Nanopore Sensing of Biomolecule

Translocation of peptide through MoS2 solid state nanopore

Omega E. HIKON

January 26, 2024

 Introduction: Nanobiomodelling

Signi cance: Understanding of biomolecules -> protein structure & interaction forces

Protein: Informative polymer Protein: Biomakers of early diseases

Some Applications:
Experimental:
• X - Ray di raction
• Biology and healthcare: Nanomanipulation
and design of targeted drugs • NMR
• Quantitative estimate of characteristics and • Cryo-electron microscopy
functions

• Detection of proteins A nsen’s Principle: One sequence -> One structure

HIKON, O. E
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 Detection of Proteins

Current Techniques:

• Single molecule uorescence

• Tunnelling current analysis
• Nanopore sequencing, which is the interest of this project

HIKON, O. E
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 Project Goal

Simulation of the full device

To simulate the translocation of a peptide through an MoS2 SSN in order to:

• characterise the performance of MoS2 as a biosensor.

• link current uctuations to the presence of a peptide.
• This is possible if the position of the peptide is known at every time step of
the translocation experiment.

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 Solid State Nanopores (SSN)

Danda & Drndic´ (2019) Current Opinion in Biotechnology, 55:124–133

HIKON, O. E
 Materials and Methods

3 - D Atomistic Modelling

Nicolaï, A., Senet, P. (2022). Challenges in Protein Sequencing Using 2-D MoS Nanopores. In: Bowen,
W., Vollmer, F., Gordon, R. (eds) Single Molecule Sensing Beyond Fluorescence . Nanostructure
HIKON, O. E Science and Technology. Springer, Cham. https://doi.org/10.1007/978-3-030-90339-8_11
 Materials and Methods

Interest: Methionine (M or MET) E3 - MET - K5

✴Encoded by AUG, is an alpha amino acid (AA) First isolated by John

Howard Mueller, 1921
✴Precursor of other non-essential amino acids

✴Cannot be synthesised by mammals, must be ingested

★2 Capping groups (ACE, NME) ->grey

✴Supplementary to the treatment of copper poisoning ★3 GLU (-) -> red

✴Dietary sources: Egg, sesame seeds, sh, beef ★METHIONINE -> green

★5 LYS (+) -> blue

HIKON, O. E

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 Materials and Methods

Molecular Dynamics: Theory

✴3D Structure: Python Script
• MoS2 SSN:
✴Topology: Force- eld equations

• Force-Field Equations:

✴3D Structure: VMD

• Peptide: ✴Topology: GROMACS

• Solvation: ✴3D Structure: GROMACS

+ KCl

✴Topology: TIP3P Water Model

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 Materials and Methods

Molecular Dynamics

• Energy minimisation, equilibration: GROMACS

• Voltage application: V = -EL
• Structural dynamics of the subsystems:

• Analysis of MD trajectory: Python script

• Ionic current:

HIKON, O. E
 Materials and Methods

Synthesis of MD Simulation

Equilibration scene

HIKON, O. E
 Materials and Methods
Equilibration & System structural 2 Info.: stability & peptide dynamics

Characterisation

Peptide: linear equil.

Peptide: Entrance

Membrane, being rigid,

maintains relative
stability

Peptide: globular

Rg for peptide only

Peptide: linear/extended after passage

HIKON, O. E
 Analysis of Production MD
Characterisation of E3-MET-K5 Translocation

Visualisation/movie of MD Translocation Event

Traj. of z coord. peptide

Mem. de ned with given

thickness around 0.

C.O.M negative -> translocation

Just few AA above

Using the radial coordinate

C.O.M compared to
radius of pore ->
translocation

HIKON, O. E Translocation Time = 45 ns

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 Analysis of Production MD
Free Energy Pro le; probability distribution Info.:
Di usion in bulk
Peptide goes to the surface
Huge energy barrier to cross
Translocation

FEP in 2D: Z vs rho coord.

Peptide translocation
HIKON, O. E In normal & radial coord.
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 Analysis of Production MD
Characterisation of Ionic Current Idea: Peptide translocation -> current drop

Open pore current

Device resolution/
most probable Ic
drop

Blocked pore current

HIKON, O. E
 Analysis of Production MD
Characterisation of Ionic Current and Comparison
(with another’s: Alanine)

HIKON, O. E 3.3 - 2.2 = 1.1 nA

 Analysis of Production MD
Sequencing of the peptide/Residues

Idea: track the position of the

COM of each AA to get the
sequence of passage

None of the negatively charged

MET right in the pore
glutamine is inside the pore

HIKON, O. E
 Analysis of Production MD
Sequencing of the peptide/Residues

Idea: estimate for each AA

how much time it spent inside
the pore & associated current
(mean & SD)

Here, one assumes each AA is

inside the pore one by one

Movie indicates motifs

possible

HIKON, O. E
 CONCLUSION AND PERSPECTIVES

✤ It is possible to simulate peptide translocation & sequence it.

✤ Protein sequencing with nanopore is still challenging: mostly 20 - 80 AA limit.

✤ To visually discriminate between polypeptides has no systemic solution.

✤MD simulations of protein/sequencing makes it easier to comprehend the

complexity of translocation of polypeptides.

✤ Union of AI/Machine Learning and MD could make it easier to correlate

parameters to peptide structures and to identify them.

HIKON, O. E
 ACKNOWLEGEMENT

❖ Special thanks to CCuB (Université de Bourgogne) HPC for the

computational resources.
❖ Special thanks to the EIPHI Graduate school for this opportunity.

HIKON, O. E