Identification of distinct communication networks in human ?2 adrenergic receptor via molecular dynamics simulation
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Date
2020
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Kadir Has Üniversitesi
Abstract
G-protein-bağlı reseptörler (GPCR), hücre dışı ligand bağlanma işlemini hücre içi tepkilere dönüştürerek çok çeşitli insan fizyolojik fonksiyonlarına aracılık eden ve yedi transmembran (TM) yapısından oluşan proteinlerdir. Karşılıklı sinyal aktarımı, ancak iki uzak bölge arasında allosterik iletişimle oluşur. Hem inaktif hem de aktif kristal yapıların mevcut olduğu bir arketipik GPCR olan insan β2-adrenerjik reseptörüne (β2AR) odaklandık. β2AR 'ın farklı konformasyonlarının yörüngelerini oluşturmak için moleküler dinamik (MD) simülasyonları gerçekleştirildi. Burada, β2AR'a ait orijinal inaktif durum (Faz I), çok inaktif durum (Faz II), ara durum ve G-proteine bağlı aktif durumun yörüngelerini kullanarak potansiyel iletişim ağlarını araştırdık. Bu nedenle, bu tezde nedenselliğe bağlı potansiyel allosterik etkileşim ve bilgi aktarımını ortaya çıkarmak için proteindeki Cα dalgalanmaları ve omurga/yan zincir dihedral açı rotasyonları üzerinde hem korelasyon hem de entropi bazlı olasılıksal yaklaşımlar kullanılmıştır. Serbest ICL3 içeren yapılarda bilgi akışı yönü hücre içinden hücre dışına doğru iken, ICL3'ün hareketinin kısıtlandığı yapılarda bu akış yönünün tam tersine olduğu görüldü. Ayrıca, esnek alanlarda lokalize olmuş amino asitler genellikle polar özelliklere sahip olup iletişime büyük katkıda bulunmuşlardır. aktif-Gp için bağımsız iki çalışma, ICL3'ün z-yönünde hareketi ile birbirinden ayrılmış ve burada G proteini etkisinden dolayı iletişim ve polarite gücünün azaldığı saptanmıştır. Son olarak, mutlak Cα dalgalanma değerleri ve sterik engeller farklı dihedral açılarının oluşmasına neden olabildiğinden, Cα dalgalanmaları ve dihedral açıların ortak hareketi gözlemlenmemiştir. Bu nedenle de dihedral verilerde çoğunlukla ilmik alanlarının ortaya çıktığı görüntülenmiştir. Bu sonuçlar β2AR 'daki allosterik iletişimi açıklamak için yapı temelli bir mekanizma sağlamakta ve dahası rasyonel ilaç tasarımı ve protein mühendisliği gibi uygulamalar için bir temel oluşturmaktadır.
G-protein-coupled receptors (GPCRs) are seven-transmembrane (TM) proteins mediating a wide range of human physiological functions by transducing extracellular events into intracellular responses. The signal relay requires allosteric communication between two distant sites. We focused on the human β2-adrenergic receptor (β2AR), for which crystal structures were available in inactive and active states. Here, we investigated communication networks using five distinct trajectories of β2AR, including both inactive and active conformations. Correlation and entropy-based approaches on Cα fluctuations and backbone/side-chain dihedral angle rotations were used to identify potential allosteric coupling and investigate information transfer due to causality. For conformations with freely moving ICL3, the information flow was directed from intracellular to extracellular parts, whereas those with constrained ICL3, this direction was reversed. Residues located on flexible domains generally had polar characteristics and contributed heavily to communication. Two independent runs conducted for the active state, which were complexed with partner G protein (Gp) displayed different dynamics.. Also, both the degree of communication and dominancy of polar residues in information transfer were decreased in active states, which was attributed to the presence of Gp. In addition, the mutual information (MI) based on Cα fluctuations was different from that based on dihedrals. Cα-based MI was dominant in regions with high RMSF values, whereas dihedral-based MI was dominant in loop regions where dihedral flexibility was high. Moreover, Cα-based transfer entropy (TE) was distinct in each state, whereas dihedral-based TE was high between loop and TM regions in all five states. These results led the way to a new approach in which the protein allostery was described with a combination of Cα- and dihedral-based MI and TE. This approach was suggested for applications including rational drug design and protein engineering.
G-protein-coupled receptors (GPCRs) are seven-transmembrane (TM) proteins mediating a wide range of human physiological functions by transducing extracellular events into intracellular responses. The signal relay requires allosteric communication between two distant sites. We focused on the human β2-adrenergic receptor (β2AR), for which crystal structures were available in inactive and active states. Here, we investigated communication networks using five distinct trajectories of β2AR, including both inactive and active conformations. Correlation and entropy-based approaches on Cα fluctuations and backbone/side-chain dihedral angle rotations were used to identify potential allosteric coupling and investigate information transfer due to causality. For conformations with freely moving ICL3, the information flow was directed from intracellular to extracellular parts, whereas those with constrained ICL3, this direction was reversed. Residues located on flexible domains generally had polar characteristics and contributed heavily to communication. Two independent runs conducted for the active state, which were complexed with partner G protein (Gp) displayed different dynamics.. Also, both the degree of communication and dominancy of polar residues in information transfer were decreased in active states, which was attributed to the presence of Gp. In addition, the mutual information (MI) based on Cα fluctuations was different from that based on dihedrals. Cα-based MI was dominant in regions with high RMSF values, whereas dihedral-based MI was dominant in loop regions where dihedral flexibility was high. Moreover, Cα-based transfer entropy (TE) was distinct in each state, whereas dihedral-based TE was high between loop and TM regions in all five states. These results led the way to a new approach in which the protein allostery was described with a combination of Cα- and dihedral-based MI and TE. This approach was suggested for applications including rational drug design and protein engineering.