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51. Bioinspired Silicification Reveals Structural Detail in Self-Assembled Peptide Cages

Author

Galloway, Johanna M., primary, Senior, Laura, additional, Fletcher, Jordan M., additional, Beesley, Joseph L., additional, Hodgson, Lorna R., additional, Harniman, Robert L., additional, Mantell, Judith M., additional, Coombs, Jennifer, additional, Rhys, Guto G., additional, Xue, Wei-Feng, additional, Mosayebi, Majid, additional, Linden, Noah, additional, Liverpool, Tanniemola B., additional, Curnow, Paul, additional, Verkade, Paul, additional, and Woolfson, Derek N., additional

Published
2017
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54. Decorating Self-Assembled Peptide Cages with Proteins

Author

Ross, James F., primary, Bridges, Angela, additional, Fletcher, Jordan M., additional, Shoemark, Deborah, additional, Alibhai, Dominic, additional, Bray, Harriet E. V., additional, Beesley, Joseph L., additional, Dawson, William M., additional, Hodgson, Lorna R., additional, Mantell, Judith, additional, Verkade, Paul, additional, Edge, Colin M., additional, Sessions, Richard B., additional, Tew, David, additional, and Woolfson, Derek N., additional

Published
2017
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56. The Dukes' Club fundamentals of colorectal surgery video series: A stepwise approach to laparoscopic right hemicolectomy– A video vignette.

Author

El‐Sayed, Charlotte, Fletcher, Jordan A., Sarmah, Panchali, Sivathondan, Pamela, and Vaughan‐Shaw, Peter G.

Subjects
*PROCTOLOGY, *RIGHT hemicolectomy, *LAPAROSCOPIC surgery, *VIGNETTES, *COLON cancer, *VIDEOS
Abstract

The Dukes' Club fundamentals of colorectal surgery video series: A stepwise approach to laparoscopic right hemicolectomy- A video vignette This Video S1 is a stepwise approach to a laparoscopic right hemicolectomy in a female patient and forms part of the educational "Fundamental of Colorectal Surgery" series presented by the Dukes' Club. Robotic-assisted surgery has grown in popularity over the years due to the ergonomic advantages over laparoscopic surgery; however, the benefits of right colon cancer surgery remain limited with only a few studies demonstrating improved outcomes [[7]]. [Extracted from the article]

Published
2023
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57. Interactions of HIV-1 antibodies 2F5 and 4E10 with a gp41 epitope prebound to host and viral membrane model systems

Author

Veiga, Ana S., Pattenden, Leonard K., Fletcher, Jordan M., Castanho, Miguel A. R. B., Aguilar, Marie Isabel, and Repositório da Universidade de Lisboa

Subjects
Membranes, Surface plasmon resonance, Membrane proteins, Immunogen design, Antibodies
Abstract

© 2009 Wiley, Two HIV-1 recognition domains for the human monoclonal ACHTUNGTRENUNGantibodies (MAb) 2F5, which recognises the core sequence ELDKWA, and 4E10, which recognises the core sequence NWFNIT, serve as promising models for immunogens in vaccine development against HIV-1. However, the failure of these recognition domains to generate broadly reactive neutralizing antibodies, and the putative membrane-binding properties of the antibodies raised to these recognition domains, suggest that additional features or recognition motifs are required to form an efficient immunogen, which could possibly include the membrane components. In this study we used an extended peptide epitope sequence derived from the gp41 native ACHTUNGTRENUNGsequence (H-NEQELLELDKWASLWNWFNITNWLWYIK-NH), which contains the two recognition domains for 2F5 and 4E10, to examine the role of model cell (POPC) and viral (POPC/cholesterol/sphingomyelin) membranes in the recognition of these two antibodies. By using a surface plasmon resonance biosensor, the binding of 2F5 and 4E10 to membranes was compared and contrasted in the presence and absence of prebound peptide epitope. The recognition of the peptide epitope by each MAb was found to be distinct; 2F5 exhibited strong and almost irreversible binding to both membranes in the presence of the peptide, but bound weakly in the absence of the peptide epitope. In contrast, 4E10 exhibited strong membrane binding in the presence or absence of the peptide epitope, and the binding was essentially irreversible in the presence of the peptide epitope. Overall, these results demonstrate that both 2F5 and 4E10 can bind to membranes prior to epitope recognition, but that high-affinity recognition of gp41-derived epitope sequences by 2F5 and 4E10 occurs in a membrane context. Moreover, 4E10 might utilise the membrane to access and bind to gp41; such membrane properties of 2F5 and 4E10 could be exploited in immunogen design., This project was partially funded by FCT-MCTES (Portugal), including a grant (SFRH/BD/14 336/2003) under the program POCTI to A.S.V. Bifonds travel allowance is also acknowledged. Monoclonal antibodies 2F5 and 4E10 were provided by Dr. Hermann Katinger and Polymun Scientific, through the NIBSC Centralised Facility for AIDS Reagents supported by EU Programme EVA and the UK Medical Research Council. The support of the Australian Research Council is also acknowledged.

Published
2009

60. Engineered synthetic scaffolds for organizing proteins within the bacterial cytoplasm

Author

Lee, Matthew J, Mantell, Judith, Hodgson, Lorna, Alibhai, Dominic, Fletcher, Jordan M, Brown, Ian R, Frank, Stefanie, Xue, Wei-Feng, Verkade, Paul, Woolfson, Derek N, and Warren, Martin J

Abstract

We have developed a system for producing a supramolecular scaffold that permeates the entire Escherichia coli cytoplasm. This cytoscaffold is constructed from a three-component system comprising a bacterial microcompartment shell protein and two complementary de novo coiled-coil peptides. We show that other proteins can be targeted to this intracellular filamentous arrangement. Specifically, the enzymes pyruvate decarboxylase and alcohol dehydrogenase have been directed to the filaments, leading to enhanced ethanol production in these engineered bacterial cells compared to those that do not produce the scaffold. This is consistent with improved metabolic efficiency through enzyme colocation. Finally, the shell-protein scaffold can be directed to the inner membrane of the cell, demonstrating how synthetic cellular organization can be coupled with spatial optimization through in-cell protein design. The cytoscaffold has potential in the development of next-generation cell factories, wherein it could be used to organize enzyme pathways and metabolite transporters to enhance metabolic flux.

Published
2018
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62. A Basis Set of de Novo Coiled-Coil Peptide Oligomers for Rational Protein Design and Synthetic Biology

Author

Fletcher, Jordan M., primary, Boyle, Aimee L., additional, Bruning, Marc, additional, Bartlett, Gail J., additional, Vincent, Thomas L., additional, Zaccai, Nathan R., additional, Armstrong, Craig T., additional, Bromley, Elizabeth H. C., additional, Booth, Paula J., additional, Brady, R. Leo, additional, Thomson, Andrew R., additional, and Woolfson, Derek N., additional

Published
2012
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63. N@aand N@d: Oligomer and Partner Specification by Asparagine in Coiled-Coil Interfaces

Author

Fletcher, Jordan M., Bartlett, Gail J., Boyle, Aimee L., Danon, Jonathan J., Rush, Laura E., Lupas, Andrei N., and Woolfson, Derek N.

Abstract

The α-helical coiled coil is one of the best-studied protein–protein interaction motifs. As a result, sequence-to-structure relationships are available for the prediction of natural coiled-coil sequences and the de novodesign of new ones. However, coiled coils adopt a wide range of oligomeric states and topologies, and our understanding of the specification of these and the discrimination between them remains incomplete. Gaps in our knowledge assume more importance as coiled coils are used increasingly to construct biomimetic systems of higher complexity; for this, coiled-coil components need to be robust, orthogonal, and transferable between contexts. Here, we explore how the polar side chain asparagine (Asn, N) is tolerated within otherwise hydrophobic helix–helix interfaces of coiled coils. The long-held view is that Asn placed at certain sites of the coiled-coil sequence repeat selects one oligomer state over others, which is rationalized by the ability of the side chain to make hydrogen bonds, or interactions with chelated ions within the coiled-coil interior of the favored state. We test this with experiments on de novopeptide sequences traditionally considered as directing parallel dimers and trimers, and more widely through bioinformatics analysis of natural coiled-coil sequences and structures. We find that when located centrally, rather than near the termini of such coiled-coil sequences, Asn does exert the anticipated oligomer-specifying influence. However, outside of these bounds, Asn is observed less frequently in the natural sequences, and the synthetic peptides are hyperthermostable and lose oligomer-state specificity. These findings highlight that not all regions of coiled-coil repeat sequences are equivalent, and that care is needed when designing coiled-coil interfaces.

Published
2017
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65. Synthesis of Stapled β3-Peptides through Ring-Closing Metathesis

Author

Bergman, Ylva E., primary, Del Borgo, Mark P., additional, Gopalan, Romila D., additional, Jalal, Sania, additional, Unabia, Sharon E., additional, Ciampini, Marisa, additional, Clayton, Daniel J., additional, Fletcher, Jordan M., additional, Mulder, Roger J., additional, Wilce, Jacqueline A., additional, Aguilar, Marie-Isabel, additional, and Perlmutter, Patrick, additional

Published
2009
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70. Bioinspired Silicification Reveals Structural Detail in Self-Assembled Peptide Cages.

Author

Galloway JM, Senior L, Fletcher JM, Beesley JL, Hodgson LR, Harniman RL, Mantell JM, Coombs J, Rhys GG, Xue WF, Mosayebi M, Linden N, Liverpool TB, Curnow P, Verkade P, and Woolfson DN

Subjects
Particle Size, Peptides chemistry, Surface Properties, Peptides chemical synthesis, Silicon Dioxide chemistry
Abstract

Understanding how molecules in self-assembled soft-matter nanostructures are organized is essential for improving the design of next-generation nanomaterials. Imaging these assemblies can be challenging and usually requires processing, e.g., staining or embedding, which can damage or obscure features. An alternative is to use bioinspired mineralization, mimicking how certain organisms use biomolecules to template mineral formation. Previously, we have reported the design and characterization of Self-Assembled peptide caGEs (SAGEs) formed from de novo peptide building blocks. In SAGEs, two complementary, 3-fold symmetric, peptide hubs combine to form a hexagonal lattice, which curves and closes to form SAGE nanoparticles. As hexagons alone cannot tile onto spheres, the network must also incorporate nonhexagonal shapes. While the hexagonal ultrastructure of the SAGEs has been imaged, these defects have not been observed. Here, we show that positively charged SAGEs biotemplate a thin, protective silica coating. Electron microscopy shows that these SiO 2 -SAGEs do not collapse, but maintain their 3D shape when dried. Atomic force microscopy reveals a network of hexagonal and irregular features on the SiO 2 -SAGE surface. The dimensions of these (7.2 nm ± 1.4 nm across, internal angles 119.8° ± 26.1°) are in accord with the designed SAGE network and with coarse-grained modeling of the SAGE assembly. The SiO 2 -SAGEs are permeable to small molecules (<2 nm), but not to larger biomolecules (>6 nm). Thus, bioinspired silicification offers a mild technique that preserves soft-matter nanoparticles for imaging, revealing structural details <10 nm in size, while also maintaining desirable properties, such as permeability to small molecules.

Published
2018
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71. Synthesis of stapled beta3-peptides through ring-closing metathesis.

Author

Bergman YE, Del Borgo MP, Gopalan RD, Jalal S, Unabia SE, Ciampini M, Clayton DJ, Fletcher JM, Mulder RJ, Wilce JA, Aguilar MI, and Perlmutter P

Subjects
Cyclization, Peptides chemistry, Protein Conformation, Protein Structure, Secondary, Peptides chemical synthesis
Abstract

The first synthesis of carbon-stapled beta(3)-peptides is reported. The precursor beta(3)-peptides, with O-allyl beta-serines located in an i/i+3 relationship, were prepared on solid phase. We show that efficient ring-closing metathesis (RCM) of these new beta(3)-peptides proceeds smoothly either in solution or on an appropriate solid support. All products were generated with high selectivity for the E-isomer.

Published
2009
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