Intramolecular hydrogen bonding incyclic peptides and depsipeptides
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- Tez No: 708711
- Danışmanlar: DR. LASZLO FABİAN
- Tez Türü: Yüksek Lisans
- Konular: Biyomühendislik, Moleküler Tıp, Biyokimya, Bioengineering, Molecular Medicine, Biochemistry
- Anahtar Kelimeler: Belirtilmemiş.
- Yıl: 2020
- Dil: İngilizce
- Üniversite: Unıversıty Of East Anglıa
- Enstitü: Yurtdışı Enstitü
- Ana Bilim Dalı: Belirtilmemiş.
- Bilim Dalı: Belirtilmemiş.
- Sayfa Sayısı: Belirtilmemiş.
Özet
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Özet (Çeviri)
Most of the cyclic peptides (CPs) and depsipeptides (CDPs) have low oral bioavailability. Intramolecular hydrogen bonds (IMHBs) in CPs/CDPs can increase their bioavailability. By investigating crystal structures in Cambridge Structural Database (CSD), 143 CPs and 19 CDPs containing IMHBs were identified. CPs with odd-numbered amino acids (aa) contain IMHBs at a higher ratio. Examination of aa showed that existence of alanine was positively affecting and existence of glycine was negatively affecting the IMHB formation. There are 326 H-bonded pseudo-rings in CPs, 58% of which are 10-membered rings (C10) and 17% of which are 14- membered rings (C14). Observation of C14 was unexpected. Among all peptides deposited to CSD, C10 are the most likely rings to be observed, with 43% frequency. Ramachandran plots of φ/ψ torsions in different pseudorings revealed the conformational preferences of these rings. Molecular dynamic simulations were run on a selected CP with two different force fields (RSFF2 and ff19SB) for 50 ns. RSFF2 was found to better reproduce the crystal structure conformation of CP. It was mostly stable during the simulation but partially lost its rigidity after some time.
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