Characterization of internal motions of Escherichia coli ribonuclease H by Monte Carlo simulation
Proteins: Structure, Function and Genetics, cilt.34, sa.4, ss.533-539, 1999 (SCI-Expanded, Scopus)
- Yayın Türü: Makale / Tam Makale
- Cilt numarası: 34 Sayı: 4
- Basım Tarihi: 1999
- Dergi Adı: Proteins: Structure, Function and Genetics
- Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus
- Sayfa Sayıları: ss.533-539
- Anahtar Kelimeler: Auto- and cross-correlation, Conformational dynamics, E. coli, Hydrogen exchange, Monte Carlo simulation technique, NMR, RNase, Virtual bonds
- Boğaziçi Üniversitesi Adresli: Evet
Özet
The backbone dynamics of Escherichia coli ribonuclease H (RNase H) is studied by a recently developed off-lattice Monte Carlo/Metropolis simulation technique. A low-resolution model (virtual-bond model) is used together with knowledge-based potentials. The calculated mean-square fluctuations in alpha carbons are in good agreement with crystallographic temperature factors. The conformations generated around the native state are analyzed by time- dependent orientational and conformational correlation functions to study the internal motions of RNase at different time windows. A correlation between the free-energy changes for native-state hydrogen exchange (HX) and the extent of the autocorrelation in the rotations of the virtual bonds at long times has been observed. Cross-correlations between the rotations of the bonds, which are near-neighbor in the sequence, are effective in all time windows and help the secondary structures to preserve their kinetic stability. On the other hand, the existence of cross-correlations at long times help the tertiary contacts be maintained. The order parameter of NH bond vector for each residue has been calculated and compared with 15N-NMR relaxation measurements.