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417 results on '"Kaas, Quentin"'

7. Delivery to, and Reactivation of, the p53 Pathway in Cancer Cells Using a Grafted Cyclotide Conjugated with a Cell-Penetrating Peptide

Author

Philippe, Grégoire Jean-Baptiste, primary, Huang, Yen-Hua, additional, Mittermeier, Anna, additional, Brown, Christopher J., additional, Kaas, Quentin, additional, Ramlan, Siti Radhiah, additional, Wang, Conan K., additional, Lane, David, additional, Loewer, Alexander, additional, Troeira Henriques, Sónia, additional, and Craik, David J., additional

Published
2024
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11. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat

Author

Babbitt, Patricia C, Bagos, Pantelis G, Bairoch, Amos, Bateman, Alex, Chatonnet, Arnaud, Chen, Mark Jinan, Craik, David J, Finn, Robert D, Gloriam, David, Haft, Daniel H, Henrissat, Bernard, Holliday, Gemma L, Isberg, Vignir, Kaas, Quentin, Landsman, David, Lenfant, Nicolas, Manning, Gerard, Nagano, Nozomi, Srinivasan, Narayanaswamy, O’Donovan, Claire, Pruitt, Kim D, Sowdhamini, Ramanathan, Rawlings, Neil D, Saier, Milton H, Sharman, Joanna L, Spedding, Michael, Tsirigos, Konstantinos D, Vastermark, Ake, and Vriend, Gerrit

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, 2.6 Resources and infrastructure (aetiology), 1.5 Resources and infrastructure (underpinning), Aetiology, Underpinning research, Generic health relevance, Computational Biology, Congresses as Topic, Databases, Nucleic Acid, Databases, Protein, Humans, Molecular Sequence Annotation, Proteins, Data Format, Library and Information Studies, Bioinformatics and computational biology, Data management and data science
Abstract

During 11-12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication and funding. An important outcome of this meeting was the creation of a Specialist Protein Resource Network that we believe will improve coordination of the activities of its member resources. We invite further protein database resources to join the network and continue the dialogue.

Published
2015

12. Computational Design of α‐Conotoxins to Target Specific Nicotinic Acetylcholine Receptor Subtypes.

Author

Wu, Xiaosa, Hone, Arik J., Huang, Yen‐Hua, Clark, Richard J., McIntosh, J. Michael, Kaas, Quentin, and Craik, David J.

Subjects
NICOTINIC acetylcholine receptors, CHOLINERGIC receptors, CONOTOXINS, CONUS, MOLECULAR dynamics, DRUG target, MOLECULAR models
Abstract

Nicotinic acetylcholine receptors (nAChRs) are drug targets for neurological diseases and disorders, but selective targeting of the large number of nAChR subtypes is challenging. Marine cone snail α‐conotoxins are potent blockers of nAChRs and some have been engineered to achieve subtype selectivity. This engineering effort would benefit from rapid computational methods able to predict mutational energies, but current approaches typically require high‐resolution experimental structures, which are not widely available for α‐conotoxin complexes. Herein, five mutational energy prediction methods were benchmarked using crystallographic and mutational data on two acetylcholine binding protein/α‐conotoxin systems. Molecular models were developed for six nAChR subtypes in complex with five α‐conotoxins that were studied through 150 substitutions. The best method was a combination of FoldX and molecular dynamics simulations, resulting in a predictive Matthews Correlation Coefficient (MCC) of 0.68 (85 % accuracy). Novel α‐conotoxin mutants designed using this method were successfully validated by experimental assay with improved pharmaceutical properties. This work paves the way for the rapid design of subtype‐specific nAChR ligands and potentially accelerated drug development. [ABSTRACT FROM AUTHOR]

Published
2024
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31. Melanocortin 1 Receptor Agonists Based on a Bivalent, Bicyclic Peptide Framework

Author

Durek, Thomas, primary, Kaas, Quentin, additional, White, Andrew M., additional, Weidmann, Joachim, additional, Fuaad, Abdullah Ahmad, additional, Cheneval, Olivier, additional, Schroeder, Christina I., additional, de Veer, Simon J., additional, Dellsén, Anita, additional, Österlund, Torben, additional, Larsson, Niklas, additional, Knerr, Laurent, additional, Bauer, Udo, additional, Plowright, Alleyn T., additional, and Craik, David J., additional

Published
2021
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39. Prediction of disulfide dihedral angles using chemical shifts† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c8sc01423j

Author

Armstrong, David A., Kaas, Quentin, and Rosengren, K. Johan

Subjects
Chemistry, fungi, food and beverages
Abstract

Chemical shifts can be used to predict the conformation of disulfide bonds, greatly improving resolution of solution NMR structures., Cystine residues result from the formation of disulfide bonds between pairs of cysteine residues. This cross linking of the backbone is essential for the structure and activity of peptides and proteins. The conformation of a cystine side chain can be described using five dihedral angles, χ1, χ2, χ3, χ2′, and χ1′, with cystines favouring certain combinations of these angles. 2D NMR spectroscopy is ideally suited for structure determination of disulfide-rich peptides, because of their small size and constrained nature. However, only limited information of the cystine side chain conformation can be determined by NMR spectroscopy, leading to ambiguity in the deduced 3D structures. Resolving accurate structures is important as disulfide-rich peptides have proven to be promising drug candidates in a number of fields, either as bioactive leads or scaffolds. Using a database of NMR chemical shifts combined with crystallographic structures, we have developed a method called DISH that uses support vector machines to predict the dihedral angles of cysteine side chains. It is able to successfully predict χ2 angles with 91% accuracy, and has improved performance over existing prediction methods for χ1 angles, with 87% accuracy. For 81% of cysteine residues, DISH successfully predicted both the χ1 and χ2 angles. By revisiting published solution structures of peptides determined using NMR spectroscopy, we assessed the impact of additional cystine dihedral restraints on the quality of 3D models. DISH improved the resolution and accuracy, highlighting the potential for improving the understanding of structure–activity relationships and rational development of peptide drugs.

Published
2018

40. Accurate de novo design of hyperstable constrained peptides

Author

Bhardwaj, Gaurav, Mulligan, Vikram Khipple, Bahl, Christopher D., Gilmore, Jason M., Harvey, Peta J., Cheneval, Olivier, Buchko, Garry W., Pulavarti, Surya V. S. R. K., Kaas, Quentin, Eletsky, Alexander, Huang, Po-Ssu, Johnsen, William A., Greisen, Per Jr, Rocklin, Gabriel J., Song, Yifan, Linsky, Thomas W., Watkins, Andrew, Rettie, Stephen A., Xu, Xianzhong, Carter, Lauren P., Bonneau, Richard, Olson, James M., Coutsias, Evangelos, Correnti, Colin E., Szyperski, Thomas, Craik, David J., and Baker, David

Subjects
Peptides -- Properties -- Analysis, Protein denaturation -- Analysis, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Naturally occurring, pharmacologically active peptides constrained with covalent crosslinks generally have shapes that have evolved to fit precisely into binding pockets on their targets. Such peptides can have excellent pharmaceutical properties, combining the stability and tissue penetration of small-molecule drugs with the specificity of much larger protein therapeutics. The ability to design constrained peptides with precisely specified tertiary structures would enable the design of shape-complementary inhibitors of arbitrary targets. Here we describe the development of computational methods for accurate de novo design of conformationally restricted peptides, and the use of these methods to design 1847 residue, disulfide-crosslinked peptides, a subset of which are heterochiral and/or NC backbone-cyclized. Both genetically encodable and non-canonical peptides are exceptionally stable to thermal and chemical denaturation, and 12 experimentally determined X-ray and NMR structures are nearly identical to the computational design models. The computational design methods and stable scaffolds presented here provide the basis for development of a new generation of peptide-based drugs., Author(s): Gaurav Bhardwaj [1, 2]; Vikram Khipple Mulligan [1, 2]; Christopher D. Bahl [1, 2]; Jason M. Gilmore [1, 2]; Peta J. Harvey [3]; Olivier Cheneval [3]; Garry W. Buchko [...]

Published
2016
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44. The [Lys(sup)-2-Arg(sup)-1-des(17-21)]-endothelin-1 peptide retains the specific Arg(sup)-1--Asp(sup)8 salt bridge but reveals discrepancies between NMR data and molecular dynamics simulations

Author

Kaas, Quentin, Aumelas, Andre, Kubo, Shigeru, Chino, Naoyoshi, Kobayashi, Yuji, and Chiche, Laurent

Subjects
Endothelin -- Analysis, Hydrogen-ion concentration -- Influence, Molecular dynamics -- Analysis, Biological sciences, Chemistry
Abstract

The endothelin-1 peptide, containing an N-terminal Arg-Lys dipeptide, undergoes conformational changes in the pH range of 1.5-4.5. Nuclear magnetic resonance studies show that the pH-mediated modifications are due to a salt bridge formed between Arg(sup)-1 and Asp(sup)8. However, the salt bridge shows no stability simulation.

Published
2002

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