Simulated and experimental force spectroscopy of lysozyme on silica

Physical Chemistry Chemical Physics : PCCP
Nils HildebrandLucio Colombi Ciacchi

Abstract

The force spectra of proteins detaching from oxide surfaces measured by atomic force microscopy (AFM) often present complex patterns of peaks, which are difficult to correlate with individual bond-breaking events at the atomic scale. In this work we rationalize experimental AFM force spectra of hen-egg-white lysozyme detaching from silica by means of all-atom steered molecular dynamics (SMD) simulations. In particular, we demonstrate that the native tertiary structure of lysozyme is preserved if, and only if, its four intramolecular disulfide bridges are intact. Otherwise, the protein pulled off the surface undergoes severe unfolding, which is well captured by SMD simulations in explicit solvent. Implicit solvent simulations, on the contrary, wrongly predict protein unfolding even in the presence of S-S bridges, due to the lack of additional structural stabilization provided by the water's hydrogen-bond network within and surrounding the protein. On the basis of our combined experimental and theoretical findings, we infer that the rugged force spectra characteristic of lysozyme/silica interfaces are not due to the successive breaking of internal disulfide bonds leading to partial unfolding events. Rather, they reflect the detac...Continue Reading

References

Jun 20, 1992·Journal of Molecular Biology·A CooperC M Dobson
Jan 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·R WetzelW J Becktel
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Mar 12, 1999·Science·M GrandboisH E Gaub
Apr 12, 2000·Biochemistry·W J WedemeyerH A Scheraga
Nov 9, 2000·The Journal of Biological Chemistry·N R Maiti, W K Surewicz
Apr 30, 2004·Journal of Computational Chemistry·Junmei WangDavid A Case
Jun 15, 2005·Langmuir : the ACS Journal of Surfaces and Colloids·Motoyoshi KobayashiMichal Borkovec
Feb 7, 2006·Journal of Molecular Graphics & Modelling·Junmei WangDavid A Case
Apr 22, 2006·Nature Methods·Peter Hinterdorfer, Yves F Dufrêne
Jan 11, 2007·The Journal of Chemical Physics·Giovanni BussiMichele Parrinello
Sep 22, 2007·Advanced Drug Delivery Reviews·David Filpula, Hong Zhao
Nov 2, 2007·Nature·Arun P WiitaJulio M Fernandez
Dec 7, 2007·The Journal of Chemical Physics·Daniel J ColeLucio Colombi Ciacchi
Mar 7, 2008·Biopolymers·Catalina DavidMironel Enescu
Jul 10, 2008·The Journal of Physical Chemistry. B·Biman JanaBiman Bagchi
Jul 10, 2009·Journal of the American Chemical Society·Luyuan ZhangDongping Zhong
Nov 27, 2009·Nature·Nathaniel Huebsch, David J Mooney
Dec 22, 2009·Physical Chemistry Chemical Physics : PCCP·Daniel J ColeLucio Colombi Ciacchi
May 14, 2010·Journal of the American Chemical Society·Francesco ColizziAndrea Cavalli
Sep 14, 2010·Langmuir : the ACS Journal of Surfaces and Colloids·Susan Köppen, Walter Langel
Sep 30, 2010·Langmuir : the ACS Journal of Surfaces and Colloids·Karina Kubiak-Ossowska, Paul A Mulheran
Apr 14, 2011·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Jessem Landoulsi, Vincent Dupres
Jun 16, 2011·The Journal of Physical Chemistry. B·Karina Kubiak-Ossowska, Paul A Mulheran
Dec 2, 2011·Langmuir : the ACS Journal of Surfaces and Colloids·Mojun ZhuWei Chen
Jan 14, 2012·Journal of the American Chemical Society·Julian Schneider, Lucio Colombi Ciacchi
Oct 16, 2012·Langmuir : the ACS Journal of Surfaces and Colloids·Karina Kubiak-Ossowska, Paul A Mulheran
Mar 15, 2013·Chemical Communications : Chem Comm·Gang WeiLucio Colombi Ciacchi
Sep 27, 2013·The Journal of Physical Chemistry. B·Maria Monica Castellanos, Coray M Colina
Dec 3, 2013·FEBS Letters·Alan A DombkowskiDouglas B Craig
Oct 5, 2014·Journal of Molecular Biology·Federico BenettiGiuseppe Legname
Jan 1, 2008·Journal of Chemical Theory and Computation·Berk Hess

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Citations

May 13, 2021·Annual Review of Analytical Chemistry·Tobias Weidner, David G Castner

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Methods Mentioned

BETA
AFM
X-ray
force
force spectroscopy

Software Mentioned

VMD
GROMACS
GAFF
AMBER99SB
Amber
ANTECHAMBER

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