Kumarin2 5Z/5E’nin Çekildiği Yönlendirilmiş Moleküler Dinamik Simülasyonları İnsana ait Dört Sitozolik Karbonik Anhidraz için Farklı Etkileşim Profilleri Ortaya Çıkarmaktadır

Karbonic anhidraz (CA), insanlarda herbiri farklı fonksiyonlar icra eden çeşitli izoformlara sahip önemli bir enzimdir. Karbonik anhidraz izoformlarının ligandlar ile etkileşimlerini karakterize etmek zor fakat önemli bir iştir. Son yıllarda yönlendirilmiş moleküler dinamik, ligand bağlanma ve kopma olaylarını karakterize etmek için başarıyla kullanılmıştır. Bu çalışmada, Kumarin2 5Z/5E adlı ligandı kullanarak dört sitozolik insan karbonik anhidrazının (karbonik anhidraz I, II, III ve VII) bu ligand ile etkileşimlerinin doğasını anlamak amacıyla sabit hızda yönlendirilmiş moleküler dinamik (YMD) simülasyonları uygulandı. Kuvvet sabitinin ve çekme hızının YMD simülasyonları üzerine etkisi incelendi. Kuvvet sabiti ve çekme hızı değiştirildiği zaman etkileşim profillerinde önemli bir değişim gözlenmedi. Son olarak hidrojen bağı etkileşimleri, Histidin 64 pozisyonları ve kuvvet-mesafe grafikleri tüm isozimler için analiz edildi. Bu sonuçlar, insana ait sitozolik karbonik anhidraz I, III ve VII’nin -farklı kuvvetlerle de olsa- Kumarin2 5E/5Z’den benzer kopma modellerine sahip olduğunu, buna karşın karbonik anhidraz II’nin tamamen farklı bir etkileşim profiline sahip olduğunu göstermektedir.

Steered Molecular Dynamics Simulations of Coumarin2 5Z/5E Pulling Reveal Different Interaction Profiles for Four Human Cytosolic Carbonic Anhydrases

Carbonic anhydrase (CA) is an important enzyme, which has multipleisoforms each performing different functions in humans. Characterizing theinteractions of carbonic anhydrase isoforms with ligands is a difficult butimportant task. In recent years, steered molecular dynamics (SMD) has been usedsuccessfully to characterize ligand binding and unbinding events. In this study,constant velocity SMD simulations were performed on four cytosolic humancarbonic anhydrases (carbonic anhydrase I, II, III and VII) using a ligand calledCoumarin2 5Z/5E to understand better the nature of interactions between thisligand and the various enzyme isoforms. The influence of force constant andpulling velocity on SMD simulations were investigated. When the force constantand the pulling velocity were changed, no significant effect on interaction profileswas observed. Finally, hydrogen bond interactions, Histidine 64 positions and thedifferences between force-distance profiles for all isozymes were analyzed. Theseresults demonstrate that human cytosolic carbonic anhydrases I, III, and VII showsimilar Coumarin2 5Z/5E unbinding patterns with different rupture forces, whilecarbonic anhydrase II has a distinct interaction profile.

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