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Molecular Dynamics Molecular Dynamics Lipid Lipid - - Peptide Interactions Peptide Interactions Kevin Kevin Majewski Majewski

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Page 1: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Molecular DynamicsMolecular Dynamics

LipidLipid--Peptide InteractionsPeptide Interactions

Kevin Kevin MajewskiMajewski

Page 2: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

OutlineOutline

• Molecular Simulations• Forces Behind it• The System• Results

Page 3: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Molecular SimulationsMolecular Simulations

GROMACS – Simulation ProgramUniversity of Groningen

Groningen, Netherlands

Use Newton Based Mechanics

Page 4: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Forces/EnergyForces/Energy

• Electro-Static (Non-Bonded Atoms)• Van der Waals (Non-Bonded Atoms)• Bond Stretching (Bonded Atoms)• Bond Angles (Bonded Atoms)• Proper Dihedrals (Bonded Atoms)• Improper Dihedrals (Bonded Atoms)

Page 5: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Forces & Energy (NonForces & Energy (Non--Bonded Atoms)Bonded Atoms)Electro Static (Coulomb) InteractionElectro Static (Coulomb) Interaction

Page 6: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Forces/Energy (NonForces/Energy (Non--Bonded Atoms)Bonded Atoms)Van Van derder Waals InteractionWaals InteractionLennardLennard--Jones PotentialJones Potential

Page 7: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Forces/Energy (Bonded Atoms)Forces/Energy (Bonded Atoms)Bond Stretching (Harmonic)Bond Stretching (Harmonic)

Page 8: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Forces/Energy (Bonded Atoms)Forces/Energy (Bonded Atoms)Bond Angles (Harmonic)Bond Angles (Harmonic)

Page 9: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Forces/Energy (Bonded Atoms)Forces/Energy (Bonded Atoms)Proper Dihedrals (Staggered/Eclipsed)Proper Dihedrals (Staggered/Eclipsed)

Page 10: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Forces/Energy (Bonded Atoms)Forces/Energy (Bonded Atoms)Improper DihedralsImproper Dihedrals

Page 11: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

The SystemThe System

Lipid

1 Peptide ~120ns 2 Peptides ~200ns

Size ~ 28,000 Atoms (far too large for QM~4)

Page 12: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Image of LipidImage of Lipid

Page 13: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Image PeptideImage Peptide

Page 14: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

System 1 Peptide (Time Scale)System 1 Peptide (Time Scale)

T=0ns T=120ns

Page 15: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

System 2 Peptides (Time Scale)System 2 Peptides (Time Scale)

T=0ns T=200ns

Page 16: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Antimicrobial PeptidesAntimicrobial Peptides

Antimicrobial peptides can carry drugs or antibiotics into a bacteria cell to kill the cell

Upon entering cell, cause leakage of vital cell structures

Synthetic peptide has Antimicrobial peptide type properties

Page 17: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

DSSP P1DSSP P1

Page 18: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

DSSP P2DSSP P2

Page 19: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

PeptidePeptideIle-Ile-Ser-Thr-Ile-Gky-Asp-Leu-

Val-Lys-Trp-Ile-Ile-Asp-Thr-Val-Asn-Lys-Phe-Thr-Lys-Lys

LipidCholine group (+)

Phosphorous group (-)Ester GroupTail Oxygen

Tail

Page 20: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

CholineCholine Group (+)Group (+)

Page 21: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Phosphorus Group (Phosphorus Group (--))

Page 22: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Ester Group Ester Group

Page 23: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

AspartateAspartate (Asp) ((Asp) (--) & Lysine (Lys) (+)) & Lysine (Lys) (+)

Page 24: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Minimum Distance P1

Page 25: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Minimum Distance P1Minimum Distance P1

Page 26: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Density P1

Page 27: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Density P2Density P2

Page 28: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Distance Peptide (1)Distance Peptide (1)

Page 29: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Distance Peptide (2)Distance Peptide (2)

Page 30: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Hydrogen BondingHydrogen BondingElectronegative differences (H & O,N,F)Donate & Accept (O,N,F directly connected

to H)Accept (O,N,F exists in molecule)

Page 31: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Hydrogen Bonding P1

Page 32: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Hydrogen Bond (LHydrogen Bond (L--P2)P2)

Page 33: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Hydrogen Bonds LYSHydrogen Bonds LYS--ASP P1ASP P1

Page 34: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Hydrogen Bonds LYSHydrogen Bonds LYS--ASP P2ASP P2

Page 35: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

WhatWhat’’s Next?s Next?

Increase number of peptides in system

Look at longer range of time

Page 36: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Work Cited PageWork Cited PageField, Martin. A Practical Introduction to the Simulation of Molecular

Systems. Cambridge: Cambridge UP, 1999. Print. GROMACS 4th edition ManualHinchliffe, Alan. Molecular Modelling for Beginners. Chichester, West

Sussex, England: Wiley, 2003. Print. McMurry, John. Organic Chemistry. Belmont, CA: Thomson

Brooks/Cole, 2008. Print. Pokorny, Anteje, Harry T. Birkbeck, and Paulo F F Almeida.

"Mechanism and Kinetics of Delta-Lysin Interaction with Phospholipid Vesicles." Biochemistry 41 (2002): 11044-1056. Web.

Shepherd, Craig M., Hans J. Vogel, and Peter D. Tieleman. "Interacions Fo the Designed Antimicrobial Peptide MB21 and Truncated Dermaseptin S3 with Lipid Bilayers: Molecular-dynamics Simulations." Biochem J. 370 (2003): 233-43. Web.

Page 37: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Work Cited ContWork Cited Cont’’ddhttp://www.pumma.nl/index.php/Theory/Potentialshttp://www.physicsofmatter.com/NotTheBook/Talks/Ice/Image7.gifhttp://en.wikipedia.org/wiki/Lipid_bilayerhttp://en.wikipedia.org/wiki/GROMACShttp://www.biology.arizona.edu/biochemistry/problem_sets/aa/aa.htmlhttp://zebu.uoregon.edu/~imamura/122/images/periodic_table.gifhttp://hidra.iqfr.csic.es/man/dlpoly/USRMAN/node49.htmlhttp://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/lipid.htmhttp://www.libertyzone.com/hz-Amino-Acid.html

Page 38: Molecular Dynamics · 2019-05-20 · Molecular Simulations GROMACS – Simulation Program University of Groningen Groningen, Netherlands Use Newton Based Mechanics

Thank YouThank You

• Dr. Lee

• Dr. Davis


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