Reconstruction of protein form with X-ray solution scattering and a genetic algorithm.
We have reconstructed, from experimental approximately 2 nm resolution X-ray solution scattering profiles, the corresponding shapes and sizes of myoglobin, troponin C, spermadhesin PSP-I/PSP-II, chymotrypsinogen A, superoxide dismutase, ovalbumin, tubulin, nitrite reductase, catalase, the structural change of troponin C upon dissociation of the two high affinity Ca(2+), and the solution model structure of a tandem pair of fibronectin type III cytoplasmic domains of integrin alpha6beta4 before determination of its crystal structure. To this purpose we have designed a new genetic algorithm which gradually explores a discrete search space and evolves convergent models made of several hundred beads (down to 0.3 nm radius) best fitting the scattering profile upon Debye calculation, without geometrical constraints or penalty for loose beads. This is a procedure of effective numerical transformation of the one-dimensional scattering profiles into three-dimensional model structures. The number of beads in models is correlated with the protein molecular mass (with one exception). The shape and approximate dimensions of each protein have been retrieved by a set of ten solution models, essentially superimposable with the available crystal structures.
Chacón
P
P
Centro de Investigaciones Biológicas, CSIC, Velázquez 144, Madrid, 28006, Spain.
Díaz
J F
JF
Morán
F
F
Andreu
J M
JM
D000465:Algorithms; D000818:Animals; D002118:Calcium / Q000494:pharmacology; D018360:Crystallography, X-Ray; D008957:Models, Genetic; D008958:Models, Molecular; D008969:Molecular Sequence Data; D008970:Molecular Weight; D009154:Mutation / Q000235:genetics; D020836:Protein Structure, Quaternary / Q000187:drug effects; D017434:Protein Structure, Tertiary / Q000187:drug effects; D011506:Proteins / Q000737:chemistry* / Q000235:genetics*; D012996:Solutions; D014961:X-Ray Diffraction / Q000379:methods
D011506:Proteins; D012996:Solutions; D002118:Calcium