Computational Insights into the Mechanisms and Structures of Peptide Bond Cleaving

209 Pages·2017·13.84 MB·English

by  Tingting Zhang

University of Miami
Scholarly Repository
Open Access Dissertations Electronic Theses and Dissertations
2014-11-12
Computational Insights into the Mechanisms and
Structures of Peptide Bond Cleaving
Metalloenzymes and Their Synthetic Analogues
Tingting Zhang
University of Miami, [email protected]
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Zhang, Tingting, "Computational Insights into the Mechanisms and Structures of Peptide Bond Cleaving Metalloenzymes and Their
Synthetic Analogues" (2014).Open Access Dissertations. 1313.
https://scholarlyrepository.miami.edu/oa_dissertations/1313
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UNIVERSITY OF MIAMI

COMPUTATIONAL INSIGHTS INTO THE MECHANISMS AND STRUCTURES OF
PEPTIDE BOND CLEAVING METALLOENZYMES AND THEIR SYNTHETIC
ANALOGUES

By

Tingting Zhang

A DISSERTATION

Submitted to the Faculty
of the University of Miami
in partial fulfillment of the requirements for
the degree of Doctor of Philosophy

Coral Gables, Florida
December 2014
©2014
Tingting Zhang
All Rights Reserved
UNIVERSITY OF MIAMI

A dissertation submitted in partial fulfillment of
the requirements for the degree of
Doctor of Philosophy

COMPUTATIONAL INSIGHTS INTO THE MECHANISMS AND STRUCTURES OF
PEPTIDE BOND CLEAVING METALLOENZYMES AND THEIR SYNTHETIC
ANALOGUES

Tingting Zhang

Approved:

________________ _________________
Rajeev Prabhakar, Ph.D. Françisco M. Raymo, Ph.D.
Professor of Chemistry Professor of Chemistry

________________ _________________
Jamie D. Walls, Ph.D. M. Brian Blake, Ph.D.
Professor of Chemistry Dean of the Graduate School

________________
Akira Chiba, Ph.D.
Professor of Biology
ZHANG, TINGTING (Ph.D., Chemistry)
Computational Insights into the Mechanisms and Structures of (December 2014)
Peptide Bond Cleaving Metalloenzymes and Their Synthetic Analogues

Abstract of a dissertation at the University of Miami.

Dissertation supervised by Professor Rajeev Prabhakar.
No. of pages in text. (188)

The selective hydrolysis of peptide or amide bond is required in a wide range of
biological, biotechnological and industrial applications. There are significant kinetic
barriers to these reactions since peptide bonds are extremely stable and possess a half-life
for hydrolysis of 350–600 years at room temperature and pH 4–8. Therefore, nature has
devised enzymes to rapidly and selectively cleave these bonds under physiological
conditions that are known as peptidases. Specifically, metallopeptidases, generate a
scaffold capable of binding one or two metal ions to hydrolyze peptide bonds. The
studies on metallopeptidases are important to understand the functions of these enzymes
and to design their synthetic analogues.
In this thesis, state-of-the-art theoretical and computational chemistry techniques
including quantum mechanics (QM), hybrid quantum mechanics/molecular mechanics
(QM/MM ONIOM), and molecular dynamics (MD) simulations have been utilized to
investigate the mechanisms and structures of mononuclear and binuclear
metallopeptidases and their synthetic analogues. In particular, the catalytic mechanisms
of four different synthetic complexes of mononuclear metallopeptidases and three natural
enzymes and their synthetic analogues of binuclear metallopeptidases have been
elucidated. These studies have provided the information regarding the conformation of
the reactants, ligand environment, and the role of the metal ions. In addition, the
structural properties and interactions between amyloid β peptides (Aβ40/Aβ42) and
insulin degrading enzyme (IDE) mutants have been explored using MD simulations.
Dedicated to My Parents

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ACKNOWLEDGEMENTS
I am so thankful for all the help and support that I received at the University of Miami.
First of all, I would like to express my sincere gratitude to my advisor, Dr. Rajeev
Prabhakar, for leading me into such an exciting field of chemistry. I was given the
opportunity to study complex chemical and biochemical systems which is amazing and
interesting. He always encouraged me when I faced a problem and taught me how to
think independently to solve it. He patiently helped me when I made mistakes. He
reminded me often to have a positive attitude towards anything and his kindness, freedom
of thought, and consistent support made my entire graduate life very smooth. I feel very
lucky to have had him as my mentor.
I would also like to thank Dr. Françisco Raymo, Dr. Jamie Walls, and Dr. Akira Chiba
for being my committee members and providing invaluable insight into my research. I
wish to express my sincere appreciation to Dr. V. Ramamurthy, Dr. Carl Hoff, Dr. Burjor
Captain and Dr. Norito Takenaka for sharing their extraordinary expertise. I also would
like to convey my gratitude to
 Dr. Roger Leblanc for his encouragement and concern. I
would like to thank Dr. Tegan Eve for his excellent training and coordination during my
teaching assistantship which greatly improved my teaching skills. I also would like to
thank the chemistry department staff members Lydia, Marlene, Susana, and Sara for all
their support.
I am grateful to all my wonderful and lovely lab mates Arghya, Xiaoxia, Mehmet,
Shanghao, Ram, and TJ for making the lab enjoyable and feeling like a home. Arghya,
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Xiaoxia, and Mehmet shared their experience and helped me a lot from the very
beginning of my research. Special thanks to TJ for his valuable suggestions and
corrections during the preparation of this thesis.
I would like to thank all my friends Dianting, Anhui, Cai, Zhili, Sheba, Barnali,
Xiaowen, Sanem, Anjaneyulu, Pradeep, Jeet, Hossein, Song, Yanhua, Revathy, Sumit,
Shampa, Veeranna, Rajib, Jyothi, Zhenghua, Beijun, Yang, Xu, Subu, and Ali at UM for
their great friendship that will never be forgotten.
Finally, I am forever indebted to my parents and my fiancé who give me love, support,
and encouragement. They are the driving force for me to move on. Having them in my
life is the greatest blessing for me.

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“The way to get good ideas is to get lots of ideas and throw the bad ones away.”
- Linus Pauling

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