ABEEM-ESHB: an in situ hydrogen-bond estimation model for dynamic monitoring of sulfur-containing amino acid-damaged base interactions.

Authors

Xin-Yue Miao, Zi-Zhen Jin, Tong-Tong Men, Wei Sun, Cui Liu, Zhong-Zhi Yang

Published in

Physical chemistry chemical physics : PCCP. Nov 11, 2026. Epub Nov 11, 2026.

Abstract

Hydrogen bonds between repair-enzyme active residues and damaged bases are critical for recognition. Simulating polarization effects and biological interactions remains a challenge in force field development. Here, we develop the atom-bond electronegativity equalization method polarizable force field (ABEEM PFF) for sulfur-containing residues and damaged bases, along with an estimation in situ hydrogen bond (ESHB) model for dynamic quantification. ABEEM PFF partitions molecules into atomic, bond, and lone-pair regions, allowing charges to fluctuate with the structure and environment. A distance-dependent function k_HB describes hydrogen bond electrostatic interactions. Parameters from mono-hydrogen bond complexes transfer well to multi-hydrogen bond systems (R ≥ 0.988, U_max ≤ 0.140 e). Average absolute deviation and root-mean-square deviation were 0.11/0.14 Å (bond length), 6.79°/8.89° (angle), and 0.63/0.80 kcal mol^-1 (binding energy). These parameters were integrated into ESHB to develop ABEEM-ESHB, where hydrogen bond energy comprises electrostatic and van der Waals components; electrostatics dominate, secondary interactions between different hydrogen bonds contribute up to 27% of H-bond energy in multi-hydrogen bond systems. When applied to simulations of 1EBM, ABEEM-ESHB captures the S-H⋯O bond between Cys253 and 8-oxo-G, which undergoes intermittent formation and breakdown. The hydrogen bond behavior is governed by bond length and the local environment: hydrogen bond energy becomes more negative as the bond length shortens below 2.2 Å; fluctuates between -3 and -1 kcal mol^-1 within 2.2-2.7 Å; and approaches 0 at 2.74 Å, indicating weakened stabilization. This suggests an auxiliary contribution. The method provides theoretical support for studying hydrogen bond interactions in biomacromolecules.

PMID:
43013815
Bibliographic data and abstract were imported from PubMed on 12 Nov 2026.

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