hnRNPA1 PY-NLS Bölgesinde N267S Mutasyonunun Amiloid Fibril Stabilitesi ve Dinamikleri Üzerine Etkileri: Moleküler Dinamik Simülasyonlardan Bulgular

Abstract

hnRNPA1 proteininin düşük komplekslik (LC) bölgesi, hem normal hücresel süreçlerde hem de nörodejeneratif hastalıkların patogenezinde kritik bir role sahiptir. Bu bölge içerisinde yer alan PY-NLS motifi, nükleer taşınımda karyoforin-β2 ile yüksek afiniteli etkileşimler kurmasının yanı sıra amiloid fibril çekirdeğinin oluşumuna da katkı sağlamaktadır. Bu çalışmada, PY-NLS dizisinin merkezinde bulunan N267 kalıntısındaki serin ikamesinin (N267S) fibril yapısının stabilitesi ve dinamikleri üzerindeki etkileri araştırılmıştır. Deneysel olarak çözümlenmiş fibril yapısı temel alınarak oluşturulan WT ve N267S modelleri, 500 ns süreli atomistik moleküler dinamik simülasyonlarına tabi tutulmuş ve sonuçlar RMSD, Rg, RMSF, inter- ve intra-protofilament mesafeler ile hidrojen bağı profilleri üzerinden değerlendirilmiştir. Bulgular, N267S mutasyonunun fibril yapısını global ölçekte daha kompakt ve başlangıç formuna yakın bir konformasyonda koruduğunu ortaya koymuştur. WT formunda zamanla artan genlikli dalgalanmalar ve coil-2 bölgesinde belirgin esneklik gözlenirken, N267S mutantı daha düşük genlikli hareketlerle rijit bir mimari sergilemiştir. N268–N268 fibriller arası arayüz mesafesi mutant formda WT’ye kıyasla daha dar aralıkta korunmuş, F263–F273 hattındaki aromatik π-π yığınlaşması ise her iki formda da kararlı biçimde sürdürülmüştür. Protofilament içi mesafe analizleri, WT’de yeniden hizalanma ve daralma eğilimlerini gösterirken, mutant formda bu değişimlerin sınırlı kaldığı tespit edilmiştir. Hidrojen bağı analizleri, özellikle protofilamentler arası bağların mutantta artış gösterdiğini ve arayüz stabilitesini güçlendirdiğini ortaya koymuştur. Tüm veriler bir arada değerlendirildiğinde, N267S mutasyonunun fibril yapısını daha sıkı paketlenmiş, daha stabil ve daha az esnek bir mimariye yönlendirdiği sonucuna varılmıştır. Bu bulgular, hnRNPA1 fibril oluşumunun moleküler düzeyde anlaşılmasına katkı sunmakta ve mutasyona bağlı nörodejeneratif süreçlerin aydınlatılmasında yeni ipuçları sağlamaktadır.

Keywords

• hnRNPA1
• PY-NLS
• amiloid fibril
• N267S mutasyonu
• moleküler dinamik simülasyon

Supporting Institution

Zonguldak Bülent Ecevit Üniversitesi

Project Number

2025-22794455-01

Ethical Statement

Bu çalışmada etik kurul onayı gerektiren bir durum bulunmamaktadır.

Thanks

Bu çalışma Zonguldak Bülent Ecevit Üniversitesi Bilimsel Araştırma Projeleri Birimi tarafından 2025-22794455-01 nolu proje ile desteklenmiştir.

Effects of the N267S Mutation on Amyloid Fibril Stability and Dynamics in the hnRNPA1 PY-NLS Region: Insights from Molecular Dynamics Simulations

Abstract

The low-complexity (LC) domain of hnRNPA1 plays a critical role both in normal cellular processes and in the pathogenesis of neurodegenerative diseases. Within this region, the PY-NLS motif not only mediates high-affinity interactions with karyopherin-β2 during nuclear import but also contributes to amyloid fibril formation. In this study, we investigated the impact of a serine substitution at residue N267 (N267S) on the stability and dynamics of the hnRNPA1 fibril core. Wild-type (WT) and N267S models were subjected to 500-ns atomistic molecular dynamics simulations, and the results were analyzed using RMSD, Rg, RMSF, inter- and intra-protofilament distance measurements, and hydrogen bond profiles. The findings revealed that the N267S mutation maintains the fibril structure in a more compact and stable conformation, closer to its initial state. While WT fibrils exhibited larger amplitude fluctuations and increased flexibility in the coil-2 region, the N267S mutant displayed reduced mobility and a more rigid architecture. The N268–N268 inter-protofilament distance remained narrower in the mutant compared to WT, whereas the F263–F273 aromatic π-π stacking persisted robustly in both forms. Intra-protofilament distance analysis demonstrated compaction and rearrangements in WT fibrils, while the mutant maintained a more preserved geometry. Hydrogen bond analysis indicated that N267S increases inter-protofilament interactions, reinforcing the stability of the fibril interface. Collectively, these results suggest that the N267S mutation enhances fibril stability by restricting flexibility, tightening interfacial packing, and strengthening hydrogen bonding networks. This provides molecular-level insight into hnRNPA1 fibril formation and its potential contribution to mutation-driven neurodegenerative processes.

Keywords

• hnRNPA1
• PY-NLS
• amyloid fibril
• N267S mutation
• molecular dynamics simulation

Supporting Institution

Zonguldak Bülent Ecevit University

Project Number

2025-22794455-01

Ethical Statement

There is no situation in this study that requires approval from an ethics committee.

Thanks

This study was supported by the Zonguldak Bülent Ecevit University Scientific Research Projects Unit under project number 2025-22794455-01.

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