title: A first principle particle mesh method for solution SAXS of large bio-molecular systems.
abstract: This paper will show that the solution small angle X-ray scattering (SAXS) intensity of globular and membrane proteins can be efficiently and accurately computed from molecular dynamics trajectories using 3D fast Fourier transforms (FFTs). A suitable particle meshing interpolation, similar to the one used in smooth particle mesh Ewald for electrostatic energies and forces, was combined with a uniform solvent density FFT padding scheme to obtain a convenient SAXS spectral resolution. The CPU time scaling of the method, as a function of system size, is highly favorable and its application to large systems such as solutions of solvated membrane proteins is computationally undemanding. Differently from other approaches, all contributions from the simulation cell are included. This means that the subtraction of the buffer from the solution scattering intensity is straightforward and devoid of artifact due to ad hoc definitions of proximal and distal solvent intensity contributions.
authors.affiliation: Commissariat à l'Energie Atomique, DRF/IBITECS/SB2SM, Centre d'Etudes de Saclay, 91191 Gif-sur-Yvette Cedex, France.
authors.forename: Massimo
authors.initials: M
authors.lastname: Marchi
mesh_terms: D000818:Animals; D020346:Aquaporins / Q000737:chemistry; D002417:Cattle; D002645:Chickens; D002919:Chymotrypsinogen / Q000737:chemistry; D003198:Computer Simulation; D005136:Eye Proteins / Q000737:chemistry; D005583:Fourier Analysis; D008823:Micelles; D056004:Molecular Dynamics Simulation; D009113:Muramidase / Q000737:chemistry; D053838:Scattering, Small Angle; D012996:Solutions / Q000737:chemistry; D012997:Solvents / Q000737:chemistry; D055672:Static Electricity; D014961:X-Ray Diffraction / Q000379:methods*
chemical_list: D020346:Aquaporins; D005136:Eye Proteins; D008823:Micelles; D012996:Solutions; D012997:Solvents; C030328:aquaporin 0; D002919:Chymotrypsinogen; D009113:Muramidase