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Molecular Dynamics Simulated Unfolding of von Willebrand Factor A Domains by Force

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Abstract

The three tandem A domains (A1, A2, and A3) of von Willebrand factor (VWF) play critical roles for its functions. The A1 and A3 domains contain respective binding sites for platelet glycoprotein Ib (GPIb) and collagen. The A2 domain hosts a proteolytic site for the VWF-cleavage enzyme A Disintegrin And Metalloprotease with a ThromboSpondin type 1 motifs 13 (ADAMTS-13). Previous studies suggested that shear flow assists the ADAMTS-13 cleavage of VWF by unfolding the A2 domain and thus exposing the cryptic proteolytic site. Here we used steered molecular dynamics (SMD) to simulate the unfolding of the A1 and A2 domains by tensile force. The forced unfolding of A2 started from the C-terminus because of its specific topology. The β-strands of A2 were pulled out sequentially, generating sawtooth-like peaks in the force-extension curves. The disulfide bond between A1 N- and C-termini prevented it from unfolding. After eliminating the disulfide bond, A1 was unfolded similarly as A2 in terms of the β-strand pullouts, but differed in the unfolding of helices. The major resistance of A1 and A2 to unfolding came from the hydrogen bond networks of the central β-sheets. Two different unfolding pathways of the β-strands were observed, where the sliding pathway encountered much higher energy barrier than the unzipping pathway.

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Acknowledgments

We thank Dr. Stephen Harvey for kindly providing computational resources for the MD simulations. We are also grateful for supercomputer time provided by TeraGrid via NCSA DAC grant MCB080011N and LRAC grant MCA08X014. This work is supported by NIH grant HL091020 (C.Z.) and a Scientist Development Grant from American Heart Association (J.L.).

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Authors and Affiliations

  1. George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA

    Wei Chen & Cheng Zhu

  2. Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA

    Jizhong Lou & Cheng Zhu

  3. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332-0363, USA

    Cheng Zhu

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  1. Wei Chen
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Correspondence to Cheng Zhu.

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Video 1

A2 was pulled at the C-terminal Cα atom while the N-terminal Cα atom was fixed. α-helices are shown as coiled ribbons, β-strands as ribbons with arrows, and loops as tubes. A blue and a red sphere indicate, respectively, the N- and C-terminal Cα atoms. The backbone atoms of Tyr1605 and Met1606 adjacent to the proteolytic site are shown as green spheres. (AVI 13994 kb)

Video 2

A2 was pulled at the N-terminal Cα atom while the C-terminal Cα atom was fixed. To facilitate comparison with Video 1, A2 in each frame has been translated such that the N-terminal Cα atom stays at its starting position to allow the structured portion of A2 to remain in view. The representations of A2 are the same as in Video 1. (AVI 17066 kb)

A1 with an intact disulfide bond was pulled at the C-terminal Cα atom while the N-terminal Cα atom was fixed. α-helices are shown as coiled ribbons, β-strands as ribbons with arrows, and loops as tubes. A blue and a red sphere indicate, respectively, the N- and C-terminal Cα atoms. The disulfide bond atoms are shown as bonds. (AVI 2814 kb)

Video 4

A1 with a broken disulfide bond was pulled at the C-terminal Cα atom while the N-terminal Cα atom was fixed. The representations of A1 are the same as in Video 3. (AVI 13738 kb)

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Chen, W., Lou, J. & Zhu, C. Molecular Dynamics Simulated Unfolding of von Willebrand Factor A Domains by Force. Cel. Mol. Bioeng. 2, 75–86 (2009). https://doi.org/10.1007/s12195-009-0051-0

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