140 Pages
English

Single molecule sensors to study hydrophobic phenomena [Elektronische Ressource] / Michael Geisler

-

Gain access to the library to view online
Learn more

Informations

Published by
Published 01 January 2009
Reads 19
Language English
Document size 3 MB

PHYSIK-DEPARTMENT

Single Molecule Sensors to
Study Hydrophobic Phenomena

Dissertation
von
Michael Geisler




















TECHNISCHE UNIVERSITÄT MÜNCHEN


Physik Department
Lehrstuhl für Biophysik E22


Single Molecule Sensors to
Study Hydrophobic Phenomena



Michael Geisler


Vollständiger Abdruck der von der Fakultät für Physik der Technischen
Universität München zur Erlangung des akademischen Grades eines

Doktors der Naturwissenschaften (Dr. rer. nat.)

genehmigten Dissertation.



Vorsitzender: Univ.-Prof. Dr. Friedrich Simmel
Prüfer der Dissertation:
1. Univ.-Prof. Dr. Thorsten Hugel
2. Univ.-Prof. Dr. Roland Netz





Die Dissertation wurde am 02.11.2009 bei der Technischen Universität
München eingereicht und durch die Fakultät für Physik am 14.12.2009
angenommen.






























127




This work is dedicated to my wife
Jutta
and my children
Zoe and René

















“…One is reminded of the story of the drunk who, one dark night, lost
his keys. He is seen looking for them under a street light. When asked
where he lost them, he points across the street, where all is dark. “Why,
then, are you looking for them here?” He replies, “Because there is
more light here”. Until more searching is done in the darkness, our
understanding of the hydrophobic effect must be considered quite
incomplete.”
Walter Kauzman, Nature, 325 (1987)







“I know a man who grabbed a cat by the tail and learned 40 per cent
more about cats than the man who didn’t.”
Mark Twain,
cited by Carlos Bustamante, Nature, 1 (2000)

















Table of Contents

Summary ......................................................................................................................................................... 1
Introduction and Outline ................................................................................................................................... 3
1. Armamentarium ........................................................................................................................................... 5
1.1 The conceptions of hydrophobicity ......................................................................................................... 5
1.2 The role of cosolvents for the hydrophobic effect.................................................................................... 6
1.3 AFM based force spectroscopy .............................................................................................................. 9
1.4 Thermodynamics of polymer desorption – Equilibrium theory ................................................................ 10
1.5 Non-equilibrium theory......................................................................................................................... 16
1.6 Forced unfolding of proteins.................. 19
1.7 Probability distributions of unfolding forces........................................................................................... 20
1.8 Equilibrium theory of cosolute binding onto a single polymer................................................................. 22
1.9 All atomistic molecular dynamics simulations........................................................................................ 23
2. Single Molecule Adhesion Mechanics ......................................................................................................... 27
2.1 Equilibrium desorption of a single molecule .......................................................................................... 28
2.2 Indications of non-equilibrium effects ................................................................................................... 32
2.3 Desorption free energy of single polymers............................................................................................ 33
2.4 Macromolecular friction of single polymers on solid surfaces ................................................................ 34
2.5 A comparison to MD-simulations............. 35
2.6 Sensor passivation - Suppression of unspecific tip adhesion................................................................. 36
2.7 Error estimate for SMFS experiments................................................................................................... 37
2.8 Concluding remarks ............................................................................................................................. 38
3. Hydrophobic Interactions at the Solid-Liquid Interface................................................................................. 39
3.1 Effect of surface roughness.................................................................................................................. 40
3.2 Impact of substrate hydrophobicity (wettability) on molecular adhesion ................................................. 42
3.3 Influence of substrate electronic properties on single polymer adhesion................................................ 42
3.4 Contribution of polymer composition to single molecule adhesion ......................................................... 45
3.5 Effect of ions on single polymer adhesion – The Hofmeister effect ........................................................ 45
3.6 Influence of solvent pH ........................................................................................................................ 49
3.7 Concluding remarks ............................................................................................................................. 49
4. Aging of Hydrophobic and Hydrophilic Diamond.......................................................................................... 51
4.1 Alteration of adhesion properties of PAAm onto diamond over time...................................................... 51
4.2 Change of diamond surface potential over time .................................................................................... 53
4.3 Origins of the diamond aging process................................................................................................... 55
4.4 Concluding remarks ............................................................................................................................. 57
5. Hydrophobicity and the Concept of Entropy Convergence ........................................................................... 59
5.1 Universal convergence for different types of polymers .......................................................................... 60
5.2 Ion induced shift in convergence temperatures ..................................................................................... 63
5.3 Concluding remarks................ 64
6. Surface Induced Protein Folding................................................................................................................. 67
6.1 Temperature facilitated folding of eADF-4 on hydrophilic steel surfaces ................................................ 68
6.2 MD simulations of forced eADF-4 unfolding – parallel vs. antiparallel arrangement................................ 72
6.3 Surface induced folding of eADF-4 facilitated by increased ion concentration........................................ 75
6.4 Toughness Estimation of silk fibers from molecular parameters ............................................................ 76
6.5 Concluding remarks ............................................................................................................................. 77
7. Surface-Differential Cosolute Binding onto Polymers .................................................................................. 79
7.1 Surface differential binding of glucose onto PAAm at different temperatures ......................................... 80
7.2 Effect of substrate material on cosolute binding affinity......................................................................... 81
7.3 Comparison to standard methods for binding studies ............................................................................ 83
7.4 Concluding remarks................ 85
Future Prospects ........................................................................................................................................... 87
A. Inherent Limitations to AFM Force Resolution ............................................................................................ 89
B. Direct Comparison of Different Polymers.................................................................................................... 91
C. Enhanced Molecular Sensor for Force Spectroscopy with small Molecules ................................................. 93
D. Materials and Methods .............................................................................................................................. 97
D.1 Substrate preparation...................................................................................................... 97
Hydrogenated and oxidized polycrystalline diamond............................................................................... 97
Surgical stainless steel (316L) ............................................................................................................... 97
Poly(tetrafluorethylene) (PTFE)............. 98
Self assembled monolayers (SAM)........ 98
D.3 Homopolymers for SMFS..................................................................................................................... 98
D.2 Production of recombinant proteins eADF-3 and eADF-4...................................................................... 99
D.4 Covalent coupling of type I antifreeze protein (AFP) and PF-555 to PAAm...........................................100
D.5 Native PAGE gel electrophoresis ........................................................................................................100
D.6 Cantilever tip preparation ...................................................................................................................101
D.7 Cantilever calibration and error analysis in SMFS ...............................................................................102
D.8 Error estimate of cosolute binding parameters ....................................................................................102
D.9 Contact angle measurements............103
D.10 Scanning Electron Microscopy (SEM) ...............................................................................................103
D.11 Atomic Force Microscopy (AFM) .......................................................................................................103