Dynamics Govern Specificity of a Protein-Protein Interface: Substrate Recognition by Thrombin

Abstract

Biomolecular recognition is crucial in cellular signal transduction. Signaling is mediated through molecular interactions at protein-protein interfaces. Still, specificity and promiscuity of protein-protein interfaces cannot be explained using simplistic static binding models. Our study rationalizes specificity of the prototypic protein-protein interface between thrombin and its peptide substrates relying solely on binding site dynamics derived from molecular dynamics simulations. We find conformational selection and thus dynamic contributions to be a key player in biomolecular recognition. Arising entropic contributions complement chemical intuition primarily reflecting enthalpic interaction patterns. The paradigm “dynamics govern specificity” might provide direct guidance for the identification of specific anchor points in biomolecular recognition processes and structure-based drug design.

Electrostatic recognition in substrate binding to serine proteases

“…Correlation of substrate specificity with backbone flexibility and orientational ordering of water molecules in the non‐prime site (S6‐S1) of Thrombin's binding cleft (ranging from red—specific, rigid and ordered, via yellow to green—promiscuous, flexible and disordered)…”

“…32 The biggest error, however, is included when using different protonation states for the FIGURE 1 Peptide substrate amino acid (Pi and Pi′) and protease subpocket enumeration (Si and Si′) with respect to the cutting position (vertical line). The N-terminal side of the substrate is located on the left FIGURE 2 Correlation of substrate specificity with backbone flexibility and orientational ordering of water molecules in the non-prime site (S6-S1) of Thrombin's binding cleft (ranging from red-specific, rigid and ordered, via yellow to green-promiscuous, flexible and disordered) 27 model, as introducing an extra charge, or removing one, changes the entire electrostatic field significantly.…”

Intrinsic flexibility of NLRP pyrin domains is a key factor in their conformational dynamics, fold stability, and dimerization

“…We extracted torsion angles from the simulation trajectory and derived a continuous probability density function using non‐parametric kernel density estimation . Data was periodically duplicated to avoid bias at boundaries and integrated to yield a thermodynamic entropy arising from conformational flexibility . Ordered states correspond to low entropies with a single dihedral peak with a width of 1 degree corresponding to an entropy of 0 J (mol K −1 ) −1 .…”

Enzyme Selectivity Fine‐Tuned through Dynamic Control of a Loop

“…and computationally. [14] However,t he concept of conformational selection and its effect on protein function is becoming increasingly popular. [3d-g] Our system opens up possibilities to introduce specific time scales of loop motion by further mutations.L inking these time scales to catalytic activities would help to elucidate the role of time-scale dependent dynamic allostery.…”