Interaction of polyoxometalates and model proteins: structural and luminescence investigation ...

94 Pages·2017·53 MB·English

Interaction of polyoxometalates and model
proteins: structural and luminescence
investigation
Jeroen De Cock
Promoter: prof. dr. Kristof Van Hecke
Co-promoter: prof. dr. Rik Van Deun
Co-promoter: dr. Anna Kaczmarek
Academic Year 2016–2017
A dissertation submitted to Ghent University in partial fulfilment of
the requirements for the degree of Master of Science in Chemistry
Knowing without seeing
is at the heart of chemistry.
— ROALD HOFFMANN
Acknowledgement
First and foremost, I would like to thank my promoter, Prof. dr. Van Hecke, for giving me the
opportunity to work in his research group. His expertise in crystallography has helped me a lot to
obtain valuable single-crystal X-ray diffraction skills for finishing my thesis.
I would also like to thank Prof. dr. Rik Van Deun for giving me the opportunity to perform lu-
minescence experiments, which was an essential part in the scope of my thesis.
I am very grateful to have dr. Anna Kaczmarek to support me throughout my thesis. Her profes-
sionalism in polyoxometalates and luminescence was very profound. She was very kind and although
she had a very busy schedule, she tried to help me as much as she can throughout my thesis. I have
learned a lot of new valuable skills thanks to her.
Special thanks goes to Prof. dr. Savvas Savvides, dr. Kenneth Verstraete, dr. Romain Merceron and
William Shepard for giving me the opportunity to perform experiments at the Proxima-2A beamline
dedicated for macromolecular X-ray diffraction experiments in the SOLEIL synchrotron. Especially
Dr. Kenneth Verstraete, for guiding me throughout the synchrotron X-ray diffraction experiments.
The help of Nigel Moriarty, who has responded for my request in solving PHENIX-related prob-
lems, was greatly appreciated.
I would also like to thank my colleagues at XStruct and L3-Luminescence Lanthanide Lab: Tim
Verdonck, Ken Princen, Dimitrije Mara, Jing Liu, Min Zeng and Kai Li and my fellow thesis stu-
dents: Camille Baetsl´e, Elena Quintero Gonzales and Giovanni Pampararo for their support and for
the pleasant times.
Furthermore, I would like to thank my classmates for their support and all the pleasant times we
had throughout the past five years.
Last, but not least, I would like to show my immense gratitude to my parents,
my brothers and my friends for their support throughout this especially challenging thesis subject, as
a I started this thesis with little background in biochemistry and macromolecular crystallography.
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Contents
1 Introduction 1
1.1 Polyoxometalates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.1.1 Anderson-Evans type POMs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.1.2 Keggin type POMs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.2 Hen Egg-White Lysozyme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.3 HEWL-POM co-crystallization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2 Single-crystal X-ray diffraction 11
2.1 Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.1.1 Crystals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.1.2 Point groups and space groups . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
2.1.3 Miller indices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
2.1.4 X-ray diffraction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
2.1.5 Fourier transform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
2.2 Macromolecular X-ray diffraction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
2.2.1 Molecular replacement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
2.2.2 Anomalous dispersion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
2.2.3 Isomorphous replacement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.2.4 Refinement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.3 X-ray sources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.3.1 X-ray tube . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.3.2 Synchrotron . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
3 Synthesis and structural characterization of polyoxometalates 23
3.1 Reaction mechanism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
3.2 Synthesis of Na [TeW O ]¨22H O . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
6 6 24 2
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3.2.1 Crystal data for Na [TeW O ]¨22H O . . . . . . . . . . . . . . . . . . . . . . 24
6 6 24 2
3.3 Synthesis of Na [SbW O ]¨16H O . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
7 6 24 2
3.3.1 Crystal data for Na [SbW O ]¨16H O . . . . . . . . . . . . . . . . . . . . . . 25
7 6 24 2
3.4 Synthesis of H [W SiO ] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
4 12 40
3.5 Synthesis of K [Ln(W SiO ) ]¨18H O . . . . . . . . . . . . . . . . . . . . . . . . . 26
13 11 39 2 2
3.5.1 Crystal data for K [Eu(W SiO ) ]¨18H O . . . . . . . . . . . . . . . . . . . 27
13 11 39 2 2
3.6 UV-Vis investigation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
3.6.1 Na [TeW O ]¨22H O . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
6 6 24 2
3.6.2 K [Eu(W SiO ) ] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
13 11 39 2
4 Soaking technique and crystal analysis 31
4.1 Protein crystallization via hanging-drop method . . . . . . . . . . . . . . . . . . . . . 31
4.2 Soaking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
4.3 Analysis of soaked crystals with in-house
X-ray diffraction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
4.4 Analysis of soaked crystals with
synchrotron X-ray diffraction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
4.4.1 HEWL crystal soaked with [TeW O ]6– . . . . . . . . . . . . . . . . . . . . . 33
6 24
4.4.2 HEWL crystal soaked with [Eu(SiW O ) ]13– . . . . . . . . . . . . . . . . . . 34
11 39 2
5 Lanthanide photoluminescence 41
5.1 Photoluminescence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
5.2 Lanthanide photoluminescence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
5.3 K [Eu(SiW O ) ] luminescence investigation . . . . . . . . . . . . . . . . . . . . . . 43
13 11 39 2
5.3.1 Excitation spectrum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
5.3.2 Emission spectrum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
5.3.3 Decay measurement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
5.4 K [Tb(SiW O ) ] luminescence investigation . . . . . . . . . . . . . . . . . . . . . . 46
13 11 39 2
5.4.1 Excitation spectrum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
5.4.2 Emission spectrum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
5.5 HEWL-EuPOM interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
6 Conclusion 51
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List of Figures
1.1 Types of polyoxometalates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.2 Anderson-Evans and Keggin type POM . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.3 The five isomers of the Keggin type POM . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.4 Dimeric 1:2 species and monomeric 1:1 species of sandwich type Keggin POMs . . . . 5
1.5 HEWL protein . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.6 Binding sites of POMs in HEWL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.7 Electrostatic potential map plotted on the surface of HEWLs with the POMs present
in the structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2.1 The 14 Bravais lattices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
2.2 Point groups and space groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
2.3 Some examples of Miller indices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
2.4 Bragg’s law . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
2.5 Phase problem visualization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
2.6 Rotating anode X-ray tube . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
2.7 SOLEIL beamlines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
3.1 Synthesis of polyoxometalates reaction mechanism . . . . . . . . . . . . . . . . . . . . 24
3.2 Structure of Na [TeW O ] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
6 6 24
3.3 Structure of Na [SbW O ] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
7 6 24
3.4 Structure of H [W SiO ] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
4 12 40
3.5 Structure of K [Eu(SiW O ) ] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
13 11 39 2
3.6 UV-Vis measurement of [TeW O ]6– stability in pH range 1-11 . . . . . . . . . . . . 29
6 24
3.7 UV-Vis lifetime measurement of [TeW O ]6– . . . . . . . . . . . . . . . . . . . . . . . 29
6 24
3.8 UV-Vis measurement of [Eu(SiW O ) ]13– stability in pH range 1-13 . . . . . . . . . 30
11 39 2
4.1 Protein crystallization phase diagram and hanging-drop procedure . . . . . . . . . . . 32
v
4.2 Data-collection statistics of HEWL-TEW in-house XRD measurement . . . . . . . . . 33
4.3 Initial 2F -F and F -F electron density map contoured at a σ level of 2.5 of TEW
o c o c
obtained from in-house X-ray diffraction . . . . . . . . . . . . . . . . . . . . . . . . . . 33
4.4 [TeW O ]6– electron density in HEWL unit cell . . . . . . . . . . . . . . . . . . . . . 34
6 24
4.5 TEW-HEWL electron density . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
4.6 [TeW O ]6– sites in HEWL. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
6 24
4.7 HEWL-EuPOM electron density . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
4.8 HEWL-EuPOM electron density . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
4.9 Electrostatic potential surface map projected on HEWL with TEW and EuPOM inter-
acting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
5.1 Jablonski diagram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
5.2 Successive introductions of perturbations. . . . . . . . . . . . . . . . . . . . . . . . . . 43
5.3 Antenna effect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
5.4 Excitation Spectra of [Eu(SiW O ) ]13– in solution and as a solid. . . . . . . . . . . 44
11 39 2
5.5 Emission spectra of [Eu(SiW O ) ]13– in solution and as a solid. . . . . . . . . . . . 45
11 39 2
5.6 The square antiprism-like environment of Eu3` within EuPOM . . . . . . . . . . . . . 46
5.7 Decay plots of EuPOM in solution and as a solid . . . . . . . . . . . . . . . . . . . . . 47
5.8 K [Tb(SiW O ) ] excitation spectrum . . . . . . . . . . . . . . . . . . . . . . . . . . 48
13 11 39 2
5.9 K [Tb(SiW O ) ] emission spectra. . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
13 11 39 2
5.10 Emission spectra of EuPOM with titration of HEWL . . . . . . . . . . . . . . . . . . . 49
5.11 Higher resolution emission graph of EuPOM before and after adding HEWL . . . . . . 50
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Abbreviations
POM: Polyoxometalate
HEWL: Hen Egg-White lysozyme
TEW: Tellurium-centered Polytungstate, TeW O
6 24
EuPOM: Europium sandwich type Keggin Polytungstate, Eu(SiW O )
11 39 2
SbPOM: Antimony-centered Polytungstate, SbW O
6 24
PDB: Protein Data Bank
XRD: X-Ray Diffraction
ALF186: fac-([Mo(CO) (histidinate)]Na, where fac stands for facial isomer.
3
TbPOM: Terbium sandwich type Keggin Polytungstate, Tb(SiW O )
11 39 2
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