1
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Van Agthoven JF, Shams H, Cochran FV, Alonso JL, Kintzing JR, Garakani K, Adair BD, Xiong JP, Mofrad MRK, Cochran JR, Arnaout MA. Structural Basis of the Differential Binding of Engineered Knottins to Integrins αVβ3 and α5β1. Structure 2019; 27:1443-1451.e6. [PMID: 31353240 DOI: 10.1016/j.str.2019.06.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/29/2019] [Accepted: 06/28/2019] [Indexed: 01/06/2023]
Abstract
Targeting both integrins αVβ3 and α5β1 simultaneously appears to be more effective in cancer therapy than targeting each one alone. The structural requirements for bispecific binding of ligand to integrins have not been fully elucidated. RGD-containing knottin 2.5F binds selectively to αVβ3 and α5β1, whereas knottin 2.5D is αVβ3 specific. To elucidate the structural basis of this selectivity, we determined the structures of 2.5F and 2.5D as apo proteins and in complex with αVβ3, and compared their interactions with integrins using molecular dynamics simulations. These studies show that 2.5D engages αVβ3 by an induced fit, but conformational selection of a flexible RGD loop accounts for high-affinity selective binding of 2.5F to both integrins. The contrasting binding of the highly flexible low-affinity linear RGD peptides to multiple integrins suggests that a "Goldilocks zone" of conformational flexibility of the RGD loop in 2.5F underlies its selective binding promiscuity to integrins.
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Affiliation(s)
- Johannes F Van Agthoven
- Leukocyte Biology and Inflammation Program, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA; Structural Biology Program, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA; Division of Nephrology/Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Hengameh Shams
- Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA 94720, USA
| | - Frank V Cochran
- Departments of Bioengineering and Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - José L Alonso
- Leukocyte Biology and Inflammation Program, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA; Structural Biology Program, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA; Division of Nephrology/Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - James R Kintzing
- Departments of Bioengineering and Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Kiavash Garakani
- Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA 94720, USA
| | - Brian D Adair
- Leukocyte Biology and Inflammation Program, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA; Structural Biology Program, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA; Division of Nephrology/Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Jian-Ping Xiong
- Leukocyte Biology and Inflammation Program, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA; Structural Biology Program, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA; Division of Nephrology/Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Mohammad R K Mofrad
- Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA 94720, USA
| | - Jennifer R Cochran
- Departments of Bioengineering and Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - M Amin Arnaout
- Leukocyte Biology and Inflammation Program, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA; Structural Biology Program, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA; Division of Nephrology/Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA.
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2
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Abstract
Homochirality is a general feature of biological macromolecules, and Nature includes few examples of heterochiral proteins. Herein, we report on the design, chemical synthesis, and structural characterization of heterochiral proteins possessing loops of amino acids of chirality opposite to that of the rest of a protein scaffold. Using the protein Ecballium elaterium trypsin inhibitor II, we discover that selective β-alanine substitution favors the efficient folding of our heterochiral constructs. Solution nuclear magnetic resonance spectroscopy of one such heterochiral protein reveals a homogeneous global fold. Additionally, steered molecular dynamics simulation indicate β-alanine reduces the free energy required to fold the protein. We also find these heterochiral proteins to be more resistant to proteolysis than homochiral l-proteins. This work informs the design of heterochiral protein architectures containing stretches of both d- and l-amino acids.
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Affiliation(s)
- Surin K Mong
- Department of Chemistry, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Frank V Cochran
- Department of Bioengineering, Stanford University , 450 Serra Mall, Stanford, California 94305, United States
| | - Hongtao Yu
- Department of Chemistry, Tufts University , 62 Talbot Avenue, Medford, Massachusetts 02155, United States
| | - Zachary Graziano
- Department of Chemistry, Tufts University , 62 Talbot Avenue, Medford, Massachusetts 02155, United States
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University , 62 Talbot Avenue, Medford, Massachusetts 02155, United States
| | - Jennifer R Cochran
- Department of Bioengineering, Stanford University , 450 Serra Mall, Stanford, California 94305, United States
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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3
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Kim JW, Cochran FV, Cochran JR. A chemically cross-linked knottin dimer binds integrins with picomolar affinity and inhibits tumor cell migration and proliferation. J Am Chem Soc 2014; 137:6-9. [PMID: 25486381 PMCID: PMC4304478 DOI: 10.1021/ja508416e] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
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Molecules that target and inhibit
αvβ3, αvβ5, and α5β1 integrins have
generated great interest
because of the role of these receptors in mediating angiogenesis and
metastasis. Attempts to increase the binding affinity and hence the
efficacy of integrin inhibitors by dimerization have been marginally
effective. In the present work, we achieved this goal by using oxime-based
chemical conjugation to synthesize dimers of integrin-binding cystine
knot (knottin) miniproteins with low-picomolar binding affinity to
tumor cells. A non-natural amino acid containing an aminooxy side
chain was introduced at different locations within a knottin monomer
and reacted with dialdehyde-containing cross-linkers of different
lengths to create knottin dimers with varying molecular topologies.
Dimers cross-linked through an aminooxy functional group located near
the middle of the protein exhibited higher apparent binding affinity
to integrin-expressing tumor cells compared with dimers cross-linked
through an aminooxy group near the C-terminus. In contrast, the cross-linker
length had no effect on the integrin binding affinity. A chemical-based
dimerization strategy was critical, as knottin dimers created through
genetic fusion to a bivalent antibody domain exhibited only modest
improvement (less than 5-fold) in tumor cell binding relative to the
knottin monomer. The best oxime-conjugated knottin dimer achieved
an unprecedented 150-fold increase in apparent binding affinity over
the knottin monomer. Also, this dimer bound 3650-fold stronger and
inhibited tumor cell migration and proliferation compared with cilengitide,
an integrin-targeting peptidomimetic that performed poorly in recent
clinical trials, suggesting promise for further therapeutic development.
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Affiliation(s)
- Jun W Kim
- Departments of †Bioengineering and ‡Chemical Engineering, Stanford University , Stanford, California 94305, United States
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4
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Kryshtafovych A, Moult J, Bales P, Bazan JF, Biasini M, Burgin A, Chen C, Cochran FV, Craig TK, Das R, Fass D, Garcia-Doval C, Herzberg O, Lorimer D, Luecke H, Ma X, Nelson DC, van Raaij MJ, Rohwer F, Segall A, Seguritan V, Zeth K, Schwede T. Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10. Proteins 2014; 82 Suppl 2:26-42. [PMID: 24318984 PMCID: PMC4072496 DOI: 10.1002/prot.24489] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Revised: 11/01/2013] [Accepted: 11/09/2013] [Indexed: 11/12/2022]
Abstract
For the last two decades, CASP has assessed the state of the art in techniques for protein structure prediction and identified areas which required further development. CASP would not have been possible without the prediction targets provided by the experimental structural biology community. In the latest experiment, CASP10, more than 100 structures were suggested as prediction targets, some of which appeared to be extraordinarily difficult for modeling. In this article, authors of some of the most challenging targets discuss which specific scientific question motivated the experimental structure determination of the target protein, which structural features were especially interesting from a structural or functional perspective, and to what extent these features were correctly reproduced in the predictions submitted to CASP10. Specifically, the following targets will be presented: the acid-gated urea channel, a difficult to predict transmembrane protein from the important human pathogen Helicobacter pylori; the structure of human interleukin (IL)-34, a recently discovered helical cytokine; the structure of a functionally uncharacterized enzyme OrfY from Thermoproteus tenax formed by a gene duplication and a novel fold; an ORFan domain of mimivirus sulfhydryl oxidase R596; the fiber protein gene product 17 from bacteriophage T7; the bacteriophage CBA-120 tailspike protein; a virus coat protein from metagenomic samples of the marine environment; and finally, an unprecedented class of structure prediction targets based on engineered disulfide-rich small proteins.
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Affiliation(s)
- Andriy Kryshtafovych
- Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, California 95616,
| | - John Moult
- Institute for Bioscience and Biotechnology Research, Department of Cell Biology and Molecular genetics, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA;
| | - Patrick Bales
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA;
| | - J. Fernando Bazan
- (1) Departments of Protein Engineering and (2) Structural Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, (3) Present address: 44th & Aspen Life Sciences, 924 4th St. N., Stillwater, MN 55082,
| | - Marco Biasini
- (1) Biozentrum, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland; (2) SIB Swiss Institute of Bioinformatics, Klingelbergstrasse 50, 4056 Basel, Switzerland;
| | - Alex Burgin
- Broad Institute, 5 Cambridge Center, Cambridge, MA 02142, USA;
| | - Chen Chen
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA;
| | - Frank V. Cochran
- Department of Biochemistry, Stanford University, Stanford, California, 94305, USA;
| | | | - Rhiju Das
- (1) Department of Biochemistry, Stanford University, Stanford, California, 94305, USA; (2) Department of Physics, Stanford University, Stanford, California, 94305, USA,
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100 Israel, Tel: +972-8-934-3214; Fax: +972-8-934-4136;
| | - Carmela Garcia-Doval
- Centro Nactional de Biotecnologia (CNB-CSIC), calle Darwin 3, E-28049 Madrid, Spain.
| | - Osnat Herzberg
- (1) Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA; (2) Department of Chemistry and Biochemistry, University of Maryland, College Park;
| | - Donald Lorimer
- Emerald Bio, 7869 NE Day Rd W, Bainbridge Isle, WA 98110, USA;
| | - Hartmut Luecke
- Center for Biomembrane Systems and Depts. of Biochemistry, Biophysics & Computer Science, 3205 McGaugh Hall, University of California, Irvine, CA 92697-3900, USA;
| | - Xiaolei Ma
- (1) Departments of Protein Engineering and (2) Structural Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080 (3) Present address: Novartis Institutes for Biomedical Research, 4560 Horton St., Emeryville, CA 94608, USA;
| | - Daniel C. Nelson
- (1) Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA; (2) Department of Veterinary Medicine, University of Maryland, College Park,
| | - Mark J. van Raaij
- Centro Nactional de Biotecnologia (CNB-CSIC), calle Darwin 3, E-28049 Madrid, Spain.
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, CA 92182, USA;
| | - Anca Segall
- Department of Biology, San Diego State University, San Diego, CA 92182, USA;
| | - Victor Seguritan
- Department of Biology, San Diego State University, San Diego, CA 9218
| | - Kornelius Zeth
- Unidad de Biofisica (CSIC-UPV/EHU), Barrio Sarriena s/n 48940, Leioa, Vizcaya, SPAIN, and IKERBASQUE, Basque Foundation for Science, Bilbao, Spain;
| | - Torsten Schwede
- (1) Biozentrum, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland; (2) SIB Swiss Institute of Bioinformatics, Klingelbergstrasse 50, 4056 Basel, Switzerland;
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5
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Lutz AM, Willmann JK, Drescher CW, Ray P, Cochran FV, Urban N, Gambhir SS. Early Diagnosis of Ovarian Carcinoma: Is a Solution in Sight? Radiology 2011; 259:329-45. [DOI: 10.1148/radiol.11090563] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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6
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Kimura RH, Levin AM, Cochran FV, Cochran JR. Engineered cystine knot peptides that bind alphavbeta3, alphavbeta5, and alpha5beta1 integrins with low-nanomolar affinity. Proteins 2009; 77:359-69. [PMID: 19452550 DOI: 10.1002/prot.22441] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
There is a critical need for compounds that target cell surface integrin receptors for applications in cancer therapy and diagnosis. We used directed evolution to engineer the Ecballium elaterium trypsin inhibitor (EETI-II), a knottin peptide from the squash family of protease inhibitors, as a new class of integrin-binding agents. We generated yeast-displayed libraries of EETI-II by substituting its 6-amino acid trypsin binding loop with 11-amino acid loops containing the Arg-Gly-Asp integrin binding motif and randomized flanking residues. These libraries were screened in a high-throughput manner by fluorescence-activated cell sorting to identify mutants that bound to alpha(v)beta(3) integrin. Select peptides were synthesized and were shown to compete for natural ligand binding to integrin receptors expressed on the surface of U87MG glioblastoma cells with half-maximal inhibitory concentration values of 10-30 nM. Receptor specificity assays demonstrated that engineered knottin peptides bind to both alpha(v)beta(3) and alpha(v)beta(5) integrins with high affinity. Interestingly, we also discovered a peptide that binds with high affinity to alpha(v)beta(3), alpha(v)beta(5), and alpha(5)beta(1) integrins. This finding has important clinical implications because all three of these receptors can be coexpressed on tumors. In addition, we showed that engineered knottin peptides inhibit tumor cell adhesion to the extracellular matrix protein vitronectin, and in some cases fibronectin, depending on their integrin binding specificity. Collectively, these data validate EETI-II as a scaffold for protein engineering, and highlight the development of unique integrin-binding peptides with potential for translational applications in cancer.
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Affiliation(s)
- Richard H Kimura
- Department of Bioengineering, Cancer Center, Bio-X Program, Stanford University, Stanford, California 94305, USA
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7
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Liu Y, Adams JD, Turner K, Cochran FV, Gambhir SS, Soh HT. Controlling the selection stringency of phage display using a microfluidic device. Lab Chip 2009; 9:1033-6. [PMID: 19350081 DOI: 10.1039/b820985e] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
We report the utilization of microfluidic technology to phage selection and demonstrate that accurate control of washing stringency in our microfluidic magnetic separator (MMS) directly impacts the diversity of isolated peptide sequences. Reproducible generation of magnetic and fluidic forces allows controlled washing conditions that enable rapid convergence of selected peptide sequences. These findings may provide a foundation for the development of automated microsystems for rapid in vitro directed evolution of affinity reagents.
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Affiliation(s)
- Yanli Liu
- Neuroscience Research Institute, University of California, Santa Barbara, CA93106, USA
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8
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Lutz AM, Willmann JK, Cochran FV, Ray P, Gambhir SS. Cancer screening: a mathematical model relating secreted blood biomarker levels to tumor sizes. PLoS Med 2008; 5:e170. [PMID: 18715113 PMCID: PMC2517618 DOI: 10.1371/journal.pmed.0050170] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Accepted: 07/04/2008] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Increasing efforts and financial resources are being invested in early cancer detection research. Blood assays detecting tumor biomarkers promise noninvasive and financially reasonable screening for early cancer with high potential of positive impact on patients' survival and quality of life. For novel tumor biomarkers, the actual tumor detection limits are usually unknown and there have been no studies exploring the tumor burden detection limits of blood tumor biomarkers using mathematical models. Therefore, the purpose of this study was to develop a mathematical model relating blood biomarker levels to tumor burden. METHODS AND FINDINGS Using a linear one-compartment model, the steady state between tumor biomarker secretion into and removal out of the intravascular space was calculated. Two conditions were assumed: (1) the compartment (plasma) is well-mixed and kinetically homogenous; (2) the tumor biomarker consists of a protein that is secreted by tumor cells into the extracellular fluid compartment, and a certain percentage of the secreted protein enters the intravascular space at a continuous rate. The model was applied to two pathophysiologic conditions: tumor biomarker is secreted (1) exclusively by the tumor cells or (2) by both tumor cells and healthy normal cells. To test the model, a sensitivity analysis was performed assuming variable conditions of the model parameters. The model parameters were primed on the basis of literature data for two established and well-studied tumor biomarkers (CA125 and prostate-specific antigen [PSA]). Assuming biomarker secretion by tumor cells only and 10% of the secreted tumor biomarker reaching the plasma, the calculated minimally detectable tumor sizes ranged between 0.11 mm(3) and 3,610.14 mm(3) for CA125 and between 0.21 mm(3) and 131.51 mm(3) for PSA. When biomarker secretion by healthy cells and tumor cells was assumed, the calculated tumor sizes leading to positive test results ranged between 116.7 mm(3) and 1.52 x 10(6) mm(3) for CA125 and between 27 mm(3) and 3.45 x 10(5) mm(3) for PSA. One of the limitations of the study is the absence of quantitative data available in the literature on the secreted tumor biomarker amount per cancer cell in intact whole body animal tumor models or in cancer patients. Additionally, the fraction of secreted tumor biomarkers actually reaching the plasma is unknown. Therefore, we used data from published cell culture experiments to estimate tumor cell biomarker secretion rates and assumed a wide range of secretion rates to account for their potential changes due to field effects of the tumor environment. CONCLUSIONS This study introduced a linear one-compartment mathematical model that allows estimation of minimal detectable tumor sizes based on blood tumor biomarker assays. Assuming physiological data on CA125 and PSA from the literature, the model predicted detection limits of tumors that were in qualitative agreement with the actual clinical performance of both biomarkers. The model may be helpful in future estimation of minimal detectable tumor sizes for novel proteomic biomarker assays if sufficient physiologic data for the biomarker are available. The model may address the potential and limitations of tumor biomarkers, help prioritize biomarkers, and guide investments into early cancer detection research efforts.
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Affiliation(s)
- Amelie M Lutz
- Department of Radiology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Juergen K Willmann
- Department of Radiology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Frank V Cochran
- Department of Radiology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Pritha Ray
- Department of Radiology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Sanjiv S Gambhir
- Department of Radiology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Bioengineering, the Bio-X Program, Stanford University School of Medicine, Stanford, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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9
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McAllister KA, Zou H, Cochran FV, Bender GM, Senes A, Fry HC, Nanda V, Keenan PA, Lear JD, Saven JG, Therien MJ, Blasie JK, DeGrado WF. Using alpha-helical coiled-coils to design nanostructured metalloporphyrin arrays. J Am Chem Soc 2008; 130:11921-7. [PMID: 18710226 DOI: 10.1021/ja800697g] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have developed a computational design strategy based on the alpha-helical coiled-coil to generate modular peptide motifs capable of assembling into metalloporphyrin arrays of varying lengths. The current study highlights the extension of a two-metalloporphyrin array to a four-metalloporphyrin array through the incorporation of a coiled-coil repeat unit. Molecular dynamics simulations demonstrate that the initial design evolves rapidly to a stable structure with a small rmsd compared to the original model. Biophysical characterization reveals elongated proteins of the desired length, correct cofactor stoichiometry, and cofactor specificity. The successful extension of the two-porphyrin array demonstrates how this methodology serves as a foundation to create linear assemblies of organized electrically and optically responsive cofactors.
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Affiliation(s)
- Karen A McAllister
- Department of Biochemistry and Molecular Biophysics, Johnson Foundation, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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10
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Cochran FV, Wu SP, Wang W, Nanda V, Saven JG, Therien MJ, DeGrado WF. Computational De Novo Design and Characterization of a Four-Helix Bundle Protein that Selectively Binds a Nonbiological Cofactor [J. Am. Chem. Soc. 2005, 127, 1346−1347]. J Am Chem Soc 2005. [DOI: 10.1021/ja059923q] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Cochran FV, Wu SP, Wang W, Nanda V, Saven JG, Therien MJ, DeGrado WF. Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor. J Am Chem Soc 2005; 127:1346-7. [PMID: 15686346 DOI: 10.1021/ja044129a] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the complete de novo design of a four-helix bundle protein that selectively binds the nonbiological DPP-Fe(III) metalloporphyrin cofactor (DPP-Fe(III) = 5, 15-Di[(4-carboxymethyleneoxy)phenyl]porphinato iron(III)). A tetrameric, D2-symmetric backbone scaffold was constructed to encapsulate two DPP-Fe(III) units through bis(His) coordination. The complete sequence was determined with the aid of the statistical computational design algorithm SCADS. The 34-residue peptide was chemically synthesized. UV-vis and CD spectroscopy, size-exclusion chromatography, and analytical ultracentrifugation indicated the peptide undergoes a transition from a predominantly random coil monomer to an alpha-helical tetramer upon binding DPP-Fe(III). EPR spectroscopy studies indicated the axial imidazole ligands were oriented in a perpendicular fashion, as defined by second-shell interactions that were included in the design. The 1-D 1H NMR spectrum of the assembled protein displayed features of a well-packed interior. The assembled protein possessed functional redox properties different from those of structurally similar systems containing the heme cofactor. The designed peptide demonstrated remarkable cofactor selectivity with a significantly weaker binding affinity for the natural heme cofactor. These findings open a path for the selective incorporation of more elaborate cofactors into designed scaffolds for constructing molecularly well-defined nanoscale materials.
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Affiliation(s)
- Frank V Cochran
- Department of Biochemistry and Molecular Biophysics, Johnson Foundation, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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12
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Cochran FV, Hock AS, Schrock RR. Molybdenum and Tungsten Complexes That Contain the Diamidoamine Ligands [(C6F5NCH2CH2)2NMe]2-, [(3,4,5-C6H2F3NCH2CH2)2NMe]2-, and [(3-CF3C6H4NCH2CH2)2NMe]2-. Organometallics 2004. [DOI: 10.1021/om030638u] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Frank V. Cochran
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Adam S. Hock
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Richard R. Schrock
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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13
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Affiliation(s)
- Frank V. Cochran
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Richard R. Schrock
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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14
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Cochran FV, Bonitatebus PJ, Schrock RR. Molybdenum, Tungsten, and Rhenium d2 Complexes That Contain the [(C6F5NCH2CH2)2NMe]2- Ligand. Organometallics 2000. [DOI: 10.1021/om0001117] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Frank V. Cochran
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139
| | - Peter J. Bonitatebus
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139
| | - Richard R. Schrock
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139
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