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Unraveling a Trap-and-Trigger Mechanism in the pH-Sensitive Self-Assembly of Spider Silk Proteins

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† ‡ Department of Chemistry and Biochemistry and School of Chemical, Biological and Materials Engineering, University of Oklahoma, Norman, Oklahoma 73019, United States
Cite this: J. Phys. Chem. Lett. 2012, 3, 5, 658–662
Publication Date (Web):February 15, 2012
Copyright © 2012 American Chemical Society

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    When the major ampullate spidroins (MaSp1) are called upon to form spider dragline silk, one of nature’s most amazing materials, a small drop in pH must occur. Using a state-of-the-art simulation technique, constant pH molecular dynamics, we discovered a few residues that respond to the pH signal in the dimerization of the N-terminal domain (NTD) of MaSp1, which is an integral step in the fiber assembly. At neutral pH, the deprotonation of Glu79 and Glu119 leads to water penetration and structural changes at the monomer–monomer binding interface. At strongly acidic pH, the protonation of Asp39 and Asp40 weakens the electrostatic attraction between the monomers. Thus, we propose a “trap-and-trigger” mechanism whereby the intermolecular salt bridges at physiologically relevant pH conditions always act as a stabilizing “trap” favoring dimerization. As the pH is lowered to about 6, Glu79 and Glu119 become protonated, triggering the dimerization and subsequent silk formation. We speculate that this type of mechanism is operative in many other pH-sensitive biological processes.

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    4. Lucie da Rocha, António M. Baptista, Sara R. R. Campos. Approach to Study pH-Dependent Protein Association Using Constant-pH Molecular Dynamics: Application to the Dimerization of β-Lactoglobulin. Journal of Chemical Theory and Computation 2022, 18 (3) , 1982-2001.
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    7. Robert C. Harris, Cheng-Chieh Tsai, Christopher R. Ellis, and Jana Shen . Proton-Coupled Conformational Allostery Modulates the Inhibitor Selectivity for β-Secretase. The Journal of Physical Chemistry Letters 2017, 8 (19) , 4832-4837.
    8. Fernando Luís Barroso da Silva and Donal MacKernan . Benchmarking a Fast Proton Titration Scheme in Implicit Solvent for Biomolecular Simulations. Journal of Chemical Theory and Computation 2017, 13 (6) , 2915-2929.
    9. Anıl Kurut, Cedric Dicko, and Mikael Lund . Dimerization of Terminal Domains in Spiders Silk Proteins Is Controlled by Electrostatic Anisotropy and Modulated by Hydrophobic Patches. ACS Biomaterials Science & Engineering 2015, 1 (6) , 363-371.
    10. Afra Panahi and Charles L. Brooks, III . Membrane Environment Modulates the pKa Values of Transmembrane Helices. The Journal of Physical Chemistry B 2015, 119 (13) , 4601-4607.
    11. Julia Ries, Simone Schwarze, Christopher M. Johnson, and Hannes Neuweiler . Microsecond Folding and Domain Motions of a Spider Silk Protein Structural Switch. Journal of the American Chemical Society 2014, 136 (49) , 17136-17144.
    12. Garrett B. Goh, Elena N. Laricheva, and Charles L. Brooks, III . Uncovering pH-Dependent Transient States of Proteins with Buried Ionizable Residues. Journal of the American Chemical Society 2014, 136 (24) , 8496-8499.
    13. Garrett B. Goh, Jennifer L. Knight, and Charles L. Brooks, III . Toward Accurate Prediction of the Protonation Equilibrium of Nucleic Acids. The Journal of Physical Chemistry Letters 2013, 4 (5) , 760-766.
    14. Garrett B. Goh, Jennifer L. Knight, and Charles L. Brooks, III . pH-Dependent Dynamics of Complex RNA Macromolecules. Journal of Chemical Theory and Computation 2013, 9 (2) , 935-943.
    15. George C. Schatz (Editor-in-Chief) . Emerging Themes in Biophysical Chemistry. The Journal of Physical Chemistry Letters 2012, 3 (8) , 1072-1073.
    16. Vinicius Martins de Oliveira, Ruibin Liu, Jana Shen. Constant pH molecular dynamics simulations: Current status and recent applications. Current Opinion in Structural Biology 2022, 77 , 102498.
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    19. Yandong Huang, Jack A. Henderson, Jana Shen. Continuous Constant pH Molecular Dynamics Simulations of Transmembrane Proteins. 2021, 275-287.
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    21. Giulia Locatelli, Chiara Ponzio, Elia Bari. Silk. 2020, 25-63.
    22. Nicholas N. Ashton, Russell J. Stewart. Aquatic caddisworm silk is solidified by environmental metal ions during the natural fiber‐spinning process. The FASEB Journal 2019, 33 (1) , 572-583.
    23. Tasneem Kausar, Shahid M. Nayeem. Correlating interfacial water dynamics with protein-protein interaction in complex of GDF-5 and BMPRI receptors. Biophysical Chemistry 2018, 240 , 50-62.
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    26. Yunhui Peng, Emil Alexov. Computational investigation of proton transfer, pKa shifts and pH-optimum of protein-DNA and protein-RNA complexes. Proteins: Structure, Function, and Bioinformatics 2017, 85 (2) , 282-295.
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    28. Thierry Lefèvre, Michèle Auger. Spider silk as a blueprint for greener materials: a review. International Materials Reviews 2016, 61 (2) , 127-153.
    29. Shichang Zhang, I-Min Tso. Spider Silk: Factors Affecting Mechanical Properties and Biomimetic Applications. 2016, 489-513.
    30. D.N. Breslauer, D.L. Kaplan. Silks. 2016
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    32. A. Lin, T. Chuang, T. Pham, C. Ho, Y. Hsia, E. Blasingame, C. Vierra. Advances in understanding the properties of spider silk. 2015, 17-40.
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