Characterization of NMR relaxation-active motions of a partially folded A-state analogue of ubiquitin

The dominant dynamics of a partially folded A-state analogue of ubiquitin t hat give rise to NMR N-15 spin relaxation have been investigated using mole cular dynamics (MD) computer simulations and reorientational quasiharmonic analysis. Starting from the X-ray structure of native ubiquitin with a prot onation state corresponding to a low pH, the A-state analogue was generated by a MD simulation of a total length of 33 ns in a 60 %/40 % methanol/wate r mixture using a variable temperature scheme to control and speed up the s tructural transformation. The N-terminal half of the A-state analogue consi sts of loosely coupled native-like secondary structural elements, while the C-terminal half is mostly irregular in structure. Analysis of dipolar N-H backbone correlation functions reveals reorientational amplitudes and time- scale distributions that are comparable to those observed experimentally. T hus, the trajectory provides a realistic picture of a partially folded prot ein that can be used for gaining a better understanding of the various type s of reorientational motions that are manifested in spin-relaxation paramet ers of partially folded systems. For this purpose, a reorientational quasih armonic reorientational analysis was performed on the final 5 ns of the tra jectory of the A-state analogue, and for comparison on a 5 ns trajectory of native ubiquitin. The largest amplitude reorientational modes show a marke dly distinct behavior for the two states. While for native ubiquitin, such motions have a more local character involving loops and the C-terminal end of the polypeptide chain, the A-state analogue shows highly collective moti ons in the nanosecond time-scale range corresponding to larger-scale moveme nts between different segments. Changes in reorientational backbone entropy between the A-state analogue and the native state of ubiquitin, which were computed from the reorientational quasiharmonic analyses, are found to dep end significantly on motional correlation effects. (C) 2001 Academic Press.