1mak

File:1mak.jpg

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SOLUTION STRUCTURE OF AN ISOLATED ANTIBODY VL DOMAIN

OverviewOverview

The solution structure of the isolated VL domain of the anti-digoxin, antibody 26-10 has been determined using data derived from heteronuclear, multi-dimensional nuclear magnetic resonance (n.m.r.) experiments., Analytical ultracentrifugation and n.m.r. data demonstrate that the VL, domain is only weakly associating (Kd = 2.5 (+/- 0.7) mM) and that it, experiences a rapid monomer/dimer equilibrium under the n.m.r., experimental conditions. Therefore, the results reported here represent, the first structure determination of an antibody VL domain in the absence, of fixed quaternary interactions. The structure determination is based on, 930 proton-proton distance constraints, 113 dihedral angle constraints, and 46 hydrogen bond constraints. Eighty initial structures were, calculated with the variable target function program DIANA; of these, 31, were accepted on the basis of satisfaction of constraints (no distance, constraint violations > 0.5 A; target function < 3.0 A2). Accepted DIANA, structures were refined by restrained energy minimization using the X-PLOR, program. The 15 best energy-minimized DIANA structures were chosen as a, representative ensemble of solution conformations. The average, root-mean-square differences (r.m.s.d.) between the individual structures, of this ensemble and the mean coordinates is 0.85 (+/- 0.10) A for all, backbone atoms and 1.29 (+/- 0.10) A for all heavy atoms. For beta-strands, A, B, C, D, E and F, the average backbone atom r.m.s.d. to the mean, structure is 0.46 (+/- 0.06) A. A higher-resolution ensemble, with all, backbone atom and all heavy atom r.m.s.d.s. to the mean coordinates of, 0.54 (+/- 0.08) A and 0.98 (+/- 0.12) A, respectively, was obtained by, X-PLOR simulated annealing refinement of the 15 energy-minimized DIANA, structures. A detailed analysis of the original ensemble of 15, energy-minimized DIANA structures is presented, as this ensemble retains a, broader, and possibly more realistic, sampling of conformation space. The, backbone atom and all heavy atom r.m.s.d.s between the mean, energy-minimized DIANA structure and the X-ray derived coordinates of the, VL domain within the Fab/digoxin complex are 1.05 A and 1.56 A, respectively. Subtle differences between the solution and X-ray structures, occur primarily in CDR2, CDR3, beta-strands A, F and G, and localized, regions of hydrophobic packing. Overall, these results demonstrate that, the 26-10 VL domain conformation is determined primarily by intradomain, interactions, and that quaternary VL-VH association induces relatively, minor conformational adjustments.

About this StructureAbout this Structure

1MAK is a Single protein structure of sequence from Mus musculus. Full crystallographic information is available from OCA.

ReferenceReference

Solution structure of an isolated antibody VL domain., Constantine KL, Friedrichs MS, Metzler WJ, Wittekind M, Hensley P, Mueller L, J Mol Biol. 1994 Feb 11;236(1):310-27. PMID:8107112

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