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 that give rise to NMR 15N spin relaxation have been investigated using molecular dynamics (MD) computer simulations and reorientational quasiharmonic analysis. Starting from the X-ray structure of native ubiquitin with a protonation 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/water mixture using a variable temperature scheme to control and speed up the structural transformation. The N-terminal half of the A-state analogue consists 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. Thus, the trajectory provides a realistic picture of a partially folded protein that can be used for gaining a better understanding of the various types of reorientational motions that are manifested in spin-relaxation parameters of partially folded systems. For this purpose, a reorientational quasiharmonic reorientational analysis was performed on the final 5 ns of the trajectory of the A-state analogue, and for comparison on a 5 ns trajectory of native ubiquitin. The largest amplitude reorientational modes show a markedly 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 motions in the nanosecond time-scale range corresponding to larger-scale movements 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 depend significantly on motional correlation effects.
Prompers
J J
JJ
Carlson School of Chemistry and Biochemistry, Clark University, Worcester, MA 01610, USA.
Scheurer
C
C
Brüschweiler
R
R
D003198:Computer Simulation; D019277:Entropy; D006801:Humans; D007700:Kinetics; D009682:Magnetic Resonance Spectroscopy; D000432:Methanol / Q000378:metabolism; D009038:Motion; D011489:Protein Denaturation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012984:Software; D013696:Temperature; D014452:Ubiquitins / Q000737:chemistry* / Q000378:metabolism*; D014867:Water / Q000378:metabolism
D014452:Ubiquitins; D014867:Water; D000432:Methanol