Electrostatic recognition in substrate binding to serine proteases

Abstract

Serine proteases of the Chymotrypsin family are structurally very similar but have very different substrate preferences. This study investigates a set of 9 different proteases of this family comprising proteases that prefer substrates containing positively charged amino acids, negatively charged amino acids, and uncharged amino acids with varying degree of specificity. Here, we show that differences in electrostatic substrate preferences can be predicted reliably by electrostatic molecular interaction fields employing customized GRID probes. Thus, we are able to directly link protease structures to their electrostatic substrate preferences. Additionally, we present a new metric that measures similarities in substrate preferences focusing only on electrostatics. It efficiently compares these electrostatic substrate preferences between different proteases. This new metric can be interpreted as the electrostatic part of our previously developed substrate similarity metric. Consequently, we suggest, that substrate recognition in terms of electrostatics and shape complementarity are rather orthogonal aspects of substrate recognition. This is in line with a 2‐step mechanism of protein‐protein recognition suggested in the literature.

Protein-Protein Binding as a Two-Step Mechanism: Preselection of Encounter Poses during the Binding of BPTI and Trypsin

“…Overall, the binding mechanism that we observe is similar to the concepts that Grünberg et al. ( 9 ) describe and is in line with our previously proposed hypothesis ( 20 ). However, in this study, we provide a substantially more exhaustive approach, in which we explicitly trace the recognition pathway in atomistic detail.…”

“…( 18 ) investigate peptide-protein association with molecular dynamics (MD) simulations and find that omitting electrostatic interactions in most cases results in a decreased ratio between native-like encounter poses and transient encounter configurations. Electrostatic interactions shape a funnel-like energy landscape that directs the binding, pulling the interface together ( 19 , 20 ). Likely during this step, electrostatic interactions also contribute strongly to the discrimination between possible binding partners as described for the substrate recognition of serine proteases ( 20 , 21 ).…”

“…Electrostatic interactions shape a funnel-like energy landscape that directs the binding, pulling the interface together ( 19 , 20 ). Likely during this step, electrostatic interactions also contribute strongly to the discrimination between possible binding partners as described for the substrate recognition of serine proteases ( 20 , 21 ). After the formation of the encounter complex, a free energy barrier hinders a fast transition to the native complex ( 10 , 22 ).…”

Protein electrostatics: From computational and structural analysis to discovery of functional fingerprints and biotechnological design

“…Medicinal chemistry studies devoted to developing and optimizing hits and leads that could target the activity of enzymes or receptors rely on the availability of structural data as well as on our proficiency in predicting such interactions where direct experimental evidence is missing [110] , [111] . Although with different degree of success, a large number of strategies have been recently proposed to evaluate and simulate the impact of electrostatic interactions on this process [80] , [112] , [113] , [114] …”

“…For example, Waldner and co-workers developed an algorithm that was able to predict the correlation between electrostatic features and substrate specificity of nine representative members of the chymotrypsin family of serine proteases [113] . In serine protease, target recognition occurs through a pattern of sub-pockets that build up the active site cleft features and define upstream and downstream amino acids selectivity within the peptide substrate [113] .…”