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In silico docking of forchlorfenuron (FCF) to septins suggests that FCF interferes with GTP binding
Journal article   Open access

In silico docking of forchlorfenuron (FCF) to septins suggests that FCF interferes with GTP binding

Dimitrios Angelis, Eva Pauline Karasmanis, Xiaobo Bai and Elias T Spiliotis
PloS one, v 9(5), pp e96390-e96390
2014
DOI: https://doi.org/10.1371/journal.pone.0096390
PMID: 24787956
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https://doi.org/10.1371/journal.pone.0096390View
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Abstract

Pyridines - chemistry Amino Acids - chemistry Guanosine Triphosphate - metabolism Isoenzymes - chemistry Amino Acids - genetics Amino Acids - metabolism Thermodynamics Isoenzymes - metabolism Phenylurea Compounds - chemistry Computer Simulation Databases, Protein Guanosine Triphosphate - chemistry Phenylurea Compounds - metabolism Septins - metabolism Guanosine Diphosphate - chemistry Guanosine Diphosphate - metabolism Protein Stability Binding, Competitive Protein Structure, Tertiary Recombinant Proteins - metabolism Septins - genetics Isoenzymes - genetics Recombinant Proteins - chemistry Binding Sites - genetics Pyridines - metabolism Protein Binding Molecular Docking Simulation Septins - chemistry
Septins are GTP-binding proteins that form cytoskeleton-like filaments, which are essential for many functions in eukaryotic organisms. Small molecule compounds that disrupt septin filament assembly are valuable tools for dissecting septin functions with high temporal control. To date, forchlorfenuron (FCF) is the only compound known to affect septin assembly and functions. FCF dampens the dynamics of septin assembly inducing the formation of enlarged stable polymers, but the underlying mechanism of action is unknown. To investigate how FCF binds and affects septins, we performed in silico simulations of FCF docking to all available crystal structures of septins. Docking of FCF with SEPT2 and SEPT3 indicated that FCF interacts preferentially with the nucleotide-binding pockets of septins. Strikingly, FCF is predicted to form hydrogen bonds with residues involved in GDP-binding, mimicking nucleotide binding. FCF docking with the structure of SEPT2-GppNHp, a nonhydrolyzable GTP analog, and SEPT7 showed that FCF may assume two alternative non-overlapping conformations deeply into and on the outer side of the nucleotide-binding pocket. Surprisingly, FCF was predicted to interact with the P-loop Walker A motif GxxxxGKS/T, which binds the phosphates of GTP, and the GTP specificity motif AKAD, which interacts with the guanine base of GTP, and highly conserved amino acids including a threonine, which is critical for GTP hydrolysis. Thus, in silico FCF exhibits a conserved mechanism of binding, interacting with septin signature motifs and residues involved in GTP binding and hydrolysis. Taken together, our results suggest that FCF stabilizes septins by locking them into a conformation that mimics a nucleotide-bound state, preventing further GTP binding and hydrolysis. Overall, this study provides the first insight into how FCF may bind and stabilize septins, and offers a blueprint for the rational design of FCF derivatives that could target septins with higher affinity and specificity.

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Biochemistry & Molecular Biology
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