(6ka) Membrane Remodelling by Proteins and Self-Assembled Nanostructure

Title: Membrane
remodelling by proteins and self-assembled nanostructure

Amir  H.  Bahrami,  Gauss  Fellow,  Department
 of  Living
 Matter  Physics,  Max  Planck  Institute
 of

Dynamics and Self-organisation, Göttingen, Germany.

amir.bahrami@ds.mpg.de

Carol Hall, Department of Chemical and Biomolecular Engineering, NC State University, Raleigh,
North

Carolina, USA.

hall@ncsu.edu

Abstract

Membrane remodelling plays a critical role in many physical and biological/cellular
processes including synthetic biology, drug delivery, cellular uptake of
nano containers, and self-assembly of nanostructures at membrane interface.
The atomistic membrane simulations are however extremely
slow to simulate membrane behaviour at large time and length scales. We have developed a triangulated
coarse-grained membrane model which is capable of rapid and efficient simulation
of membrane remodelling. We performed Monte Carlo simulations of the model to investigate membrane interaction with nanoparticles and proteins. We report tubular membrane structures induced by adsorbed
nanoparticles on vesicles
[1] and investigate the role of membrane
curvature [2,3] and size and shape of the particles
[4] on cellular uptake of the particles. We also show how membrane curvature
determines pairwise interactions induced between adsorbed Janus nanoparticles on the vesicles
[5] and reveal that the area fraction
of the adhesive Janus particle surface
is an important control parameter
for the assembly of the
particles [5].

We
also performed simulations to understand how tubular membrane structures of the Endoplasmic reticulum , Golgi, mitochondria, and other cellular
organelles are created and maintained. Our simulations
show that the membrane area growth and volume reduction can induce tubular
membrane structure in concert with curved proteins
previously found to shape these tubules
[6].

We
use our model to simulate
membrane remodelling induced by protein molecules
in biological processes. Our simulations reveal the scaffolding role of
Atg protein complexes in autophagosome biogenesis in autophagy, a critical physiological process winning the Nobel prize
of medicine in 2016.
We show that cooperative
interaction of aggregates of several protein chains is essential
to remodel the memberne appropriately [7]. Our outstanding results, in collaboration with experimental
colleagues from Berkeley, indicate how ESCRT (endosomal sorting
complex required for transport) machinery can induce membrane remodelling and scission [8]. Our
 recent simulations reveal spontaneous vesicle constriction
by rings of Janus nanoparticles and clusters of curved proteins,
relevant for membrane
scission by proteins and applicable to synthetic biology
[9].

Keywords:
Membrane remodelling,
proteins, nanostructures, self-assembly, drug delivery, cellular
processes, synthetic biology, nanomaterials

References

(1) Bahrami, A. H.,
Lipowsky, R., & Weikl, T. R., Phys.
Rev.
Lett. 2012, 109, 188102. (2) Bahrami,
A. H. et. al, Advances
in colloid and interface science
2014, 208, 214-224. (3) Bahrami, A. H., Lipowsky, R., & Weikl, T. R., Soft Matter 2016, 12(2), 581-587.

(4) Bahrami,
A. H., Soft Matter 2013, 9(36), 8642-8646.

(5) Bahrami,
A. H., & Weikl, Nano Letters
2018, 18(2), 1259-1263.

(6) Bahrami,
A. H., & Hummer, G., ACS Nano
2017, 11(9), 9558-9565.

(7) Bahrami,
A. H., Lin, M. G., Ren, X., Hurley, J. H., & Hummer, G., PLOS Comput.
Biol. 2017,

13(10).

(8)  Schoeneberg, J. et. al, Science
362 (6421), 1423-1428.

(9) Bahrami,
A., Bahrami, A.H., Nanotechnology 30.34 (2019): 345101.

Research accomplishments

Statement of research

During  my  BS  and  MSC
 in  mechanical engineering, I performed  molecular  dynamics  simulations
 of  particle-
based coarse grained fluid models to investigate capillary flow  of
 liquid  bislugs  in  nanotubes.  I  also  simulated vesicle  membrane  formation  and  curvatrue-mediated interactions between
transmembrane proteins in vesicles.
Our   interesting  results,
 appeared
 in  
the  Journal  of Chemical Physics, earned me a second
PhD scholarship in

(a)           (b)           (c)

Figure 1

soft matter
physics in Max
Planck Institute for Colloids and Interfaces,

before finishing
the first one, within the international
program SSNI– Self-Assembled Soft Matter
Nano-Structures at Interfaces.
Answering a long-standing question of the field, our results on
membrane-mediated aggregation and tubulation of adsorbed nano particles on vesicles (Fig.
1(a)) appeared in  Physical Review Letters in a suggested
paper by the editor (97 citations) and
a chosen paper for synopsis of physics [1]. Among other publications including
an invited review to the International Journal
of Colloid and Interface Science (86 citations) on wrapping of nano
particles by membranes [2], I published a single-author
paper [3] on the role of nano particle shape in
engulfment orientation (Fig. 1(c)), which appeared on the  cover of Soft Matter (41 citations). I also
developed a continuum membrane model for theoretical calculations of axisymmetric membrane shapes. The model was successfully used to demonstrate, for the first time, the important
role of membrane curvature in
wrapping of spherical nano particles by vesicles [4], appeared in Soft
Matter (29 citations). I spent a 6-month visiting
period in North Carolina State University in the
group of Prof. C. K. Hall. Our results on size-dependent
translocation of nano particles across lipid
bilayers using discrete molecular dynamics simulations appeared
in Nanoscale [5].

Finishing  a  successful
 3-year  PhD,  I  was  offered  an
 immediate Postdoctoral  position
 by  Prof. Gerhard Hummer to start
in the department

of  theoretical
 biophysics  at  the  MPI  for

Biophysics.
During my Postdoctoral period, I

used   my  tessellated  membrane  model
 to i n v e s t i g a t e   m e m b r a n e   r e m o d e l l i n g 
 i
n biological processes. We demonstrated for the first time the significant role of membrane
area growth by lipid synthesis in the formation
and stability  of  the  membrane tubular  structures
(Fig. 2(b)) in cellular organelles. Our results,
appeared in  ACS  Nano,  also  provides a  new

(a)

Figure 2

(b)

technique for creating
stable tubules of synthetic membranes
for applications in synthetic biology [6]. Our collaboration with experimentalists
in Biocenter of The Goethe Institute on atomistic
simulations of eukaryotic sensors
for membrane lipid saturation appeared in Molecular Cell.

My current collaboration with neuroscientists in FIAS (Frankfurt Institute for Advanced Studies) on
how tubular structure of
the nerve cells are related
to the cell function is in preparation for PNAS.

I also extended the tessellated membrane
model by including
coarse-grained representation of proteins, interacting with the membrane.
My suggestion on the scaffolding role of
ATG
protein complex in autophagosome biogenesis in autophagy
(Fig. 2(a)), confirmed by our experimental
collaborators at  Berkeley, appeared
recently in  PLOS Computational Biology, where the  good agreement of experiments and theory was praised by the referees
[7]. The referees
also recognised the importance of our interesting model
for simulating protein-induced membrane remodelling and wide
range of potential
applications of the model for future investigations. Our model is particularly successful in simulating protein aggregation
at the membrane interface. Our outstanding results,
in collaboration with experimental colleagues from Berkeley, on how ESCRT (endosomal sorting complex required for transport) machinery can induce membrane remodelling and scission recently appeared in Science [8].

My continuous collaboration with my colleagues at MPI Colloids
and Interfaces, working on one of
my old ideas about curvature-mediated interactions between
Janus nano particle (Fig. 1(b)), led to interesting results appeared in  Nano
Letters, in which I am a corresponding author
[9]. We revealed,
for the first time, that the membrane
curvature determines the nature
of interactions between partially-

adsorbed Janus
nano particles on vesicles. Our recent work on membrane
scission by nanoparticle rings and protein aggregates has just appeared
in Nanotechnology [10].

Future research

Membrane remodelling plays a critical role in self assembly of proteins and nanostructure
and pattern formation at the membrane interface, in shaping cellular
organelles, in cellular processes
such as cell division/migration, autophagy, and in designing synthetic
nano materials for biological applications [11-13].

Model. Computational methods
have been increasingly used to better understand experimental results and to suggest new experiments. Limited time and length scales in simulations of atomistic membrane models,  however,  highlight  the  demand  for  much
 faster,  more  efficient
 coarse-grained  models including continuum and tessellated membrane models. Monte Carlo (MC) simulation
of the tessellated model with sequential moves of the mesh nodes, however, is not efficient to simulate
membranes with proteins and the cytoskeleton and the the current continuum model is limited to axisymmetric membranes. I will develop
a novel much more efficient, faster membrane model by
inducing global membrane
undulations using a Hybrid Monte Carlo (HMC) algorithm
[14], combined of MC and Molecular Dynamics
(MD), which allows simultaneous
moves of all nodes during MD steps. To involve the role of mechanical forces in cellular
processes such as cell migration and cell division, I will incorporate a coarse-grained representation of the cytoskeleton and of protein molecules
into the new model. The HMC simulations of the new membrane model with
proteins and the cytoskeleton, together with general continuum membrane
model, thus provide
a strong package for simulating membrane
remodelling over long time and length
scales with wide applications some of which follow.

Designing Nano materials
and synthetic biology. The new field of synthetic biology
aims at constructing a living cell [15]. Nano structures such as DNA origami scaffolds are promising tools to
induce  synthetic  membrane  remodelling.
 I  will
 build  a  coarse-grained  model  of
 DNA  origami scaffolds and use simulations, for the first time, to understand how these scaffolds might be
effectively used to synthetically reproduce cellular processes. Self-assembled structures of nano particles are also
used for designing new materials
at the nanoscale. We revealed
that membrane curvature determines pairwise interactions between adsorbed Janus nano particles. I will design synthetic
nano structures composed of linear rings of aggregated Janus nano particles
on membranes, as promising synthetic counterparts of ESCRT
complexes and membrane cytoskeleton, to induce membrane
fission, furrow constriction and cell division.

Drug delivery
and nano drug containers. Recent advances
in nanotechnology have led to an increasing use of nano particles for drug delivery
purposes in medicine
particularly in cancer therapy [16]. I will study how membrane
curvature modifies cooperative internalisation of several rigid and
deformable drug containers with a variety
of sizes and shapes to design drug containers with optimal
shape, size, and mechanical flexibility.

Protein aggregation
and protein-induced cellular
and biological processes.
I will perform simulations to understand how proteins create and maintain membrane
shapes and aggregate at the membrane
interface. I will also investigate how membrane properties such as spontaneous curvature, volume regulation, area growth, and membrane
asymmetry affect the formation
and stability of different membrane shapes. HMC simulations of the novel fast membrane model allow me to efficiently investigate how protein complexes and membrane properties regulate autophagy [17], a cellular mechanism for material degradation (nobel prize in physiology and medicine 2016). I will perform simulations to understand membrane budding and scission
induced by the endosomal sorting complexes required
for transport (ESCRT), essential
for the multivesicular body pathway, cytokinesis
and HIV budding [18].

Micro- and nano-fluidics.
I will use my tessellated membrane model to study rheology of colloidal
particles of different sizes and shapes,
red blood cell dynamics
and related diseases, and swimming dynamics of bacterial cells in low Reynolds
numbers. The swimming
dynamics is crucial for building
a minimal model of synthetic cells.

Mechanobiology and tissue
growth. The newly-emerging field of mechonobiology focuses on the role
of mechanical forces in biological and cellular processes
[19]. I have successfully used the
tessellated membrane model to simulate
membrane adhesion to rigid surfaces such as nano particles.
I will include mechanical
forces by introducing a coarse-grained representation of the cytoskeleton as a new aspect into the model. I will use simulations
to understand how cell adhesion and migration
depend on the membrane
cytoskeleton, on membrane properties, and on substrate
rigidity for applications in cell development and tissue growth. I will also distinguish the role of membrane
cytoskeleton and protein
molecules such as BAR domain
family in cell division and mitochondrial
fission. The new model allows
me to investigate, for the first time,
how membrane cytoskeleton affects nano particle
intrenalisation.

References

(1) Bahrami, A. H., Lipowsky, R., & Weikl, T. R., Phys. Rev. Lett. 2012,
109, 188102. (2) Bahrami, A. H. et. al, Advances in colloid and interface science
2014, 208, 214-224.
(3) Bahrami, A. H., Soft Matter 2013, 9(36),
8642-8646.

(4) Bahrami, A. H., Lipowsky, R., & Weikl, T. R., Soft Matter 2016, 12(2), 581-587. (5) EM Curtis, AH Bahrami, TR Weikl, CK
Hall, Nanoscale 7 (34), 14505-14514. (6)  Bahrami, A. H., & Hummer, G., ACS Nano
2017, 11(9), 9558-9565.

(7) Bahrami, A. H., Lin, M. G., Ren, X., Hurley, J. H., & Hummer, G., PLOS Comput. Biol. 2017,

13(10).

(8) Schoeneberg, J. et. al, Science
362 (6421), 1423-1428.

(9) Bahrami, A. H., & Weikl, Nano Letters 2018, 18(2), 1259-1263.

(10) Bahrami, A., Bahrami, A.H., Nanotechnology 30.34 (2019): 345101.

(11) Shibata,
Y., Hu, J., Kozlov, M. M., & Rapoport, T. A., Annu Rev Cell Dev Biol 2009, 25,

329-354.

(12) McMahon, H. T., & Gallop, J. L.,
Nature 2005, 438(7068), 590.

(13) Zimmerberg, J., & Kozlov, M. M. , Nature reviews Molecular cell biology 2006, 7(1), 9.

(14) Duane, S., Kennedy, A.
D., Pendleton, B. J., &
Roweth, D. , Physics letters
B 1987, 195(2), 216. (15) Schwille, P., Science 2011,
333(6047), 1252-1254.

(16) Della Rocca, J., Liu,
D., & Lin, W., Accounts
of chemical research 2011,
44(10), 957-968. (17) Kuma, A. et. al, Nature 2004,
432, 1032; Mercer, T. J.,
et. al, J. Biol. Chem. 2018, jbc-R117. (18) Wollert,
T., & Hurley, J.
H., Nature 2010, 464(7290), 864..

(19) Wang, N., Butler, J. P., &
Ingber, D. E.,
M, Science 1993, 260(5111), 1124-1127.

Statement of Teaching

I
regard teaching as an important part of my academic career. During my career, I have devoted
considerable attention to the teaching of engineering
labs and courses as well as to mentoring
undergraduate and graduate students. Successful teaching relies
on the instructor’s ability to motivate
students. My favorite teachers always established the need for learning
the subject by raising the basic
question: “why do we learn this concept?” Scientific advances are often brought about by deep insights
into the fundamental principles underlying new ideas or concepts.
While covering a wide range of
materials broadens students’
viewpoints on the subject, I believe that successful teaching
lies in keeping these fundamental concepts in the forefront of students’ understanding in order to train them as creative scientists and researchers. In my classrooms I develop lectures
that encourage student learning through
different approaches such as class lectures,
texts and visual presentations. I incorporate
up-to-date knowledge about the subject area and strong teaching and communication skills
in order to create an interactive learning environment and guide students
to think deeply about the subject. In my opinion,
the success  in  teaching  relies
 heavily  on  striking  a  balance 
between  lecturing  and  class
 discussion, particularly in interdisciplinary
courses. Style, professional ethics and respectfulness are among the fine
qualities of an outstanding and successful teacher
who can serve as a role model for the
students.

During the last year of my bachelor degree in the department
of mechanical engineering in Tehran Polytechnic (Amirkabir University of Technology), I was offered to serve as teaching
assistant of classical
mechanics (engineering dynamics), a basic course in mechanical
engineering. The course deals with
newtonian equations of motions for mechanical
systems of particles and rigid bodies and their numerical solutions. The dean of mechanical engineering department had to convince the faculty to offer a TA
to a bachelor student as by the time only MSc and PhD students were allowed to serve as teaching assistant. As TA my duties ranged from giving
lectures, assigning quizzes,
grading reports, and holding office hours to
address students’ questions. My devotion and interest put me in position to cooperate in some teaching sessions of the main course as well. In the same year I also started teaching laboratory
of dynamics and vibration in the same department.

During my Masters degree in mechanical engineering department at Sharif University of Technology, I was granted a research assistantship at the Centre of Excellence for Design, Robotics,
and Automation. Working in the lab, I was offered to teach the robotics
laboratory course the year after. My teaching
period in the lab extended
to two years after my graduation as MSc in mechanical
engineering. Robotics course deals with formulating and solving the equations of motion of robotic manipulators as multi rigid or
flexible bodies. The equations of motion of robotic manipulator resemble those of polymer chains
with flexible links between the particles. In the meanwhile, I started to learn machine
learning methods including neural networks and genetic algorithms for applications in artificial
intelligence in particular
in robotic and automation systems.

Starting from classical mechanics
of systems of particles and rigid bodies
in my bachelors and continuing to mechanics of robotic manipulators, I got interested in simulations of soft matter and fluid systems and statistical mechanics as I was accepted
to PhD. For soft matter simulations, I learned a variety of particle-
based and continuum methods including Molecular
Dynamics, Monte Carlo, Dissipative Particle Dynamics, Computational Fluid Dynamics,
and Multi-Particle Collision
Dynamics.

As
I was accepted to start
a PhD in mechanical engineering, I had the choice between
a 5-year-long course-research-based PhD and a 3-year-long research-based PhD. Choosing the 5-year-lomg PhD, I had
two teach to complete courses before graduation. I chose “Molecular
Dynamics and Monte Carlo
Simulations” and “Neural
Networks” and taught
these two courses
in a complete semester.

Having an interdisciplinary
background in mechanical engineering and soft matter statistical physics allows me to teach a variety
of different courses
with a particular focus on interdisciplinary courses.

I will welcome the opportunity to teach core courses in my future academic career. I am prepared to offer a variety of courses at both undergraduate and graduate
levels with the emphasis on “Computational Soft Matter”, “Simulation Methods in Chemistry and Physics”, ”Thermodynamics and Fluid Mechanics”, and “Statistical Thermodynamics”.
I am
enthusiastic about teaching
core and elective undergraduate
and graduate courses including
“Introduction to Statistical Thermodynamics”, “Soft Matter Simulation Methods”, “Introduction to Molecular Dynamics
Simulations”, “Introduction to Biological Physics”, “Fluid Mechanics”, and “Classical Thermodynamics”. I especially enjoy teaching
and consulting undergraduate senior design projects. In addition, I will welcome the opportunity to develop new upper
division undergraduate and graduate courses pertaining to “Molecular Driving
Forces”, “Cellular and Biological Processes”, “Statistical Thermodynamics”, and “Advanced Molecular Dynamics and Monte Carlo Simulations”. Some of the graduate
level courses will be mainly seminar-based
courses, which will include lectures, class discussions, reading, summarising papers, and presentation assignments. I am confident that my teaching and research experience will enhance the current strengths
of your school and will provide
a desirable addition
to the preexisting cadre of brilliant scholars and dedicated teachers.