA 02115, USA. Department of Surgery, Harvard Medical School, Boston, MA 02115, USA. Centre for Cancer Biomarkers (CCBIO), Department of Clinical Medicine, University of Bergen, NO-5020 Bergen, Norway
| | - Tina El Rayes
- Department of Cardiothoracic Surgery, Weill Cornell Medical College, New York, NY 10065, USA. Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY 10065, USA. Neuberger Berman Lung Cancer Center, Weill Cornell Medical College, New York, NY 10065, USA
| | - Joyce F Liu
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Michelle S Hirsch
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Karsten Gravdal
- Centre for Cancer Biomarkers (CCBIO), Department of Clinical Medicine, University of Bergen, NO-5020 Bergen, Norway. Department of Pathology, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Sangeetha Palakurthi
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Diane R Bielenberg
- Vascular Biology Program, Boston Children's Hospital, Boston, MA 02115, USA. Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Lars A Akslen
- Centre for Cancer Biomarkers (CCBIO), Department of Clinical Medicine, University of Bergen, NO-5020 Bergen, Norway. Department of Pathology, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Ronny Drapkin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA. Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Vivek Mittal
- Department of Cardiothoracic Surgery, Weill Cornell Medical College, New York, NY 10065, USA. Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY 10065, USA. Neuberger Berman Lung Cancer Center, Weill Cornell Medical College, New York, NY 10065, USA
| | - Randolph S Watnick
- Vascular Biology Program, Boston Children's Hospital, Boston, MA 02115, USA. Department of Surgery, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
52
|
Hammack LJ, Kusmierczyk AR. Assembly of proteasome subunits into non-canonical complexes in vivo. Biochem Biophys Res Commun 2016; 482:164-169. [PMID: 27833017 DOI: 10.1016/j.bbrc.2016.11.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 11/05/2016] [Indexed: 01/25/2023]
Abstract
Proteasomes exist in all domains of life. In general, they are comprised of a compartmentalized protease whose activity is modulated by one or more regulatory complexes with which it interacts. The quaternary structure of this compartmentalized protease, called the 20S proteasome, is absolutely conserved and consists of four heptameric rings stacked coaxially. The rings are made of structurally related α and β subunits. In eukaryotes, assembly factors chaperone the α and β subunits during 20S biogenesis. Here we demonstrate that proteasome subunits can assemble into structures other than the canonical 20S proteasome in vivo. Specifically, the yeast α4 subunit forms high molecular weight complexes whose abundance increases when proteasome function is compromised. Results from a disulfide crosslinking approach are consistent with these complexes being ring-shaped. Though several eukaryotic α subunits can form rings when expressed recombinantly in bacteria, this is the first evidence that such non-canonical complexes exist in vivo.
Collapse
Affiliation(s)
- Lindsay J Hammack
- Department of Biology, Indiana University-Purdue University Indianapolis, 723 West Michigan Street, Indianapolis, IN, 46202, United States
| | - Andrew R Kusmierczyk
- Department of Biology, Indiana University-Purdue University Indianapolis, 723 West Michigan Street, Indianapolis, IN, 46202, United States.
| |
Collapse
|
53
|
Ciragan A, Aranko AS, Tascon I, Iwaï H. Salt-inducible Protein Splicing in cis and trans by Inteins from Extremely Halophilic Archaea as a Novel Protein-Engineering Tool. J Mol Biol 2016; 428:4573-4588. [PMID: 27720988 DOI: 10.1016/j.jmb.2016.10.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Revised: 09/29/2016] [Accepted: 10/01/2016] [Indexed: 10/20/2022]
Abstract
Intervening protein sequences (inteins) from extremely halophilic haloarchaea can be inactive under low salinity but could be activated by increasing the salt content to a specific concentration for each intein. The halo-obligatory inteins confer high solubility under both low and high salinity conditions. We showed the broad utility of salt-dependent protein splicing in cis and trans by demonstrating backbone cyclization, self-cleavage for purification, and scarless protein ligation for segmental isotopic labeling. Artificially split MCM2 intein derived from Halorhabdus utahensis remained highly soluble and was capable of protein trans-splicing with excellent ligation kinetics by reassembly under high salinity conditions. Importantly, the MCM2 intein has the active site residue of Ser at the +1 position, which remains in the ligated product, instead of Cys as found in many other efficient split inteins. Since Ser is more abundant than Cys in proteins, the novel split intein could widen the applications of segmental labeling in protein NMR spectroscopy and traceless protein ligation by exploiting a Ser residue in the native sequences as the +1 position of the MCM2 intein. The split halo-obligatory intein was successfully used to demonstrate the utility in NMR investigation of intact proteins by producing segmentally isotope-labeled intact TonB protein from Helicobacter pylori.
Collapse
Affiliation(s)
- Annika Ciragan
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki, FI-00014, Finland
| | - A Sesilja Aranko
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki, FI-00014, Finland
| | - Igor Tascon
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki, FI-00014, Finland
| | - Hideo Iwaï
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki, FI-00014, Finland.
| |
Collapse
|
54
|
Boll E, Drobecq H, Lissy E, Cantrelle FX, Melnyk O. Kinetically Controlled Chemoselective Cyclization Simplifies the Access to Cyclic and Branched Peptides. Org Lett 2016; 18:3842-5. [DOI: 10.1021/acs.orglett.6b01847] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Emmanuelle Boll
- Université de Lille, CNRS, Institut Pasteur de Lille, UMR 8161, F-59000 Lille, France
| | - Hervé Drobecq
- Université de Lille, CNRS, Institut Pasteur de Lille, UMR 8161, F-59000 Lille, France
| | - Elizabeth Lissy
- Université de Lille, CNRS, Institut Pasteur de Lille, UMR 8161, F-59000 Lille, France
| | - François-Xavier Cantrelle
- Université de Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Oleg Melnyk
- Université de Lille, CNRS, Institut Pasteur de Lille, UMR 8161, F-59000 Lille, France
| |
Collapse
|
55
|
Rasche N, Tonillo J, Rieker M, Becker S, Dorr B, Ter-Ovanesyan D, Betz UAK, Hock B, Kolmar H. PROLink-Single Step Circularization and Purification Procedure for the Generation of an Improved Variant of Human Growth Hormone. Bioconjug Chem 2016; 27:1341-7. [PMID: 27108993 DOI: 10.1021/acs.bioconjchem.6b00137] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human growth hormone (hGH) plays an important role during human development and is also an approved therapeutic for the treatment of several diseases. However, one major drawback of hGH is its short circulating half-life requiring frequent administration, which is inconvenient and painful for the patients. Recent publications indicate that circularization greatly increases the stability of proteins due to their protection from exoproteolytic attack and a higher thermal stability of the circular form. Using sortase A, a transpeptidase isolated from Staphylococcus aureus, we developed a single step solid-phase circularization and purification procedure resulting in a circular version of hGH with improved properties. We could show that circular hGH binds to the recombinant hGH receptor with binding kinetics similar to those of linear hGH and that circularization does not alter the biological activity of hGH in vitro. Besides, circular hGH showed almost complete resistance toward exoproteolytic attack and slightly increased thermal stability which could possibly translate into an extended plasma half-life. The single step solid-phase circularization and purification procedure is in principle a generic process, which could also be applied for other proteins that meet the requirements for circularization.
Collapse
Affiliation(s)
- Nicolas Rasche
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt , 64287 Darmstadt, Germany.,Merck KGaA , Frankfurterstrasse 250, 64293 Darmstadt, Germany
| | - Jason Tonillo
- Merck KGaA , Frankfurterstrasse 250, 64293 Darmstadt, Germany
| | - Marcel Rieker
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt , 64287 Darmstadt, Germany.,Merck KGaA , Frankfurterstrasse 250, 64293 Darmstadt, Germany
| | - Stefan Becker
- Merck KGaA , Frankfurterstrasse 250, 64293 Darmstadt, Germany
| | | | - Dmitry Ter-Ovanesyan
- Department of Molecular and Cellular Biology, Harvard University , Cambridge, Massachusetts 02138, United States.,Wyss Institute for Biologically Inspired Engineering , Boston, Massachusetts 02115, United States
| | - Ulrich A K Betz
- Merck KGaA , Frankfurterstrasse 250, 64293 Darmstadt, Germany
| | - Björn Hock
- Merck KGaA , Frankfurterstrasse 250, 64293 Darmstadt, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt , 64287 Darmstadt, Germany
| |
Collapse
|
56
|
Borra R, Camarero JA. Recombinant expression of backbone-cyclized polypeptides. Biopolymers 2016; 100:502-9. [PMID: 23893781 DOI: 10.1002/bip.22306] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/13/2013] [Accepted: 05/28/2013] [Indexed: 01/08/2023]
Abstract
Here we review the different biochemical approaches available for the expression of backbone-cyclized polypeptides, including peptides and proteins. These methods allow for the production of circular polypeptides either in vitro or in vivo using standard recombinant DNA expression techniques. Polypeptide circularization provides a valuable tool to study the effects of topology on protein stability and folding kinetics. Furthermore, having biosynthetic access to backbone-cyclized polypeptides makes the production of genetically encoded libraries of cyclic polypeptides possible. The production of such libraries, which was previously restricted to the domain of synthetic chemistry, now offers biologists access to highly diverse and stable molecular libraries that can be screened using high-throughput methods for the rapid selection of novel cyclic polypeptide sequences with new biological activities.
Collapse
Affiliation(s)
- Radhika Borra
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, 90033
| | | |
Collapse
|
57
|
Schoene C, Bennett SP, Howarth M. SpyRing interrogation: analyzing how enzyme resilience can be achieved with phytase and distinct cyclization chemistries. Sci Rep 2016; 6:21151. [PMID: 26861173 PMCID: PMC4748275 DOI: 10.1038/srep21151] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/18/2016] [Indexed: 12/23/2022] Open
Abstract
Enzymes catalyze reactions with exceptional selectivity and rate acceleration but are often limited by instability. Towards a generic route to thermo-resilience, we established the SpyRing approach, cyclizing enzymes by sandwiching between SpyTag and SpyCatcher (peptide and protein partners which lock together via a spontaneous isopeptide bond). Here we first investigated the basis for this resilience, comparing alternative reactive peptide/protein pairs we engineered from Gram-positive bacteria. Both SnoopRing and PilinRing cyclization gave dramatic enzyme resilience, but SpyRing cyclization was the best. Differential scanning calorimetry for each ring showed that cyclization did not inhibit unfolding of the inserted β-lactamase. Cyclization conferred resilience even at 100 °C, where the cyclizing domains themselves were unfolded. Phytases hydrolyze phytic acid and improve dietary absorption of phosphate and essential metal ions, important for agriculture and with potential against human malnutrition. SpyRing phytase (PhyC) resisted aggregation and retained catalytic activity even following heating at 100 °C. In addition, SpyRing cyclization made it possible to purify phytase simply by heating the cell lysate, to drive aggregation of non-cyclized proteins. Cyclization via domains forming spontaneous isopeptide bonds is a general strategy to generate resilient enzymes and may extend the range of conditions for isolation and application of enzymes.
Collapse
Affiliation(s)
- Christopher Schoene
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - S Paul Bennett
- Sekisui Diagnostics UK Ltd., Operations Building, Liphook Way, Allington, Maidstone, Kent, ME16 0LQ, UK
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| |
Collapse
|
58
|
|
59
|
Nguyen GKT, Kam A, Loo S, Jansson AE, Pan LX, Tam JP. Butelase 1: A Versatile Ligase for Peptide and Protein Macrocyclization. J Am Chem Soc 2015; 137:15398-401. [PMID: 26633100 DOI: 10.1021/jacs.5b11014] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Macrocyclization is a valuable tool for drug design and protein engineering. Although various methods have been developed to prepare macrocycles, a general and efficient strategy is needed. Here we report a highly efficient method using butelase 1 to macrocyclize peptides and proteins ranging in sizes from 26 to >200 residues. We achieved cyclizations that are 20,000 times faster than sortase A, the most widely used ligase for protein cyclization. The reactions completed within minutes with up to 95% yields.
Collapse
Affiliation(s)
- Giang K T Nguyen
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore
| | - Antony Kam
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore
| | - Shining Loo
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore
| | - Anna E Jansson
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore
| | - Lucy X Pan
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore
| |
Collapse
|
60
|
Pierre B, Labonte JW, Xiong T, Aoraha E, Williams A, Shah V, Chau E, Helal KY, Gray JJ, Kim JR. Molecular Determinants for Protein Stabilization by Insertional Fusion to a Thermophilic Host Protein. Chembiochem 2015; 16:2392-402. [DOI: 10.1002/cbic.201500310] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Indexed: 12/26/2022]
Affiliation(s)
- Brennal Pierre
- Othmer-Jacobs Department of Chemical and Biomolecular Engineering; New York University; 6 MetroTech Center Brooklyn NY 11201 USA
| | - Jason W. Labonte
- Department of Chemical and Biomolecular Engineering; Johns Hopkins University; 3400 North Charles Street Baltimore MD 21218 USA
| | - Tina Xiong
- Othmer-Jacobs Department of Chemical and Biomolecular Engineering; New York University; 6 MetroTech Center Brooklyn NY 11201 USA
- Department of Chemical and Biomolecular Engineering; Johns Hopkins University; 3400 North Charles Street Baltimore MD 21218 USA
| | - Edwin Aoraha
- Othmer-Jacobs Department of Chemical and Biomolecular Engineering; New York University; 6 MetroTech Center Brooklyn NY 11201 USA
| | - Asher Williams
- Othmer-Jacobs Department of Chemical and Biomolecular Engineering; New York University; 6 MetroTech Center Brooklyn NY 11201 USA
| | - Vandan Shah
- Othmer-Jacobs Department of Chemical and Biomolecular Engineering; New York University; 6 MetroTech Center Brooklyn NY 11201 USA
| | - Edward Chau
- Othmer-Jacobs Department of Chemical and Biomolecular Engineering; New York University; 6 MetroTech Center Brooklyn NY 11201 USA
| | - Kazi Yasin Helal
- Othmer-Jacobs Department of Chemical and Biomolecular Engineering; New York University; 6 MetroTech Center Brooklyn NY 11201 USA
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering; Johns Hopkins University; 3400 North Charles Street Baltimore MD 21218 USA
| | - Jin Ryoun Kim
- Othmer-Jacobs Department of Chemical and Biomolecular Engineering; New York University; 6 MetroTech Center Brooklyn NY 11201 USA
| |
Collapse
|
61
|
Li Y. Split-inteins and their bioapplications. Biotechnol Lett 2015; 37:2121-37. [DOI: 10.1007/s10529-015-1905-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 06/29/2015] [Indexed: 01/01/2023]
|
62
|
Schumann FH, Varadan R, Tayakuniyil PP, Grossman JH, Camarero JA, Fushman D. Changing the topology of protein backbone: the effect of backbone cyclization on the structure and dynamics of a SH3 domain. Front Chem 2015; 3:26. [PMID: 25905098 PMCID: PMC4389572 DOI: 10.3389/fchem.2015.00026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 03/23/2015] [Indexed: 12/02/2022] Open
Abstract
Understanding of the effects of the backbone cyclization on the structure and dynamics of a protein is essential for using protein topology engineering to alter protein stability and function. Here we have determined, for the first time, the structure and dynamics of the linear and various circular constructs of the N-SH3 domain from protein c-Crk. These constructs differ in the length and amino acid composition of the cyclization region. The backbone cyclization was carried out using intein-mediated intramolecular chemical ligation between the juxtaposed N- and the C-termini. The structure and backbone dynamics studies were performed using solution NMR. Our data suggest that the backbone cyclization has little effect on the overall three-dimensional structure of the SH3 domain: besides the termini, only minor structural changes were found in the proximity of the cyclization region. In contrast to the structure, backbone dynamics are significantly affected by the cyclization. On the subnanosecond time scale, the backbone of all circular constructs on average appears more rigid than that of the linear SH3 domain; this effect is observed over the entire backbone and is not limited to the cyclization site. The backbone mobility of the circular constructs becomes less restricted with increasing length of the circularization loop. In addition, significant conformational exchange motions (on the sub-millisecond time scale) were found in the N-Src loop and in the adjacent β-strands in all circular constructs studied in this work. These effects of backbone cyclization on protein dynamics have potential implications for the stability of the protein fold and for ligand binding.
Collapse
Affiliation(s)
- Frank H Schumann
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
| | - Ranjani Varadan
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
| | - Praveen P Tayakuniyil
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
| | - Jennifer H Grossman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
| | - Julio A Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California Los Angeles, CA, USA ; Department of Chemistry, University of Southern California Los Angeles, CA, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland College Park, MD, USA
| |
Collapse
|
63
|
Site-specific in situ growth of a cyclized protein-polymer conjugate with improved stability and tumor retention. Biomaterials 2015; 47:13-9. [DOI: 10.1016/j.biomaterials.2015.01.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 01/11/2015] [Indexed: 11/18/2022]
|
64
|
Michel E, Allain FHT. Selective Amino Acid Segmental Labeling of Multi-Domain Proteins. Methods Enzymol 2015; 565:389-422. [DOI: 10.1016/bs.mie.2015.05.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
65
|
Waldhauer MC, Schmitz SN, Ahlmann-Eltze C, Gleixner JG, Schmelas CC, Huhn AG, Bunne C, Büscher M, Horn M, Klughammer N, Kreft J, Schäfer E, Bayer PA, Krämer SG, Neugebauer J, Wehler P, Mayer MP, Eils R, Di Ventura B. Backbone circularization of Bacillus subtilis family 11 xylanase increases its thermostability and its resistance against aggregation. MOLECULAR BIOSYSTEMS 2015; 11:3231-43. [DOI: 10.1039/c5mb00341e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
While using a serine (S) as linker for circularization increases the thermostability, a longer linker (RGKCWE) leads to reduced aggregation after heat shock at elevated temperatures.
Collapse
|
66
|
Boll E, Ebran JP, Drobecq H, El-Mahdi O, Raibaut L, Ollivier N, Melnyk O. Access to large cyclic peptides by a one-pot two-peptide segment ligation/cyclization process. Org Lett 2014; 17:130-3. [PMID: 25506740 DOI: 10.1021/ol503359w] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The use of the N-acetoacetyl protecting group for N-terminal cysteine residue enabled creation of an efficient and mild one-pot native chemical ligation/SEA ligation sequence giving access to large cyclic peptides.
Collapse
Affiliation(s)
- Emmanuelle Boll
- UMR CNRS 8161, Université de Lille, Pasteur Institute of Lille 59021 Lille, France
| | | | | | | | | | | | | |
Collapse
|
67
|
Tarasava K, Freisinger E. An optimized intein-mediated protein ligation approach for the efficient cyclization of cysteine-rich proteins. Protein Eng Des Sel 2014; 27:481-8. [PMID: 25335928 DOI: 10.1093/protein/gzu048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Head-to-tail backbone cyclization of proteins is a widely used approach for the improvement of protein stability. One way to obtain cyclic proteins via recombinant expression makes use of engineered Intein tags, which are self-cleaving protein domains. In this approach, pH-induced self-cleavage of the N-terminal Intein tag generates an N-terminal cysteine residue at the target protein, which then attacks in an intramolecular reaction the C-terminal thioester formed by the second C-terminal Intein tag resulting in the release of the cyclic target protein. In the current work we aimed to produce a cyclic analog of the small γ-Ec-1 domain of the wheat metallothionein, which contains six cysteine residues. During the purification process we faced several challenges, among them premature cleavage of one or the other Intein tag resulting in decreasing yields and contamination with linear species. To improve efficiency of the system we applied a number of optimizations such as the introduction of a Tobacco etch virus cleavage site and an additional poly-histidine tag. Our efforts resulted in the production of a cyclic protein in moderate yields without any contamination with linear protein species.
Collapse
Affiliation(s)
- Katsiaryna Tarasava
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Eva Freisinger
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| |
Collapse
|
68
|
Shi J, Zhang H, Fang L, Xi Y, Zhou Y, Luo R, Wang D, Xiao S, Chen H. A novel firefly luciferase biosensor enhances the detection of apoptosis induced by ESAT-6 family proteins of Mycobacterium tuberculosis. Biochem Biophys Res Commun 2014; 452:1046-53. [DOI: 10.1016/j.bbrc.2014.09.047] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 09/11/2014] [Indexed: 12/14/2022]
|
69
|
Veggiani G, Zakeri B, Howarth M. Superglue from bacteria: unbreakable bridges for protein nanotechnology. Trends Biotechnol 2014; 32:506-12. [PMID: 25168413 DOI: 10.1016/j.tibtech.2014.08.001] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/13/2014] [Accepted: 08/04/2014] [Indexed: 11/28/2022]
Abstract
Biotechnology is often limited by weak interactions. We suggest that an ideal interaction between proteins would be covalent, specific, require addition of only a peptide tag to the protein of interest, and form under a wide range of conditions. Here we summarize peptide tags that are able to form spontaneous amide bonds, based on harnessing reactions of adhesion proteins from the bacterium Streptococcus pyogenes. These include the irreversible peptide-protein interaction of SpyTag with SpyCatcher, as well as irreversible peptide-peptide interactions via SpyLigase. We describe existing applications, including polymerization to enhance cancer cell capture, assembly of living biomaterial, access to diverse protein shapes, and improved enzyme resilience. We also indicate future opportunities for resisting biological force and extending the scope of protein nanotechnology.
Collapse
Affiliation(s)
- Gianluca Veggiani
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Bijan Zakeri
- MIT Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| |
Collapse
|
70
|
Schoene C, Fierer JO, Bennett SP, Howarth M. SpyTag/SpyCatcher Cyclization Confers Resilience to Boiling on a Mesophilic Enzyme. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402519] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
71
|
Schoene C, Fierer JO, Bennett SP, Howarth M. SpyTag/SpyCatcher cyclization confers resilience to boiling on a mesophilic enzyme. Angew Chem Int Ed Engl 2014; 53:6101-4. [PMID: 24817566 DOI: 10.1002/anie.201402519] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Indexed: 11/09/2022]
Abstract
SpyTag is a peptide that spontaneously forms an amide bond with its protein partner SpyCatcher. SpyTag was fused at the N terminus of β-lactamase and SpyCatcher at the C terminus so that the partners could react to lock together the termini of the enzyme. The wild-type enzyme aggregates above 37 °C, with irreversible loss of activity. Cyclized β-lactamase was soluble even after heating at 100 °C; after cooling, the catalytic activity was restored. SpyTag/SpyCatcher cyclization led to a much larger increase in stability than that achieved through point mutation or alternative approaches to cyclization. Cyclized dihydrofolate reductase was similarly resilient. Analyzing unfolding through calorimetry indicated that cyclization did not increase the unfolding temperature but rather facilitated refolding after thermal stress. SpyTag/SpyCatcher sandwiching represents a simple and efficient route to enzyme cyclization, with potential to greatly enhance the robustness of biocatalysts.
Collapse
Affiliation(s)
- Christopher Schoene
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU (UK)
| | | | | | | |
Collapse
|
72
|
Wood DW, Camarero JA. Intein applications: from protein purification and labeling to metabolic control methods. J Biol Chem 2014; 289:14512-9. [PMID: 24700459 DOI: 10.1074/jbc.r114.552653] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The discovery of inteins in the early 1990s opened the door to a wide variety of new technologies. Early engineered inteins from various sources allowed the development of self-cleaving affinity tags and new methods for joining protein segments through expressed protein ligation. Some applications were developed around native and engineered split inteins, which allow protein segments expressed separately to be spliced together in vitro. More recently, these early applications have been expanded and optimized through the discovery of highly efficient trans-splicing and trans-cleaving inteins. These new inteins have enabled a wide variety of applications in metabolic engineering, protein labeling, biomaterials construction, protein cyclization, and protein purification.
Collapse
Affiliation(s)
- David W Wood
- From the Department of Chemical and Biomolecular Engineering, Ohio State University, Columbus, Ohio 43210 and
| | - Julio A Camarero
- the Departments of Pharmacology and Pharmaceutical Sciences and Department of Chemistry, University of Southern California, Los Angeles, California 90033
| |
Collapse
|
73
|
Melnyk O, Ollivier N, Besret S, Melnyk P. Phenylthiocarbamate or N-carbothiophenyl group chemistry in peptide synthesis and bioconjugation. Bioconjug Chem 2014; 25:629-39. [PMID: 24641212 PMCID: PMC4064696 DOI: 10.1021/bc500052r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
The design of novel chemoselective
and site-specific ligation methods
provides new tools for obtaining complex scaffolds, peptidomimetics,
and peptide conjugates. The chemistry of the N-phenylthiocarbonyl
group has led to several developments in peptide ligation chemistry
and peptide bioconjugation during the last 10 years. The aim of this
review is to provide an overview of this emerging field.
Collapse
|
74
|
Topilina NI, Mills KV. Recent advances in in vivo applications of intein-mediated protein splicing. Mob DNA 2014; 5:5. [PMID: 24490831 PMCID: PMC3922620 DOI: 10.1186/1759-8753-5-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/07/2014] [Indexed: 01/27/2023] Open
Abstract
Intein-mediated protein splicing has become an essential tool in modern biotechnology. Fundamental progress in the structure and catalytic strategies of cis- and trans-splicing inteins has led to the development of modified inteins that promote efficient protein purification, ligation, modification and cyclization. Recent work has extended these in vitro applications to the cell or to whole organisms. We review recent advances in intein-mediated protein expression and modification, post-translational processing and labeling, protein regulation by conditional protein splicing, biosensors, and expression of trans-genes.
Collapse
Affiliation(s)
| | - Kenneth V Mills
- Department of Chemistry, College of the Holy Cross, 1 College Street, Worcester, MA 01610, USA.
| |
Collapse
|
75
|
Zhulenkovs D, Jaudzems K, Zajakina A, Leonchiks A. Enzymatic activity of circular sortase A under denaturing conditions: An advanced tool for protein ligation. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2013.11.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
76
|
Solution structure of the circular γ-domain analog from the wheat metallothionein E(c)-1. Molecules 2013; 18:14414-29. [PMID: 24284492 PMCID: PMC6269658 DOI: 10.3390/molecules181114414] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 11/06/2013] [Accepted: 11/19/2013] [Indexed: 11/28/2022] Open
Abstract
The first cyclic analog of a metallothionein (MT) was prepared and analyzed by UV and (magnetic) circular dichroism spectroscopy, ESI-MS as well as NMR spectroscopy. Results reveal that the evaluated cyclic γ-Ec-1 domain of the wheat MT Ec-1 retains its ability to coordinate two Zn(II) or Cd(II) ions and adopts a three-dimensional structure that is highly similar to the one of the linear wild-type form. However, the reduced flexibility of the protein backbone facilitates structure solution significantly and results in a certain stabilization of metal binding to the protein.
Collapse
|
77
|
Zhang WB, Sun F, Tirrell DA, Arnold FH. Controlling Macromolecular Topology with Genetically Encoded SpyTag–SpyCatcher Chemistry. J Am Chem Soc 2013; 135:13988-97. [DOI: 10.1021/ja4076452] [Citation(s) in RCA: 158] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Wen-Bin Zhang
- Division of Chemistry and
Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Fei Sun
- Division of Chemistry and
Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - David A. Tirrell
- Division of Chemistry and
Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Frances H. Arnold
- Division of Chemistry and
Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| |
Collapse
|
78
|
Pappa EV, Zompra AA, Diamantopoulou Z, Spyranti Z, Pairas G, Lamari FN, Katsoris P, Spyroulias GA, Cordopatis P. Structure-activity studies of lGnRH-III through rational amino acid substitution and NMR conformational studies. Biopolymers 2013. [PMID: 23203758 DOI: 10.1002/bip.22123] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Lamprey gonadotropin-releasing hormone type III (lGnRH-III) is an isoform of GnRH isolated from the sea lamprey (Petromyzon marinus) with negligible endocrine activity in mammalian systems. Data concerning the superior direct anticancer activity of lGnRH-III have been published, raising questions on the structure-activity relationship. We synthesized 21 lGnRH-III analogs with rational amino acid substitutions and studied their effect on PC3 and LNCaP prostate cancer cell proliferation. Our results question the importance of the acidic charge of Asp⁶ for the antiproliferative activity and indicate the significance of the stereochemistry of Trp in positions 3 and 7. Furthermore, conjugation of an acetyl-group to the side chain of Lys⁸ or side chain cyclization of amino acids 1-8 increased the antiproliferative activity of lGnRH-III demonstrating that the proposed salt bridge between Asp⁶ and Lys⁸ is not crucial. Conformational studies of lGnRH-III were performed through NMR spectroscopy, and the solution structure of GnRH-I was solved. In solution, lGnRH-III adopts an extended backbone conformation in contrast to the well-defined β-turn conformation of GnRH-I.
Collapse
Affiliation(s)
- Eleni V Pappa
- Department of Pharmacy, University of Patras, Greece.
| | | | | | | | | | | | | | | | | |
Collapse
|
79
|
Byrne A, Kier BL, Williams DV, Scian M, Andersen NH. Circular Permutation of the Trp-cage: Fold Rescue upon Addition of a Hydrophobic Staple. RSC Adv 2013; 2013. [PMID: 24376912 DOI: 10.1039/c3ra43674h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The Trp-cage, at 20 residues in length, is generally acknowledged as the smallest fully protein-like folding motif. Linking the termini by a two-residue unit and excising one residue affords circularly permuted sequences that adopt the same structure. This represents the first successful circular permutation of any fold of less than 50-residue length. As was observed for the original topology, a hydrophobic staple near the chain termini is required for enhanced fold stability.
Collapse
Affiliation(s)
- Aimee Byrne
- Department of Chemistry, University of Washington Seattle, Washington, 98195, USA
| | - Brandon L Kier
- Department of Chemistry, University of Washington Seattle, Washington, 98195, USA
| | - D V Williams
- Department of Chemistry, University of Washington Seattle, Washington, 98195, USA
| | - Michele Scian
- Department of Chemistry, University of Washington Seattle, Washington, 98195, USA
| | - Niels H Andersen
- Department of Chemistry, University of Washington Seattle, Washington, 98195, USA
| |
Collapse
|
80
|
van Lieshout JFT, Gutiérrez ONP, Vroom W, Planas A, de Vos WM, van der Oost J, Koutsopoulos S. Thermal stabilization of an endoglucanase by cyclization. Appl Biochem Biotechnol 2012; 167:2039-53. [PMID: 22653681 PMCID: PMC3416981 DOI: 10.1007/s12010-012-9674-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 04/09/2012] [Indexed: 10/28/2022]
Abstract
An intein-driven protein splicing approach allowed for the covalent linkage between the N- and C-termini of a polypeptide chain to create circular variants of the endo-β-1,3-1,4-glucanase, LicA, from Bacillus licheniformis. Two circular variants, LicA-C1 and LicA-C2, which have connecting loops of 20 and 14 amino acids, respectively, showed catalytic activities that are approximately two and three times higher, respectively, compared to that of the linear LicA (LicA-L1). The thermal stability of the circular variants was significantly increased compared to the linear form. Whereas the linear glucanase lost half of its activity after 3 min at 65 °C, the two circular variants have 6-fold (LicA-C1) and 16-fold (LicA-C2) increased half-life time of inactivation. In agreement with this, fluorescence spectroscopy and differential scanning calorimetry studies revealed that circular enzymes undergo structural changes at higher temperatures compared to that of the linear form. The effect of calcium on the conformational stability and function of the circular LicAs was also investigated, and we observed that the presence of calcium ions results in increased thermal stability. The impact of the length of the designed loops on thermal stability of the circular proteins is discussed, and it is suggested that cyclization may be an efficient strategy for the increased stability of proteins.
Collapse
Affiliation(s)
- Johan F. T. van Lieshout
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - Odette N. Pérez Gutiérrez
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - Wietse Vroom
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - Antoni Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - Sotirios Koutsopoulos
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
- Center for Biomedical Engineering, NE47-307, Massachusetts Institute of Technology, Cambridge, MA 02139-4307 USA
| |
Collapse
|
81
|
Abstract
Here, we review the use of different biochemical approaches for biological synthesis of circular or backbone-cyclized proteins and peptides. These methods allow the production of circular polypeptides either in vitro or in vivo using standard recombinant DNA expression techniques. Protein circularization can significantly impact protein engineering and research in protein folding. Basic polymer theory predicts that circularization should lead to a net thermodynamic stabilization of a folded protein by reducing the entropy associated with the unfolded state. Protein cyclization also provides a valuable tool for exploring the effects of topology on protein folding kinetics. Furthermore, the biological production of cyclic polypeptides makes possible the production of cyclic polypeptide libraries. The generation of such libraries, which was previously restricted to the domain of synthetic chemists, now offers biologists access to highly diverse and stable molecular libraries for probing protein structure and function.
Collapse
Affiliation(s)
- Teshome L Aboye
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90033, USA
| | | |
Collapse
|
82
|
Gould A, Ji Y, Aboye TL, Camarero JA. Cyclotides, a novel ultrastable polypeptide scaffold for drug discovery. Curr Pharm Des 2012; 17:4294-307. [PMID: 22204428 DOI: 10.2174/138161211798999438] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2011] [Accepted: 09/15/2011] [Indexed: 11/22/2022]
Abstract
Cyclotides are a unique and growing family of backbone cyclized peptides that also contain a cystine knot motif built from six conserved cysteine residues. This unique circular backbone topology and knotted arrangement of three disulfide bonds makes them exceptionally stable to thermal, chemical, and enzymatic degradation compared to other peptides of similar size. Aside from the conserved residues forming the cystine knot, cyclotides have been shown to have high variability in their sequences. Consisting of over 160 known members, cyclotides have many biological activities, ranging from anti-HIV, antimicrobial, hemolytic, and uterotonic capabilities; additionally, some cyclotides have been shown to have cell penetrating properties. Originally discovered and isolated from plants, cyclotides can also be produced synthetically and recombinantly. The high sequence variability, stability, and cell penetrating properties of cyclotides make them potential scaffolds to be used to graft known active peptides or engineer peptide-based drug design. The present review reports recent findings in the biological diversity and therapeutic potential of natural and engineered cyclotides.
Collapse
Affiliation(s)
- Andrew Gould
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90033, USA
| | | | | | | |
Collapse
|
83
|
Boll E, Dheur J, Drobecq H, Melnyk O. Access to Cyclic or Branched Peptides Using Bis(2-sulfanylethyl)amido Side-Chain Derivatives of Asp and Glu. Org Lett 2012; 14:2222-5. [DOI: 10.1021/ol300528r] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Emmanuelle Boll
- CNRS UMR 8161, Université Lille Nord de France, Institut Pasteur de Lille, 59021, Lille, France
| | - Julien Dheur
- CNRS UMR 8161, Université Lille Nord de France, Institut Pasteur de Lille, 59021, Lille, France
| | - Hervé Drobecq
- CNRS UMR 8161, Université Lille Nord de France, Institut Pasteur de Lille, 59021, Lille, France
| | - Oleg Melnyk
- CNRS UMR 8161, Université Lille Nord de France, Institut Pasteur de Lille, 59021, Lille, France
| |
Collapse
|
84
|
Getz JA, Rice JJ, Daugherty PS. Protease-resistant peptide ligands from a knottin scaffold library. ACS Chem Biol 2011; 6:837-44. [PMID: 21615106 PMCID: PMC3158827 DOI: 10.1021/cb200039s] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Peptides within the knottin family have been shown to possess inherent stability, making them attractive scaffolds for the development of therapeutic and diagnostic agents. Given its remarkable stability to proteases, the cyclic peptide kalata B1 was employed as a scaffold to create a large knottin library displayed on the surface of E. coli. A library exceeding 10(9) variants was constructed by randomizing seven amino acids within a loop of the kalata B1 scaffold and screened using fluorescence-activated cell sorting to identify peptide ligands specific for the active site of human thrombin. Refolded thrombin binders exhibited high nanomolar affinities in solution and slow dissociation rates and were able to inhibit thrombin's enzymatic activity. Importantly, 80% of a knottin-based thrombin inhibitor remained intact after a 2 h incubation both with trypsin and with chymotrypsin, demonstrating that modifying the kalata B1 sequence did not compromise its stability properties. In addition, the knottin variant mediated 20-fold enhanced affinity for thrombin, when compared to the same seven residue binding epitope constrained by a single disulfide bond. Our results indicate that peptide libraries derived from the kalata B1 scaffold can yield high-affinity protein ligands that retain the remarkable protease resistance associated with the parent scaffold. More generally, this strategy may prove useful in the development of stable peptide ligands suitable for in vivo applications.
Collapse
Affiliation(s)
- Jennifer A. Getz
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106
- Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA 93106
| | - Jeffrey J. Rice
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106
- Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA 93106
| | - Patrick S. Daugherty
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106
- Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA 93106
- Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106
| |
Collapse
|
85
|
Appleby-Tagoe JH, Thiel IV, Wang Y, Wang Y, Mootz HD, Liu XQ. Highly efficient and more general cis- and trans-splicing inteins through sequential directed evolution. J Biol Chem 2011; 286:34440-7. [PMID: 21832069 DOI: 10.1074/jbc.m111.277350] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Inteins are internal protein sequences that post-translationally self-excise and splice together the flanking sequences, the so-called exteins. Natural and engineered inteins have been used in many practical applications. However, inteins are often inefficient or inactive when placed in a non-native host protein and may require the presence of several amino acid residues of the native exteins, which will then remain as a potential scar in the spliced protein. Thus, more general inteins that overcome these limitations are highly desirable. Here we report sequential directed evolution as a new approach to produce inteins with such properties. Random mutants of the Ssp (Synechocystis sp. PCC 6803) DnaB mini-intein were inserted into the protein conferring kanamycin resistance at a site where the parent intein was inactive for splicing. The mutants selected for splicing activity were further improved by iterating the procedure for two more cycles at different positions in the same protein. The resulting improved inteins showed high activity in the positions of the first rounds of selection, in multiple new insertion sites, and in different proteins. One of these inteins, the M86 mutant, which accumulated 8 amino acid substitutions, was also biochemically characterized in an artificially split form with a chemically synthesized N-terminal intein fragment consisting of 11 amino acids. When compared with the unevolved split intein, it exhibited an ∼60-fold increased rate in the protein trans-splicing reaction and a K(d) value for the interaction of the split intein fragments improved by an order of magnitude. Implications on the intein structure-function, practical application, and evolution are discussed.
Collapse
Affiliation(s)
- Julia H Appleby-Tagoe
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 1X5, Canada
| | | | | | | | | | | |
Collapse
|
86
|
Katoh T, Goto Y, Reza MS, Suga H. Ribosomal synthesis of backbone macrocyclic peptides. Chem Commun (Camb) 2011; 47:9946-58. [PMID: 21766105 DOI: 10.1039/c1cc12647d] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A wealth of knowledge has been accumulated on ribosomal synthesis of macrocyclic peptides in the past decade. In nature, backbone cyclization of the translated linear peptides is generally catalyzed by specific enzymes, giving them peptidase resistance, thermodynamic stability and various other physiological activities. Due to these biochemical traits, backbone cyclic peptides have become an attractive resource for the discovery of drug leads. Recently, various new methodologies have also been established to generate man-made cyclic peptides. Here, we describe the biosynthetic mechanisms of naturally occurring backbone macrocyclic peptides focusing on cyclotides, sunflower trypsin inhibitors (SFTIs) and cyanobactins as well as several new emerging methodologies, such as sortase mediated ligation, protein splicing method and genetic code reprogramming.
Collapse
Affiliation(s)
- Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | | | | | | |
Collapse
|
87
|
Lyskowski A, Oeemig JS, Jaakkonen A, Rommi K, DiMaio F, Zhou D, Kajander T, Baker D, Wlodawer A, Goldman A, Iwaï H. Cloning, expression, purification, crystallization and preliminary X-ray diffraction data of the Pyrococcus horikoshii RadA intein. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:623-6. [PMID: 21543876 DOI: 10.1107/s1744309111008372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Accepted: 03/05/2011] [Indexed: 11/10/2022]
Abstract
The RadA intein from the hyperthermophilic archaebacterium Pyrococcus horikoshii was cloned, expressed and purified for subsequent structure determination. The protein crystallized rapidly in several conditions. The best crystals, which diffracted to 1.75 Å resolution, were harvested from drops consisting of 0.1 M HEPES pH 7.5, 3.0 M NaCl and were cryoprotected with Paratone-N before flash-cooling. The collected data were processed in the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 58.1, b = 67.4, c = 82.9 Å. Molecular replacement with Rosetta using energy- and density-guided structure optimization provided the initial solution, which is currently under refinement.
Collapse
Affiliation(s)
- Andrzej Lyskowski
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, PO Box 65, Helsinki FIN-00014, Finland
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
88
|
Tae HS, Cui Y, Karunasekara Y, Board PG, Dulhunty AF, Casarotto MG. Cyclization of the intrinsically disordered α1S dihydropyridine receptor II-III loop enhances secondary structure and in vitro function. J Biol Chem 2011; 286:22589-99. [PMID: 21525002 DOI: 10.1074/jbc.m110.205476] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A key component of excitation contraction (EC) coupling in skeletal muscle is the cytoplasmic linker (II-III loop) between the second and third transmembrane repeats of the α(1S) subunit of the dihydropyridine receptor (DHPR). The II-III loop has been previously examined in vitro using a linear II-III loop with unrestrained N- and C-terminal ends. To better reproduce the loop structure in its native environment (tethered to the DHPR transmembrane domains), we have joined the N and C termini using intein-mediated technology. Circular dichroism and NMR spectroscopy revealed a structural shift in the cyclized loop toward a protein with increased α-helical and β-strand structure in a region of the loop implicated in its in vitro function and also in a critical region for EC coupling. The affinity of binding of the II-III loop binding to the SPRY2 domain of the skeletal ryanodine receptor (RyR1) increased 4-fold, and its ability to activate RyR1 channels in lipid bilayers was enhanced 3-fold by cyclization. These functional changes were predicted consequences of the structural enhancement. We suggest that tethering the N and C termini stabilized secondary structural elements in the DHPR II-III loop and may reflect structural and dynamic characteristics of the loop that are inherent in EC coupling.
Collapse
Affiliation(s)
- Han-Shen Tae
- John Curtin School of Medical Research, Australian National University, PO Box 334, Canberra, Australian Capital Territory 2601, Australia
| | | | | | | | | | | |
Collapse
|
89
|
Schlesinger SR, Kim SG, Lee JS, Kim SK. Purification development and characterization of the zinc-dependent metallo-β-lactamase from Bacillus anthracis. Biotechnol Lett 2011; 33:1417-22. [PMID: 21369909 DOI: 10.1007/s10529-011-0569-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 02/14/2011] [Indexed: 11/29/2022]
Abstract
Metallo-β-lactamase from Bacillus anthracis (Bla2) catalyzes the hydrolysis of β-lactam antibiotics which are commonly prescribed to combat bacterial infections. Bla2 contributes to the antibiotic resistance of this bacterium. An understanding of it is necessary to design potential inhibitors that can be introduced with current antibiotics for effective eradication of anthrax infections. We have purified Bla2 using Ni(2+)-affinity chromatography with over 140-fold increase in activity with a yield of 3.5%. The final specific activity was 19,000 units/mg. Purified Bla2 displays different K ( m ), V ( max ), and (k ( cat ) /K (M)) with penicillin G and cephalexin as substrates and is also sensitive to pH, with maximum activity between pH 7.0-9.0. The IC(50) (50% inhibition concentration) value of EDTA against Bla2 is 630 nM, which can be understood by observing its three-dimensional interaction with the enzyme.
Collapse
Affiliation(s)
- Sara R Schlesinger
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798-7348, USA.
| | | | | | | |
Collapse
|
90
|
Sortase-catalyzed transformations that improve the properties of cytokines. Proc Natl Acad Sci U S A 2011; 108:3169-74. [PMID: 21297034 DOI: 10.1073/pnas.1016863108] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recombinant protein therapeutics often suffer from short circulating half-life and poor stability, necessitating multiple injections and resulting in limited shelf-life. Conjugation to polyethylene glycol chains (PEG) extends the circulatory half-life of many proteins, but the methods for attachment often lack specificity, resulting in loss of biological activity. Using four-helix bundle cytokines as an example, we present a general platform that uses sortase-mediated transpeptidation to facilitate site-specific attachment of PEG to extend cytokine half-life with full retention of biological activity. Covalently joining the N and C termini of proteins to obtain circular polypeptides, again executed using sortase, increases thermal stability. We combined both PEGylation and circularization by exploiting two distinct sortase enzymes and the use of a molecular suture that allows both site-specific PEGylation and covalent closure. The method developed is general, uses a set of easily accessible reagents, and should be applicable to a wide variety of proteins, provided that their termini are not involved in receptor binding or function.
Collapse
|
91
|
Ozawa T, Umezawa Y. Peptide Assemblies in Living Cells. Methods for Detecting Protein-Protein Interactions†. Supramol Chem 2010. [DOI: 10.1080/10610270290026185] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Takeaki Ozawa
- a Department of Chemistry, School of Science , The University of Tokyo , Hongo, Bunkyo-ku, Tokyo , 113-0033 , Japan
- b Japan Science and Technology Corporation , Tokyo , Japan
| | - Yoshio Umezawa
- a Department of Chemistry, School of Science , The University of Tokyo , Hongo, Bunkyo-ku, Tokyo , 113-0033 , Japan
- b Japan Science and Technology Corporation , Tokyo , Japan
| |
Collapse
|
92
|
Deschuyteneer G, Garcia S, Michiels B, Baudoux B, Degand H, Morsomme P, Soumillion P. Intein-mediated cyclization of randomized peptides in the periplasm of Escherichia coli and their extracellular secretion. ACS Chem Biol 2010; 5:691-700. [PMID: 20527881 DOI: 10.1021/cb100072u] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Split-inteins can be used to generate backbone cyclized peptide as a source of new bioactive molecules. In this work we show that cysteine-mediated splicing can be performed in the oxidative environment of the periplasm of Escherichia coli. Cyclization of the TEM-1 beta-lactamase and of small randomized peptides was demonstrated using an artificially permuted version of the DnaB mini-intein from Synechocystis sp. PCC6803 strain fused to a signal sequence. For small peptides, a signal sequence that promotes cotranslational translocation had to be used. Efficient backbone cyclization was observed for more than 50% of combinatorial peptides featuring a fully randomized sequence inserted between a serine and glycine that are necessary for fast splicing. Furthermore, by coexpressing a mutant of the pIV outer membrane pore protein of fd bacteriophage, we showed that peptides can diffuse in the extracellular medium. These results open new routes for searching compounds acting on new targets such as exported and membrane proteins or pathogen microorganisms.
Collapse
Affiliation(s)
| | | | | | | | - Hervé Degand
- Physiologie Moléculaire, Institut des Sciences de la Vie, Université catholique de Louvain, Place Croix du Sud 4-5, B-1348 Louvain-la-Neuve, Belgium
| | - Pierre Morsomme
- Physiologie Moléculaire, Institut des Sciences de la Vie, Université catholique de Louvain, Place Croix du Sud 4-5, B-1348 Louvain-la-Neuve, Belgium
| | | |
Collapse
|
93
|
Kaas Q, Craik DJ. Analysis and classification of circular proteins in CyBase. Biopolymers 2010; 94:584-91. [DOI: 10.1002/bip.21424] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
94
|
Abstract
AbstractOptimal stereospecific and regiospecific labeling of proteins with stable isotopes enhances the nuclear magnetic resonance (NMR) method for the determination of the three-dimensional protein structures in solution. Stereo-array isotope labeling (SAIL) offers sharpened lines, spectral simplification without loss of information and the ability to rapidly collect and automatically evaluate the structural restraints required to solve a high-quality solution structure for proteins up to twice as large as before. This review gives an overview of stable isotope labeling methods for NMR spectroscopy with proteins and provides an in-depth treatment of the SAIL technology.
Collapse
|
95
|
Volkmann G, Iwaï H. Protein trans-splicing and its use in structural biology: opportunities and limitations. MOLECULAR BIOSYSTEMS 2010; 6:2110-21. [DOI: 10.1039/c0mb00034e] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
96
|
Skrisovska L, Schubert M, Allain FHT. Recent advances in segmental isotope labeling of proteins: NMR applications to large proteins and glycoproteins. JOURNAL OF BIOMOLECULAR NMR 2010; 46:51-65. [PMID: 19690964 DOI: 10.1007/s10858-009-9362-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2009] [Accepted: 07/17/2009] [Indexed: 05/19/2023]
Abstract
In the last 15 years substantial advances have been made to place isotope labels in native and glycosylated proteins for NMR studies and structure determination. Key developments include segmental isotope labeling using Native Chemical Ligation, Expressed Protein Ligation and Protein Trans-Splicing. These advances are pushing the size limit of NMR spectroscopy further making larger proteins accessible for this technique. It is just emerging that segmental isotope labeling can be used to define inter-domain interactions in NMR structure determination. Labeling of post-translational modified proteins like glycoproteins remains difficult but some promising developments were recently achieved. Key achievements are segmental and site-specific labeling schemes that improve resonance assignment and structure determination of the glycan moiety. We adjusted the focus of this perspective article to concentrate on the NMR applications based on recent developments rather than on labeling methods themselves to illustrate the considerable potential for biomolecular NMR.
Collapse
Affiliation(s)
- Lenka Skrisovska
- Institute for Molecular Biology and Biophysics, ETH Zürich, Zurich, Switzerland
| | | | | |
Collapse
|
97
|
Gao Y, Cui T, Lam Y. Synthesis and disulfide bond connectivity-activity studies of a kalata B1-inspired cyclopeptide against dengue NS2B-NS3 protease. Bioorg Med Chem 2009; 18:1331-6. [PMID: 20042339 DOI: 10.1016/j.bmc.2009.12.026] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2009] [Revised: 12/07/2009] [Accepted: 12/08/2009] [Indexed: 10/20/2022]
Abstract
Kalata B1 is a plant protein with remarkable thermal, chemical and enzymatic stability. Its potential applications could be centered on the possibility of using its cyclic structure and cystine knot motif as a scaffold for the design of stable pharmaceuticals. To discover potent dengue NS2B-NS3 protease inhibitors, we have prepared various kalata B1 analogues by varying the amino acid sequence. Mass spectrometric and biochemical investigations of these analogues revealed a cyclopeptide whose two fully oxidized forms are substrate-competitive inhibitors of the dengue viral NS2B-NS3 protease. Both oxidized forms showed potent inhibition with K(i) of 1.39+/-0.35 and 3.03+/-0.75 microM, respectively.
Collapse
Affiliation(s)
- Yaojun Gao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | | | | |
Collapse
|
98
|
Berrade L, Camarero JA. Expressed protein ligation: a resourceful tool to study protein structure and function. Cell Mol Life Sci 2009; 66:3909-22. [PMID: 19685006 PMCID: PMC3806878 DOI: 10.1007/s00018-009-0122-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2009] [Revised: 07/23/2009] [Accepted: 07/28/2009] [Indexed: 01/21/2023]
Abstract
This review outlines the use of expressed protein ligation (EPL) to study protein structure, function and stability. EPL is a chemoselective ligation method that allows the selective ligation of unprotected polypeptides from synthetic and recombinant origin for the production of semi-synthetic protein samples of well-defined and homogeneous chemical composition. This method has been extensively used for the site-specific introduction of biophysical probes, unnatural amino acids, and increasingly complex post-translational modifications. Since it was introduced 10 years ago, EPL applications have grown increasingly more sophisticated in order to address even more complex biological questions. In this review, we highlight how this powerful technology combined with standard biochemical analysis techniques has been used to improve our ability to understand protein structure and function.
Collapse
Affiliation(s)
- Luis Berrade
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, PSC 616, Los Angeles, CA 90033 USA
| | - Julio A. Camarero
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, PSC 616, Los Angeles, CA 90033 USA
| |
Collapse
|
99
|
Sancheti H, Camarero JA. "Splicing up" drug discovery. Cell-based expression and screening of genetically-encoded libraries of backbone-cyclized polypeptides. Adv Drug Deliv Rev 2009; 61:908-17. [PMID: 19628015 PMCID: PMC3329944 DOI: 10.1016/j.addr.2009.07.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Revised: 07/02/2009] [Accepted: 07/08/2009] [Indexed: 01/22/2023]
Abstract
The present paper reviews the use of protein splicing for the biosynthesis of backbone cyclic polypeptides. This general method allows the in vivo and in vitro biosynthesis of cyclic polypeptides using recombinant DNA expression techniques. Biosynthetic access to backbone cyclic peptides opens the possibility to generate cell-based combinatorial libraries that can be screened inside living cells for their ability to attenuate or inhibit cellular processes thus providing a new way for finding therapeutic agents.
Collapse
Affiliation(s)
- Harshkumar Sancheti
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90033
| | - Julio A. Camarero
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90033
| |
Collapse
|
100
|
Austin J, Kimura RH, Woo YH, Camarero JA. In vivo biosynthesis of an Ala-scan library based on the cyclic peptide SFTI-1. Amino Acids 2009; 38:1313-22. [PMID: 19685144 DOI: 10.1007/s00726-009-0338-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Accepted: 07/30/2009] [Indexed: 10/20/2022]
Abstract
We present the in vivo biosynthesis of wild-type sunflower trypsin inhibitor 1 (SFTI-1) inside E. coli cells using an intramolecular native chemical ligation in combination with a modified protein splicing unit. SFTI-1 is a small backbone cyclized polypeptide with a single disulfide bridge. A small library containing multiple Ala mutants was also biosynthesized and its activity was assayed using a trypsin-binding assay. This study clearly demonstrates the exciting possibility of generating large cyclic peptide libraries in live E. coli cells, and is a critical first step for developing in vivo screening and directed evolution technologies using the cyclic peptide SFTI-1 as a molecular scaffold.
Collapse
Affiliation(s)
- Jeffrey Austin
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | | | | | | |
Collapse
|