Force-based analysis of multidimensional energy landscapes: application of dynamic force spectroscopy and steered molecular dynamics simulations to an antibody fragment-peptide complex.

Full 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 Gly(H)-H40 of the antibody fragment and Glu(Oepsilon)-6(peptide) 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.

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Author information

Author/s: Morfill, Julia (J); Neumann, Jan (J); Blank, Kerstin (K); Steinbach, Uta (U); Puchner, Elias M (EM); Gottschalk, Kay-E (KE); Gaub, Hermann E (HE);

Affiliation: Lehrstuhl für Angewandte Physik & Center for Nanoscience, LMU München, Amalienstrasse 54, D-80799 München, Germany.

Journal and publication information

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal: Journal of molecular biology (J Mol Biol), published in England. (Language: eng)

Reference: 2008-Sep; vol 381 (issue 5) : pp 1253-66

Dates: Created 2008/08/12; Completed 2008/09/15;

PMID: 18619976, status: MEDLINE (last retrieval date: 11/6/2008)

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MeSH headings (categories)

This article was linked to the MESH Headings shown below.

Computer Simulation
Immunoglobulin Fragments - chemistry
Microscopy, Atomic Force
Models, Molecular
Peptides - chemistry

Associated Chemicals: Immunoglobulin Fragments (0) ; Peptides (0)

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