HYDROGEN BOND AND INTERNAL SOLVENT DYNAMICS OF BPTI PROTEIN *
HYDROGEN BOND AND INTERNAL SOLVENT DYNAMICS OF BPTI PROTEIN *
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BPTI 蛋白的氢键和内部溶剂动力学*
DOI：
10.1111/j.1749-6632.1981.tb50567.x
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发表时间：
1981
影响因子：
5.2
通讯作者：
M. Levitt
中科院分区：
文献类型：
--
作者：
M. Levitt
The powerful technique of x-ray crystallography has, over the past 20 years, revealed the atomic detail of over a hundred different protein molecules. While these studies do provide the time-averaged positions of the atoms in the crystal and can also indicate the amplitude of their fluctuations about these positions, they cannot provide information about the rates and pathways of conformational fluctuations. Fortunately, theoretical methods may be able to complement the x-ray studies by using the well-established methods of molecular dynamics to simulate the motion about the mean positions observed in protein crystals.'*' The results of molecular dynamics simulations depend on the molecular potential energy from which the forces acting on the atoms are calculated. Present calculations use an approximate empirical potential energy function and omit the thousands of solvent molecules that normally surround the A quantitative comparison of the results of the simulation with experimentally observed quantities is, therefore, essential. Two observed properties of globular proteins seem particularly well suited to such a comparison: (I) the amplitudes of atomic vibration available from the highest resolution x-ray studies can be checked against amplitudes computed from a dynamics run and (2) the different stabilities of peptide protons available from 'H nuclear magnetic resonance (nmr) studies can be checked against the computed fluctuations in the peptide hydrogen bond lengths. A preliminary attempt to correlate the observed vibration amplitudes of rubredoxin obtained at 1.2 b; resolution6 with those calculated from a 32 picosecond (ps) dynamic simulation failed due to changes in conformation that were not associated with fluctuations about an equilibrium structure.' Here we analyze the results of molecular dynamics simulations of BPTI [bovine pancreatic trypsin inhibitor] in terms of the fluctuations of peptide hydrogen bonds and the mobility of the four internal water molecules included in the calculation. We focused our attention on the following two questions.
