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. Author manuscript; available in PMC: 2011 Aug 31.
Published in final edited form as: Biochemistry. 2010 Aug 31;49(34):7323–7343. doi: 10.1021/bi100588a

Table 3.

Predicted inter-chain salt bridges in nascent HDL during molecular dynamics simulation

Salt bridge DSH model Simulation trajectory
Distance
(Å)		 Minimum a
distance (Å)		 Average b
distance (Å)		 Maximum c
distance (Å)		 Persistence d
(%)
Arg10A–Glu234B 1.53 2.17 2.72 3.21 14.3
Lys12A–Glu234B 1.67 1.97 2.83 3.96 14.3
Arg27A–Glu223B 1.68 2.47 2.47 2.47 4.8
Lys40A–Asp213B 1.65 2.23 2.50 2.77 57.1
Asp48A–Lys206B 1.69 2.19 2.70 3.94 23.8
Asp48A–Lys208B 7.25 2.02 3.16 3.85 57.1
Asp51A–Lys206B 5.88 3.95 3.95 3.95 4.8
Lys59A–Glu198B 1.52 2.30 2.30 2.3 4.8
Glu62A–Lys195B 1.61 2.08 2.08 2.08 4.8
Glu70A–Arg188B 1.53 1.92 3.07 3.75 57.1
Lys77A–Glu183B 1.55 2.03 2.03 2.03 4.8
Glu78A–Arg177B 1.68 1.95 2.69 4.00 85.7
Glu85A–Arg177B 10.55 1.95 2.71 3.87 66.7
Asp89A–Arg173B 1.65 1.81 2.14 3.34 100
Glu92A–Arg171B 1.53 1.72 2.66 3.99 33.3
Glu92A-Arg173B 1.53 1.94 2.31 3.14 95.2
Lys96A-Glu169B 1.56 2.73 2.73 2.73 4.8
Lys107A-Asp157B 1.5 2.10 2.63 3.97 80.9
Glu110A-Arg151B 9.11 3.66 3.66 3.66 4.8
Glu111A-Arg151B 1.54 2.82 2.82 2.82 4.8
Glu111A-His155B 1.42 1.61 1.79 2.01 100
Lys118A-Glu147B 1.51 2.02 2.64 3.81 85.7
Glu125A-Lys133B 10.33 2.03 2.41 3.16 66.7
Glu125A-Lys140B 1.59 2.06 2.42 3.30 80.9
Glu128A-Lys133B 10.25 2.26 2.98 3.92 28.6
Glu136A-Arg123B 1.6 2.21 2.21 2.21 4.8
Lys140A-Glu125B 1.76 2.23 2.50 2.77 9.5
Glu147A-Lys118B 1.62 2.04 2.59 3.09 33.3
Arg151A-Glu111B 1.65 1.82 2.83 3.80 61.9
His155A-Glu110B 4.2 3.84 3.84 3.84 4.8
His155A-Glu111B 1.49 1.61 1.83 2.40 95.2
Asp157A-Lys107B 9.2 3.90 3.90 3.90 4.8
Arg171A-Glu85B 7.29 3.14 3.55 3.99 19.0
Arg171A-Glu92B 13.81 3.97 3.97 3.97 4.8
Arg173A-Glu78B 1.51 2.27 2.58 3.45 28.6
Arg173A-Glu85B 5.55 2.02 2.62 3.83 38.1
Arg177A-Glu70B 19.97 2.28 3.31 3.96 38.1
Arg177A-Asp73B 13.68 2.95 3.47 3.95 14.3
Glu191A-Lys59B 1.47 2.10 2.78 3.45 66.7
Lys195A-Asp48B 13.46 2.19 2.96 3.52 19.0
Lys195A-Asp51B 11.74 2.10 3.26 3.96 38.1
Glu198A-Lys45B 8.82 3.63 3.84 3.97 14.3
His199A-Asp48B 6.37 1.63 1.91 2.71 95.2
Glu212A-Lys40B 7.34 1.99 2.69 3.96 19.0
Asp213A-Lys40B 7.64 3.08 3.08 3.08 4.8
Lys238A-Glu2B 2.69 2.43 3.35 3.94 42.8
Lys239A-Glu2B 1.66 2.27 2.79 3.30 9.5
a

Minimum distance between charged residues detected during the entire trajectory.

b

Average distance between charged residues calculated from all snapshots.

c

Maximum distance between charged residues detected during the entire trajectory.

d

Salt bridge persistence calculated as the fraction of the snapshots in which the salt bridge was detected (i.e. that distance between charged residue was less than 4 Å. Salt bridges with light shaded background are located in the half domain of the apoA1 dimer that contains the Nβ/Cα termini pair. Salt bridges with a darker background persist more than 80% of the simulation.