Methods for hybrid modeling of solution scattering data and their applications [Elektronische Ressource] / Alexander V. Shkumatov. Betreuer: Dmitri Svergun

Ashkumat

Sujets

• Biologie

Informations

• Publié par: julius-maximilians-universitat_wurzburg
• Publié le: 01 janvier 2011
• Nombre de lectures: 23
• Langue: Deutsch
• Poids de l'ouvrage: 9 Mo

Extrait

Methods for Hybrid Modeling of Solution
Scattering Data and their Applications




Dissertation zur Erlangung
des naturwissenschaftlichen Doktorgrades
der Bayerischen Julius-Maximilians-Universität Würzburg




vorgelegt von
Alexander V. Shkumatov
aus
Minsk, Belarus

Würzburg 2011



















Eingereicht am:

Mitglieder der Promotionskommission:
Vorsitzender:
- 1. Gutachter: Dr. habil. Matthias Wilmanns
- 2. Gutachter: Prof. Dr. Thomas Dandekar


Tag des Promotionskolloquiums:
Doktorurkunde ausgehändigt am:
Contents
Abstract..............................................................................................................................vi
Zusammenfassung............................................................................................................ viii
List of figures.....................................................................................................................x
List of tables.......................................................................................................................xii
List of abbreviations......................................................................................................... xiii
1 Introduction..................................................................................................................1
1.1 SAXS history........................................................................................................... 2
1.2 SAXS theory............................................................................................................ 3
1.3 Characterization of Intrinsically Disordered Proteins (IDPs) using SAXS.............5
1.4 Scope of the thesis................................................................................................... 7
1.5 Further reading.........................................................................................................9
2. Methods for SAXS data analysis……………............................................................. 10
2.1 Data collection and reduction.................................................................................. 11
2.2 Ab initio shape reconstruction..................................................................................12
2.3 Rigid body modeling................................................................................................13
2.4 Combined ab initio and rigid body modeling..........................................................13
2.5 Flexibility assessment.............................................................................................. 14
3. Improvements and new developments in the SAXS data program suite
(ATSAS)………………………………………………………………………….............15
3.1 Improvements and new features in CRYSOL and CRYSON.................................. 16
3.1.1 Implementation of novel minimization algorithm and new options in
CRYSOL………………………………………………………………………….............16
3.1.2 Implementation of new minimization algorithm in CRYSON………………18
Page | iii
  3.2 RANLOGS – a tool to generate random loops and linkers ab initio.......................19
3.3 Validation of low-resolution models: EM2DAM tool.............................................22
3.4 MW estimation using excluded and Porod volumes................................................25
4. Novel developments utilizing bioinformatics predictors…………………...............30
4.1 Post processing of ab initio decoys generated by ROSETTA................................. 31
4.2 Selection and refinement of HADDOCK solutions.................................................35
4.3 Automatic selection and HADDOCK refinement of models.................................. 39
4.4 NMA-based refinement of binary complexes..........................................................43
4.5 Application of bioinformatics tools to proteome analysis of tardigrades................49
5. Structural flexibility of biological macromolecules studied by SAXS.……...……. 62
5.1 Structural insights into the extracellular assembly of the hematopoietic Flt3
signaling complex……....................................................................................................... 65
5.2 Oligomerization propensity and flexibility of yeast frataxin studied by X-ray
crystallography and SAXS…………………………........................................................ 83
5.3 Insights into the molecular activation mechanism of the RhoA-specific guanine
nucleotide exchange factor, PDZRHOGEF…….............................................................. 96
5.4 Structural memory of natively unfolded tau protein detected by SAXS…………..110
Concluding discussion...................................................................................................... 120
Appendix A: supporting documents for subchapter 4.5............................................... 125
Appendix B: supporting documents for subchapter 5.1............................................... 126
Appendix C: supporting documents for subchapter 5.3............................................... 132
Appendix D: supporting documents for subchapter 5.4............................................... 134
References..........................................................................................................................136
Page | iv
 List of publications............................................................................................................154
Contributions.................................................................................................................... 155
Poster contributions, visits and participations...............................................................160
Participation in other courses..........................................................................................161
Acknowledgements........................................................................................................... 162
Erklärung.......................................................................................................................... 164
Curriculum Vitae..............................................................................................................165
Lebenslauf..........................................................................................................................166
 














Page | v
 Abstract
Small-angle X-ray scattering (SAXS) is a universal low-resolution method to study proteins
in solution and to analyze structural changes in response to variations of conditions (pH,
temperature, ionic strength etc). SAXS is hardly limited by the particle size, being applicable
to the smallest proteins and to huge macromolecular machines like ribosomes and viruses.
SAXS experiments are usually fast and require a moderate amount of purified material.
Traditionally, SAXS is employed to study the size and shape of globular proteins, but recent
developments have made it possible to quantitatively characterize the structure and structural
transitions of metastable systems, e.g. partially or completely unfolded proteins.
In the absence of complementary information, low-resolution macromolecular shapes can be
reconstructed ab initio and overall characteristics of the systems can be extracted. If a high-
or low-resolution structure or a predicted model is available, it can be validated against the
experimental SAXS data. If the measured sample is polydisperse, the oligomeric state and/or
oligomeric composition in solution can be determined. One of the most important approaches
for macromolecular complexes is a combined ab initio/rigid body modeling, when the
structures (either complete or partial) of individual subunits are available and SAXS data is
employed to build the entire complex. Moreover, this method can be effectively combined
with information from other structural, computational and biochemical methods. All the
above approaches are covered in a comprehensive program suite ATSAS for SAXS data
analysis, which has been developed at the EMBL-Hamburg.
In order to meet the growing demands of the structural biology community, methods for
SAXS data analysis must be further developed. This thesis describes the development of two
new modules, RANLOGS and EM2DAM, which became part of ATSAS suite. The former
program can be employed for constructing libraries of linkers and loops de novo and became
a part of a combined ab initio/rigid body modeling program CORAL. EM2DAM can be
employed to convert electron microscopy maps to bead models, which can be used for
modeling or structure validation. Moreover, the programs CRYSOL and CRYSON, for
computing X-ray and neutron scattering patterns from atomic models, respectively, were
refurbished to work faster and new options were added to them.
Two program