Formins catalyze nucleation and growth of actin filaments. Here, we study the structure and interactions of actin with the FH2 domain of budding yeast formin Bni1p. We built an all-atom model of the formin dimer on an Oda actin filament 7-mer and studied structural relaxation and interprotein interactions by molecular dynamics simulations. These simulations produced a refined model for the FH2 dimer associated with the barbed end of the filament and showed electrostatic interactions between the formin knob and actin target-binding cleft. Mutations of two formin residues contributing to these interactions (R1423N, K1467L, or both) reduced the interaction energies between the proteins, and in coarse-grained simulations, the formin lost more interprotein contacts with an actin dimer than with an actin 7-mer. Biochemical experiments confirmed a strong influence of these mutations on Bni1p-mediated actin filament nucleation, but not elongation, suggesting that different interactions contribute to these two functions of formins.
Bibliographical noteFunding Information:
J.L.B., D.L.P., and G.A.V. were supported by the National Science Foundation (NSF) through the Center for Multiscale Theory and Simulation (grant CHE-1136709 ). M.M. was supported by a Ruth L. Kirschstein National Research Service Award ( GM101848 ) from the National Institute of General Medical Sciences . N.C. and T.D.P. were supported by NIH research grant GM-026338 (awarded to T.D.P.) and a postdoctoral fellowship from the Leukemia and Lymphoma Society (awarded to N.C.). Simulations were performed using the Extreme Science and Engineering Discovery Environment, which is supported by NSF grant OCI-1053575 . This research also used resources of the Argonne Leadership Computing Facility (ALCF) and the ALCF-2 Early Science Program at the Argonne National Laboratory, which is supported by the U.S. Department of Energy Office of Science under contract DE-AC02-06CH11357 .