Söğünmez Erdoğan, Nuray

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Sogunmez Erdogan,Nuray
NURAY SÖĞÜNMEZ ERDOĞAN
S., Nuray
Sogunmez Erdogan,N.
Sogunmez Erdogan, Nuray
Nuray Söğünmez Erdoğan
N. Söğünmez Erdoğan
Nuray, Sogunmez Erdogan
SÖĞÜNMEZ ERDOĞAN, NURAY
Söğünmez Erdoğan, N.
S.,Nuray
Söğünmez Erdoğan, Nuray
Söğünmez Erdoğan,N.
Nuray SÖĞÜNMEZ ERDOĞAN
Söğünmez Erdoğan, NURAY
SÖĞÜNMEZ ERDOĞAN, Nuray
Söğünmez, Nuray
Soğünmez, Nuray
Job Title
Dr. Öğr. Üyesi
Email Address
nuray.erdogan@khas.edu.tr
ORCID ID
0000-0003-0909-064X
Scopus Author ID
58772066800
Turkish CoHE Profile ID
Google Scholar ID
WoS Researcher ID
Scholarly Output

2

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2

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0

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2019 - 20202
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Now showing 1 - 2 of 2
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    Article
    Citation Count: 5
    Distinctive communication networks in inactive states of beta(2)-adrenergic receptor: Mutual information and entropy transfer analysis
    (Wiley, 2020) Söğünmez Erdoğan, Nuray; Akdoğan, Ebru Demet
    Mutual information and entropy transfer analysis employed on two inactive states of human beta-2 adrenergic receptor (beta(2)-AR) unraveled distinct communication pathways. Previously, a so-called "highly" inactive state of the receptor was observed during 1.5 microsecond long molecular dynamics simulation where the largest intracellular loop (ICL3) was swiftly packed onto the G-protein binding cavity, becoming entirely inaccessible. Mutual information quantifying the degree of correspondence between backbone-C(alpha)fluctuations was mostly shared between intra- and extra-cellular loop regions in the original inactive state, but shifted to entirely different regions in this latest inactive state. Interestingly, the largest amount of mutual information was always shared among the mobile regions. Irrespective of the conformational state, polar residues always contributed more to mutual information than hydrophobic residues, and also the number of polar-polar residue pairs shared the highest degree of mutual information compared to those incorporating hydrophobic residues. Entropy transfer, quantifying the correspondence between backbone-C(alpha)fluctuations at different timesteps, revealed a distinctive pathway directed from the extracellular site toward intracellular portions in this recently exposed inactive state for which the direction of information flow was the reverse of that observed in the original inactive state where the mobile ICL3 and its intracellular surroundings drove the future fluctuations of extracellular regions.
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    Article
    Citation Count: 2
    Intrinsic Dynamics and Causality in Correlated Motions Unraveled in Two Distinct Inactive States of Human beta(2)-Adrenergic Receptor
    (Amer Chemical Soc, 2019) Akdoğan, Ebru Demet; Söğünmez Erdoğan, Nuray
    The alternative inactive state of the human beta(2)-adrenergic receptor originally exposed in molecular dynamics simulations was investigated using various analysis tools to evaluate causality between correlated residue-pair fluctuations and suggest allosteric communication pathways. A major conformational shift observed in the third intracellular loop (ICL3) displayed a novel inactive state featuring an inaccessible G protein binding site blocked by ICL3 and an expanded orthosteric ligand binding site. Residue-based mean square fluctuation and stiffness calculations revealed a significant mobility decrease in ICL3 which induced a mobility increase in the remaining loop regions. This indicates conformational entropy loss in one mobile region being compensated by residual intermolecular motions in other mobile regions. Moreover the extent motions decreased and correlations that once existed between transmembrane helices shifted toward regions with increased mobility. Conditional time-delayed cross-correlation analysis identified distinct driver follower relationship profiles. Prior to its packing freely moving ICL3 was markedly driven by transmembrane helix-8 whereas once packed ICL3 controlled future fluctuations of nearby helices. Moreover two transmembrane helices (H5 and H6) started to control future fluctuations of a remote site the extracellular loop ECL2. This clearly suggests that allosteric coupling between extra- and intracellular parts intensified in agreement with the receptor's well recognized feature which is the inverse proportionality between activity and the degree of coupling.