MCM supplemental data

Supplemental data published before 2011 can be found in our archive.

Supplemental data relating to papers published in or after 2011 can be found below:

• Comparative electrostatic analysis of adenylyl cyclase for isoform dependent regulation properties. Rudi Tong, Rebecca C. Wade and Neil J. Bruce (2016), Proteins: Struct. Func. Bioinf., 84, 1844-1858. DOI: 10.1002/prot.25167

^  Structures   ^    Grids    ^
|{{ :projects:modelledisoformstructuresnorefine.tgz |Unrefined modelled AC isoforms for small molecule analysis}} |{{ :projects:electrostaticgridsnorefine.tgz |Electrostatic potential grids from unrefined structures, UHBD format}} |
|{{ :projects:modelledisoformstructures.tgz |Modelled AC isoforms}}  |{{ :projects:electrostaticgrids.tgz |Electrostatic potential grids, UHBD format}} |

• On the structure and dynamics of the complex of the nucleosome and the linker histone, Georgi V. Pachov, Razif R. Gabdoulline and Rebecca C. Wade. Nucl. Acid. Res., (2011) 1:9.: PDB files for the encounter complexes (zipped)

• For simulation of the cysteine synthase complex ( A mechanistic model of the cysteine synthase complex, Feldman-Salit et al, J Mol Biol. 2009 Feb 13;386(1):37-59):
  • Parameters derived using Antechamber for simulations with AMBER8 using parm99.dat and gaff.dat:
    • Coenzyme A (CoA): lib, parm
    • Pyridoxal 5′-phosphate covalently bound to a lysine residue (K-PLP): lib, parm
  • For PDB coordinates, see Supplementary material.

• A tightly regulated molecular toggle controls AAA+ disaggregase, Oguchi Y, Kummer E, Seyffer F, Berynskyy M, Anstett B, Zahn R, Wade RC, Mogk A, Bukau B., Nat Struct Mol Biol. (2012) 19:1338-46. doi: 10.1038/nsmb.2441 : PDB files for models (zipped).

• Dynamic enzyme docking to the ribosome coordinates N-terminal processing with polypeptide folding, Sandikci A, Gloge F, Martinez M, Mayer MP, Wade R, Bukau B, Kramer G, Nat Struct Mol Biol. (2013) 20:843-50. doi: 10.1038/nsmb.2615 : PDB files for MAP-ribosome encounter complexes (zipped (bzip2) tar file).

• Atomic Detail Brownian Dynamics Simulations of Concentrated Protein Solutions with a Mean Field Treatment of Hydrodynamic Interactions, Mereghetti P, Wade, RC, J. Phys. Chem. B. (2012) 116:8523-8533. doi: 10.1021/jp212532h : Movie of diffusion of a solution of hemoglobin tetramers at a 0.11 volume fraction simulated with the SDA software (zipped (zip) file).

• Three steps to gold: mechanism of protein adsorption revealed by Brownian and molecular dynamics simulations, Ozboyaci M, Kokh DB, Wade, RC, Phys. Chem. Chem. Phys. (2016) 18:10191-10200. doi: 10.1039/C6CP00201C : Movie showing adsorption of beta-lactamase inhibitor protein (BLIP) onto an Au(111) surface in molecular dynamics simulations starting from two encounter complexes generated by Brownian dynamics simulation. (zipped (zip) file).