University of Groningen
The Role of Structural Dynamics in Protein Function and Evolvability
Muthahari, Yusran
DOI:
10.33612/diss.155494424
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Publication date:
2021
Link to publication in University of Groningen/UMCG research database
Citation for published version (APA):
Muthahari, Y. (2021). The Role of Structural Dynamics in Protein Function and Evolvability. University of
Groningen. https://doi.org/10.33612/diss.155494424
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The Role of Structural Dynamics in Protein
Function and Evolvability
Yusran Abdillah Muthahari
Zernike PhD Thesis Series:
Financially supported by:
Cover Design : Hanifah Az Zahra Zernike Institute PhD Thesis: 2021-04
ISSN: 1570-1530
Dutch Summary: Jochem Hessel Smit
Printed by Proefschriftmaken | www.proefschriftmaken.nl
The research described in this thesis was carried out at Zernike Institute of Advanced Materials of the University of Groningen, the Netherlands and Laboratory of Molecular Bacteriology REGA Institute, KU Leuven, the Belgium. The research is financially supported by the Netherlands Organisation for Scientific Research (NWO) and the European Research Council (ERC). The author (Y.A.M.) is financially supported by The Doctoral Scholarship of Indonesia Endowment Fund for Education (Lembaga Pengelola Dana Pendidikan – Republik Indonesia/LPDP-RI).
Copyright 2021 by Yusran A. Muthahari. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means without the prior written permission of the author.
The Role of Structural Dynamics in Protein
Function and Evolvability
PhD thesis
to obtain the degree of PhD at the University of Groningen
on the authority of the Rector Magnificus Prof. C. Wijmenga
and in accordance with the decision by the College of Deans
and
to obtain the degree of Doctor in Biomedical Sciences at Katholieke Universiteit Leuven
on the authority of the Rector Prof. Luc Sels and in accordance with
the decision by the Doctoral School Committee Double PhD degree
This thesis will be defended in public on Friday, 5th February 2021 at 11.00 hours
by
Yusran Abdillah Muthahari
born on 29th April 1993
Supervisors Prof. A. Economou Prof. T. Cordes Prof. W. Roos Co-supervisors Dr. G. Gkouridis Assessment Committee Prof. E. A. Lemke Prof. F. Rousseau Prof. G. Maglia Prof. J. Schymkowitz
Contents
Contents ... 5
Chapter 1.Introduction ... 7
The Structure of a Protein... 10
The Path of Protein Folding ... 12
Protein Evolution ... 18
Bibliography ... 23
Chapter 2. Plasticity and Conformational Variability of Cherry-core Proteins ... 27
Abstract ... 28
Introduction ... 29
Results ... 31
Discussion and Outlooks ... 40
Materials and Methods ... 42
Supplementary Information ... 44
Bibliography ... 47
Chapter 3. The Role of C-tails on The Evolution of Structural Dynamics in Bilobed Proteins .... 53
Abstract ... 54
Introduction ... 55
Results ... 58
Discussion ... 64
Materials and Methods ... 73
Supplementary Information ... 81
Bibliography ... 84
Abstract ... 92
Introduction ... 93
Results ... 95
Discussion ... 104
Materials and Methods ... 106
Supplementary Information ... 111
Bibliography ... 112
Chapter 5. The Modules dictate the Functional Specialization of the Ancestral Protein ... 115
Abstract ... 116
Introduction ... 117
Results ... 119
Discussion ... 139
Materials and Methods ... 143
Supplementary Information ... 150
Bibliography ... 154
Supplementary Information and Files ... 158
Samenvatting ... 171
Summary ... 174
