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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptHHS Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
 
From:
Neuron. Author manuscript; available in PMC 2010 October 15.
Published in final edited form as:
Neuron. 2010 April 15; 66(1): 85–100.
doi: 10.1016/j.neuron.2010.03.028

Table 2

Overview of Simulations.

Label#PDBBinding Sitetsim (ns)Slowest SMD Speed (nm/ns)Size (# atoms)Size (nm3)
0123
C23 WT EC1S1a-g2wbxCa2+---102.720.165,59218.0 × 6.0 × 6.5
C23 WT EC1S2a-f2wbx----85.490.165,81518.0 × 6.0 × 6.5
C23 WT EC1S3a-g2wbx----92.620.165,59118.0 × 6.0 × 6.5
C23 WT EC1 βS4a-g2wbxCa2+ at 2 available sites56.300.184,90418.0 × 6.9 × 7.3
C23 WT EC1 βS5a-g2wbx----61.320.184,90218.0 × 6.9 × 7.3
C23 WT EC1+2S6a-l2wcpCa2+Na+Ca2+Ca2+191.490.1130,91924.8 × 7.6 × 7.4
C23 WT EC1+2S7a-b2wcpCa2+Na+Ca2+Ca2+49.49-125,35014.8 × 9.6 × 9.4
C23 WT EC1+2S8a-b2wcpCa2+Na+Ca2+Ca2+43.63-172,80713.8 × 11.6 × 11.4
C23 WT EC1+2S9a-k2wcp----165.860.1130,90924.8 × 7.6 × 7.4
C23 WT EC1+2S10a-b2wcp----32.950.1125,34314.8 × 9.6 × 9.4
C23 WT EC1+2S11a-j2wcpCa2+Na+Na+Ca2+103.670.1130,91824.8 × 7.6 × 7.4
C23 WT EC1+2S12a-k2whvCa2+Ca2+Ca2+Ca2+175.300.1132,32524.8 × 7.6 × 7.4
C23 WT EC1+2S13a-b2whvCa2+Ca2+Ca2+Ca2+33.00-126,92414.8 × 9.6 × 9.4
C23 WT EC1+2S14a-b2whvCa2+Ca2+Ca2+Ca2+25.00-174,61513.8 × 11.6 × 11.4
C23 WT EC1+2 CUTS15a-j2whvCa2+Ca2+Ca2+Ca2+121.860.1132,30724.8 × 7.6 × 7.4
C23 WT EC1+2 WS16a-g2whvCa2+ at 8 available sites65.770.1231,80023.6 × 9.9 × 10.4
C23 D101G EC1+2S17a-l2wd0Ca2+Na+Ca2+Ca2+180.640.1115,30324.6 × 7.4 × 6.8
C23 D101G EC1+2S18a-b2wd0Ca2+Na+Ca2+Ca2+45.48-112,88214.6 × 9.4 × 8.8
C23 D101G EC1+2S19a-b2wd0Ca2+Na+Ca2+Ca2+37.95-182,22613.6 × 12.0 × 11.8
C23 D101G EC1+2S20a-f2wd0----77.330.1115,29924.6 × 7.4 × 6.8
C23 D101G EC1+2S21a-b2wd0----26.21-112,88014.6 × 9.4 × 8.8
C23 D101G EC1+2S22a-j2wd0Ca2+Na+Na+Ca2+97.560.1115,30224.6 × 7.4 × 6.8
C23 E21A IS EC1+2S23a-c2whvCa2+Ca2+Ca2+Ca2+46.47-155,69014.8 × 10.6 × 10.4
C23 D101G IS EC1+2S24a-c2whvCa2+Ca2+Ca2+Ca2+46.54-155,69014.8 × 10.6 × 10.4
C23 E73V IS EC1+2S25a-c2whvCa2+Ca2+Ca2+Ca2+46.63-155,69614.8 × 10.6 × 10.4
C23 E21A IS EC1+2S26a-k2whvCa2+Ca2+Ca2+Ca2+151.530.1121,22824.6 × 7.6 × 6.9
C23 E73V IS EC1+2S27a-k2whvCa2+Ca2+Ca2+Ca2+166.100.1129,16524.3 × 7.6 × 7.5
C WTS28a-e1l3wCa2+ at 12 available sites50.311355,20837.4 × 10.5 × 9.4
C E69A ISS29a-i1l3wCa2+ at 12 available sites78.681355,20837.4 × 10.5 × 9.4
C E11A ISS30a-c1l3wCa2+ at 12 available sites13.1010355,20537.4 × 10.5 × 9.4
C WT DIMS31a-m1l3wCa2+ at 12 available sites154.390.1203,76927.8 × 9.4 × 8.2
C8 WT DIMS32a-f2a62Ca2+ at 12 available sites35.101155,37925.9 × 8.5 × 7.6
C8 WT DIMS33a-i2a62Ca2+ at 12 available sites139.670.1203,37627.9 × 9.5 × 8.2
C11 WT DIMS34a-c2a4eCa2+ at 6 available sites9.881150,10824.2 × 9.2 × 7.2

Overview of cadherin simulations. Labels indicate the system and protein variant (C23: cadherin-23; WT: wild-type; EC1: extracellular repeat 1; β: dimer interface mediated by β-strands; EC1+2: extracellular repeats 1 & 2; CUT: peptide bond N103-C-D104-N deleted; W: dimer interface mediated by W65; IS: in silico mutation; DIM: strand-exchanged dimer interface). Unique simulation identifiers are denoted by Snnx. Initial size of the system (in nm3) is indicated in the last column for each system. A detailed list of all simulations is in Tables S1-S6. The overall computational effort involved a cumulative total of 2,810.04 nanoseconds of simulation for systems ranging in size from 65K to 355K atoms (equivalent to a single simulation of a 25K-atom system lasting 16 μs using a uniform time-step of 2 fs).