Han, Eol

Lee, Hwankyu

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98a Sunday, February 16, 2014518-Pos Board B273
Role of M2 Influenza Protein on Viral Budding and Scission
Eduardo Mendez-Villuendas, Peter Tieleman.
Biological Sciences, University of Calgary, Calgary, AB, Canada.
M2 is a pH-dependent matrix protein from influenza virus widely known for its
role in viral uncoating and the target of the amantadine flu drug that prevents
proton transport. An additional role played by M2 relies on collective effects
where clusters of M2-homotetramer proteins have been hypothesized to induce
local membrane curvature effects (Rossman et al., Cell 142, pp. 902-913,
2010).
We use molecular dynamics simulations with the MARTINI coarse grained
parametrization to study a system comprised by two model membranes linked
by an hour-glass shaped structure. We study the role played by M2 homote-
tramers in the scission step, leading to lipid-bilayer separation. The geometry
of the model and the membrane-lipid interaction details are further used to
adjust parameters on a Helfrich-like functional in order to propose a minimal
model for viral scission at the mesoscopic scale.
519-Pos Board B274
Comparative Analysis of Inorganic Phosphate Binding in a Synthetic and a
Native P-Loop Peptide Using Molecular Dynamics Simulations
Mathias F. Gruber1, Elizabeth Wood1, Andrea Bordoni1, Henrik Bohr1,
Per Amstrup Pedersen2, Claus He´lix-Nielsen1.
1Physics, Technical University of Denmark, Copenhagen N, Denmark,
2Molecular Integrative Physiology, University of Copenhagen, Copenhagen
N, Denmark.
Binding of anions by proteins is a topic of great interest, the binding being due
to interactions either with the protein’s positively charged side chains and/or
with the main chain. In particular the phosphate anion is essential for a large
number of functions and pathways within cells, and the specific binding of
phosphate anion has been widely studied. However, investigation of the struc-
tural features in phosphate binding sites and the mechanisms for phosphate
binding is still a field that warrants more research.
One of the most common ways in which proteins bind to phosphate is via a
highly conserved consensus sequence that folds into what is known as a P-
loop. Here, we use molecular mechanics and quantum mechanical calcula-
tions to characterize interactions of the phosphate anion with 1) a native
P-loop whose structure available in the PDB database (1MAB), and 2) a
synthetic peptide designed to bind phosphate by mimicking the P-loop func-
tion. Whereas the structure of the native P-loop is fairly well characterized
and restricted within the 1MAB structure, the synthetic peptide explores a
larger conformational space - yet the synthetic peptide is able to bind
phosphate.
Specifically we investigate the structural properties and the conformational
space of both the peptides, we characterize how they interact with phosphate,
and we examine the mechanism by which the peptides fold into the P-loop
structure and bind phosphate.
520-Pos Board B275
Computational Study of Transmembrane Helix-Helix Interactions in
Model Peptides Derived from the DesK Minimal Sensor
Moussatova Anastassiia1, Wassenaar A. Tsjerk2, Cybulski E. Larisa3,
Ballering Joost4, Killian J. Antoinette4, Tieleman D. Peter1.
1Biological Sciences, University of Calgary, Calgary, AB, Canada,
2Univeristy of Groningen, Groningen, Netherlands, 3Universidad Nacional
de Rosario, Rosario, Argentina, 4Utrecht University, Utrecht, Netherlands.
DesK is a bacterial transmembrane protein that acts as a molecular switch to
regulate membrane fluidity as a function of temperature change. The full func-
tion of DesK has been experimentally modeled by a chimeric construct, de-
nominated minimal sensor (MS), consisting of a single transmembrane (TM)
helix. Multiple mutants based on the TM part of DesK-MS have been reported,
suggesting that DesK is sensitive to changes in membrane thickness as a result
of changes in temperature. The current view of DesK-MS signaling mechanism
points towards formation of a dimer capable of switching its conformation de-
pending on the temperature.
In this study we investigate the molecular details of the functioning of the
DesK-MS using experimentally developed model peptides of the TM part
only, both the wild type and some of its mutants. We employ a method recently
developed in our group for exploring the energy landscape of helix-helix inter-
actions in the membrane environment, which allows high throughput screening
of trans-membrane helix dimers. In order to gain more insight into the interac-
tions between the dimers and their lipid environment, a multiscale approach is
used. The results presented here are compared to the available experimental
data and provide basis for further exploration of the molecular basis of the
switch mechanism in DesK-MS.521-Pos Board B276
Charged Protein-Lipid Interactions in Bilayers with Wide-Ranging
Thickness
Peiran Chen1, Igor Vorobyov1, Toby W. Allen1,2.
1Chemistry, University of California Davis, Davis, CA, USA, 2School of
Applied Sciences & Health Innovations Research Institute, RMIT University,
Melbourne, Australia.
Charged amino acids play important roles inmembrane protein structure and func-
tion. All-atommolecular dynamics (MD) studies have previously been applied to
investigate themechanisms bywhich charged groupsmove through lipid bilayers,
but have not fully explored thewide range ofmembrane topologies thatmay influ-
ence charge transport. Here we have performed simulations of the arginine (Arg)
side chain analog, MguanHþ, moving across bilayers of mono-unsaturated phos-
phatidylcholine (PC)with 14-24 carbon tails,with andwithout cholesterol (in a 2:1
lipid:cholesterol ratio), generating hydrophobic thickness increasing systemati-
cally from 24 to 42 Angstrom.We demonstrate that free energies grow in propor-
tion to membrane thickness due to an ion-induced defect mechanism, where the
presence of the ion leads tomembrane deformations and sharp free energy barriers
ranging from 14 kcal/mol in D14:1PC to 40 kcal/mol in D24:1PCþcholesterol.
Our findings provide a deeper understanding of membrane charge transport phe-
nomena, including uncatalyzed ion permeation and the actions of membrane-
active charged peptides for a range of membrane compositions.
522-Pos Board B277
Capturing Spontaneous Binding of Human Islet Amyloid Polypeptide to
Anionic Membranes using a Highly Mobile Membrane Mimetic Model
Katrine K. Skeby1, Emad Tajkhorshid2, Schiøtt Birgit1.
1Department of Chemistry, Interdisciplinary Nanoscience Center (iNANO),
Center for Insoluble Protein Structures (inSPIN), Aarhus University, Aarhus
C, Denmark, 2Department of Biochemistry, Beckman Institute, Urbana-
Champaign, IL, USA.
Human islet amyloid polypeptide (hIAPP) aggregates and forms amyloid fibrils
in the pancreas of patients with type2 diabetes. Anionic membranes bind hIAPP
and accelerate the fibril formation. During this process, hIAPP disrupts the
membrane, a toxic process that has been associated with the N-terminal 19 res-
idues and proposed to lead to the destruction of the insulin-producing b-cells in
the pancreas. The mechanism by which the membrane is disrupted is therefore
key to our understanding of toxicity of hIAPP, and to design of effective disease
modifying treatments.
Employing molecular dynamics (MD) simulations, we have investigated the
molecular events key to hIAPP binding to anionic phospholipid bilayers. The
diffusion of lipids in conventional membrane models is too slow to allow for
hIAPP-membrane binding on the time-scale feasible with conventional MD
simulations. In order to overcome the slow diffusion of lipids in conventional
membranes which might not allow for adequate sampling of the binding of hI-
APP binding to the membrane, we have employed a highly mobile membrane
mimetic (HMMM) model.
Multiple independentMDsimulations, amounting to 1.2ms, both for theN-termi-
nal 19-residue peptide, and for the full (37-residue) hIAPP, resulted in sponta-
neous binding to mixed anionic/zwitterionic HMMM membranes. Initial
contacts between the peptide and lipids, which form rapidly (within the first 10
ns of the simulations), are mediated by a group of positively charged residues,
Lys1, Arg11, and His18, indicating that the N-terminal part of hIAPP is respon-
sible for its interactionwith anionicmembranes. These simulations haveprovided
anunprecedented level of statistic on lipid-protein interaction for hIAPPpeptides,
characterizing residues and lipid chemical groups key for bindig and interaction,
as well as the structure and dynamics of the peptide in its membrane-bound form.
523-Pos Board B278
Molecular Dynamics Studies of PEGylated Antimicrobial Peptides with
Lipid Bilayers
Eol Han, Hwankyu Lee*.
Department of Chemical Engineering, Dankook University, Yongin,
448-701, South Korea.
*Correspondence: leeh@dankook.ac.kr
We performed all-atom molecular dynamics (MD) simulations of polyethylene
glycol (PEG)-graftedmagainin 2 and tachyplesin Iwith lipid bilayers. In the sim-
ulations of PEGylated magainin 2 and tachyplesin I in water, both peptides are
wrapped by PEG chains because of the interaction between oxygens of PEGs
and the cationic residues of peptides. The a-helical structure of PEGylated mag-
ainin 2 is broken, while b-sheet of PEGylated tachyplesin I keeps stable, similar
to the structural behavior of unPEGylated peptides, in agreement with experi-
ments. Simulations of PEGylated peptides with lipid bilayers show that PEG
chains block the electrostatic interaction between cationic residues of peptides
and anionic phosphates of lipids, leading to the less binding of the peptide to
the bilayer surface, which is observed more significantly for magainin 2 than
Sunday, February 16, 2014 99afor tachyplesin I. Since the random-coiled magainin 2 can be more completely
covered by PEGs than does the b-sheet tachyplesin I, the PEGylation effect on
the decreased binding is larger for magainin 2, showing the dependence of PE-
Gylation on the peptide structure. These results qualitatively support that
PEGylated magainin 2 and tachyplesin I have the different extents of the
membrane-permeabilizing activity on lipid bilayer surface.
524-Pos Board B279
Double-Belt a Novel Structure of Membrane Pore
Robert Vacha1, Daan Frenkel2.
1Masaryk University, Brno, Czech Republic, 2University of Cambridge,
Cambridge, United Kingdom.
Amphiphilic proteins andpeptides can induce formation of stable andmetastable
pores in phospholipid membranes, which has been associated with toxicity or
antimicrobial activity. Using coarse-grained simulations we have studied pep-
tide orientation within the pores and have found that peptides can be oriented
perpendicular, parallel, or tilted with respect to the membrane plane. The orien-
tation depends on the length of the peptide and its hydrophobicity distribution,
which we rationalized in terms of the hydrophobic mismatch. Apart from
well-known barrel-stave or toroidal pores our simulations suggest a novel ’dou-
ble-belt’ pore structure, where peptides within the membrane pore are oriented
parallel to the membrane plane. This result
was verified usingmore detailed simulations
with the MARTINI force field, where the
double-belt structure was stable in micro-
second time scale of our simulation.525-Pos Board B280
Interaction of the Inward Rectifier Potassium Channel Kir 2.2 with Phos-
phatidylserine
Mercedes Alfonso Prieto, Lucie Delemotte, Michael L. Klein.
Institute for Computational Molecular Science, Temple University,
Philadelphia, PA, USA.
Inward-rectifier Kþ (Kir) channels are ion channels that transport potassium
into the cell. They are essential to maintain the resting membrane potential
and to regulate the action potential duration in excitable cells [1]. As a conse-
quence, Kir mutations result in several diseases, such as periodic paralysis or
cardiac arrhythmia [1, 2].
The activity of Kir channels is regulated by phosphatidylinositol-(4,5)-bisphos-
phate (PIP2), a negatively charged phospholipid that has been recognized as one
of the major regulators of membrane excitability [2]. Moreover, it has been
suggested that Kir activation is not only regulated by PIP2, but it has a second-
ary, non-specific requirement for other anionic phospholipids [3].
Here we have investigated the interaction of phosphatidylserine (PS) with Kir
2.2 by means of all-atom molecular dynamics (MD). Simulations have been
performed on both the apo and PIP2-bound states of the channel [4], embedded
in a POPS membrane in the presence of KCl. These trajectories reveal the key
protein residues interacting with POPS, complementing previous docking [3]
and coarse-grain [5] studies. Furthermore, they suggest that the Kir 2.2-
POPS interactions drive the cytoplasmic domain closer to the membrane and
help to pre-assemble the PIP2 binding site. In other words, our simulations pro-
vide a molecular picture of the sensitized state proposed by Nichols and co-
workers to explain the synergistic effect of anionic phospholipids [3].
[1] Physiol. Rev. 90:291-366 (2010).
[2] Pflugers Arch. 460:321-341 (2010).
[3] (a) Biophys. J. 100:620-628 (2011). (b) J. Biol. Chem. 288:16726-16737
(2013). (c) Biophys. J., 104:433a (2013).
[4] (a) Science, 326:1668-1674 (2009). (b) Nature (Letter), 477:495-499 (2011)
[5] Biochemistry, 52:279-281 (2013).
526-Pos Board B281
Permeation of Lipidated Protein in Bilayer using Unbiased Simulations
Reveals Signature Motif for Protein-Membrane Binding
Lipi Thukral1, Durba Sengupta2, Rajesh S. Gokhale1.
1CSIR- Institute of Genomics and Integrative Biology, New Delhi, India,
2CSIR- National chemical laboratory, Pune, India.
Structural and dynamic reorganization of membrane domains by proteins is a
central theme in many biological processes. Eukaryotic cells possess potential
regulatory mechanisms to mediate many of its protein-membrane interactions
in form of lipid-modified proteins. Two forms of these proteins exist; cytosolic
conformers and functional membrane bound complexes. At present, there are
many questions that remain to be answered with regard to the molecular mech-
anism of interaction of lipidated proteins with membrane that generates a
trigger for physiological response, only upon membrane binding.
A particularly exciting area of membrane trafficking, autophagy, has been
receiving increasing attention. It is a cellular degradative process that involvesthe formation of autophagosome, a specialized vesicle to deliver the dispensable
cellular cargo to the lysosome.During initiation of autophagy, key regulator pro-
tein, LC3-I (cytosolic form) is conjugated reversibly to phosphotidylethanol-
amine (PE) resulting in a nonsoluble form of LC3 that stably associates with
the autophagosomal membrane. The present work reports partitioning of PE
chain of LC3 in bilayer usingMARTINI force field based coarse grainmolecular
dynamics simulations.
Spontaneous insertion of PE chain at microseconds timescale is observed in
fourteen out of fifteen trajectories. This unbiased insertion of lipidated protein
reveals a novel insertion pathway through an arginine rich patch that drives the
insertion of PE chain. Interestingly, membrane curvature properties reveal var-
iations in spontaneous curvature of the membrane, confirming the role of LC3
in forming a vesicle during autophagy. This first unbiased study of active inser-
tion of a lipid chain provides future avenues to investigate detailed regulatory
aspects of this phenomenon using experimental techniques.
527-Pos Board B282
Structural Basis of Lipid Exchange in the Oxysterol-Binding Protein Ho-
mologue (OSH) Family
Stefano Vanni, JoachimMoser, von Filseck, BrunoMesmin, Bruno Antonny,
Guillaume Drin.
Institut de PharmacologieMole´culaire et Cellulaire, CNRS,Valbonne, France.
Oxysterol-binding proteins, long known to be involved in the non-vesicular
transport of sterol, have recently been shown to also transfer glycerophospho-
lipids, such as phosphatidyl-inositol-4-phosphate (PI4P) and phosphatidyl-
serine (PS) between membranes.
Using a combination of atomistic molecular dynamics simulations and in vitro
lipid transport assays, we characterized the structural determinants that regulate
the extraction and release of different lipids by the various Osh proteins.
Our results define how distinct lipid-binding modes govern the ability of Osh
proteins to transport or exchange lipids between organelles.
528-Pos Board B283
Study of the Mecanism of Action of a Hybrid Peptide in POPG:POPC
Bilayers
Gabriel C. Da Hora, Thereza Ame´lia Soares.
Departament of Fundamental Chemistry, Federal University of Pernambuco,
Recife - Pernambuco, Brazil.
A hybrid peptide sequence has been synthesized from the antimicrobial peptides
pediocin A and plantaricin 149A. Previous studies of circular dichroism and fluo-
rescence spectroscopic studies have shown a disordered to ordered conforma-
tional transition of the peptide upon binding to POPG but not to POPC. Further,
single vesicle experiments under optical microscopy observation have indicated
that at low concentrations the peptide causes the disruption of POPG membrane
and formation of small, heterogeneous complexes of phospholipids and peptides.
In order to analyze those interactions, concentration effects and to propose a
disruption mechanism, molecular dynamics simulations were carried out using
the GROMOS parameter set 54A7 and MARTINI. The systems were analyzed
with respect to time-dependent (peptide secondary structure and lipid tilt angle),
and average properties (density profiles and deuterium order parameters).
It was found that the peptides adsorb on both PG and PC membranes via elec-
trostatic interactions. Only upon binding to the PG surface there is an increase
of helical content compared to the peptide in solution. Higher helical content is
also observed for the single peptide embedded in PG compared to PC mem-
branes. The density of the membrane medium makes conformational transition
of the peptide embedded slower than on the surface of the membrane. Our sim-
ulations indicate disruption of the membrane without deep penetration of the
peptides. Evidence for that comes from increased disorder of the membrane
and persistent interactions between the peptide and membrane headgroups
throughout the membrane disruption process. Our findings suggest that the
hybrid peptide disrupt the membrane via a carpet-like mechanism which has
also been postulated for the action of Pediocin A and Plantaricin 149A [1,2].
[1] Gaussier et al. App. Environm. MicroBiol, 69, 6777 (2003);
[2] Lopes et al., BBA, 1788, 2252 (2009).
529-Pos Board B284
Oligomerization of Huntingtin N-Terminal Fragment on a Phospholipid
Bilayer Revealed by Molecular Dynamics Simulations
Sebastien Cote1, Vincent Binette1, Evgeniy S. Salnikov2,
Burkhard Bechinger2, Guanghong Wei3, Normand Mousseau1.
1Physique, Universite de Montreal, Montreal, QC, Canada, 2University of
Strasbourg, Strasbourg, France, 3Physics, Fudan University, Shanghai, China.
The Huntingtin protein is characterized by a consecutive segment of glutamines
that leads,when thenumberof repeats exceeds a certain length, tofibrillation.Mis-
folding of this amyloid protein is related to theHuntington’s disease through path-
ways that could involve interactions with phospholipid membranes. For instance,


Molecular Dynamics Studies of PEGylated Antimicrobial Peptides with Lipid Bilayers 

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Molecular Dynamics Studies of PEGylated Antimicrobial Peptides with Lipid Bilayers

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