Coarse-grained simulations of the conformational dynamics of proteins
Computational and Theoretical Polymer Science, cilt.9, sa.3-4, ss.255-260, 1999 (SCI-Expanded, Scopus)
- Yayın Türü: Makale / Tam Makale
- Cilt numarası: 9 Sayı: 3-4
- Basım Tarihi: 1999
- Doi Numarası: 10.1016/s1089-3156(99)00012-4
- Dergi Adı: Computational and Theoretical Polymer Science
- Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus
- Sayfa Sayıları: ss.255-260
- Anahtar Kelimeler: Autocorrelations, Conformational dynamics, Monte Carlo/Metropolis simulation technique, Unfolding α-Helices, Virtual bonds, β-Sheets
- Boğaziçi Üniversitesi Adresli: Evet
Özet
The conformational dynamics of a set of proteins, cytochrome c, α-lactalbumin and barnase, is studied by an off-lattice Monte Carlo (MC)/Metropolis simulation technique. A low-resolution model (virtual bond model) for the protein structure is used with recently extracted knowledge-based potentials. The calculated root-mean-square fluctuations in the α-carbons are in good agreement with X-ray crystallographic temperature factors. The potentially yielding or non-yielding regions of the protein for unfolding, in the kinetic sense, are identified from the correlation analysis of the rotational motions of the backbone bonds. The bonds which display highly auto-correlated rotational motions, in general, belong to those regions which are experimentally identified to be highly resistant to unfolding.