Using molecular modeling to identify zinc finger protein-DNA recognition patterns : a study of four finger proteins and dimer binding to DNA
Other Title(s)
استخدام التمثيل الجزيئي لتحديد أنماط تعرف بروتين أصبع الزنك على الحمض النووي : دراسة ارتباط أربعة أنماط من بروتين أصبع الزنك و البروتين الثنائي مع الحمض النووي
Dissertant
Thesis advisor
Comitee Members
Karain, Wail
Sayyid Ahmad, Abd Allah
University
Birzeit University
Faculty
Faculty of Science
Department
Department of Chemistry
University Country
Palestine (West Bank)
Degree
Master
Degree Date
2017
English Abstract
Binding of Zinc finger proteins to their DNA targets is an important process for regulating many biological processes.
In this study, four finger and dimers Znf proteins bound to their target DNA are simulated using Molecular dynamics simulations to obtain their equilibrium structures and extract important interactions determining these zinc finger proteins-DNA binding specificity.
Furthermore, binding free energies of these zinc finger proteins to their DNA targets are calculated using MM/GBSA and MM/PBSA approaches.
In particular, the multidomain zinc finger (ZnF) protein PRDM9 (PDB ID: 5EGB) and its variants L9/L24, L13, L20 bind AT, and L20 bind GC calculated binding free energies were -29.48,-31.92 , -27.83, -22.44 ,-9.97 kcal/mol, respectively.
While calculated binding free energies of dimer transcription factors PPR1 (PDB ID: 1PYI) and PUT3 (PDB ID:1ZME) to their target DNA were -7.35 and -15.79 kcal/mol.
The aforementioned calculated binding free energies showed low correlation with experimentally obtained energies (R = 0.69 and 0.59 for MM/PBSA and MM/GBSA, respectively).
Main Subjects
No. of Pages
131
Table of Contents
Table of contents.
Abstract.
Abstract in Arabic.
Chapter 1 : Introduction.
Chapter 2 : Computational methods.
Chapter 3 : Results and discussion.
Chapter 4 : Conclusion.
References.
American Psychological Association (APA)
Siyam, Rima Mazin. (2017). Using molecular modeling to identify zinc finger protein-DNA recognition patterns : a study of four finger proteins and dimer binding to DNA. (Master's theses Theses and Dissertations Master). Birzeit University, Palestine (West Bank)
https://search.emarefa.net/detail/BIM-779853
Modern Language Association (MLA)
Siyam, Rima Mazin. Using molecular modeling to identify zinc finger protein-DNA recognition patterns : a study of four finger proteins and dimer binding to DNA. (Master's theses Theses and Dissertations Master). Birzeit University. (2017).
https://search.emarefa.net/detail/BIM-779853
American Medical Association (AMA)
Siyam, Rima Mazin. (2017). Using molecular modeling to identify zinc finger protein-DNA recognition patterns : a study of four finger proteins and dimer binding to DNA. (Master's theses Theses and Dissertations Master). Birzeit University, Palestine (West Bank)
https://search.emarefa.net/detail/BIM-779853
Language
English
Data Type
Arab Theses
Record ID
BIM-779853
