Proteins in Bionanotechnology Computational Studies

1. Proteins in Bionanotechnology Computational Studies Andrew Hung, Oliver Beckstein, Robert D’Rozario, Sylvanna S.W. Ho and Mark S.P. Sansom Laboratory of Molecular Biophysics Department of Biochemistry, University of Oxford, OX1 3QU, United Kingdom Molecular Biosensors : Real and Virtual • Biosensor : properties and components • - High specificity/sensitivity • - Extracellular domain • (sensing element) • Ion-permeable transmembrane • (TM) domain • - Lipid bilayer • - Conducting surface (eg. Au) • - Ion channel current = analyte conc. • Atomistic simulations : • Towards a virtual biosensor • - Atomic-level description of : • - Pore structure and permeation • - Mechanical properties and stability • Influence of solvent environment • Protein-linker interactions • -Protein-inorganic surface interactions H. Bayley et al., Nature 413, pp226 (2001) Pore Structure and Permeation Protein-Surface Interactions Water and cation permeation (Beckstein) Pore structure and dynamics (Hung) Protein on gold : preliminary studies (Ho) • - MD of unrestrained M2 in rigid scaffold of outer helices (nAChR) • - Bending of 40-600 observed • - Hinge point coincident with hydrophobic ring • - Pore radius reduced significantly from initial structure (LEFT) • - Anisotropic Network Model calculation reveals major motions : bending (LOWER LEFT) and twisting (LOWER RIGHT) • - Variations in inter-residue connectivity along the pore axis results in M2 bending • -Nicotinic acetylcholine receptor (nAChR) • Pore-lining M2 helices backbone-restrained • 60ns MD collected with 1.3 Molar NaCl • 5-fold symmetry of pore imprinted on water density (LEFT) • Na+ density shows no cation permeation to pore centre (RIGHT) • Both -barrel and -helical proteins and peptides have potential biosensor applications • MD simulations performed for proteins in biological (eg. NspA and SP-C in lipid bilayer, LEFT and LOWER LEFT respectively) and non-native environments (LOWER RIGHT) • Surfactant protein C (SP-C) embedded in bilayer • MD simulations reveal preferential tilting relative to bilayer normal • Preliminary studies : SP-C tethered to gold (Au) lowest energy surface • Influence of non-biological environment on protein conformations • Potential of mean force shows free energy required to place molecule/ion at specific regions along pore • High permeation barrier at hydrophobic girdle (L251-V255) • -Conclusion: nAChR gate is formed by hydrophobic ring Mechanical Properties and Stability Future Directions Applied compressional deformation (Hung) Bending helix : ion channel “switch” (D’Rozario) • Helix flexibility and pore gating (Hung and D’Rozario) • -haemolysin/cyclodextrin simulations (Beckstein and Hagan Bayley Group, Oxford) • Coarse-grain simulations of ion flux through pores (Beckstein and Asen Asenov Group, Glasgow) • In silico biosensor modelling and design (Ho in collaboration with National Physical Laboratory) - Electron conductance of Cu azurin studied with respect to applied compressional force (BELOW) -Conductance-atomic force microscopy (C-AFM) - Protein covalently bonded to Au AFM tip, compressed on C surface - Tunneling coefficient variations measured at various applied force • - Ion channel mechanical "switch" • - Many IC contain helix-bending motifs, allowing rapid conformation changes between functional states • - MD simulations performed on helix F from rhodopsin (RIGHT, red) • Superimposed snapshots of helix F over 10ns MD • (LOWER LEFT AND RIGHT) • - Proline induces highly directionally-biased hinge bending motion Group Publications J-w Zhao, J.J. Davis, M.S.P. Sansom and A. Hung, “Exploring the electronic and mechanical properties of protein using conductance atomif force microscopy”, Journal of the American Chemical Society 126 (17), p5601-5609 (2004) O. Beckstein, K. Tai and M.S.P. Sansom, “Not ions alone: barriers to ion permeation in nanopores and channels”, Journal of the American Chemical Society 126 (45), p14694-14695 (2004) A. Hung, K. Tai and M.S.P. Sansom, “Molecular dynamics simulation of the M2 helices within the nicotinic acetylcholine receptor: structure and collective motions”, Biophysical Journal (in press) S. Amiri, K. Tai, O. Beckstein, P.C. Biggin and M.S.P. Sansom, “The 7 nicotinic acetylcholine receptor: molecular modelling, electrostatics, and energetics”, Molecular Membrane Biology (in press) J. Zhao, J. J. Davis, Nanotechnology 14(9), p1023 (2003) • MD simulations of unidirectional compression performed (LEFT) • “Compression” achieved by manipulating cell geometry • Protein atomic density correlated with experimentally-observed tunneling coefficient