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Molecular Biotechnology Programme Uppsala University School of Engineering

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Molecular Biotechnology Programme

Uppsala University School of Engineering

UPTEC X 04 025 Date of issue 2004-04

Author

Jens Carlsson

Title (English)

Proton binding in proteins: pKa calculations with explicit and implicit solvent

Title (Swedish)

Abstract

Accurate and reliable pKa prediction is of significant interest, because it provides direct information of the protonation state of a protein and can be compared to experimental data. In this work pKa shifts of three aminoacids in proteins have been calculated using molecular dynamics free energy simulations with an explicit solvent and implicit Generalized Born solvent model. The direction of the shifts were correctly predicted in both the explicit and implicit solvent calculations, but the results were not in perfect agreement with experimental data.

Keywords

Proton binding, pKa, free energy calculations, molecular dynamics

Supervisors

David A. Case

Department of Molecular Biology, The Scripps Research Institute, San Diego, USA

Scientific reviewer

Johan Åqvist

Department of Cell and Molecular biology, Uppsala University

Project name Sponsors

Language

English

Security

ISSN 1401-2138 Classification

Supplementary bibliographical information Pages

34

Biology Education Centre Biomedical Center Husargatan 3 Uppsala Box 592 S-75124 Uppsala Tel +46 (0)18 4710000 Fax +46 (0)18 555217

References

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