simulation studies of biomolecules @ soft interfaces : continuing challenge of bridging length-...

Simulation Studies ofSimulation Studies ofBiomolecules @ Soft Interfaces :Biomolecules @ Soft Interfaces :

Continuing challenge of Continuing challenge of bridging length- & bridging length- &

time-scalestime-scales

Third Computational Chemistry Conference on “use of Third Computational Chemistry Conference on “use of computational techniques in chemistry, biology, computational techniques in chemistry, biology,

biochemistry, and materials science” biochemistry, and materials science” SURA NCSA UoK ARL www.2003SURA NCSA UoK ARL www.2003

It gives me great pleasure to talk to you today about research going on in my group at UPenn that is focused on membranes and membrane-bound species.

* DISCLAIMER - This talk contains no equations – theoreticians may find the extensive use of color images offensive

SURA-NCSA-UoK-ARL CCC2003*SURA-NCSA-UoK-ARL CCC2003*

My early computations dealt with ATOMIC systems. But, in the mid-1970’s, computers became more powerful I shifted to MOLECULAR solids & liquids.

Since the 1980’s my research has dealt with simulation algorithms and applications ranging from materials to bio-membranes.

Current interests - ab initio based (DFT) methods for chemical & enzyme reactions and coarse-grain simulations of self-assembling soft matter systems.

In the 1960’s COMPUTATION started to become respectable….

PROLOGUEPROLOGUE

Use computer to follow the motion of a Use computer to follow the motion of a system of atoms or molecules using system of atoms or molecules using principles of physics (Newton, Lagrange, principles of physics (Newton, Lagrange, Feynman) and statistical mechanics Feynman) and statistical mechanics (Onsager, Kubo, van Hove) to go from (Onsager, Kubo, van Hove) to go from trajectories to observables. trajectories to observables.

Interactions can be from empirical Interactions can be from empirical potentials or from quantum mechanics, potentials or from quantum mechanics, often via DFT - Car-Parrinello often via DFT - Car-Parrinello methodology.methodology.

MethodologyMethodology

Biomolecules @ Soft Biomolecules @ Soft InterfacesInterfaces*

Carlos Lopez, Steve Nielsen, Carlos Lopez, Steve Nielsen,

Preston Moore, Robert Doerksen,Preston Moore, Robert Doerksen,

Srinivas Goundla,Srinivas Goundla,

Rosalind Allen, Bin Chen, Rosalind Allen, Bin Chen,

John & Mee ShelleyJohn & Mee Shelley

* * Bridging from atoms to the Bridging from atoms to the mesoscalemesoscale

Infection Pathway of a Virus in a Living Infection Pathway of a Virus in a Living Cell*Cell*

Single-molecule real-time visualization of the infection pathway of single viruses in living cells, each labeled with only one fluorescent dye molecule.

Trajectories show various modes of motion of adeno-associated viruses (AAV) during their infection pathway into living HeLa cells:

(i) Consecutive virus touching at the cell surface and fast endocytosis;

(ii) Free and anomalous diffusion of the endosome and the virus in the cytoplasm and the nucleus; and

(iii) Directed motion by motor proteins in the cytoplasm and in nuclear tubular structures.

* Munich Group Science

Polymersomes (Penn Polymersomes (Penn MRSEC)*MRSEC)*

*Discher, Hammer, Bates (*Discher, Hammer, Bates (ScienceScience 1997)1997)

Nature’s Nanoworld *Nature’s Nanoworld *

*Cell membranes are complex, containing lipids, proteins, cholesterol, carbohydrates, plus actin filements, etc… Design principles for Nature’s devices, plus their self- & supramolecular assembly can yield new materials.

Membranes – A Playground for Membranes – A Playground for

Molecular Dynamics Simulation Molecular Dynamics Simulation

MANY ACHIEVEMENTSMANY ACHIEVEMENTS

MANY ACTIVE GROUPS:MANY ACTIVE GROUPS:

Schulten, Carloni, Sansom,Schulten, Carloni, Sansom,Tielman, Roux, Pastor, etc.Tielman, Roux, Pastor, etc.

M2 pentamer in a lipid bilayer at T=303K

94 DMPC lipids plus5 M2-TM peptides

Channels well-studied Schulten Roux Carloni Sansom Teilman

Ion Channel in a Lipid Bilayer Ion Channel in a Lipid Bilayer ––

n-AChR (M2-TM)n-AChR (M2-TM)

N-terminal intracellular on topN-terminal intracellular on top

Nature’s Ion ChannelsNature’s Ion Channels

Transmembrane – Assembly & Function Difficult with classical MD

Mostly pre-assembled systems Simulated structures Open/Closed?

Gramicidin (Warshel, Roux – Karplus,…) K+ (Carloni, Roux, Tielman, Sansom,…) OMP, Porins (Carloni, Sansom, Schulten,

…)

Design Principles ?Design Principles ?

Carbon Nanotube as Nanosyringe Carbon Nanotube as Nanosyringe ??

G. Hummer, J. Rasaiah, & J.P. NoworytaNature 414, 188-190 (2001)

Tube:13.4 Å long8.1 Å diameter

“We observe pulse like transmission of waterthrough the nanotube…two-state transitions betweenempty and filled states on nanosecond timescale..”

Water in a Water in a

carbon carbon nanotubenanotube

Why Coarse Grain ? *Why Coarse Grain ? *

Atomistic ModelsEmpirical potentials -

local structuresLimited system sizeLimited timescale

**One million lipids / m2

A Coarse-grain Model for Soft

Interfaces

Strategy for Simulations of Advanced MaterialsStrategy for Simulations of Advanced Materials

A Coarse-grain ModelA Coarse-grain Modelfor Soft Interfacesfor Soft Interfaces*

Carlos Lopez, Steve Nielsen, Carlos Lopez, Steve Nielsen,

Preston Moore, Robert Doerksen,Preston Moore, Robert Doerksen,

Srinivas Goundla,Srinivas Goundla,

Rosalind Allen, Bin Chen, Rosalind Allen, Bin Chen,

John & Mee ShelleyJohn & Mee Shelley

* * Bridging from atoms to the Bridging from atoms to the mesoscalemesoscale

From hundreds of From hundreds of atoms to billions - the atoms to billions - the challenge of the challenge of the mesoscalemesoscale

Coarse grain models & soft interfacesCoarse grain models & soft interfaces

Coarse Grain DMPCCoarse Grain DMPC

Choline Head Group

Phosphate Group

Glycerol Groups

Acyl Chains

Chain Ends

Self Assembly of DMPC-Self Assembly of DMPC-CGCG

NVT Ensemble:46 Å X 45 Å X 59 Å 64 DMPC,T: 30°C, 1ns (20fs/step)

MUCH faster thanMUCH faster thanatomistic modelsatomistic models

See JPC 2001See JPC 2001

Coarse Grain Membrane - ResultsCoarse Grain Membrane - Results

J Phys Chem 2001J Phys Chem 2001

DMPC-CG 1024 BilayerDMPC-CG 1024 Bilayer

NPT Ensemble Orthorhombic Cell 1024 Lipids 1 ns (20fs/step) T: 30°C, P: 1atm Equilibration

340psSnapshots of

ConfigurationsComp Phys Comm 2002Comp Phys Comm 2002

Membrane Surface DynamicsMembrane Surface Dynamics

Area: 18nm X 20nm Note Transient Holes P(Blue), N(Orange)

Water Removed for Clarity

Challenges & OpportunitiesChallenges & Opportunities

Nothing amuses more harmlessly than Nothing amuses more harmlessly than computation, and nothing is oftener computation, and nothing is oftener applicable to real business and speculative applicable to real business and speculative inquiry.inquiry.

A thousand stories which the ignorant tell and A thousand stories which the ignorant tell and believe die away at once when the computist believe die away at once when the computist takes them in his grip.takes them in his grip.

Samuel JohnsonSamuel Johnson: 1709-1784: 1709-1784

Nanosyringe - Nature’s Nanosyringe - Nature’s DesignDesign

Protein Helix BundleProtein Helix Bundle Coarse Grain TubeCoarse Grain Tube

Pore diameter sized to accommodate “water”

Hydrophobic

NanosyringeNanosyringe

CG-tube mimic of nanotube or viral channel

insertion into membrane

NPT-MD 30°C, 1atm

Transmembrane Transmembrane NanotubeNanotube

CG-tube mimic of membrane-bound

nanotube or viral channel

NPT-MD 30°C, 1atm

Hydrophobic NanotubeHydrophobic Nanotube

Tube gets blocked with lipids after 15,000 steps

First lipid inserted at 5000 steps (10 ns ?)

Tube tilts to fit bilayer

Q: How to make a nanosyringe…? A: Nature uses

hydrophilic caps

CG nanotube (nanosyringe) in CG DMPCCG nanotube (nanosyringe) in CG DMPC

Nanosyringe - Nature’s Nanosyringe - Nature’s DesignDesign

Protein Helix BundleProtein Helix Bundle Coarse Grain TubeCoarse Grain Tube

Hydro - philic

Pore diameter sized to accommodate “water”

Hydro-phobic

Insertion into MembraneInsertion into Membrane

Start outside the membrane (water not shown)

Tube inserts into the membrane, favoring hydrophobic interactions

Insertion into MembraneInsertion into Membrane

Tube drags lipids into the middle of the bilayer. Then “sees” the other side of the membrane.

Tube straightens up and then remains in this position through the run.

Nature’s DesignNature’s Design

CG tube in CG tube in DMPCDMPC:

“Water” goes through tube

NPT 30°C, 1atm

PoreationSnapshot of tube in CG Snapshot of tube in CG DMPCDMPC Two waters are present in the tube. Lipids removed from bottom leaflet to reveal the tube/lipid interface

Insertion into MembraneInsertion into Membrane

Antibacterial Peptide Molecules

Common traits of AB peptides:Common traits of AB peptides: Relatively short peptides.Relatively short peptides. Charged and hydrophobic groups segregate Charged and hydrophobic groups segregate

onto opposite sides of a structure.onto opposite sides of a structure. Believed to kill cells by disrupting Believed to kill cells by disrupting

membranes.membranes.

Q: De novo design of biomimetic antimicrobial molecules?

Anti-microbial Peptide Anti-microbial Peptide MimicsMimics

Bin Chen, Carlos Lopez,Bin Chen, Carlos Lopez,Robert Doerksen, Bill Robert Doerksen, Bill

DeGradoDeGrado

HN

O O

HN

S

R

n

Polyarylamide n = 3Polyarylamide n = 3

1

MagaininMagaininMimicMimic

de novo design and synthesis of antimicrobialsde novo design and synthesis of antimicrobials

• Gradient-corrected density Gradient-corrected density functional theory calculationsfunctional theory calculations

• Atomistic molecular dynamics and Atomistic molecular dynamics and Monte Carlo calculationsMonte Carlo calculations

• Coarse-grained molecular dynamics Coarse-grained molecular dynamics simulationssimulations

Build initial target

polymer backbones

A schematic flow-chart showing the whole design process

Search low-energy conformations,parameterize

torsion potentials

Test force fields, investigate the polymer’s conformations at vacuum

and interfaces and its hydrophobicity, select the potential target

Evaluate the polymer’s antibacterial activity and

other important properties, determine the final target

Provide microscopic-level insights on the antibacterial mechanisms and

guidelines for improving the antibacterial polymer

Density functional theory calculations

Monte Carlo andmolecular dynamics

Experimental synthesis and assay tests

molecular dynamics simulations at membrane/water interface

DeNovo Designed Anti-microbial PolymersDeNovo Designed Anti-microbial Polymers

0

10

20

30

40

50

60

70

0 60 120 180 240 300 360

X : HX : S-CH

3

E [

kJ

/mo

l]

[degree]

HN

O

X

HN

O O

HN

S

R

n

PNAS 2002PNAS 2002

Antibacterial Activity of Antibacterial Activity of PolyamidesPolyamides

H N

O O

H N

S

NH2

n

n MIC E. coliE. coli K. pneumoniaeK. pneumoniae B. subtilisB. subtilis 2 19 66 12 3 <19 N/A 19 4 7.5-15 31-50 16 6 >500 250 >500

(AB)(AB)nn

0

20

40

60

80

100

0 50 100 150 200 250 300

Le

ak

ag

e F

rac

ton

(%

)Time (s)

15 µg/mL

7.5 µg/mL

3.75 µg/mL

1.88 µg/mL

A Coarse-grain Simulation Model A Coarse-grain Simulation Model for Probing Mechanisms of for Probing Mechanisms of

Anti-bacterial ActionAnti-bacterial Action*

Srinivas Goundla, Carlos Lopez, Steve NielsenSrinivas Goundla, Carlos Lopez, Steve Nielsen

Michael L. Klein*

Center for Molecular Modeling

University of Pennsylvania

CG-AB with CG LipidCG-AB with CG Lipid

Approximation to AB: Use existing CG

types to emulate the AB molecule.

AB Dimer in CG LipidAB Dimer in CG Lipid

Peptide mimics are adsorbed

at the lipid surface.

Peptide mimics first enter bilayer and eventually settle under the head groups

AcknowledgementsAcknowledgements

Thanks to friends & Thanks to friends & collaboratorscollaborators

NPACI @ NCSA, SDSC, PSCNPACI @ NCSA, SDSC, PSC

NSFNSF NIHNIH

Many thanks Many thanks for inviting me tofor inviting me to

talk to you! talk to you!

ENDEND

Challenges & OpportunitiesChallenges & Opportunities

It will surely come to the desktop…It will surely come to the desktop…

Phenomena at longer-length and time Phenomena at longer-length and time scales will be accessible…scales will be accessible…

HPC will participate in discovery of HPC will participate in discovery of advanced materials and more…advanced materials and more…

Terascale Computing has arrivedTerascale Computing has arrived

Challenges & OpportunitiesChallenges & Opportunities

Nothing amuses more harmlessly than Nothing amuses more harmlessly than computation, and nothing is oftener computation, and nothing is oftener applicable to real business and speculative applicable to real business and speculative inquiry.inquiry.

A thousand stories which the ignorant tell and A thousand stories which the ignorant tell and believe die away at once when the computist believe die away at once when the computist takes them in his grip.takes them in his grip.

Samuel JohnsonSamuel Johnson: 1709-1784: 1709-1784