What does this research mean for the field?

In silico models predict that transition-metal coordination of a histidine hexamer shifts its DNA binding preference from a major-groove pose with adenine contacts to a minor-groove pose with guanine contacts. Novelty: ClaimNovelty.INCREMENTAL. Consensus alignment: ConsensusAlignment.NEUTRAL.

What question did this study set out to answer?

Evaluate how transition-metal coordination alters the predicted DNA groove localization, nucleobase contacts, and structural stability of a histidine hexamer (His6) interacting with B-DNA.

August 29, 2026Journal of Biomolecular Structure and Dynamics

Transition-metal coordination modulates predicted DNA groove recognition and nucleobase contacts in oligohistidine complexes

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Authors

SASoykan Ağar AYA. Yıldız MYMine Yurtsever

Discussion

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Overview

In silico modeling demonstrates that transition-metal coordination shifts oligohistidine from major-groove to minor-groove DNA binding, indicating metal-dependent modulation of DNA recognition.

Key Points

Evaluate how transition-metal coordination alters the predicted DNA groove localization, nucleobase contacts, and structural stability of a histidine hexamer (His6) interacting with B-DNA.
Conducted molecular docking and molecular dynamics simulations comparing metal-free His6 with tri-metal complexes ([Zn3(His6)]6+, [Ni3(His6)]6+, and [Cu3(His6)]6+).
Evaluated structural binding poses, hydrogen bonding, and trajectory-based persistence against a canonical B-DNA dodecamer model [d(CGCGAATTCGCG)].
Metal-free His6 predominantly engaged the major groove with adenine contacts and a docking score of −8.9 kcal/mol, whereas tri-metal complexes shifted to minor-groove binding with guanine contacts.
Tri-metal models yielded docking scores of −9.5 kcal/mol for Zn(II), −13.5 kcal/mol for Ni(II), and −10.8 kcal/mol for Cu(II), with Ni(II) and Cu(II) exhibiting lower RMSD values than the metal-free complex.

Cite This Study

Ağar et al. (2026) studied this question.

synapsesocial.com/papers/6a9299088e5d7d1fc0c10cc2 https://doi.org/10.1080/07391102.2026.2723209

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August 29, 2026Journal of Biomolecular Structure and Dynamics

Transition-metal coordination modulates predicted DNA groove recognition and nucleobase contacts in oligohistidine complexes

View Full Paper

Ask AI

Bookmark

Authors

SASoykan Ağar AYA. Yıldız MYMine Yurtsever

Discussion

Member takes

Overview

In silico modeling demonstrates that transition-metal coordination shifts oligohistidine from major-groove to minor-groove DNA binding, indicating metal-dependent modulation of DNA recognition.

Key Points

Evaluate how transition-metal coordination alters the predicted DNA groove localization, nucleobase contacts, and structural stability of a histidine hexamer (His6) interacting with B-DNA.
Conducted molecular docking and molecular dynamics simulations comparing metal-free His6 with tri-metal complexes ([Zn3(His6)]6+, [Ni3(His6)]6+, and [Cu3(His6)]6+).
Evaluated structural binding poses, hydrogen bonding, and trajectory-based persistence against a canonical B-DNA dodecamer model [d(CGCGAATTCGCG)].
Metal-free His6 predominantly engaged the major groove with adenine contacts and a docking score of −8.9 kcal/mol, whereas tri-metal complexes shifted to minor-groove binding with guanine contacts.
Tri-metal models yielded docking scores of −9.5 kcal/mol for Zn(II), −13.5 kcal/mol for Ni(II), and −10.8 kcal/mol for Cu(II), with Ni(II) and Cu(II) exhibiting lower RMSD values than the metal-free complex.

Cite This Study

Ağar et al. (2026) studied this question.

synapsesocial.com/papers/6a9299088e5d7d1fc0c10cc2 https://doi.org/10.1080/07391102.2026.2723209

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