Molecular Dynamics Simulation Analysis of Anti-MUC1 Aptamer and Mucin 1 Peptide Binding

Abstract

Aptasensors utilize aptamers as bioreceptors. Aptamers are highly efficient, have a high specificity and are reusable. Within the biosensor the aptamers are immobilized to maximize their access to target molecules. Knowledge of the orientation and location of the aptamer and peptide during binding could be gained through computational modeling. Experimentally, the aptamer (anti-MUC1 S2.2) has been identified as a bioreceptor for breast cancer biomarker mucin 1 (MUC1) protein. However, within this protein lie several peptide variants with the common sequence APDTRPAP that are targeted by the aptamer. Understanding orientation and location of the binding region for a peptide-aptamer complex is critical in their biosensor applicability. In this study, we investigate through computational modeling how this peptide sequence and its minor variants affect the peptide-aptamer complex binding. We use molecular dynamics simulations to study multiple peptide-aptamer systems consisting of MUC1 (APDTRPAP) and MUC1-G (APDTRPAPG) peptides with the anti-MUC1 aptamer under similar physiological conditions reported experimentally. Multiple simulations of the MUC1 peptide and aptamer reveal that the peptide interacts between 3' and 5' ends of the aptamer but does not fully bind. Multiple simulations of the MUC1-G peptide indicate consistent binding with the thymine loop of the aptamer, initiated by the arginine residue of the peptide. We find that the binding event induces structural changes in the aptamer by altering the number of hydrogen bonds within the aptamer and establishes a stable peptide-aptamer complex. In all MUC1-G cases the occurrence of binding was confirmed by systematically studying the distance distributions between peptide and aptamers. These results are found to corroborate well with experimental study reported in the literature that indicated a strong binding in the case of MUC1-G peptide and anti-MUC1 aptamer. Present MD simulations highlight the role of the arginine residue of MUC1-G peptide in initiating the binding. The addition of the glycine residue to the peptide, as in the case of MUC1-G, is shown to yield a stable binding. Our study clearly demonstrates the ability of MD simulations to obtain molecular insights for peptide-aptamer binding, and to provide details on the orientation and location of binding between the peptide-aptamer that can be instrumental in biosensor development.

Label-free sensing of the binding state of MUC1 peptide and anti-MUC1 aptamer solution in fluidic chip by terahertz spectroscopy

“…The initial interaction causes the number of hydrogen bonds to decrease, then gradually increase as the complex structure achieves stable conformation corresponding to the final binding combination. The variation of the hydrogen bonds along with the binding process is consistent with the results obtained by Rhinehardt [26]. THz spectra of biological solutions mainly reflect the change in the hydrogen bond network around the biomolecules [42,43].…”

“…The binding duration of the peptide and aptamer stays at the nanosecond time scale [26], which cannot be monitored in real-time by THz spectroscopy owing to the latter's millisecond-scale sampling time. The PBS solution and D-PBS solution, showing main discrepancy of divalent metal ions, are selected to control the binding state of the specific aptamer (anti-MUC1) and MUC1 peptide, as divalent metal ions (e.g., Mg 2+ , Ca 2+ ) are crucial for forming the characteristic secondary structure of the aptamer [11].…”

“…Instead, only the initial and final states can be measured in the actual experiment. However, from the MD simulation, according to the time-dependent change in the number of hydrogen bonds between the biomolecules and water, we can observe the binding process as it occurs, and estimate an approximate binding time of 25 ns [26]. …”

“…This suggests the existence of a heterogeneous hydrogen bond network that assists molecular recognition and binding. Meaningful molecular details for MUC1 peptide and aptamer binding were successfully obtained by molecular dynamics (MD) simulation, which showed the number of hydrogen bonds in and around the aptamer changed with the binding process [26]. On account of hydration shell alteration, the binding reaction of hemagglutinin (HA) subtypes H9 with a human HA-specific neutralizing monoclonal antibody F10 was detected by THz spectroscopy [27].…”

Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors

“…The atomistic details available in MD simulations with explicit solvent have been fundamental at uncovering the molecular level mechanisms of key experimental observations and deepen our understanding of the interactions and properties of biological complexes in their natural environment 24–28 . Partly because of the lack of solved 3D structures, very few MD simulation studies have focused on aptamers 29, 30 . Our results show that MD simulations can, indeed, be used to further improve the structural predictions and that the predictions are representative of those obtained from the dynamics of the systems under conditions that mimic their targeted environment.…”