SEB’e Bağlanan Tekrarlı Peptid Dizilimlerinin REMD Çalışması

Değişikliğe uğramış peptitlerin konformasyonel farklılıklarının, afinite üzerinde rol oynayıp oynamadığını araştırdık. Bu amaçla, staphylococcal enterotoxin B SEB ’e bağlanma afinitesini değiştiren tekrarlı peptit dizilimlerinin ikincil yapı eğilimlerini ve konformasyonel durumlarını elde etmek için Replica Exchange Moleküler Dinamik REMD simülasyonlar yaptık. REMD simülasyonlardan elde edilen sonuçlar bu tekrarlı peptit dizilimlerinin ikincil yapılarının tüm sıcaklıklar için az miktarda heliks ve β-bridge yapılarla birlikte çoğunlukla random coil, bend ve turn yapılar olduğunu gösterdi. Bunların yanısıra, dizilimlerin tekrarlanmasıyla random coil yapıların yüzdesi azalırken, bend yapılarda artış gözlenmiştir. Bu sonuçlar Circular Dicroism CD spektroskopiden elde edilen sonuçlarla uyumludur. Temel Bileşen Analizi PCA vasıtasıyla, peptit dizilimlerinin serbest enerji yüzeyleri elde edilmiş ve birkaç yerel minimum bulunmuştur. Bu minimumlara karşılık gelen ikincil yapılar her iki peptit için de çoğunlukla coil, bend ve turn yapılara sahiptir. Bu baskın yapılara ek olarak bir de önemli miktarda heliks ve β-bridge yapılar göze çarpmıştır. Peptit dizilimlerini tekrar sayısı arttıkça random coil yapıların yüzdesi azalır ve random coil yapılardaki bu dönüşüm seçilen sıcaklık ve bölgeye bağlı olarak bend, turn, heliks ve β-bridge yapılardaki artış şeklinde ortaya çıkar. Sonuçlar, tekrarlı peptit dizilimlerinin ikincil yapı eğilimleri ve afinite arasında doğrudan bir ilişki görüntülenemediğini işaret etmiştir

Anahtar Kelimeler:

Serbest enerji yüzeyi, Peptit ligand, Temel bileşen analizi, Kopya değiş-tokuş moleküler dinamik, SEB’e bağlanan peptitler, İkincil yapı

The Study of REMD Simulation of SEB-Binding Repetitive Peptide Sequences

We investigated whether the conformational differences of modified peptides play a role for affinity or not. For this purpose, we have performed the replica exchange molecular dynamic simulation REMD to obtain the conformational states and secondary structural propensities of repetitive peptide sequences changed the affinity of binding to staphylococcal enterotoxin B SEB . The results obtained from REMD simulations have shown that the secondary structures of these repetitive peptide sequences were mainly random coil, bend and turn structures with a small amount of helix and β-bridge structures for all temperatures. Besides it was shown that, with repeating the sequence, while the percentage of random coil structures decreased, the ones of bend structures increased. These results are consistent with the ones which obtained from circular dicroism spectroscopy. In terms of principal component analysis PCA , the free energy landscapes of peptide sequences were obtained and found several local minima. The secondary structures corresponding with these minima have mainly coil, turn and bend structures for both peptides. In addition to these dominant structures considerable amount of helix and β-bridge structures were also outstanding. Its observed that while the number of repetition of peptide sequence increases, the percentage of random coil structures are decreases and this transformation in the random coil structures emerges in the form of increases in the rates of bend, turn, helix and β-bridge structures with the chosen temperature and region. The results pointed that it was not monitored a directly relationship between the affinity and secondary structures propensities of repetitive peptides.

Keywords:

replica exchange molecular dynamics, secondary structure, peptide ligands, principal component analysis, free energy landscape, SEB-binding peptides,

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