Dynamics fingerprints of active conformers of epidermal growth factor receptor kinase

Abstract

Epidermal growth factor receptor (EGFR) is a prototypical cellsurface receptor that plays a key role in the regulation of cellular signaling, proliferation and differentiation. Mutations of its kinase domain have been associated with the development of a variety of cancers and, therefore, it has been the target of drug design. Single amino acid substitutions (SASs) in this domain have been proven to alter the equilibrium of pre-existing conformer populations. Despite the advances in structural descriptions of its so-called active and inactive conformations, the associated dynamics aspects that characterize them have not been thoroughly studied yet. As the dynamic behaviors and molecular motions of proteins are important for a complete understanding of their structure-function relationships we present a novel procedure, using (or based on) normal mode analysis, to identify the collective dynamics shared among different conformers in EGFR kinase. The method allows the comparison of patterns of low-frequency vibrational modes defining representative directions of motions. Our procedure is able to emphasize the main similarities and differences between the collective dynamics of different conformers. In the case of EGFR kinase, two representative directions of motions have been found as dynamics fingerprints of the active conformers. Protein motion along both directions reveals to have a significant impact on the cavity volume of the main pocket of the active site. Otherwise, the inactive conformers exhibit a more heterogeneous distribution of collective motions.

Impact of protein conformational diversity on AlphaFold predictions

“…These differences are also relevant for signal transduction [16] and define metabolic regulation by mechanisms like cooperativity and allosterism [10,[17][18][19]. Conformers in the native ensemble could be identical in their backbones but differ just in the conformations of some residues, defining open and close transitions of tunnels [20,21] and/or volume variations in their cavities [22,23]. Increasing differences involve backbone movements comprising loops, secondary structural elements rearrangements, and relative domains movements [24][25][26].…”

Analysis of changes of cavity volumes in predefined directions of protein motions and cavity flexibility

“…44 Its native state is mainly clustered into active and inactive conformers, whose main pockets can be structurally and dynamically differentiated. 45,46 with respect to the inactive conformer can be directly related to the required functional hinge and shear motions between the C-and N-lobe associated to its collective low-frequency dynamics. This is consistent with previous studies that identify the two lowest frequency normal modes as dynamics fingerprints of active conformers that allow them to be differentiated from inactive conformers.…”

“…This is consistent with previous studies that identify the two lowest frequency normal modes as dynamics fingerprints of active conformers that allow them to be differentiated from inactive conformers. 46 Relative displacements in the direction of these modes lead to greater changes in cavity volumes than movements in the direction of the corresponding modes of inactive conformers, that is, a more flexible cavity in the active conformers with respect to inactive conformers.…”