RT Journal Article
SR Electronic
T1 Martini bead form factors for nucleic-acids and their application in the refinement of protein/nucleic-acid complexes against SAXS data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 498147
DO 10.1101/498147
A1 Cristina Paissoni
A1 Alexander Jussupow
A1 Carlo Camilloni
YR 2018
UL http://biorxiv.org/content/early/2018/12/16/498147.abstract
AB Small-angle X-ray scattering (SAXS) use in combination with molecular dynamics simulation is hampered by its heavy computational cost. The calculation of SAXS from atomic structures can be speed up by using a coarse grain representation of the structure. Here following the work of Niebling, et al. (J. Appl. Cryst., (2014), 47, 1190) we derived the Martini beads form factors for nucleic acids and we implemented them, together with those previously determined for proteins, in the publicly available PLUMED library. We also implemented a hybrid multi-resolution strategy to perform SAXS restrained simulations at atomic resolution by calculating on-the-fly the virtual position of the Martini beads and using them for the calculation of SAXS. The accuracy and efficiency of the method is demonstrated by refining the structure of two protein/nucleic acid complexes. Instrumental for this result is the use of metainference that allows considering and alleviating the approximations at play in our SAXS calculation.