Decomposing Dynamical Couplings in Mutated scFv Antibody Fragments into Stabilizing and Destabilizing Effects

Abstract

Conformational fluctuations within scFv antibodies are characterized by a novel perturbation-response decomposition of molecular dynamics trajectories. Both perturbation and response profiles are stratified into stabilizing and destabilizing conditions. The linker between the VH and VL domains exhibits the dominant dynamical response by being coupled to nearly the entire protein, responding to both stabilizing and destabilizing perturbations. Perturbations within complementarity-determining regions (CDR) induce rich behavior in dynamic response. Among many effects, stabilizing any CDR loop in the VH domain triggers a destabilizing response in all CDR loops in the VL domain and vice versa. Destabilizing residues within the VL domain are likely to stabilize all CDR loops in the VH domain, and, when these residues are not buried the CDR loops in the VL domain are also likely to be stabilized. These effects, described by shifts in normal mode characteristics, initiate a propensity for dynamic allostery with possible functional implications in bispecific antibodies.

Peptide–MHC (pMHC) binding to a human antiviral T cell receptor induces long-range allosteric communication between pMHC- and CD3-binding sites

“…8C). In a similar case, a recent MD simulation of single-chain Fv antibodies found that the linker between the V H and V L domains exhibited the dominant dynamical response by being coupled to nearly the entire protein (38). Our MD simulations are consistent with previous H/D exchange experiments showing that pMHC binding induced a global reduction in TCR A6 flexibility that included the C␤ FG loop (28).…”

Dissecting Conformational Changes in APP’s Transmembrane Domain Linked to ε-Efficiency in Familial Alzheimer’s Disease

“…Given the fluctuations in the pre-bound state, the reorganization of conformational dynamics can be probed for a variety of model interactions. Similar perturbation-based analyses have been employed in various previous studies (Ettayapuram Ramaprasad et al, 2017; Guarnera & Berezovsky, 2016; Ming & Wall, 2006; Zheng & Brooks, 2005; Zheng, Liao, Brooks, & Doniach, 2007). For further details and comparison with related approaches see Methods.…”

“…Differences in the local structural dynamics alone cannot explain the impact of FAD mutations on ε-cleavage. Although localized at a single Cα-atom or H-bond, these fluctuations may cooperate to produce functional backbone flexibility enabling (i) large-scale conformational changes conducive to recognition and binding, (ii) induced conformational relaxations, and (iii) communication between functional sites distal in the sequence (Clarkson, Gilmore, Edgell, & Lee, 2006; Csermely, Palotai, & Nussinov, 2010; Ettayapuram Ramaprasad, Uddin, Casas-Finet, & Jacobs, 2017; Guarnera & Berezovsky, 2016; Haliloglu & Bahar, 2015; Marcos, Crehuet, & Bahar, 2011; Nashine, Hammes-Schiffer, & Benkovic, 2010). The dynamic cross-correlation mainly depends on the fold and is fine-tuned by sequence.…”

“…The effect on ε-cleavage efficiency observed after glycine to alanine substitution at G33 (Higashide, Ishihara, Nobuhara, Ihara, & Funamoto, 2017) as well as the shifted cleavage pattern concomitant with the creation of an alternative ε-site at M51 in the G33Q mutant (Oestereich et al, 2015; Olsson et al, 2014) can be considered as direct hints to this communication. The propagation of effects arising from localized perturbations along the network of coupled protein fluctuations has been reported for several proteins even in the absence allosteric function (Bouguet-Bonnet & Buck, 2008; Clarkson et al, 2006; Ettayapuram Ramaprasad et al, 2017; Freire, 1999; Liu et al, 2006; Pan et al, 2000) and their general relation to disease has been discussed (Kucukkal, Petukh, Li, & Alexov, 2015). The synergy between binding and presentation of the ε-sites emerging from the current analysis is summarized in Figure 12 .…”

“…In various studies the initial state’s average structure was perturbed by forces and the displacements of residues were monitored (Atilgan, Aykut, & Atilgan, 2011; Echave & Fernández, 2010; Ikeguchi, Ueno, Sato, & Kidera, 2005; Naritomi & Fuchigami, 2011). In other studies residue flexibility and connectivity were perturbed by adding interaction energies and the redistribution of conformational states was recorded (Erman, 2006; Ettayapuram Ramaprasad et al, 2017; Guarnera & Berezovsky, 2016; Ming & Wall, 2006; Zheng & Brooks, 2005; Zheng et al, 2007). Here we applied dynamic perturbations, because (i) the mean structures of the TMDs did not show substantial conformational changes even for the mutants, (ii) a reasonable model for functionally relevant forces was missing, and (iii) given the importance of the direction of perturbing forces (Atilgan et al, 2011) applying random kicks might not by sufficiently informative enough.…”