Interface-Driven Peptide Folding: Quantum Computations on Simulated Membrane Surfaces
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arXiv
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| Format: | Preprint |
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2024
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| author | Conde-Torres, Daniel Mussa-Juane, Mariamo Faílde, Daniel Gómez, Andrés García-Fandiño, Rebeca Piñeiro, Ángel |
| author_facet | Conde-Torres, Daniel Mussa-Juane, Mariamo Faílde, Daniel Gómez, Andrés García-Fandiño, Rebeca Piñeiro, Ángel |
| contents | Antimicrobial peptides (AMPs) play important roles in cancer, autoimmune diseases, and aging. A critical aspect of AMP functionality is their targeted interaction with pathogen membranes, which often possess altered lipid compositions. Designing AMPs with enhanced therapeutic properties relies on a nuanced understanding of these interactions, which are believed to trigger a rearrangement of these peptides from random coil to alpha-helical conformations, essential for their lytic action. Traditional supercomputing has consistently encountered difficulties in accurately modeling these structural changes, especially within membrane environments, thereby opening an opportunity for more advanced approaches. This study extends an existing quantum computing algorithm to address the complexities of antimicrobial peptide interactions at interfaces. Our approach enables the prediction of the optimal conformation of peptides located in the transition region between hydrophilic and hydrophobic phases, akin to lipid membranes. The new method has been applied to model the structure of three 10-amino-acid-long peptides, each exhibiting hydrophobic, hydrophilic, or amphipathic properties in different media and at interfaces between solvents of different polarity. Notably, our approach does not demand a higher number of qubits compared to simulations in homogeneous media, making it more feasible with current quantum computing resources. Despite existing limitations in computational power and qubit accessibility, our findings demonstrate the significant potential of quantum computing in accurately characterizing complex biomolecular processes, particularly the folding of AMPs at membrane models. This research paves the way for future advances in quantum computing to enhance the accuracy and applicability of biomolecular simulations. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2401_05075 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Interface-Driven Peptide Folding: Quantum Computations on Simulated Membrane Surfaces Conde-Torres, Daniel Mussa-Juane, Mariamo Faílde, Daniel Gómez, Andrés García-Fandiño, Rebeca Piñeiro, Ángel Quantum Physics Biological Physics Biomolecules Antimicrobial peptides (AMPs) play important roles in cancer, autoimmune diseases, and aging. A critical aspect of AMP functionality is their targeted interaction with pathogen membranes, which often possess altered lipid compositions. Designing AMPs with enhanced therapeutic properties relies on a nuanced understanding of these interactions, which are believed to trigger a rearrangement of these peptides from random coil to alpha-helical conformations, essential for their lytic action. Traditional supercomputing has consistently encountered difficulties in accurately modeling these structural changes, especially within membrane environments, thereby opening an opportunity for more advanced approaches. This study extends an existing quantum computing algorithm to address the complexities of antimicrobial peptide interactions at interfaces. Our approach enables the prediction of the optimal conformation of peptides located in the transition region between hydrophilic and hydrophobic phases, akin to lipid membranes. The new method has been applied to model the structure of three 10-amino-acid-long peptides, each exhibiting hydrophobic, hydrophilic, or amphipathic properties in different media and at interfaces between solvents of different polarity. Notably, our approach does not demand a higher number of qubits compared to simulations in homogeneous media, making it more feasible with current quantum computing resources. Despite existing limitations in computational power and qubit accessibility, our findings demonstrate the significant potential of quantum computing in accurately characterizing complex biomolecular processes, particularly the folding of AMPs at membrane models. This research paves the way for future advances in quantum computing to enhance the accuracy and applicability of biomolecular simulations. |
| title | Interface-Driven Peptide Folding: Quantum Computations on Simulated Membrane Surfaces |
| topic | Quantum Physics Biological Physics Biomolecules |
| url | https://arxiv.org/abs/2401.05075 |