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Probing How Defects in Self-assembled Monolayers Affect Peptide Adsorption with Molecular Simulation

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Foundations of Molecular Modeling and Simulation

Part of the book series: Molecular Modeling and Simulation ((MMAS))

Abstract

Due to their flexible chemical functionality and simple formulation, self-assembled monolayer (SAM) surfaces have become an ideal choice for a multitude of wide-ranging applications. However, a major issue in the preparation of SAM surfaces is naturally occurring defects that manifest in a number of different ways, including depressions in the underlying gold substrate that cause surface roughness or through incorrect self-assembly of the chains that causes domain boundary effects. Molecular simulations can provide valuable insight into the origins of these defects and the effect they have on biological and other processes. Molecular dynamics (MD) simulations have been performed on a SAM surface with a carboxylic acid/carboxylate terminal functionality and induced with two types of experimentally observed defects. The enhanced sampling method PTMetaD-WTE has been used to model the adsorption of LKα14 onto the two types of defective SAM surfaces and onto a control SAM surface with no defective chains. An advanced clustering algorithm has been used to elucidate the effect of the surface defects on the conformations of the adsorbed peptide. Results show significant structural differences arise as a result of the defects. Specifically, both types of defects lead to a near-complete loss of secondary structure of the adsorbed peptide as compared to the control simulation, in which LKα14 adopts a perfect helical structure at the SAM/water interface. On the surface with domain boundary effects, extended conformations of the peptide are stabilized, whereas on the SAM with surface roughness (i.e., chains of various lengths), random coil conformations dominate the ensemble of surface-bound structures.

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Acknowledgments

JP and KGS acknowledge financial support from NSF award CBET-1264459. This work was facilitated through the use of computational, storage, and networking infrastructure provided by the Hyak supercomputer system, supported in part by the University of Washington and the UW Student Technology Fee Proposal program (award 2015-028). This research was also supported by the National Natural Science Foundation of China through grant numbers 21450110411, 21476191, and 91434110, and by the Scientific Research Fund of the Zhejiang Provincial Education Department through grant number Y201329422.

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Authors and Affiliations

  1. Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA

    K. G. Sprenger & Jim Pfaendtner

  2. College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China

    Yi He

Authors
  1. K. G. Sprenger
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  2. Yi He
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  3. Jim Pfaendtner
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Correspondence to Jim Pfaendtner .

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Editors and Affiliations

  1. Department of Chemical &, Northwestern University, Evanston, Illinois, USA

    Randall Q Snurr

  2. Chemical Engineering, Imperial College London, London, United Kingdom

    Claire S. Adjiman

  3. York Buffalo, The State University of New, Buffalo, New York, USA

    David A. Kofke

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Sprenger, K., He, Y., Pfaendtner, J. (2016). Probing How Defects in Self-assembled Monolayers Affect Peptide Adsorption with Molecular Simulation. In: Snurr, R., Adjiman, C., Kofke, D. (eds) Foundations of Molecular Modeling and Simulation. Molecular Modeling and Simulation. Springer, Singapore. https://doi.org/10.1007/978-981-10-1128-3_2

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