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Download (7Mb) University of Warwick institutional repository: http://go.warwick.ac.uk/wrap A Thesis Submitted for the Degree of PhD at the University of Warwick http://go.warwick.ac.uk/wrap/61709 This thesis is made available online and is protected by original copyright. Please scroll down to view the document itself. Please refer to the repository record for this item for information to help you to cite it. Our policy information is available from the repository home page. AUTHOR: Louise B Wright DEGREE: Ph.D. TITLE: Modelling the Adsorption of Peptides at aqueous Quartz and Gold Interfaces DATE OF DEPOSIT: ................................. I agree that this thesis shall be available in accordance with the regulations governing the University of Warwick theses. I agree that the summary of this thesis may be submitted for publication. I agree that the thesis may be photocopied (single copies for study purposes only). Theses with no restriction on photocopying will also be made available to the British Library for microfilming. The British Library may supply copies to individuals or libraries. subject to a statement from them that the copy is supplied for non-publishing purposes. All copies supplied by the British Library will carry the following statement: “Attention is drawn to the fact that the copyright of this thesis rests with its author. This copy of the thesis has been supplied on the condition that anyone who consults it is understood to recognise that its copyright rests with its author and that no quotation from the thesis and no information derived from it may be published without the author’s written consent.” AUTHOR’S SIGNATURE: ................................................... .... USER’S DECLARATION 1. I undertake not to quote or make use of any information from this thesis without making acknowledgement to the author. 2. I further undertake to allow no-one else to use this thesis while it is in my care. DATE SIGNATURE ADDRESS ................................................... ............................... ................................................... ............................... ................................................... ............................... ................................................... ............................... ................................................... ............................... www.warwick.ac.uk MENS T A T A G I MOLEM U N IS IV S E EN RS IC ITAS WARW Modelling the Adsorption of Peptides at aqueous Quartz and Gold Interfaces by Louise B Wright Thesis Submitted to the University of Warwick for the degree of Doctor of Philosophy Chemistry March 2014 Contents List of Tables vi List of Figures xiv Acknowledgments xxiii Declarations xxiv Abstract xxv Abbreviations xxvii Chapter 1 Introduction 1 1.1 The Potential of material and facet selective Peptides . ....... 1 1.2 SelectionofMaterialBindingPeptides . ... 5 1.2.1 Biocombinatorial Peptide Selection . 5 1.2.2 Towards the Rational Design of Peptide Sequences . 6 1.2.3 Biointerfacial Experimental Techniques . 7 1.2.4 BiointerfacialSimulation. 10 1.3 AqueousQuartzInterface . 13 1.3.1 Experiment ............................ 13 1.3.2 Simulation ............................ 17 1.3.3 CrystallographicSurfaces . 19 1.4 AqueousGoldInterface . 21 1.4.1 Experiment ............................ 21 1.4.2 Simulation ............................ 23 1.4.3 CrystallographicSurfaces . 25 Chapter 2 Methods 28 2.1 Describing the Potential Energy Landscape . 28 i 2.1.1 FirstPrinciplesMethods. 28 2.1.2 AtomisticForce-Fields . 33 2.2 MolecularDynamics ........................... 36 2.2.1 TimeEvolution.......................... 37 2.2.2 Thermostats ........................... 37 2.2.3 Barostats ............................. 38 2.2.4 First-PrinciplesMD . 39 2.3 ReplicaExchangeMethods . 40 2.3.1 T-REMD ............................. 41 2.3.2 H-REMD ............................. 42 2.3.3 ReplicaExchangewithSoluteTempering . 43 2.4 FreeEnergyMethods........................... 44 2.4.1 PotentialofMeanForce . 45 2.4.2 Metadynamics .......................... 46 2.5 Analysis.................................. 48 2.5.1 HydrogenBonding ........................ 48 2.5.2 PeptideStructureClustering . 49 2.6 PeptideSecondaryStructure . 51 Chapter 3 Free Energy Calculations of Amino-Acid Analogue Ad- sorption at Aqueous α-Quartz Interfaces. 53 3.1 Introduction................................ 53 3.2 Methods.................................. 54 3.2.1 Analysis.............................. 55 3.3 Results................................... 55 3.3.1 Methane.............................. 56 3.3.2 Ammonium............................ 57 3.3.3 Butylammonium......................... 59 3.3.4 Benzene.............................. 61 3.3.5 Ethanoate............................. 63 3.4 Discussion................................. 66 3.5 Conclusions ................................ 67 Chapter 4 First-Principles Molecular Dynamics Simulations of Am- monium and Ethanoate Adsorption at the Aqueous (100) α-Quartz Interface. 68 4.1 Introduction................................ 68 4.2 Methods.................................. 69 ii 4.2.1 Car-Parrinello Molecular Dynamics Simulations . 70 4.2.2 Force-fieldMDSimulations . 71 4.2.3 Analysis.............................. 72 4.3 Results................................... 73 4.3.1 Ethanoate............................. 73 4.3.2 Ammonium............................ 74 4.4 Discussion................................. 77 4.5 Conclusions ................................ 80 Chapter 5 Benchmarking Replica Exchange with Solute Tempering for Bio-interfacial Systems: QBP-1 Adsorption onto the (100) α- Quartz Surface. 81 5.1 Introduction................................ 81 5.2 Methods.................................. 82 5.2.1 SystemDetails .......................... 82 5.2.2 Temperature-REMD . 83 5.2.3 ReplicaExchangewithSoluteTempering . 84 5.2.4 Analysis.............................. 86 5.3 Results................................... 87 5.3.1 ReplicaMobility ......................... 87 5.3.2 ClusteringAnalysis. 88 5.3.3 Peptide Structures and Ramachandran Analysis . 91 5.3.4 HydrogenBonding ........................ 96 5.3.5 BindingResiduesandMotifs . 96 5.3.6 Energetics............................. 98 5.4 Discussion................................. 99 5.5 Conclusions ................................ 101 Chapter 6 GolP-CHARMM: A First-Principles Based Force-field for modelling protein adsorption to Au(111), Au(100)(1 1) and Au(100)(5 1).103 × × 6.1 Introduction................................ 103 6.2 Methods.................................. 104 6.2.1 in Vacuo Force-FieldCalculations . 113 6.2.2 Force-field MD Simulations of Aqueous Gold Interfaces . 115 6.2.3 Analysis.............................. 115 6.3 Results................................... 116 6.3.1 EvaluationofvdW-DFT. 116 6.3.2 Force-fieldParameterisation . 118 iii 6.3.3 AqueousAu(111)andAu(100)Interfaces . 129 6.4 Conclusions ................................ 133 Chapter 7 Material Selectivity of QBP-1 Adsorption. 135 7.1 Disclaimer................................. 135 7.2 Introduction................................ 135 7.3 Methods.................................. 136 7.3.1 SystemDetails .......................... 136 7.3.2 ReplicaExchangewithSoluteTempering . 137 7.3.3 Analysis.............................. 138 7.4 Results................................... 139 7.4.1 PeptideConformation . 139 7.4.2 SurfaceBinding. 144 7.5 Discussion................................. 146 7.6 Conclusions ................................ 149 Chapter 8 Facet Selectivity of AuBP-1 adsorption onto Gold: A Replica Exchange with Solute Tempering Metadynamics Study. 150 8.1 Disclaimer................................. 150 8.2 Introduction................................ 150 8.3 Methods.................................. 151 8.3.1 SystemDetails .......................... 151 8.3.2 ReplicaExchangewithSoluteTempering . 153 8.3.3 Analysis.............................. 153 8.4 Schemes for Reweighting Structural Data from a Metadynamics Sim- ulation................................... 156 8.4.1 Scheme1:Totalbias‘V’. 157 8.4.2 Scheme2: RelativeBias‘∆V’. 157 8.4.3 Scheme3: RelativeBias‘∆Vequilib’. 157 8.4.4 Scheme4:‘Timeperiod’. 158 8.4.5 Scheme5:Tianamethod . 160 8.4.6 Scheme6: BonomiMethod . 161 8.4.7 Evaluation ............................ 162 8.5 Results................................... 166 8.5.1 BindingStrength. 166 8.5.2 ClusterAnalysis . 170 8.5.3 SecondaryStructure . 171 8.5.4 BindingMechanism . 171 iv 8.6 Conclusions ................................ 174 Chapter 9 Conclusions and Future Prospects 176 Appendix A Additional Information: Free Energy Calculations of Amino-Acid Analogue Adsorption at Aqueous α-Quartz Interfaces.181 Appendix B Additional Information: First-Principles Molecular Dy- namics Simulations of Ammonium and Ethanoate Adsorption at the Aqueous (100) α-Quartz Interface. 188 Appendix C Additional Information:Benchmarking Replica Exchange with Solute Tempering for Bio-interfacial Systems: QBP-1 Adsorp- tion onto the (100) α-Quartz Surface. 194 Appendix D Additional Information:GolP-CHARMM: A First-Principles Based Force-field for modelling protein adsorption to Au(111), Au(100)(1 1) and Au(100)(5 1). 203 × × Appendix E Additional Information:Material Selectivity of QBP-1 Adsorption. 225 Appendix F Additional Information:Facet Selectivity of AuBP-1 ad- sorption onto Gold: A Replica Exchange with Solute Tempering Metadynamics Study. 236 v List of Tables 1.1 Silica-binding peptide sequences along
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