We
present an in silico approach for modeling
the noncovalent interactions between the human mitochondrial voltage-dependent
anion channel (hVDAC1) and a family of single-walled carbon nanotubes
(SWCNTs) with a defined pattern of topological vacancies (v = 1–16), obtained by removing atoms from the SWCNT
surface. The general results showed more stable docking interaction
complexes (SWCNT–hVDAC1), with more negative Gibbs free energy
of binding affinity values, and a strong dependence on the vacancy
number (R
2 = 0.93) and vacancy formation
energy (R
2 = 0.96). In addition, for most
of the SWCNT vacancies that were analyzed, the interatomic distances
for the interactions of the SWCNT–hVDAC1 complex with the functional
catalytic residues (i.e., Pro7, Gln199, Gln182, Phe181, Val20, Asp19,
Lys15, Gly14, Asp12, Ala11, and Arg18) that form the hVDAC1 active
site (i.e., the voltage-sensing N-terminal α-helix segment)
were very similar to or shorter than the interatomic distances of
these residues for ATP–hVDAC1 interactions. In particular,
the hVDAC1 residues that can be phosphorylated like Tyr10, Tyr198,
and Se16 were significantly perturbed by the interactions with SWCNT
with at least nine vacancies. In addition, the SWCNT vacancy family
members can affect the flexibility properties of the hVDAC1 N-terminal
α-helix segment inducing different patterns of local perturbations
in inter-residue communication. Finally, vacancy quantitative structure–binding
relationships (V-QSBRs) were unveiled for setting up a robust model
that can predict the strength of docking interactions between SWCNTs
with a specific topological vacancy and hVDAC1. The developed V-QSBR
model classified properly all of the SWCNTs with a different number
of SWCNT vacancies with exceptional sensitivity and specificity (both
equal to 100%), indicating a strong potential to unequivocally predict
the influence of SWCNT vacancies on the mitochondrial channel interactions.