SASREF: Global Rigid Body Modelling
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1 SASREF: Global Rigid Body Modelling Starts from arbitrary initial positions and orientations of the subunits Employs simulated annealing to search interconnected arrangement of the subunits without clashes Random movement/rotation at one SA step Fitting the SAXS/SANS data by minimizing the target function E (X) = Σχ 2 [I exp (s), I(X,s)] + Σα i P i (X) Penalty terms describe additional restraints Petoukhov, M. V., and Svergun, D. I. (2006). Eur Biophys J., 35,
![one SA step Fitting the SAXS/SANS data by minimizing the target function E (X) = Σχ 2 [I exp (s), I(X,s)] + Σα i P i](/docs-images/41/17459067/images/page_1.jpg "(X) Penalty terms describe additional restraints Petoukhov, M. V., and Svergun, D. I. (2006). Eur Biophys J.")
2 Interconnectivity and steric clashes (natural restraints) Subunit arrangements with steric clashes and disconnected models are penalized. Overlap: C a -C a distance < 4 A.
3 Interconnectivity and steric clashes (natural restraints) To ensure the interconnectivity of the entire complex each subunit should have a contact with at least one other subunit. The contact distance between Cα atoms of distinct subunits: 4-7 A.
4 From binding affinity studies or from mutagenesis data the information on contacting subunits and even individual residues can be available. Such information is accounted for by specifying the ranges of residues or nucleotides which can be involved in interactions between the partners. Spring force potentials are added as penalties Contacts restraints
5 Symmetry Possible constraints Groups Pn / Pn2 (n=1..6), P23, P432 and icosahedral symmetry can be taken into account. - fewer spatial parameters to describe the model - selection rules for the partial amplitudes: m equal to 0 or multiples of n, for Pn2, terms of order l0 with odd l and all imaginary parts vanish Fixation of subset A Some subunits can be fixed at the initial positions and orientations to keep their mutual arrangement B C D E
6 EMBO Practical Course on Solution Scattering from Biological Macromolecules Test examples Symmetric tetramer of pyruvate oxidase Dimeric & trimeric functional units of hemocyanin (Patrice) TK Met ectodomain - multidomain protein with no extended linkers
7 Modelling of multidomain proteins MRGSHHHHHH GSGVPSRVIH IRKLPIDVTE GEVISLGLPF GKVTNLLMLK GKNQAFIEMN TEEAANTMVN YYTSVTPVLR GQPIYIQFSN HKELKTDSSP NQARAQAALQ AVNSVQSGNL ALAASAAAVD AGMAMAGQSP VLRIIVENLF YPVTLDVLHQ IFSKFGTVLK IITFTKNNQF QALLQYADPV SAQHAKLSLD GQNIYNACCT LRIDFSKLTS LNVKYNNDKS RDYTRPDLPS GDSQPSLDQT MAAAFGLSVP NVHGALAPLA IPSAAAAAAA AGRIAIPGLA GAGNSVLLVS NLNPERVTPQ SLFILFGVYG DVQRVKILFN KKENALVQMA DGNQAQLAMS HLNGHKLHGK PIRITLSKHQ NVQLPREGQE DQGLTKDYGN SPLHRFKKPG
8 Modelling of multidomain proteins A combined approach is proposed to built the models of multidomain proteins with large and flexible interdomain linkers The latter are represented as DR chains which are attached to the appropriate terminals in rigid domains. A single modification of a model is a rotation about one or two randomly selected DR(s).
9 Modelling of multidomain proteins
10 Building native-like folds of linkers Dihedral angles, degrees r i+k Absence of steric clashes i Neighbors distribution along the sequence Bond angles, degrees Bond angles & dihedrals distribution Loop compactness may also be required Rg = id 33 nl
11 Simultaneous fitting of multiple data sets from deletion mutants lg I, relative s, nm -1
12 EMBO Practical Course on Solution Scattering from Biological Macromolecules PTB protein MRGSHHHHHH GSGVPSRVIH IRKLPIDVTE GEVISLGLPF GKVTNLLMLK D GKNQAFIEMN TEEAANTMVN YYTSVTPVLR GQPIYIQFSN HKELKTDSSP NQARAQAALQ AVNSVQSGNL ALAASAAAVD AGMAMAGQSP VLRIIVENLF YPVTLDVLHQ IFSKFGTVLK IITFTKNNQF QALLQYADPV SAQHAKLSLD C GQNIYNACCT LRIDFSKLTS LNVKYNNDKS RDYTRPDLPS GDSQPSLDQT MAAAFGLSVP NVHGALAPLA IPSAAAAAAA AGRIAIPGLA GAGNSVLLVS NLNPERVTPQ SLFILFGVYG DVQRVKILFN KKENALVQMA DGNQAQLAMS HLNGHKLHGK PIRITLSKHQ NVQLPREGQE DQGLTKDYGN SPLHRFKKPG B SKNFQNIFPP SATLHLSNIP PSVSEEDLKV LFSSNGGVVK GFKFFQKDRK MALIQMGSVE EAVQALIDLH NHDLGENHHL RVSFSKSTI A
13 CORAL: new in ATSAS 2.4
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15 Merging Sasref and Bunch CORAL = COmplexes with RAndom Loops
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