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Title:Detekcija ohranjenih vod na medproteinskih površinah : diplomsko delo univerzitetnega študijskega programa I. stopnje
Authors:ID Masten, Ines (Author)
ID Bren, Urban (Mentor) More about this mentor... New window
ID Jukič, Marko (Comentor)
Files:.pdf UN_Masten_Ines_2020.pdf (2,97 MB)
MD5: CD1194E704CF65FC96A83D628537D95B
PID: 20.500.12556/dkum/660a1809-099e-425b-a360-2afdf164c92e
 
Language:Slovenian
Work type:Bachelor thesis/paper
Typology:2.11 - Undergraduate Thesis
Organization:FKKT - Faculty of Chemistry and Chemical Engineering
Abstract:Študij ohranjenih vod je v sodobni farmacevtski kemiji ključnega pomena. Ne samo da ima voda pomembno vlogo v vseh bioloških procesih, temveč molekule vode ključno prispevajo pri interakcijah med proteini. Kristalne strukture kompleksov, pridobljene z visoko ločljivostjo iz različnih vendar homolognih proteinov, so pokazale, da so nekatere vode na medproteinski površini ohranjene med dvema homolognima kompleksoma. Ohranjene vode nastopajo pri tvorjenju vodikovih vezi, imajo strukturno vlogo pri makromolekulah, kjer tvorijo kompleksne mreže molekul, ki stabilizirajo njihovo strukturo. V diplomski nalogi smo s pomočjo računalniškega programa PyMOL identificirali medproteinsko površino sistema programirane celične smrt hPD-1 in njenega liganda hPD-L1 ter sistema beta rastnega faktorja Tgf-β3 in receptorja Tgf-β tipa II. Na tej medproteinski površini smo nato z orodjem ProBis H2O identificirali ohranjene molekule vode. Za vsako molekulo vode smo analizirali njene interakcije z aminokislinskimi ostanki in z ostalo medproteinsko površino. Ugotovili smo, da nekatere od teh ohranjenih molekul vod igrajo pomembno vlogo pri interakcijah med proteini ter so ključnega pomena za nujno komplementarnost. Poleg tega smo izračunali tudi energijo medproteinske interakcije in analizirali, kako vode vplivajo na celotno površino in vezavo med proteinoma. Rezultati analize nam lahko pomagajo pri predvidevanju interakcij med proteini, karakterizaciji vezavnih mest ter optimizaciji in razvoju zdravil
Keywords:ohranjene vode, medproteinska površina, vodikova vez, hidrofobni učinek, ProBiS H2O
Place of publishing:Maribor
Place of performance:Maribor
Publisher:[I. Masten]
Year of publishing:2020
Number of pages:X, 40 str.
PID:20.500.12556/DKUM-77539 New window
UDC:577.112(043.2)
COBISS.SI-ID:33831939 New window
NUK URN:URN:SI:UM:DK:49HORUC7
Publication date in DKUM:08.10.2020
Views:754
Downloads:80
Metadata:XML DC-XML DC-RDF
Categories:KTFMB - FKKT
:
MASTEN, Ines, 2020, Detekcija ohranjenih vod na medproteinskih površinah : diplomsko delo univerzitetnega študijskega programa I. stopnje [online]. Bachelor’s thesis. Maribor : I. Masten. [Accessed 28 April 2025]. Retrieved from: https://dk.um.si/IzpisGradiva.php?lang=eng&id=77539
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Licences

License:CC BY-NC-ND 4.0, Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
Link:http://creativecommons.org/licenses/by-nc-nd/4.0/
Description:The most restrictive Creative Commons license. This only allows people to download and share the work for no commercial gain and for no other purposes.
Licensing start date:02.09.2020

Secondary language

Language:English
Title:Identification of conserved waters on protein interfaces
Abstract:The study of conserved waters is crucial in modern pharmaceutical chemistry. Not only that water plays an important role in all biological processes, but water molecules play a key role in protein-protein interactions (PPI) as well. The high-resolution crystal structures from different homologous proteins show that certain waters on the protein interfaces retain their location. They are named conserved waters and paticipate in the formation of key hydrogen bonds, play a structural role and stabilize macromolecular structures. In this thesis, we used computer programme PyMOL to identify the protein interface of human programmed death-1 (PD-1)-PD-L1 complex and transforming growth factor beta Tgf-β3 and TGF-beta Type II receptor complex. Conserved water molecules were then identified on these protein interfaces using ProBis H2O software. For each water molecule, its interactions at the protein interface were analysed. We found that conserved water molecules play an important role in protein-protein interactions (PPI) and are crucial for the interface complementarity. In addition, we also calculated the energy of the interface interactions and confirmed that all of the identified conserved waters contribute favourably to the interface binding. The results of this work can help us to predict protein-protein interactions (PPI), characterize binding sites, as well as to optimize and develop novel drugs.
Keywords:conserved waters, protein-protein interface, hydrogen bond, hydrophobic effect, ProBiS H2O


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