Çağdaş Dağ

Çağdaş Dağ


Research Focus & Metrics

Academic Career Length

15Years (2012-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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1 May 2018 in LWT
Verified
Journal Article
Closed access
IÖİbrahim Sani Özdemir
İbrahim Sani Özdemir
ÇDÇağdaş Dağ
Çağdaş Dağ
GÖGizem Özinanç
Gizem Özinanç
ÖSÖznur Suçsoran
Öznur Suçsoran
EEErdal Ertaş
Erdal Ertaş
SBSomer Bekiroğlu
Somer Bekiroğlu

1 June 2018 in LWT
Verified
Journal Article
Closed access
IÖİbRahim Sani Özdemir
İbRahim Sani Özdemir
ÇDÇağdaş Dağ
Çağdaş Dağ
DMDamjan Makuc
Damjan Makuc
EEErdal Ertaş
Erdal Ertaş
JPJanez Plavec
Janez Plavec
SBSomer Bekiroğlu
Somer Bekiroğlu

20 January 2022 in Communications Biology
Verified
Journal Article
Open access
PDF file
EAEsra Ayan
Esra Ayan
BYBusra Yuksel
Busra Yuksel
EDEbru Destan
Ebru Destan
FEFatma Betul Ertem
Fatma Betul Ertem
GYGunseli Yildirim
Gunseli Yildirim
Hasan DeMirciHasan DeMirci
Hasan DeMirci
Multimeric protein assemblies are abundant in nature. Streptavidin is an attractive protein that provides a paradigm system to investigate the intra- and intermolecular interactions of multimeric protein complexes. Also, it offers a versatile tool for biotechnological applications. Here, we present two apo-streptavidin structures, the first one is an ambient temperature Serial Femtosecond X-ray crystal (Apo-SFX) structure at 1.7 Å resolution and the second one is a cryogenic crystal structure (Apo-Cryo) at 1.1 Å resolution. These structures are mostly in agreement with previous structural data. Combined with computational analysis, these structures provide invaluable information about structural dynamics of apo streptavidin. Collectively, these data further reveal a novel cooperative allostery of streptavidin which binds to substrate via water molecules that provide a polar interaction network and mimics the substrate biotin which displays one of the strongest affinities found in nature.

3 September 2021 in Journal of Biomolecular NMR
Verified
Journal Article
Open access
PDF file
SRScott A. Robson
Scott A. Robson
ÇDÇağdaş Dağ
Çağdaş Dağ
HWHongwei Wu
Hongwei Wu
JZJoshua Ziarek
Joshua Ziarek
Accurate rotational correlation times (\({\tau }_{\text{c}}\)) are critical for quantitative analysis of fast timescale NMR dynamics. As molecular weights increase, the classic derivation of \({\tau }_{c}\) using transverse and longitudinal relaxation rates becomes increasingly unsuitable due to the non-trivial contribution of remote dipole–dipole interactions to longitudinal relaxation. Derivations using cross-correlated relaxation experiments, such as TRACT, overcome these limitations but are erroneously calculated in 65% of the citing literature. Herein, we developed an algebraic solutions to the Goldman relationship that facilitate rapid, point-by-point calculations for straightforward identification of appropriate spectral regions where global tumbling is likely to be dominant. The rigid-body approximation of the Goldman relationship has been previously shown to underestimate TRACT-based rotational correlation time estimates. This motivated us to develop a second algebraic solution that employs a simplified model-free spectral density function including an order parameter term that could, in principle, be set to an average backbone S2 ≈ 0.9 to further improve the accuracy of \({\tau }_{\text{c}}\) estimation. These solutions enabled us to explore the boundaries of the Goldman relationship as a function of the H–N internuclear distance (\(r\)), difference of the two principal components of the axially-symmetric 15N CSA tensor (\(\Delta {\delta }_{N}\)), and angle of the CSA tensor relative to the N–H bond vector (\(\theta\)). We hope our algebraic solutions and analytical strategies will increase the accuracy and application of the TRACT experiment.

11 December 2018 in TURKISH JOURNAL OF AGRICULTURE AND FORESTRY
Verified
Journal Article
Open access
İÖİbrahim Sani Özdemir
İbrahim Sani Özdemir
ÖKÖznur Karaoğlu
Öznur Karaoğlu
ÇDÇağdaş Dağ
Çağdaş Dağ
SBSomer Beki̇rOğlu
Somer Beki̇rOğlu

15 October 2018 in Metabolomics
Verified
Journal Article
Closed access
PDF file
ŞÇŞükrü Serter Çatav
Şükrü Serter Çatav
EEEmine Sonay Elgin
Emine Sonay Elgin
ÇDÇağdaş Dağ
Çağdaş Dağ
JSJaime L. Stark
Jaime L. Stark
KKKöksal Küçükakyüz
Köksal Küçükakyüz