Identifying residues in unfolded whole proteins with a nanopore: a theoretical model based on linear inequalities.

ABSTRACT: A theoretical model is proposed for the identification of individual amino acids (AAs) in an unfolded whole protein's primary sequence. It is based in part on a recent report (Nat. Biotech. 41, 1130-1139, 2023) that describes the unfolding and translocation of whole proteins at constant speed through a biological nanopore (alpha-Hemolysin) of length 5 nm with a residue dwell time inside the pore of ~10 μs. Here current blockade levels in the pore due to the translocating protein are assumed to be measured with a limited precision of 70 nm³ and a bandwidth of 20 KHz for measurement with a low-bandwidth detector. Exclusion volumes in two pores of slightly different lengths are used as a computational proxy for the blockade signal; subsequence exclusion volume differences al

SUBMITTER: Sampath G 

PROVIDER: S-EPMC10491143 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature