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Length-independent transport rates in biomolecules by quantum mechanical unfurling.

ABSTRACT: Experiments on hole transfer in DNA between donor and acceptor moieties revealed transfer rates which are independent of the molecular bridge length (within experimental error). However, the physical origin of this intriguing observation is still unclear. The hopping model implies that the hole propagates in multiple steps along the bridge from one localized state to another, and therefore the longer the bridge, the slower the transfer. This can explain weak length-dependence but not a length-independent transfer rate. We show that the rigid molecular structure of a poly-A bridge supports single step transitions from a localized hole state to delocalized states, spread over the entire bridge. Since propagation to the bridge end is a single step process (termed quantum unfurling) the transfer rate becomes independent of the bridge length. This explanation is consistent with experimental results, and emphasizes the importance of structural order in charge transfer through bio-molecular systems.

SUBMITTER: Levine AD

PROVIDER: S-EPMC5530864 | biostudies-other | 2016 Feb

REPOSITORIES: biostudies-other

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Length-independent transport rates in biomolecules by quantum mechanical unfurling.

Levine Ariel D AD Iv Michael M Peskin Uri U

Chemical science 20151120 2

Experiments on hole transfer in DNA between donor and acceptor moieties revealed transfer rates which are independent of the molecular bridge length (within experimental error). However, the physical origin of this intriguing observation is still unclear. The hopping model implies that the hole propagates in multiple steps along the bridge from one localized state to another, and therefore the longer the bridge, the slower the transfer. This can explain weak length-dependence but not a length-in ...[more]

PMID: 28808530

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Project description:We performed steered molecular dynamics (SMD) and umbrella sampling simulations of Cl- ion migration through the transmembrane domain of a prototypical E. coli CLC Cl-/H+ antiporter by employing combined quantum-mechanical (QM) and molecular-mechanical (MM) calculations. The SMD simulations revealed interesting conformational changes of the protein. While no large-amplitude motions of the protein were observed during pore opening, the side chain rotation of the protonated external gating residue Glu148 was found to be critical for full access of the channel entrance by Cl-. Moving the anion into the external binding site (Sext) induced small-amplitude shifting of the protein backbone at the N-terminal end of helix F. As Cl- traveled through the pore, rigid-body swinging motions of helix R separated it from helix D. Helix R returned to its original position once Cl- exited the channel. Population analysis based on polarized wavefunction from QM/MM calculations discovered significant (up to 20%) charge loss for Cl- along the ion translocation pathway inside the pore. The delocalized charge was redistributed onto the pore residues, especially the functional groups containing π bonds (e.g., the Tyr445 side chain), while the charges of the H atoms coordinating Cl- changed almost negligibly. Potentials of mean force computed from umbrella sampling at the QM/MM and MM levels both displayed barriers at the same locations near the pore entrance and exit. However, the QM/MM PMF showed higher barriers (~10 kcal/mol) than the MM PMF (~2 kcal/mol). Binding energy calculations indicated that the interactions between Cl- and certain pore residues were overestimated by the semi-empirical PM3 Hamiltonian and underestimated by the CHARMM36 force fields, both of which were employed in the umbrella sampling simulations. In particular, CHARMM36 underestimated binding interactions for the functional groups containing π bonds, missing the stabilizations of the Cl- ion due to electron delocalization. The results suggested that it is important to explore these quantum effects for accurate descriptions of the Cl- transport.

Dataset Information

Length-independent transport rates in biomolecules by quantum mechanical unfurling.

Publications

Length-independent transport rates in biomolecules by quantum mechanical unfurling.

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