title: Allosteric response and substrate sensitivity in peptide binding of the signal recognition particle.
abstract: We characterize the conformational dynamics and substrate selectivity of the signal recognition particle (SRP) using a thermodynamic free energy cycle approach and microsecond timescale molecular dynamics simulations. The SRP is a central component of the co-translational protein targeting machinery that binds to the N-terminal signal peptide (SP) of nascent proteins. We determined the shift in relative conformational stability of the SRP upon substrate binding to quantify allosteric coupling between SRP domains. In particular, for dipeptidyl aminopeptidase, an SP that is recognized by the SRP for co-translational targeting, it is found that substrate binding induces substantial changes in the SRP toward configurations associated with targeting of the nascent protein, and it is found that the changes are modestly enhanced by a mutation that increases the hydrophobicity of the SP. However, for alkaline phosphatase, an SP that is recognized for post-translational targeting, substrate binding induces the reverse change in the SRP conformational distribution away from targeting configurations. Microsecond timescale trajectories reveal the intrinsic flexibility of the SRP conformational landscape and provide insight into recent single molecule studies by illustrating that 10-nm lengthscale changes between FRET pairs occur via the rigid-body movement of SRP domains connected by the flexible linker region. In combination, these results provide direct evidence for the hypothesis that substrate-controlled conformational switching in the SRP provides a mechanism for discriminating between different SPs and for connecting substrate binding to downstream steps in the protein targeting pathway.
authors.affiliation: Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91106.
authors.forename: Connie Y
authors.initials: CY
authors.lastname: Wang
authors.affiliation: Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91106. Electronic address: tfm@caltech.edu.
authors.forename: Thomas F
authors.initials: TF
authors.lastname: Miller
mesh_terms: D000494:Allosteric Regulation; D019843:Archaeal Proteins / Q000737:chemistry*; D057927:Hydrophobic and Hydrophilic Interactions; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D014176:Protein Biosynthesis; D055550:Protein Stability; D021381:Protein Transport; D018271:Signal Recognition Particle / Q000737:chemistry*; D048229:Sulfolobus solfataricus; D013816:Thermodynamics
chemical_list: D019843:Archaeal Proteins; D018271:Signal Recognition Particle
keywords: Allosteric Regulation; Computer Modeling; Conformational Change; Protein Targeting; Signal Recognition Particle (SRP); Single Molecule Biophysics