Application of molecular dynamics with interproton distance restraints to three-dimensional protein structure determination: A model study of crambin

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The applicability of restrained molecular dynamics for the determination of threedimensional protein structures on the basis of short interproton distances (<4 Å) that can be realistically determined from nuclear magnetic resonance measurements in solution is assessed. The model system used is the 1.2 Å resolution crystal structure of the 46 residue protein crambin, from which a set of 240 approximate distance restraints, divided into three ranges (2.5±0.5, 3.0 −1.0 +0.5 and 4±1 Å), is derived. This interproton distance set comprises 159 short-range (|i−j|≤ 5) and 56 (|i−j|>5) long-range inter-residue distances and 25 intra-residue distances. Restrained molecular dynamics are carried out using a number of different protocols starting from two initial structures: a completely extended β-strand; and an extended structure with two α-helices in the same positions as in the crystal structure (residues 7 to 19, and 23 to 30) and all other residues in the form of extended β-strands. The root-mean-square (r.m.s.) atomic differences between these two initial structures and the crystal structure are 43 Å and 23 Å, respectively. It is shown that, provided protocols are used that permit the secondary structure elements to form at least partially prior to folding into a tertiary structure, convergence to the correct final structure, both globally and locally, is achieved. The r.m.s. atomic differences between the converged restrained dynamics structures and the crystal structure range from 1.5 to 2.2 Å for the backbone atoms and from 2.0 to 2.8 Å for all atoms. The r.m.s. atomic difference between the X-ray structure and the structure obtained by first averaging the co-ordinates of the converged restrained dynamics structures is even smaller: 1.0 Å for the backbone atoms and 1.6 Å for all atoms. These results provide a measure with which to judge future experimental results on proteins whose crystal structures are unknown. In addition, from an examination of the dynamics trajectories, it is shown that the convergence pathways followed by the various simulations are different.