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Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
Published on: September 16, 2010
Electronic Transmission Signatures of Hydrogen-Bond Topology in Model Antiparallel β-Sheet Segments
Amrit Sarmah1, Dipankar Sutradhar2, Pavel Hobza3
1RIKEN, Center for Computational Science, 7-1- 26, Minatojima-minami- machi, Chuo-ku, Kobe 650-0047, Hyogo, Japan.
Abstract:
We investigate the electronic conductance of peptide-based molecular junctions modeled on antiparallel β-sheet motifs of H-bonded glycine complexes, using density functional theory (DFT) combined with the nonequilibrium Green's function (NEGF) formalism. Our results demonstrate that distinct hydrogen-bonding topologies, including central versus terminal ring closure and compact versus extended loop geometries, produce characteristic transmission spectra and stepwise, nonlinear current-voltage (I-V) responses. These features reflect quantum confinement and discrete resonant tunneling, enabling each hydrogen-bond pattern to serve as a reproducible electronic "fingerprint." Complementary analyses (SAPT, NCI-RDG, NBO, AIM) reveal that while thermodynamic stability is governed by a balance of electrostatic, induction, and dispersion contributions, electron-transport efficiency correlates most strongly with hydrogen-bond shortness and orbital delocalization rather than solely with binding energy. The methodology establishes a quantitative structure-conductance relationship for peptide backbones, with implications for bioelectronic sensing.
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