Peptide binding proclivities of calcium loaded calbindin‐D28k

Abstract

Calbindin-D28k is known to function as a calciumbuffering protein in the cell. Moreover, recent evidence shows that it also plays a role as a sensor. Using circular dichroism and NMR, we show that calbindin-D28k undergoes significant conformational changes upon binding calcium, whereas only minor changes occur when binding target peptides in its Ca 2+ -loaded state. NMR experiments also identify residues that undergo chemical shift changes as a result of peptide binding. The subsequent use of computational protein-protein docking protocols produce a model describing the interaction interface between calbindin-D28k and its target peptides.

Structural insights into the calcium‐dependent interaction between calbindin‐D28K and caspase‐3

“…We define 'not directly interacting' as a distance (Ca-Ca) of at least 4.5 Å between residues in calbindin-D28K and the catalytic residues in caspase-3. Lending support to these preliminary studies was that the binding region identified on calbindin-D28K is similar to a region on calbindin-D28K shown previously to be involved in interactions with peptides derived from known targets [11].…”

Computational Design of Cyclic Peptide Inhibitors of the Anti-Apoptotic Protein Calbindin-D28K

“…Here in our present study, we show that of the potential druggable sites within calbindin-D28K, the highest affinity location for the cyclic peptides corresponds to the area where linear peptides have previously been shown to bind (region of EF-hand 2) [8]. This location is immediately adjacent to the site where caspase-3 interacts with calbindin-D28K [10]. We also identify a general consensus sequence of potential cyclic peptide inhibitors of calbindin-D28K.…”

“…This study resulted in two high-affinity sites and several lower affinity sites ( Figure 1 and Table 1). The highest affinity site corresponds to the site on calbindin-D28K where a series of linear peptides were previously shown to bind [10]. These linear peptides were derived from the following known calbindin-D28K binding proteins: Ran-binding protein M (RanBPM), myo-inositol monophosphatase (IMPase), and caspase-3/procaspase-3 [7,28].…”

“…This suggests that binding of the cyclic peptide can allosterically alter the calbindin-D28K binding site, thereby interfering with caspase-3. To further verify our analysis, principal component analysis (PCA) (see Material and Methods) was used to analyze the: (i) calbindin-D28K:CKFSIKNRQC, (ii) calbindin-D28K:caspase-3 [8,10], and (iii) the 4-Ca 2+ loaded NMR structure of calbindin-D28K [31] (Figure 2d-f). PCA assists in defining correlations in conformational rearrangements from a family of structures [32].…”

“…These studies provided the first insights into the mechanism of caspase-3 inhibition [8]. Calbindin-D28K's interaction with linear peptides has also been characterized using circular dichroism, nuclear magnetic resonance (NMR) and molecular modeling [10]. Affecting the ability of calbindin-D28K to bind caspase-3 will induce apoptosis -helping overcome resistance to chemo-and radiation treatments.…”