Скачать презентацию Outline 1 Methods new version of the energy Скачать презентацию Outline 1 Methods new version of the energy

6b8370ba017fe419ad6bbf50c9353cc3.ppt

  • Количество слайдов: 11

Outline 1. Methods new version of the energy model PMF calculations instead of adsorption Outline 1. Methods new version of the energy model PMF calculations instead of adsorption free energy 2. Model validation PMF for amino acids Proteins 3. Outlook

Methods 1. Protein-metal non-polar interactions (sum of Lennard-Jones potentials) - checked 2. Protein-metal electrostatic Methods 1. Protein-metal non-polar interactions (sum of Lennard-Jones potentials) - checked 2. Protein-metal electrostatic interaction 3. Desolvation effects - improved 4. Electrostatic interaction between adsorbed water layer on gold and a protein – implemented (only for proteins)

Desolvation energy E 0 is water adsorption energy per unit area; Now desolvation area Desolvation energy E 0 is water adsorption energy per unit area; Now desolvation area is defined by vd. W radius of water molecule+ vd. W radius of protein atoms (i. e. ~6 Angstrom) Adsorption energy in the 2 d layer in the 1 st layer distance from the gold surface OLD R NEW = 6. 0 Å 6. 5 Å 2)-1 0. 13 k. J(mol Å2)-1 = 0. 25 k. J(mol Å = 3. 0 Å 6. 0 Å

PMF and adsorption free energy Configurational space: rotation ( i=1 -3) + translation (x=0 PMF and adsorption free energy Configurational space: rotation ( i=1 -3) + translation (x=0 -Dx; y=0 -Dy; z=0 -b); DS=Dx. Dy adsorption free energy: PMF energy

Model validation: amino acids on gold Different conformations: Gln Lys His/His. H Model validation: amino acids on gold Different conformations: Gln Lys His/His. H

Model validation: BLIP/BLIP-3 His From MD simulations BD simulations: BLIP weakly bound DG ~ Model validation: BLIP/BLIP-3 His From MD simulations BD simulations: BLIP weakly bound DG ~ 1. 6 k. T BLIP-3 HIS is strongly bound ! 3 His. H DG ~ 38 k. T

Model validation: Fibronectin on the gold surface structure from MD simulations DG ~ 36 Model validation: Fibronectin on the gold surface structure from MD simulations DG ~ 36 k. T Conformation is very important!

BLIP BLIP

Electrostatic interaction between adsorbed water and a protein Electrostatic interaction between adsorbed water and a protein

Outlook 1. Model of electrostatic interaction between adsorbed water and protein – must be Outlook 1. Model of electrostatic interaction between adsorbed water and protein – must be improved

Acknowledgements • University of Modena and Reggio Emilia • Elisa Molinari • Francesco Iori Acknowledgements • University of Modena and Reggio Emilia • Elisa Molinari • Francesco Iori • Weizmann Institute of Science - Biochemistry • EML Reasearch • Rebecca Wade • Piter Winn • Bingding Huang • Gideon Schreiber • Dana Reichmann • Ori Cohavi • Weizmann Institute of Science – Nanomaterials • Israel Rubinstein, • Alexander Vaskevich • Ludwig Maximilians University • Kay Gottschalk • Martin Hoefling • INFM-CNR National Research Center S 3 • Stefano Corni • Rosa Di Felice • Arrigo Calzolari • Alessandra Catellani Financial support