An NADH-quinone oxidoreductase was found with a valine to proline substitution in the long horizontal helix of its membrane-intrinsic region. Will this complex I be able to transport any protons?

No. Proline is a unique amino acid because its side chain is connected to the backbone twice, forming a ring. This gives it a very rigid structure that normally causes kinks because it can't form a normal helical structure.

Valine is a hydrophobic amino acid, highly suitable for transmembrane regions, and will not tolerate a substitution to proline very well at all, given they are such different structures.

Therefore, the substitution will likely completely alter the properties of this region of the protein, meaning it will not form the proper structure in the membrane and will be unable to transport protons.