Molecular modeling of biomolecular associations and quantifying allosteric effects
Başlık çevirisi mevcut değil.
- Tez No: 402162
- Danışmanlar: PROF. DR. VOLKHARD HELMS
- Tez Türü: Doktora
- Konular: Biyomühendislik, Biyoteknoloji, Bioengineering, Biotechnology
- Anahtar Kelimeler: Belirtilmemiş.
- Yıl: 2015
- Dil: İngilizce
- Üniversite: Universität des Saarlandes
- Enstitü: Yurtdışı Enstitü
- Ana Bilim Dalı: Belirtilmemiş.
- Bilim Dalı: Belirtilmemiş.
- Sayfa Sayısı: 134
Özet
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Özet (Çeviri)
Molecular dynamics simulation technique is a very popular approach to investigate the structure, dynamics and thermodynamics of biological molecules and their complexes. Using extensive standard molecular dynamics simulations and variants thereof, we probed in this work structural and energetic aspects of either specific or non--‐specific protein--‐protein complexes formed by hydrophilic proteins and of the interfacial water between the two proteins. For the specific complexes, the standard free energies of binding are in overall good agreement with the experimental values. In comparison to their specific counterparts, non specific encounters bear smaller interaction interfaces and are attracted by shorter ranged direct interactions between the proteins. In order to quantify the allosteric effect, we calculated the allosteric coupling energy between the ATP binding pocket and the PIF ‐pocket of phosphoinostide dependent kinase 1. For this system, we found that the main contribution to the allosteric coupling energy comes from electrostatic interactions. Utilizing molecular docking we modeled the interaction of the ER luminal binding immunoglobulin protein (BIP) with loop 7 of the Sec61 translocon. Additionally we used a cyclic peptide as a scaffold to design new competitive compounds that bind to Casein kinase II 𝛼 in a competitive manner to Casein kinase II 𝛽 using molecular docking.
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