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High-resolution structure of a BRICHOS domain and its implications for anti-amyloid chaperone activity on lung surfactant protein C
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular and Morphological Pathology. (Per Westermark)
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2012 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, no 7, 2325-2329 p.Article in journal (Refereed) Published
Abstract [en]

BRICHOS domains are encoded in >30 human genes, which are associated with cancer, neurodegeneration, and interstitial lung disease (ILD). The BRICHOS domain from lung surfactant protein C proprotein (proSP-C) is required for membrane insertion of SP-C and has anti-amyloid activity in vitro. Here, we report the 2.1 angstrom crystal structure of the human proSP-C BRICHOS domain, which, together with molecular dynamics simulations and hydrogen-deuterium exchange mass spectrometry, reveals how BRICHOS domains may mediate chaperone activity. Observation of amyloid deposits composed of mature SP-C in lung tissue samples from ILD patients with mutations in the BRICHOS domain or in its peptide-binding linker region supports the in vivo relevance of the proposed mechanism. The results indicate that ILD mutations interfering with proSP-C BRICHOS activity cause amyloid disease secondary to intramolecular chaperone malfunction.

Place, publisher, year, edition, pages
2012. Vol. 109, no 7, 2325-2329 p.
Keyword [en]
interstitial lung disease, SFTPC mutations, beta-sheet aggregates, transmembrane segment, discordant helix
National Category
Medical and Health Sciences
URN: urn:nbn:se:uu:diva-171673DOI: 10.1073/pnas.1114740109ISI: 000300489200038OAI: oai:DiVA.org:uu-171673DiVA: diva2:512249
Available from: 2012-03-27 Created: 2012-03-25 Last updated: 2015-01-23Bibliographically approved
In thesis
1. Advances in Ligand Binding Predictions using Molecular Dynamics Simulations
Open this publication in new window or tab >>Advances in Ligand Binding Predictions using Molecular Dynamics Simulations
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Biochemical processes all involve associations and dissociations of chemical entities. Understanding these is of substantial importance for many modern pharmaceutical applications. In this thesis, longstanding problems with regard to ligand binding are treated with computational methods, applied to proteins of key pharmaceutical importance. Homology modeling, docking, molecular dynamics simulations and free-energy calculations are used here for quantitative characterization of ligand binding to proteins. By combining computational tools, valuable contributions have been made for pharmaceutically relevant areas: a neglected tropical disease, an ion channel anti-drug-target, and GPCR drug-targets.

We report three compounds inhibiting cruzain, the main cysteine protease of the protozoa causing Chagas’ disease. The compounds were found through an extensive virtual screening study and validated with experimental enzymatic assays. The compounds inhibit the enzyme in the μM-range and are therefore valuable in further lead optimization studies.

A high-resolution crystal structure of the BRICHOS domain is reported, together with molecular dynamics simulations and hydrogen-deuterium exchange mass spectrometry studies. This work revealed a plausible mechanism for how the chaperone activity of the domain may operate.

Rationalization of structure-activity relationships for a set of analogous blockers of the hERG potassium channel is given. A homology model of the ion channel was used for docking compounds and molecular dynamics simulations together with the linear interaction energy method employed for calculating the binding free-energies.

The three-dimensional coordinates of two GPCRs, 5HT1B and 5HT2B, were derived from homology modeling and evaluated in the GPCR Dock 2013 assessment. Our models were in good correlation with the experimental structures and all of them placed among the top quarter of all models assessed. 

Finally, a computational method, based on molecular dynamics free-energy calculations, for performing alanine scanning was validated with the A2A adenosine receptor bound to either agonist or antagonist. The calculated binding free-energies were found to be in good agreement with experimental data and the method was subsequently extended to non-alanine mutations. With extensive experimental mutation data, this scheme is a valuable tool for quantitative understanding of ligand binding and can ultimately be used for structure-based drug design.

Place, publisher, year, edition, pages
Uppsala: Uppsala universitet, 2014. 51 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1172
free-energy perturbation, molecular dynamics, ligand binding, free-energy perturbation, linear interaction energy, binding free-energy, homology modeling, virtual screening, alanine scanning, amino acid mutagenesis, hERG, GPCR, adenosine receptor, serotonin receptor, BRICHOS, cruzain
National Category
Theoretical Chemistry Biological Sciences
urn:nbn:se:uu:diva-230777 (URN)978-91-554-9020-1 (ISBN)
Public defence
2014-10-15, B41, BMC, Husargatan 3, Uppsala, 13:15 (English)
Available from: 2014-09-23 Created: 2014-08-29 Last updated: 2015-01-23

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Westermark, PerKeränen, HenrikÅqvist, JohanPresto, JennyKnight, Stefan D.
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