Our method is utterly general and can be applied in many contexts

Our method is utterly general and can be applied in many contexts. for the functioning of life. Like other large biomolecular assemblies, they are progressively being exploited in modern nanobiotechnology1and biomedical2applications. Immunoglobulins G (IgG) are large molecules comprising three grossly ellipsoidal domains of length about 6 nm, two Fab arms (prolate) and an Fc stem (oblate), connected by a flexible hinge3,4,5. GSK 269962 The suggestions of the Fab domain name host hypervariable regions6. These are often referred to as theactivesites orparatopes, as these are the portions of the structure where antigens are bound (at theirepitopes). The Fc stem is usually acknowledged at its lower end by the match system7and by phagocytic cells8in the early steps of an immune response. A key house of IgGs is usually their extreme flexibility, which allows them to adopt a wide range of conformations. Atomic-force microscopy9and single-molecule cryo-electron microscopy (cryo-EM)10measurements have revealed that Fab-Fab and Fab-Fc angles are virtually limited only by steric clashes, with measured values ranging from 15 to 128 (Fab-Fc angle) and from about 20 to 180 (Fab-Fc angle)10. The intrinsic flexibility of IgG molecules reflects their astonishing ability to bind antigens of different sizes, from small molecules such as hormones to large viruses11,12. Moreover, high flexibility is also important to double-Fab (bivalent) binding to large viruses13, a process quantified GSK 269962 by the so-called bindingavidity14,15, as opposed to the single-binding affinity. Bivalent binding increases the overall strength of the immune response and also allows for IgG-mediated virion aggregation16. Recently, it was exhibited that this intrinsic flexibility of antibodies can be exploited to have them literallywalkingon antigen-covered surfaces with specific lattice-like plans of haptens with lattice spacing matching the IgGstride17. In this paper we focussed on the following question. Given their great flexibility, it is interesting to assess whether IgGs are more effective in binding a co-diffusing antigen when adopting certain specific conformations. More generally, it would be extremely informative to establish a GSK 269962 quantitative link between the large-scale dynamics of antibodies and their bindingeffectiveness. Here we concentrated on this problem in the case of small antigens, where the dynamics of substrate and IgG molecules are characterized by widely separated time scales. More precisely, our model assumes that this characteristic time scale of relaxation of fluctuations of antigen concentration is much faster than the time scale associated with large-scale conformational rearrangements of IgG molecules. In practice, the antigens should diffuse sufficiently fast so toseethe antibody virtually frozen in one of the many allowed configurations (counted with their associated weights, as dictated by the dynamics). Working in this framework, we shall sophisticated around the role of IgG conformation on antigen-antibody diffusion-limited reaction rate. In order to tackle the above problem, we first constructed Rabbit Polyclonal to HUCE1 a simple coarse-grained (CG) model of the antibody, where each domain name is replaced by a rigid structure made of a collection of hard spheres joined by stiff bonds. This was made so as to preserve the overall three-dimensionalshapeof the domains, which are joined GSK 269962 together at the hinge and are free to fluctuate about one another, except for the mutual excluded-volume interactions10. Amazingly, we show that this mechanical model is enough to recover the experimental distributions of inter-domain angles. In order to quantify the role of the IgG conformation in the diffusive encounter with small antigens, we then elaborated a theory to compute exactly the rate to capture of a small molecule to one of the active Fab methods for an arbitrary configuration of the CG antibodies. == Results == Despite the recent astonishing progresses exhibited by the massively parallel supercomputer Anton18, atomistic molecular dynamics simulations of proteins19,20is still an impractical tool for obtaining many conformations of large, flexible molecules GSK 269962 such as antibodies. In order to generate many impartial configurations of an IgG, we constructed a bead-based CG model (seeFig. 1). In our model, effective beads are joined by stiff springs, that preserve the crystallographic shape of the three domains while they fluctuate about the common hinge region (see Methods). == Physique 1. Coarse-grained representation of an IgG withN= 96 beads. == TheN-bead structure was obtained by applying the structure-based coarse-grained algorithm implemented in VMD37to the (murine) IgG crystallographic structure with PDB code 1IGT (shown as transparent surface). The dark spheres located at the outer edges of the Fab arms represent the two active sites. The radius of the beads shown in the physique corresponds approximately to the one used in the simulations (0.44 nm, see Methods). == Low-resolution, large-scale dynamics of IgGs in answer can be explained by a simple CG model in.