University of Groningen
Computational studies of influenza hemagglutinin
Boonstra, Sander
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Publication date: 2017
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Boonstra, S. (2017). Computational studies of influenza hemagglutinin: How does it mediate membrane fusion?. University of Groningen.
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Computational Studies of Influenza Hemagglutinin.
How Does it Mediate Membrane Fusion?
© 2017, Sander Boonstra
Zernike Institute PhD thesis series 2017-26
ISSN: 1570-1530
ISBN: 978-94-034-0252-9 (Printed version) ISBN: 978-94-034-0253-6 (Electronic version)
Cover design
Emmie Holtmaat
Printed by
GVO drukkers & vormgevers B.V., Ede
The work presented in this thesis was performed in the Micromechanics research group at the Zernike Institute for Advanced Materials (ZIAM) of the University of Groningen, The Netherlands. ZIAM is acknowledged for funding this research through the bonus incentive scheme. This work was sponsored by NWO Exacte Wetenschappen (Physical Sciences) for the use of supercomputer facilities.
Computational Studies of
Influenza Hemagglutinin
How Does it Mediate Membrane Fusion?
PhD thesis
to obtain the degree of PhD at the
University of Groningen
on the authority of the
Rector Magnificus Prof. E. Sterken
and in accordance with
the decision by the College of Deans.
This thesis will be defended in public on
Friday 22 December 2017 at 11.00 hours
by
Sander Boonstra
born on 26 November 1985
Supervisors
Prof. E. van der Giessen Prof. P.R. Onck
Assessment committee
Prof. S.J. Marrink Prof. W.H. Roos Prof. A. Kros
Contents
1 Introduction 1
1.1 Influenza viral entry and replication . . . 3
1.2 Entry inhibition . . . 4
1.3 Hemagglutinin-mediated membrane fusion . . . 4
1.4 Molecular dynamics simulations . . . 6
1.5 Thesis outline . . . 6
References . . . 7
2 Hemagglutinin-mediated membrane fusion: A biophysical perspective 11 2.1 Introduction . . . 12
2.2 Membrane fusion . . . 13
2.2.1 Pathway . . . 13
2.2.2 Methods . . . 14
2.2.3 Barriers . . . 15
2.3 Hemagglutinin conformational changes . . . 17
2.3.1 Structure and triggering . . . 17
2.3.2 Pathways of the conformational change . . . 18
2.3.3 Surmounting membrane-fusion barriers . . . 20
2.4 Stochastic modeling of influenza fusion . . . 21
2.4.1 Single-particle kinetic assays . . . 21
2.4.2 Influenza fusion mediated by a cluster of stochastically inserted hemagglutinins . . . 22
2.5 Future directions . . . 25
References . . . 26
2.A Appendix: Tables . . . 38
3 CHARMM TIP3P water model suppresses peptide folding by solvating the un-folded state 41 3.1 Introduction . . . 42
3.2 Method . . . 42
3.2.1 Water models . . . 43
3.2.2 System setup and equilibration . . . 43
3.2.3 Replica exchange molecular dynamics . . . 43
3.2.4 Definition of folded states . . . 44
3.2.5 Convergence . . . 44
3.3 Results . . . 44
3.3.1 Melting curves . . . 44
3.3.2 Characteristics of the unfolded state . . . 45
Contents
3.4 Discussion . . . 49
3.5 Conclusion . . . 51
References . . . 51
4 Critical interactions in the globular bottom of influenza hemagglutinin 55 4.1 Introduction . . . 56
4.2 Methods . . . 58
4.2.1 Simulation setup . . . 58
4.2.2 Analysis of simulation results . . . 61
4.3 Results . . . 63
4.3.1 Unfolding pathway of the globular bottom of H3 . . . 63
4.3.2 Identification of critical interactions . . . 64
4.3.3 Salt-bridge network . . . 66
4.3.4 Mutation studies . . . 69
4.3.5 Protonation studies . . . 69
4.3.6 Conservation of stabilizing amino acids . . . 70
4.3.7 Stability of the globular bottom of H1 . . . 71
4.3.8 Single-particle experiments . . . 72
4.4 Discussion . . . 73
4.5 Conclusion . . . 77
References . . . 77
4.A Appendix: Single-particle assay . . . 82
4.B Appendix: H1 homology modeling . . . 85
4.C Appendix: Constant pulling rate simulations . . . 86
4.D Appendix: Tables . . . 87
5 Computation of hemagglutinin free energy difference by the confinement method 89 5.1 Introduction . . . 90
5.2 Methods . . . 92
5.2.1 Confinement free energy method . . . 92
5.2.2 Thermodynamic integration and MBAR . . . 94
5.2.3 Guidelines for free energy calculation . . . 96
5.2.4 Equilibration and decorrelation of time series . . . 96
5.2.5 Crystal structures and simulation setup . . . 96
5.2.6 Window spacing and overlap coefficient . . . 98
5.3 Results . . . 99
5.3.1 Energy minimization . . . 99
5.3.2 Confinement to the harmonic regime . . . 100
5.3.3 Confinement free energies . . . 101
5.3.4 Convergence: overlapping distributions . . . 102
Contents
5.3.5 Convergence: equilibration and sampling . . . 104
5.3.6 Conformational free energy difference . . . 105
5.4 Discussion . . . 106
5.5 Conclusion . . . 109
References . . . 109
5.A Appendix: Error propagation . . . 115
5.B Appendix: Force field and MD code selection . . . 116
5.C Appendix: SHAKE test case . . . 117
Summary 119
Samenvatting 121
Acknowledgments 125
List of publications 129
