Construction and Molecular Dynamics 

of a Nanodisc for Membrane Protein 

Simulation

Ryan Franklin 

Mentored by Joseph Curtis
Overview Figure 1. Cell membrane

(Figure 1) http://www.fitwit.com/blog/2014/03/19/guest-post-good-fats-healthy-cell-structure/

(Figure 3) http://biology.usf.edu/cmmb/undergrad/bio/ 

(Figure 4) http://www.silhouettegraphics.net/man-running-silhouette/ 

Single lipid

Figure 3. 

Biological cells

Figure 4.

(-)
Prions

Figure 5. http://srxawordonhealth.com/tag/misfolded-proteins/

Figure 6. http://truthfrequencyradio.com/neurosurgery-patients-exposed-to-human-mad-cow-disease-in-n-h/ 

Figure 5. Misfolding of a protein Figure 6. Mad cow disease in humans

• Misfolded proteins can be toxic, or in some cases may behave like a disease

• These harmful misfolded proteins are prions

• Prions are associated with various diseases, such as mad cow disease (infectious and fatal 

neurodegenerative disease) 
Understanding Prions

• To prevent and study these harmful prions, the structure of properly 

folded proteins must be determined

Proper Structure

Misfolded Structure

Prevent Harmful Prions Prevent Prion Diseases

Harmful Function

Proper Function
Figure 5. MSP1E3 Nanodisc with MSP and bR

transmembrane protein

(Figure 5) Timothy H. Bayburt, Stephen G. Sligar, Membrane protein assembly into Nanodiscs, FEBS 

Letters, Volume 584, Issue 9, 3 May 2010, Pages 1721-1727, ISSN 0014-5793

Overview Two MSP1D1 nanodiscs on top. MSP belts are 

blue and orange

• Proteins are often insoluble in water, 

making crystallization and structure 

determination difficult

• Ongoing research to correlate structure 

to function

• Nanodiscs are used to stabilize several 

varieties of membrane proteins

• Transmembrane proteins 

• G-protein coupled receptors

• Cytochromes

• Blood clotting cofactors Figure 2. Cell membrane
Overview

Figure 2.

http://chronopause.com/chronopause.com/index.php/2011/02/23/does-personal-identity-survive-cryopreservation/

• Membrane proteins denature when removed from their native environment

• Proteins must retain structural integrity for experimental studies to have biological significance

• Small-angle neutron scattering (SANS) and contrast variation are used to determine 

shape/structure

• Computer-generated molecular dynamics simulations are used to validate experimental results

example MD simulation
Basic SANS Figure 3

(Figure 3) Small-Angle Neutron Scattering Study of Protein Crowding in Liquid and Solid Phases: Lysozyme in Aqueous Solution, Frozen Solution, and Carbohydrate Powders

Joseph E. Curtis, Hirsh Nanda, Sheila Khodadadi, Marcus Cicerone, Hyo Jin Lee, Arnold McAuley, and Susan Krueger

The Journal of Physical Chemistry B 2012 116 (32), 9653-9667

Determine 

scattering profile 

by radially 

averaging data

Structural conclusions based on the 

neutron scattering profile

Inverse space, q = 

2ππ

rr
Contrast Variation

Example for Visible Light

Glass Rod in Air

Glass Rod in 

Silicon Oil
Contrast Variation

CD2

Deuterated Lipid Head Group

CONTRAST

∆ρ

Lipid Head Group

CH2

a solvent

b
Contrast Variation

CD2

Deuterated Lipid Head Group

CONTRAST

∆ρ

Lipid Head Group

CH2

a solvent

b
Contrast Variation and MSP

• Small-angle neutron scattering (SANS) 

interacts directly with the nucleus of the 

atoms being studied

• Hydrogen and deuterium coherent scattering 

lengths

• Contrast variation substitutes deuterium for 

hydrogen to change the scattering length 

density and differentiate two or more 

structures

Membrane 

Scaffold Protein 

(MSP)

Lipid Protein

top down view

side view

90°
Styrene/maleic acid polymer (SMA) scattering length densities match DMPC lipid, 

leaving a clearly defined protein

SMA

DMPC Protein

(Figure 1) Jamshad, M.; Grimard, V.; Idini, I.; Knowles, T.; Dowle, M.; Schofield, N.; Sridhar, P.; Lin, Y.; 

Finka, R.; Wheatley, M.; Thomas, O.; Palmer, R.; Overduin, M.; Govaerts, C.; Ruysschaert, J.; Edler, K.; 

Dafforn, T. Nano Res. 2014, 8, 774-789.

Figure 1 DMPC Lipid

(-)
Overview

• We created a model of a nanodisc wrapped by SMA polymer

• Force field parameters for SMA did not exist, so we created them

• Validated our parameters by studying lone polymers

• Constructed models of lipid systems to study interaction with SMA polymer

• Calculated SANS profiles for SMA nanodiscs
Force Field Parameterization

• CGENFF

• Developed through collaboration and funded by the NSF

• Generated a parameter file from a given starting structure through analogy with 

known structures

• Provided a strong starting point for quantum mechanical validation of the 

parameterization (ongoing)

Maleic acid .mol2 structure Carboxylate structure Styrene .mol2 structure
Constructing SMA Polymer

.mol2 trimer constructed in maestro 30 residue styrene based polymer

• Internal coordinates written based on minimized structures to define the individual 

styrene/maleic acid residues

• Python script defined the sequence and modified dihedrals between residues to 

construct a pre-wrapped starting structure

• Five trimers: SSS (35%), MSS/SSM (54%), MSM (11%), and SMS (Never MM)

minimized trimer
Small DMPC 

block

Lipid rod 

from 

wrapped 

small block

Study 

styrene

based 

polymer

Study 

alternating 

polymer

Study 

random

polymer

Four block 

large system 

Trimmed 

DMPC 

cylinder

Wrapped 

DMPC 

nanodiscs

Main Research Paths for DMPC bilayer

35% SSS,

54% MSS/SSM, 

11% MSM

Poly SSS

Poly MSM
Small DMPC 

block

Lipid rod 

from 

wrapped 

small block

Study 

styrene

based 

polymer

Study 

alternating 

polymer

Study 

random

polymer

Four block 

large system 

Trimmed 

DMPC 

cylinder

Wrapped 

DMPC 

nanodiscs

Main Research Paths for DMPC bilayer

35% SSS,

54% MSS/SSM, 

11% MSM

Poly SSS

Poly MSM
Lipid Rod

• We created a lipid rod from the small DMPC block

• This enabled us to analyze the polymer interaction with the bilayer

• Simulation cell wrapped to create the properties of a rod while retaining short 

computation time

Replicate Interaction

Polymer

DMPC

∞ ∞

Y- y+

X- (W)

Z- (W)

Z+ (W)

X+ (W)

Small DMPC 

block

Lipid rod 

from 

wrapped 

small block

Study 

styrene

based 

polymer

Study 

alternating 

polymer

Study 

random

polymer

Four block 

large system 

Trimmed 

DMPC 

cylinder

Wrapped 

DMPC 

nanodiscs

Main Research Paths for DMPC bilayer

35% SSS,

54% MSS/SSM, 

11% MSM

Poly SSS

Poly MSM
Bilayer Interaction with Pure Styrene Polymer

• Initial simulations of the small 

block used pure styrene 

polymers to confirm 

intercalation with the lipid tails

• Small box model was limited 

by harmonic constraints on the 

lipids

• Pure styrene residue chain 

strongly interacts since it is not 

amphipathic yet

0.2 ns NPT run
Small DMPC 

block

Lipid rod 

from 

wrapped 

small block

Study 

styrene

based 

polymer

Study 

alternating 

polymer

Study 

random

polymer

Four block 

large system 

Trimmed 

DMPC 

cylinder

Wrapped 

DMPC 

nanodiscs

Main Research Paths for DMPC bilayer

35% SSS,

54% MSS/SSM, 

11% MSM

Poly SSS

Poly MSM
Small DMPC 

block

Lipid rod 

from 

wrapped 

small block

Study 

styrene

based 

polymer

Study 

alternating 

polymer

Study 

random

polymer

Four block 

large system 

Trimmed 

DMPC 

cylinder

Wrapped 

DMPC 

nanodiscs

Main Research Paths for DMPC bilayer

35% SSS,

54% MSS/SSM, 

11% MSM

Poly SSS

Poly MSM
0.2 ns random composition orientation 
Small DMPC 

block

Lipid rod 

from 

wrapped 

small block

Study 

styrene

based 

polymer

Study 

alternating 

polymer

Study 

random

polymer

Four block 

large system 

Trimmed 

DMPC 

cylinder

Wrapped 

DMPC 

nanodiscs

Main Research Paths for DMPC bilayer

35% SSS,

54% MSS/SSM, 

11% MSM

4 blocks merged 

Poly SSS

Poly MSM
Constructing the Lipid Bilayer

general large bilayer equilibration

1, NVT

Fixed lipid heads, 

harmonic water 

constraints

2, NPT 

Harmonic lipid heads and 

water constraints, 

keep_water_out.tcl force 

bias

3, NPT

Harmonic lipid head 

constraint, 

keep_water_out.tcl force 

bias

4, NPT

All constraints removed

(crashed timestep 11,400)

5, NPT

(restart) Increase Langevin 

Damping

6, NPT

Decrease Langevin damping,

do production run

• Following design process from the small 

block we made the full nanodisc bilayer

• The solvent (water) no longer interfered, 

so harmonic constraints were removed

• Packing density and dimensions match 

experimental results

Trimmed bilayer cylinder (blue) from equilibrated patch (VDW)
Small DMPC 

block

Lipid rod 

from 

wrapped 

small block

Study 

styrene

based 

polymer

Study 

alternating 

polymer

Study 

random

polymer

Four block 

large system 

Trimmed 

DMPC 

cylinder

Wrapped 

DMPC 

nanodiscs

Main Research Paths for DMPC bilayer

35% SSS,

54% MSS/SSM, 

11% MSM

1, NVT

4 blocks merged 

Poly SSS

Poly MSM
Small DMPC 

block

Lipid rod 

from 

wrapped 

small block

Study 

styrene

based 

polymer

Study 

alternating 

polymer

Study 

random

polymer

Four block 

large system 

Trimmed 

DMPC 

cylinder

Wrapped 

DMPC 

nanodiscs

Main Research Paths for DMPC bilayer

35% SSS,

54% MSS/SSM, 

11% MSM

1, NVT 2, NPT

4 blocks merged 

Poly SSS

Poly MSM
Small DMPC 

block

Lipid rod 

from 

wrapped 

small block

Study 

styrene

based 

polymer

Study 

alternating 

polymer

Study 

random

polymer

Four block 

large system 

Trimmed 

DMPC 

cylinder

Wrapped 

DMPC 

nanodiscs

Main Research Paths for DMPC bilayer

35% SSS,

54% MSS/SSM, 

11% MSM

1, NVT 2, NPT

3, NPT

4 blocks merged 

Poly SSS

Poly MSM
Small DMPC 

block

Lipid rod 

from 

wrapped 

small block

Study 

styrene

based 

polymer

Study 

alternating 

polymer

Study 

random

polymer

Four block 

large system 

Trimmed 

DMPC 

cylinder

Wrapped 

DMPC 

nanodiscs

Main Research Paths for DMPC bilayer

35% SSS,

54% MSS/SSM, 

11% MSM

1, NVT 2, NPT

3, NPT

4, NPT

4 blocks merged 

Poly SSS

Poly MSM
Small DMPC 

block

Lipid rod 

from 

wrapped 

small block

Study 

styrene

based 

polymer

Study 

alternating 

polymer

Study 

random

polymer

Four block 

large system 

Trimmed 

DMPC 

cylinder

Wrapped 

DMPC 

nanodiscs

Main Research Paths for DMPC bilayer

35% SSS,

54% MSS/SSM, 

11% MSM

1, NVT 2, NPT

3, NPT

5, NPT 4, NPT

4 blocks merged 

Poly SSS

Poly MSM
Small DMPC 

block

Lipid rod 

from 

wrapped 

small block

Study 

styrene

based 

polymer

Study 

alternating 

polymer

Study 

random

polymer

Four block 

large system 

Trimmed 

DMPC 

cylinder

Wrapped 

DMPC 

nanodiscs

Main Research Paths for DMPC bilayer

35% SSS,

54% MSS/SSM, 

11% MSM

1, NVT 2, NPT

3, NPT

5, NPT 4, NPT

6, NPT

4 blocks merged 

Poly SSS

Poly MSM
Small DMPC 

block

Lipid rod 

from 

wrapped 

small block

Study 

styrene

based 

polymer

Study 

alternating 

polymer

Study 

random

polymer

Four block 

large system 

Trimmed 

DMPC 

cylinder

Wrapped 

DMPC 

nanodiscs

Main Research Paths for DMPC bilayer

35% SSS,

54% MSS/SSM, 

11% MSM

1, NVT 2, NPT

3, NPT

5, NPT 4, NPT

6, NPT

4 blocks merged 

Poly SSS

Poly MSM
Small DMPC 

block

Lipid rod 

from 

wrapped 

small block

Study 

styrene

based 

polymer

Study 

alternating 

polymer

Study 

random

polymer

Four block 

large system 

Trimmed 

DMPC 

cylinder

Wrapped 

DMPC 

nanodiscs

Main Research Paths for DMPC bilayer

35% SSS,

54% MSS/SSM, 

11% MSM

1, NVT 2, NPT

3, NPT

5, NPT 4, NPT

6, NPT

4 blocks merged 

Poly SSS

Poly MSM
Small DMPC 

block

Lipid rod 

from 

wrapped 

small block

Study 

styrene

based 

polymer

Study 

alternating 

polymer

Study 

random

polymer

Four block 

large system 

Trimmed 

DMPC 

cylinder

Wrapped 

DMPC 

nanodiscs

Main Research Paths for DMPC bilayer

35% SSS,

54% MSS/SSM, 

11% MSM

1, NVT 2, NPT

3, NPT

5, NPT 4, NPT

6, NPT

4 blocks merged 

Poly SSS

Poly MSM
Wrapped Nanodiscs

MSP wrapped nanodisc SMA wrapped nanodisc (in progress)
Ongoing Work

• Various known proteins need to be simulated with our nanodisc

• Theoretical scattering profiles and contrast variation from the sample proteins 

should match known

• Quantum mechanical refinement of parameterization

• Validate the structure of the lipid by comparing the thickness of the bilayer and the 

surface per lipid head group

• Continue with the lipid rod/polymer interaction computational experiments
CHE-1265821

Supported via CCP-SAS a joint EPSRC (EP/K039121/1) and NSF (CHE-1265821) grant

DMR-0944772

www.ccpsas.org

Dr. Joseph Curtis

Dr. Julie Borchers

Dr. Susan Krueger