uu.seUppsala University Publications
Change search
ReferencesLink to record
Permanent link

Direct link
Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structural Molecular Biology.
Show others and affiliations
2002 (English)In: Proteins: Structure, Function, and Genetics, Vol. 46, no 1, 7- p.Article in journal (Refereed) Published
Place, publisher, year, edition, pages
2002. Vol. 46, no 1, 7- p.
URN: urn:nbn:se:uu:diva-93805OAI: oai:DiVA.org:uu-93805DiVA: diva2:167398
Available from: 2005-11-11 Created: 2005-11-11 Last updated: 2009-06-02Bibliographically approved
In thesis
1. Exploring Ligand Binding in HIV-1 Protease and K+ Channels Using Computational Methods
Open this publication in new window or tab >>Exploring Ligand Binding in HIV-1 Protease and K+ Channels Using Computational Methods
2005 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Understanding protein-ligand interactions is highly important in drug development. In the present work the objective is to comprehend the link between structure and function using molecular modelling. Specifically, this thesis has been focused on implementation of receptor flexibility in molecular docking and studying structure-activity relationships of potassium ion channels and their blockers.

In ligand docking simulations protein motion and heterogeneity of structural waters are approximated using an ensemble of protein structures. Four methods of combining multiple target structures within a single grid-based lookup table of interaction energies are tested. Two weighted average methods permit consistent and accurate ligand docking using a single grid representation of the target protein structures.

Quaternary ammonium ions (QAIs) are well known K+ channel blockers. Conformations around C–N bonds at the quaternary centre in tetraalkylammonium ions in water solution are investigated using quantum mechanical methods. Relative solvation free energies of QAIs are further estimated from molecular dynamics simulations. The torsion barrier for a two-step interconversion between the conformations D2d and S4 is calculated to be 9.5 kcal mol–1. Furthermore D2d is found to be more stable than the S4 conformation which is in agreement with experimental studies. External QAI binding to the K+ channel KcsA is also studied. Computer simulations and relative binding free energies of the KcsA complexes with QAIs are calculated. This is done with the molecular dynamics free energy perturbation approach together with automated ligand docking. In agreement with experiment, the Et4N+ blocker in D2d symmetry has better binding than the other QAIs.

Binding of blockers to the human cardiac hERG potassium channel is studied using a combination of homology modelling, automated docking and molecular dynamics simulations. The calculations reproduce the relative binding affinities of a set of drug derivatives very well and indicate that both polar interactions near the intracellular opening of the selectivity filter as well as hydrophobic complementarity in the region around F656 are important for blocker binding. Hence, the derived model of hERG should be useful for further interpretations of structure-activity relationships.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2005. 44 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 124
Cell and molecular biology, hERG, KcsA, AutoDock, LIE, molecular dynamics, ion channels, Cell- och molekylärbiologi
National Category
Biochemistry and Molecular Biology
urn:nbn:se:uu:diva-6167 (URN)91-554-6411-4 (ISBN)
Public defence
2005-12-02, B42, BMC, Husargatan 3, Uppsala, 14:00 (English)
Available from: 2005-11-11 Created: 2005-11-11 Last updated: 2009-06-02Bibliographically approved

Open Access in DiVA

No full text

By organisation
Structural Molecular Biology

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Total: 186 hits
ReferencesLink to record
Permanent link

Direct link