Yıl 2019, Cilt 20 , Sayı 1, Sayfalar 19 - 26 2019-04-15

MOLECULAR DYNAMICS STUDIES OF THE NOROVIRUS-HOST CELL INTERACTION MEDIATED BY H-TYPE 1 ANTIGEN

Abdulkadir Kocak [1] , Müslüm Yıldız [2]


Noroviruses are the main cause for acute gastroenteritis disease. They infect the host cell via interaction with HGBA receptors on the cell surface. Virus makes complex with cell surface receptors through its capsid protein VP1 to enter the cell. Although the protein has been successfully crystallized in the presence of some common glycans, the dynamic change in the protein structure when interacting with sugar moieties has yet to be fully elucidated. This is critically important since it leads to understanding the protein’s recognition mechanism of HBGAs and develop therapeutic strategies against the gastroenteritis disease. Here, we computationally assessed the dynamic features of wild type VP1 envelope protein to get insights into the interactions that can be important for virus infectivity. We have found that the binding of sugar moiety does not cause noticeable dynamic changes in the binding region. However, interestingly, a drastic change occurs in a distant loop lying at the residue numbers of 395-400, which might be indication of an allosteric effect.

Akut gastroenterit hastalığının önemli nedenlerinden biri norovirüslerdir. Konakçı hücreye, hücre yüzeyindeki çoklu şeker halkalarından oluşan HGBA reseptörleri ile etkileşerek enfekte olurlar. Hücreye girmek için virüse ait kapsid proteini hücre yüzeyi reseptörleri ile kompleksleşir. Her ne kadar protein bazı ortak glikanların varlığında kompleks olarak başarılı bir şekilde kristalize edilmiş olsa da, şeker kısımlarının bağlanmasından kaynaklanan protein yapısındaki dinamik değişim henüz tam olarak aydınlatılamamıştır. Virüs proteinin HBGA'lara bağlanma mekanizmasını anlama ve gastroenterit hastalığına karşı tedavi stratejileri geliştirmesine yardımcı olması nedeniyle bu dinamik değişimi anlamak kritik derecede öneme sahiptir. Bu çalışmada, virüs enfeksiyonu için önemli olabilecek etkileşimler hakkında bilgi edinmek için yabanıl VP1 kapsit proteininin dinamik özelliklerini moleküler dinamik metotlarla hesapladık. Şeker kısmının bağlanmasının, bağlanma bölgesinde gözle görülür dinamik değişikliklere neden olmadığını tespit ettik. Bununla birlikte, ilginç bir şekilde, allosterik bir etkinin göstergesi olabilecek 395-400 numaralı sekansa ait amino asitlerinde ihmal edilemeyecek bir hareketlilik meydana geldiğini gözlemledik. 

Norovirus, therapeutic antibody, HBGA blockage, molecular dynamics
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Birincil Dil en
Konular Biyoloji, Fen
Bölüm Araştırma Makalesi/Research Article
Yazarlar

Orcid: 0000-0001-6891-6929
Yazar: Abdulkadir Kocak (Sorumlu Yazar)
Kurum: GEBZE TECHNICAL UNIVERSITY, FACULTY OF BASIC SCIENCES
Ülke: Turkey


Orcid: 0000-0001-8396-1461
Yazar: Müslüm Yıldız
Kurum: GEBZE TECHNICAL UNIVERSITY, FACULTY OF BASIC SCIENCES
Ülke: Turkey


Tarihler

Başvuru Tarihi : 4 Ocak 2019
Kabul Tarihi : 27 Ocak 2019
Yayımlanma Tarihi : 15 Nisan 2019

Bibtex @araştırma makalesi { trkjnat508120, journal = {Trakya University Journal of Natural Sciences}, issn = {2147-0294}, eissn = {2528-9691}, address = {}, publisher = {Trakya Üniversitesi}, year = {2019}, volume = {20}, pages = {19 - 26}, doi = {10.23902/trkjnat.508120}, title = {MOLECULAR DYNAMICS STUDIES OF THE NOROVIRUS-HOST CELL INTERACTION MEDIATED BY H-TYPE 1 ANTIGEN}, key = {cite}, author = {Kocak, Abdulkadir and Yıldız, Müslüm} }
APA Kocak, A , Yıldız, M . (2019). MOLECULAR DYNAMICS STUDIES OF THE NOROVIRUS-HOST CELL INTERACTION MEDIATED BY H-TYPE 1 ANTIGEN. Trakya University Journal of Natural Sciences , 20 (1) , 19-26 . DOI: 10.23902/trkjnat.508120
MLA Kocak, A , Yıldız, M . "MOLECULAR DYNAMICS STUDIES OF THE NOROVIRUS-HOST CELL INTERACTION MEDIATED BY H-TYPE 1 ANTIGEN". Trakya University Journal of Natural Sciences 20 (2019 ): 19-26 <https://dergipark.org.tr/tr/pub/trkjnat/issue/44590/508120>
Chicago Kocak, A , Yıldız, M . "MOLECULAR DYNAMICS STUDIES OF THE NOROVIRUS-HOST CELL INTERACTION MEDIATED BY H-TYPE 1 ANTIGEN". Trakya University Journal of Natural Sciences 20 (2019 ): 19-26
RIS TY - JOUR T1 - MOLECULAR DYNAMICS STUDIES OF THE NOROVIRUS-HOST CELL INTERACTION MEDIATED BY H-TYPE 1 ANTIGEN AU - Abdulkadir Kocak , Müslüm Yıldız Y1 - 2019 PY - 2019 N1 - doi: 10.23902/trkjnat.508120 DO - 10.23902/trkjnat.508120 T2 - Trakya University Journal of Natural Sciences JF - Journal JO - JOR SP - 19 EP - 26 VL - 20 IS - 1 SN - 2147-0294-2528-9691 M3 - doi: 10.23902/trkjnat.508120 UR - https://doi.org/10.23902/trkjnat.508120 Y2 - 2019 ER -
EndNote %0 Trakya University Journal of Natural Sciences MOLECULAR DYNAMICS STUDIES OF THE NOROVIRUS-HOST CELL INTERACTION MEDIATED BY H-TYPE 1 ANTIGEN %A Abdulkadir Kocak , Müslüm Yıldız %T MOLECULAR DYNAMICS STUDIES OF THE NOROVIRUS-HOST CELL INTERACTION MEDIATED BY H-TYPE 1 ANTIGEN %D 2019 %J Trakya University Journal of Natural Sciences %P 2147-0294-2528-9691 %V 20 %N 1 %R doi: 10.23902/trkjnat.508120 %U 10.23902/trkjnat.508120
ISNAD Kocak, Abdulkadir , Yıldız, Müslüm . "MOLECULAR DYNAMICS STUDIES OF THE NOROVIRUS-HOST CELL INTERACTION MEDIATED BY H-TYPE 1 ANTIGEN". Trakya University Journal of Natural Sciences 20 / 1 (Nisan 2019): 19-26 . https://doi.org/10.23902/trkjnat.508120
AMA Kocak A , Yıldız M . MOLECULAR DYNAMICS STUDIES OF THE NOROVIRUS-HOST CELL INTERACTION MEDIATED BY H-TYPE 1 ANTIGEN. Trakya Univ J Nat Sci. 2019; 20(1): 19-26.
Vancouver Kocak A , Yıldız M . MOLECULAR DYNAMICS STUDIES OF THE NOROVIRUS-HOST CELL INTERACTION MEDIATED BY H-TYPE 1 ANTIGEN. Trakya University Journal of Natural Sciences. 2019; 20(1): 26-19.