Proteins in BionanotechnologyProteins in BionanotechnologyComputational StudiesComputational Studies

Andrew Hung, Oliver Beckstein, Robert D’Rozario, Sylvanna S.W. Ho and Mark S.P. SansomAndrew Hung, Oliver Beckstein, Robert D’Rozario, Sylvanna S.W. Ho and Mark S.P. Sansom Laboratory of Molecular BiophysicsLaboratory of Molecular Biophysics

Department of Biochemistry, University of Oxford, OX1 3QU, United KingdomDepartment of Biochemistry, University of Oxford, OX1 3QU, United Kingdom

Molecular Biosensors : Real and VirtualMolecular Biosensors : Real and VirtualBiosensor : 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

Pore Structure and PermeationPore Structure and Permeation

Mechanical Properties and StabilityMechanical Properties and Stability

Protein-Surface InteractionsProtein-Surface InteractionsWater and cation permeation (Beckstein) Pore structure and dynamics (Hung)

Applied compressional deformation (Hung)

Protein on gold : preliminary studies (Ho)

Bending helix : ion channel “switch” (D’Rozario)

Group PublicationsGroup Publications

-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)

-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

- 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

- Electron conductance of Cu azurin studied with respect toapplied 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

-MD simulations of unidirectional compression performed (LEFT)-“Compression” achieved by manipulating cell geometry-Protein atomic density correlated with experimentally-observed tunneling coefficient

- 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

-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

J. Zhao, J. J. Davis, Nanotechnology 14(9), p1023 (2003)

H. Bayley et al., Nature 413, pp226 (2001)

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)

Future DirectionsFuture Directions

-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)

- 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)