University of Pennsylvania Department of Bioengineering Hybrid Mesoscale Models For Protein- Membrane Interactions Neeraj Agrawal, Jonathan Nukpezah, Joshua Weinstein, Ravi Radhakrishnan Targeted Therapeutics Bridging Intracellular Signaling with Trafficking Endocytosis: the internalization machinery in cells

University of Pennsylvania Department of Bioengineering … “In spite of the above, we felt that it would be redundant to elaborate on his career as a scientist, for that aspect of him is rather well-known. Moreover, we wanted to celebrate one of the perhaps less awarded, but not less important, aspects of Keith: his human nature. Anyone who has worked with him will recognize this in several ways.” Coray Colina, Biography of Keith E. Gubbins, J. Phys. Chem. C, 111 (43), , 2007

University of Pennsylvania Department of Bioengineering 1997: Nagarhole Tiger Sanctuary Karnataka, India Keith M.S. Ananth: Keith’s 1 st PhD student Madhu, Guide Keith seen with his high-tech luxury Yacht

University of Pennsylvania Department of Bioengineering Hierarchical Multiscale Modeling Weinan E, Bjorn Engquist, Notices of the ACM, 2003 K E Gubbins et al., J. Phys.: Cond. Matter, 2006 Minimal model for protein-membrane interaction in endocytosis is focused on the mesoscale

University of Pennsylvania Department of Bioengineering Multiscale Modeling of Membranes Length scale Time scale nm ns µmµm s Fully-atomistic MD Coarse-grained MD Generalized elastic model Bilayer slippage Monolayer viscous dissipation Viscoelastic model Molecular Dynamics (MD)

University of Pennsylvania Department of Bioengineering C 0 :Intrinsic curvature k: Bending Modulus k: Gaussian Curvature Modulus Helfrich Free Energy Cartesian (Monge) notation: h(x,y) 1 2 R 1 >0, R 2 >0 H>0, K>0 R 1 >0, R 2 <0 H=0, K<0 H  1/2[1/R 1 +1/R 2 ] K  1/R 1  1/R 2 Plane: H=0, K=0 Nelson, Piran, Weinberg, 1987 Mesoscale linearized elastic model for membrane

University of Pennsylvania Department of Bioengineering Linearized Elastic Model For Membrane: Monge Gauge Helfrich membrane energy accounts for membrane bending and membrane area extension. In Monge notation, for small deformations, the membrane energy is Force acting normal to the membrane surface (or in z-direction) drives membrane deformation Spontaneous curvatureBending modulus Frame tension Splay modulus Consider only those deformations for which membrane topology remains same. White noise z(x,y) The Monge gauge approximation makes the elastic model amenable to Cartesian coordinate system

University of Pennsylvania Department of Bioengineering Hydrodynamics of the Linearized Elastic Membrane Non-inertial Navier-Stokes equation  Dynamic viscosity Solution of the above PDEs yields the Oseen tensor, (Generalized Mobility). Oseen tensor Fluid velocity is same as membrane velocity at the membrane boundary  no slip condition given by: This results in the Time-Dependent Ginzburg Landau (TDGL) Equation z(x,y) x y

University of Pennsylvania Department of Bioengineering Curvature-Inducing Protein Epsin Diffusion on the Membrane Each epsin molecule induces a curvature field in the membrane Membrane in turn exerts a force on epsin Epsin performs a random walk on membrane surface with a membrane mediated force field, whose solution is propagated in time using the kinetic Monte Carlo algorithm Bound epsin position For 2 D Metric epsin(a)  epsin(a+a 0 ) where a 0 is the lattice size, F is the force acting on epsin KMC-move

University of Pennsylvania Department of Bioengineering KMC-TDGL Hybrid Multiscale Integration Regime 1: Deborah number De<<1 or (a 2 /D)/(z 2 /M) << 1 Regime 2: Deborah number De~1 or (a 2 /D)/(z 2 /M) ~ 1 KMC TDGL #=1/De #=  /  t Surface hopping switching probability Weinstein, Radhakrishnan, 2006 Constant Temperature Protein- Mediated Membrane Dynamics C 0 /µm -1 R/nm R, Range C 0, Intrinsic Curvature  *, Surface Density

University of Pennsylvania Department of Bioengineering Membrane-Mediated Potential of Mean Force between Epsins PMF is dictated by both energetic and entropic components Energy: Epsin experience repulsion due to energetic component when brought close. Entropy: Regions of non-zero H 0 assume increased stiffness and hence reduced membrane fluctuations Therefore, the system can lower its free energy by localizing epsins on the membrane leading to membrane-mediated epsin- epsin attraction  2 E~ spring constant;  =test function

University of Pennsylvania Department of Bioengineering Membrane Dynamics, R= 40nm Membrane-Mediated Protein-Protein Spatial Correlations  *=0.004, C 0 =20  *=0.03, C 0 =20 Localization F/kT C 0 *=20 R*=40 nm Threshold No effective membrane-mediated attraction; no nucleation below threshold curvature and range

University of Pennsylvania Department of Bioengineering Membrane Dynamics, R=60nm Membrane-Mediated Protein-Protein Spatial Correlations  *=0.008, C 0 =10  *=0.008, C 0 =40  *=0.008, C 0 =60 Localization F/kT C 0 **: F(r)  k B Tln g(r) Nucleation limited only by diffusional timescale of association (NVA)

University of Pennsylvania Department of Bioengineering Membrane Dynamics, R=100nm Membrane-Mediated Protein-Protein Spatial Correlations  *=0.016, C 0 =30 Localization F/kT Threshold C 0 *: Nucleation occurs following spatial localization of epsin

University of Pennsylvania Department of Bioengineering x y 1 st Shell 2 nd Shell Epsin arrangement x y θjθj Sustained orientational correlations beyond nearest- neighbors drives nucleation Nucleation via Hexatic Orientational Ordering: NVOO

University of Pennsylvania Department of Bioengineering Membrane Dynamics, R=80nm Membrane Temporal Correlations  *=0.02, C 0 =5 Regions of non-zero H 0 assume increased stiffness and hence reduced membrane fluctuations High protein-surface density drives the membrane phase into a glass-like dynamical behavior

University of Pennsylvania Department of Bioengineering Global Phase Diagram ** C0C0 R NVLRO NVA No N GT GT: Glass-like transition; No N: No nucleation NVOO: Nucleation via orientational ordering NVA: Nucleation via diffusional association C 0 / µm -1 R / nm NVA NVOO No N GT g(r=r 0 )  6 (r=r 0 )

University of Pennsylvania Department of Bioengineering Conclusions The KMC-TDGL approach is successful in describing the dynamic processes associated with the interaction of proteins and membranes at a coarse-grained level Membrane-mediated protein-protein repulsion effects short- and long-ranged ordering of epsins Two modes of nucleation observed -- Nucleation via Association : Effected by large C 0 -- Nucleation via Orientational Ordering: Effected by persistence of orientational correlations In the regime of large surface density, a glass-like transition is observed A global phase diagram is proposed

University of Pennsylvania Department of Bioengineering Integrating Signaling and Trafficking Extracellular Intracellular (MAP Kinases) Ras Raf MEK ERK CblClathrin, AP2 Endphepsin Proliferation Nucleus Umbrella Sampling KMC+TDGL Hypothesis for receptor internalization Clathrin Coat

University of Pennsylvania Department of Bioengineering Acknowledgments Graduate Students Andrew Shih (PhD, BE) Yingting Liu (PhD, BE) Jeremy Purvis (PhD, GCB) Shannon Telesco (PhD, BE) Jonathan Nukpezah (PhD, BE) Neeraj Agrawal (PhD, CBE) Undergraduate Students Joshua Weinstein (Senior, PHYS) Collaborators Mark Lemmon, (Penn) Sung-Hee Choi, (Penn) Boris Kholodenko, (TJU) Funding NSF; Whitaker Foundation; NIH training grant; NPACI supercomputing allocations; Greater Philadelphia Bioinformatics Alliance Co-Authors: Neeraj Agrawal, Jonathan Nukpezah, Joshua Weinstein

University of Pennsylvania Department of Bioengineering

University of Pennsylvania Department of Bioengineering

University of Pennsylvania Department of Bioengineering Paradigms of Membrane Curvature McMahon, Gallop, Nature reviews, 2005

University of Pennsylvania Department of Bioengineering Epsin Clathrin Membrane Ap180 Imaging Endocytosis Ford et al., Nature, 2002

University of Pennsylvania Department of Bioengineering Ap180+ClathrinEpsin+ClathrinAp180+Epsin+Clathrin Ford et al., Nature, 2002 EpsinClathrinAp180 Endocytosis Machinery Receptor Inactivation to Neurotransmitters

University of Pennsylvania Department of Bioengineering Endocytosis: The Internalization Machinery in Cells Detailed molecular and physical mechanism of the process still evading. Endocytosis is a highly orchestrated process involving a variety of proteins. Attenuation of endocytosis leads to impaired deactivation of EGFR – linked to cancer Membrane deformation and dynamics linked to nanocarrier adhesion to cells