Table 1 List of MD replicas to study the opening of the E. coli MelB permease.

From: Helical unwinding and side-chain unlocking unravel the outward open conformation of the melibiose transporter

Replicaa

Length (ns)

Periplasmic Cavity Volume (Å3)c

CγY33–CγY256 Distance (Å)

OPEN

A.0

0

5,270

6.64

No

A.1

288.96b

7,969

17.23

Yes

A.2

100

6,030

9.04

Partially

A.3

100

3,229

7.03

No

A.4

100

3,898

4.87

No

A.5

100

2,953

7.03

No

A.6

100

3,664

6.40

No

B.0

0

5,230

6.85

No

B.1

100

4,555

6.87

No

B.2

100

3,544

8.28

No

B.3

100

3,764

6.28

No

B.4

100

7,464

20.15

Yes

B.5

100

2,974

11.10

No

B.6

100

3,842

8.13

No

  1. aReplica ID indicates the equilibration output (A or B) followed by the replica number.
  2. bThis replica was extended until 289 ns and analyzed in this study.
  3. cVolume of the water molecules allocated in the periplasmic cavity of MelB (Fig. 1). The volume was calculated with the Volarea plugin28 in VMD.
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