Characterizing the Diversity of the CDR-H3 Loop Conformational Ensembles in Relationship to Antibody Binding Properties

Abstract

We present an approach to assess antibody CDR-H3 loops according to their dynamic properties using molecular dynamics simulations. We selected six antibodies in three pairs differing substantially in their individual promiscuity respectively specificity. For two pairs of antibodies crystal structures are available in different states of maturation and used as starting structures for the analyses. For a third pair we chose two antibody CDR sequences obtained from a synthetic library and predicted the respective structures. For all three pairs of antibodies we performed metadynamics simulations to overcome the limitations in conformational sampling imposed by high energy barriers. Additionally, we used classic molecular dynamics simulations to describe nano- to microsecond flexibility and to estimate up to millisecond kinetics of captured conformational transitions. The methodology represents the antibodies as conformational ensembles and allows comprehensive analysis of structural diversity, thermodynamics of conformations and kinetics of structural transitions. Referring to the concept of conformational selection we investigated the link between promiscuity and flexibility of the antibodies' binding interfaces. The obtained detailed characterization of the binding interface clearly indicates a link between structural flexibility and binding promiscuity for this set of antibodies.

VH‐VL interdomain dynamics observed by computer simulations and NMR

“…Combining experimental NOE data with molecular dynamics simulations reveals in this example the same fast interdomain dynamics in the low nanosecond timescale for the different fragments analyzed. The timescale of interdomain reorientation is orders of magnitudes faster than the loop dynamics reflecting a hydrophobic interface with rather unspecific interactions that can be easily broken and result in low kinetic barriers, whereas loop dynamics is dominated by reorganization of hydrogen bond networks and electrostatic interactions characterized by strong forces and high barriers leading to much longer transition time scales . The distributions of interdomain orientations resulting from the time evolutions are very similar to distributions observed for antibody fragments in the PDB.…”

“…The fluctuations indicate that majority of the V H ‐V L movements occur on the nanosecond timescale. This timescale is orders of magnitude faster than that of the loop dynamics, especially of the CDR‐H3 loop, which occur on the microsecond to millisecond timescales . To characterize the role of the peptide linker on the V H ‐V L domain orientation, we show the analysis of 1‐μs molecular dynamics simulations without the presence of the linker in Figure S2.…”

Sodium-induced population shift drives activation of thrombin

“…The resulting MSM can then be used to investigate thermodynamic and kinetic properties of conformational changes on much longer timescales. Enhanced sampling techniques previously have successfully been used to seed simulations for the construction of MSMs 45 , used to investigate G protein activation 43 and antibody dynamics 46 .…”

Dynamics Rationalize Proteolytic Susceptibility of the Major Birch Pollen Allergen Bet v 1

“…The construction of the MSM allows to quantify thermodynamic and kinetic properties of each ensemble without the intrinsic bias resulting from the seeding process (Bowman et al, 2013;Kohlhoff et al, 2014). Similar workflows have already been proven to be extremely efficient and highly reliable (Noe et al, 2009;Nedialkova et al, 2014;Biswas et al, 2018;Fernandez-Quintero et al, 2018;Sun et al, 2018;Zimmerman et al, 2018).…”