Force-based Analysis of Multidimensional Energy Landscapes: Application of Dynamic Force Spectroscopy and Steered Molecular Dynamics Simulations to an Antibody Fragment-Peptide Complex

Julia Morfill, Jan Neumann, Kerstin Blank, Uta Steinbach, Elias M. Puchner, Kay E. Gottschalk, Hermann E. Gaub

Research output: Contribution to journalArticlepeer-review

42 Scopus citations

Abstract

Multidimensional energy landscapes are an intrinsic property of proteins and define their dynamic behavior as well as their response to external stimuli. In order to explore the energy landscape and its implications on the dynamic function of proteins dynamic force spectroscopy and steered molecular dynamics (SMD) simulations have proved to be important tools. In this study, these techniques have been employed to analyze the influence of the direction of the probing forces on the complex of an antibody fragment with its peptide antigen. Using an atomic force microscope, experiments were performed where the attachment points of the 12 amino acid long peptide antigen were varied. These measurements yielded clearly distinguishable basal dissociation rates and potential widths, proving that the direction of the applied force determines the unbinding pathway. Complementary atomistic SMD simulations were performed, which also show that the unbinding pathways of the system are dependent on the pulling direction. However, the main barrier to be crossed was independent of the pulling direction and is represented by a backbone hydrogen bond between GlyH-H40 of the antibody fragment and Glu-6peptide of the peptide. For each pulling direction, the observed barriers can be correlated with the rupture of specific interactions, which stabilize the bound complex. Furthermore, although the SMD simulations were performed at loading rates exceeding the experimental rates by orders of magnitude due to computational limitations, a detailed comparison of the barriers that were overcome in the SMD simulations with the data obtained from the atomic force microscope unbinding experiments show excellent agreement.

Original languageEnglish (US)
Pages (from-to)1253-1266
Number of pages14
JournalJournal of Molecular Biology
Volume381
Issue number5
DOIs
StatePublished - Sep 19 2008

Bibliographical note

Funding Information:
We thank Dr. Torsten Pirch and Professor Dr. Kirsten Jung for the SPR data, Professor Dr. Andreas Plückthun for the gift of the expression vector of the antibody fragment and Gert De Cremer for help in preparing Fig. 5 . This work was supported by the Center for Integrative Protein Science Munich, the European Union, the Deutsche Forschungsgemeinschaft and the Fonds der Chemischen Industrie.

Keywords

  • antibody-antigen interaction
  • atomic force microscope
  • energy landscape
  • molecular dynamics simulations
  • single molecule force spectroscopy

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