and constant domains [18]. Redistribution of flexibility in stabilizing fragments of mutant antibodies was observed in antilymphotoxin-beta receptor antibody [9]. Antibody-antigen recognition appears to also involve allosteric effects [19]. Pritsch et al.
suggested that antibodies with identical variable domains, but different isotypes have significantly different affinities when binding to
tubulin [13]. Oda et al. showed that the binding of antigen causes
conformational changes in protein G and protein A binding sites on
the heavy-chain constant domains [20]. A recent study surveyed
over 100 crystal structures of antibodies in either the apo or bound
form and found that distant loops from CH1-1 undergo significant
fluctuation upon antigen binding and this fluctuation is common
among these structures [21].
Though several studies have shown that antibody constant
domains respond to antigen binding, molecular details and dynamics are still unknown. We have studied conformational changes in
the antibody and cross-talk between its subunits and with antigens,
using MD simulations of the complex of Fab and prion-associated
peptide in the apo and bound forms. This allowed us to show that
the inter-chain disulfide bond between the CH-1 and CL domains
restrains the conformational changes of Fab, especially the loops in
the CH1 domain, resulting in inhibition of the cross-talk between
Fab subdomains which thereby may prevent prion peptide binding.
Structural cross-talks between the constant domains and the antigen were shown by several negative and positive correlations of
motions between the peptide and Fab constant domains. The crosstalk was influenced by the inter-chain disulfide bond which reduced
the number of paths between them. Importantly, network analysis
of the complex and its bound water molecules observed that those
water molecules form an integral part of the Fab/peptide network
of potential allosteric pathways. This chapter aims to provide robust
and general strategies to study allosteric effects in the antibodyantigen recognition, which may help to develop strategies to incorporate these network communications—including the associated
water molecules—in antibody design.
2 Simulation Protocols
2.1 Materials
2.1.1 Structures
of Isolated Antibody
and Prion Peptide
1. The structures of the apo forms of the Fab are based on crystal
structures PDB IDs 1cr9 [22]. The unbound form was
obtained by manually removing the peptide in the bound
(1cu4) structure (see Note 1, Fig. 1).
2. The isolated prion peptide was simulated independently starting from the conformation in 1cu4.
176
Jun Zhao et al.
suggested that antibodies with identical variable domains, but different isotypes have significantly different affinities when binding to
tubulin [13]. Oda et al. showed that the binding of antigen causes
conformational changes in protein G and protein A binding sites on
the heavy-chain constant domains [20]. A recent study surveyed
over 100 crystal structures of antibodies in either the apo or bound
form and found that distant loops from CH1-1 undergo significant
fluctuation upon antigen binding and this fluctuation is common
among these structures [21].
Though several studies have shown that antibody constant
domains respond to antigen binding, molecular details and dynamics are still unknown. We have studied conformational changes in
the antibody and cross-talk between its subunits and with antigens,
using MD simulations of the complex of Fab and prion-associated
peptide in the apo and bound forms. This allowed us to show that
the inter-chain disulfide bond between the CH-1 and CL domains
restrains the conformational changes of Fab, especially the loops in
the CH1 domain, resulting in inhibition of the cross-talk between
Fab subdomains which thereby may prevent prion peptide binding.
Structural cross-talks between the constant domains and the antigen were shown by several negative and positive correlations of
motions between the peptide and Fab constant domains. The crosstalk was influenced by the inter-chain disulfide bond which reduced
the number of paths between them. Importantly, network analysis
of the complex and its bound water molecules observed that those
water molecules form an integral part of the Fab/peptide network
of potential allosteric pathways. This chapter aims to provide robust
and general strategies to study allosteric effects in the antibodyantigen recognition, which may help to develop strategies to incorporate these network communications—including the associated
water molecules—in antibody design.
2 Simulation Protocols
2.1 Materials
2.1.1 Structures
of Isolated Antibody
and Prion Peptide
1. The structures of the apo forms of the Fab are based on crystal
structures PDB IDs 1cr9 [22]. The unbound form was
obtained by manually removing the peptide in the bound
(1cu4) structure (see Note 1, Fig. 1).
2. The isolated prion peptide was simulated independently starting from the conformation in 1cu4.
176
Jun Zhao et al.