Text A in S1 File:

Additional details of the preparation of the protein structures, MD simulations and targeted MD simulations; Table A in S1 File: Representation of the calculation of the average percentage of interaction of each possible pair of residues for the different phases, PoI(Rij)Phk, along all TMD simulations, using the free energy decomposition method; Text B in S1 File: Detailed main interactions established by residues that participate in the conformational change of HIV-1 gp41; Table B in S1 File: Correspondence between the gp160 sequence and the numbering used for TMD trajectories; Table C in S1 File: Table summarizing experimental gp41 mutagenesis data; Figure A in S1 File: Scheme illustrating the two required criteria for an intermediate to proceed to the TMD step; Figure B in S1 File: Plots of the evolution of all the defined leading interactions along the TMD pathway.
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