I. Experiments/Polymers
Gels, Surfactants, Micelles, Smart Materials, Nanoparticle Targeting, Nanoparticle-Surface Interactions, Self-Assembly, Electrospinning, Controlled Release
II. Biophysics
Lipid Bilayers, Membrane Biophysics
III. Computations
Monte Carlo, Molecular Dynamics, Brownian Dynamics
University of Michigan, Ann Arbor, MI
The study is intended to provide a fundamental understanding of the complex interaction among different components of water borne coating, including Surfactants, Rheology Modifiers and Latex Particles.
The complexed interactions among different components of water borne coatings are studied.
University of Michigan, Ann Arbor, MI
The overall project is to obtain a deep understanding of the electrochemical properties of the tethered lipid bilayers. This project has spanned and addressed different aspects of the lipid bilayers, including a) Pore Formation inside Lipid BIlayers; b) Influences of Lipid Architectures; and c) Tethered Lipid Conformation
Water pores/channels form inside lipid bilayers and are one of the important processes for many biological phenomena. We are trying to explain the formation of water pores inside lipid bilayers from molecular level using a combination of modeling and computer simulation.
Using coarse-grained molecular dynamic simulations based on the MARTINI force field, we study the self-assembly of free dipalmitoylphosphatidylcholine (DPPC) lipids onto PEGylated lipids tethered to a solid substrate. We show that upon increasing lipid concentration, structural transitions occur from tethered spherical nanoparticles, to tethered cylinders and bicelles, to a tethered lipid bilayer with pores, to an unporated tethered lipid bilayer, and finally to a tethered lipid bilayer with liposomes on top of it. The simulation results compare well with structures inferred from experimental observations. In addition, we also demonstrate the structural stability and local fluidity of the tethered lipid bilayer.
Case Western Reserve University, Cleveland, OH
The ultimate goal is to obtain a better control of the nanoparticle design in order to achieve an optimal targeting efficiency of nanoparticles. To this end, the project investigated the influences of many different design factors on the targeting affinity and specificity of nanoparticles, including: nanoparticle size, tether length, binding energy, and ligand valency, etc.
We systematically studied the influence of different design parameters of a spherical nanoparticle tethered with monovalent ligands on its efficiency of targeting planar cell surfaces containing mobile receptors. We investigate how the nanoparticle affinity can be affected by changing the binding energy, the percent of functionalization by ligands, tether length, grafting density, and nanoparticle core size. We also discuss the selectivity of nanoparticle targeting of cells with a high receptor density.
We analyze the efficiency in targeting mobile receptors on cell surfaces by nanoparticles carrying multivalent (divalent, tetravalent) ligands. We identify a few cases when using multivalent ligands innanoparticle targeting can be beneficial, especially for a high binding energy of ligand-receptor interactions and large receptor densities. We demonstrate that for nanoparticles with longer tether length or larger core size, using multivalent ligands becomes favorable. We also show that multivalent ligands can enhance the selectivity of nanoparticletargeting by increasing the nanoparticles affinity to cells with a high density of mobile receptors.
Selectivity of interactions between nanoparticles functionalized by tethered ligands and cell surfaces with different densities of receptors plays an essential role in biorecognition and its implementation in nanobiomedicine. We show that the onset of nanoparticle adsorption has a universal character for a range of nanoparticles: the onset receptor density decreases exponentially with the energy of ligand-receptor binding and inversely with the ligand density. We demonstrate that a bimodal tether distribution, which permits shielding ligands by longer nonfunctional tethers, leads to extra loss of entropy at the adsorption onset, enhancing the selectivity.
We studied how the polydispersity of the chains influences the targeting affinity and selectivity o nanoparticles.
Case Western Reserve University, Cleveland, OH
The reversibly associated polymers are based on supramolecular interactions, such as hydrogen bondings, metal-ligand coordination interactions, etc. In this project, the transition between sol and gel states of one particular types of supramolecular polymers, i.e., metallo-supramolecular polymers, and the formation of metallo-supramolecular micelles were investigated.
Formation of reversible metallo-supramolecular networks based on 3 : 1 ligand–metal complexes between end-functionalized oligomers and metal ions was studied. The formation of different ligand-metal complexes was investigated. The average molecular weight and molecular weight distribution were calculated. The formation of gel under critical condition was identified and the gel properties, i.e., mesh size, plateau modulus, were calculated.
We studied the effect of cis-trans isomerization of 2:1 ligand–metal complexes on self-assembly and network formation of metallo-supramolecular polymersin a good solvent. We show that trans-cis isomerization of ligand-metal complexes can significantly increase the average molecular weight as well as trigger formation of reversible metallosupramolecular network based on 3:1 ligand-metal complexes acting as cross-linkers. We predict conditions when trans- to cis- isomerization can trigger the sol-network transition and/or result in a significant change in materials properties, such as molecular weight and especially elastic plateau modulus. We discuss the molecular mechanisms of network transformation upon cis-trans isomerization, which vary with metal-to-oligomer ratio and originate from different morphologies of the reversible network.
We show that the equilibrium properties of metallo-supramolecular micelles are determined by the competition of 2:1 and 1:1 metal–ligand complexation in the bulk and on the surface as well as steric interactions between the neighboring corona blocks attached to the surface. We predict that by increasing the association energy for the second metal–ligand bond, or decreasing the corona block length one can achieve a larger core surface coverage for metallo-supramolecular micelles. Compared to covalently bonded block copolymer micelles, we show that metallo-supramolecular micelles have smaller monomer and end group density, especially in the vicinity of the core, which may lead to experimentally observed aggregation.
Case Western Reserve University, Cleveland, OH
The release of hydrophobic drugs, DOX and Beta-Lapchone, were influenced by the physicochemical properties of the core-forming blocks of the micelles.
Polymer micelles with two different core-forming blocks, poly(D,L -lactide) (PLA) and poly(ε-caprolactone) (PCL), but the same coronal material, poly(ethylene glycol) (PEG), were investigated in this study as nanoscopic drug carriers. The release of two different drugs, doxorubicin (DOX) and β-lapachone (β-lap), from PEG(5k)-b-PCL(5k) and PEG(5k)-b-PLA(5k) micelles was studied at pH 5.0 and 7.4. Mathematical solutions of both Higuchi’s model and Fickian diffusion equations were utilized to elucidate the differences between the micelle core materials for the two drugs.
a. RNA Spliceosomes
U6 and U2 spliceosomal small nuclear RNAs (snRNAs) play central roles in splicing, a ubiquitous and essential step in eukaryotic gene expression. In activated spliceosomes U6 and U2 form a functionally-critical basepaired complex which is thought to contribute to the formation of the spliceosomal active site. Evidence indicates that in vitro-assembled complexes of these two snRNAs can perform a two-step splicing reaction in the absence of the rest of the spliceosomal components. However, despite its functional importance, structural information on the human U6/U2 basepaired complex has been lacking.
We describe crosslinking and Small- Angle X-Ray Scattering (SAXS) structural analyses on an in vitro-assembled, basepaired complex formed by central domains of human U6 and U2 snRNAs. Psoralen crosslinking data point to the formation of the basepairing interactions previously observed in vivo between U2 and U6 snRNAs. The SAXS data indicate that snRNAs fold into a four-way junction-like structure with an overall cylindrical shape. These data offer a first glimpse into the structure of the basepaired complex of human U6 and U2 snRNAs in solution.
b. Proteins Sliding on DNA
The sequence dependence of DNA-protein interactions that allows proteins to find the correct reaction site also slows down the 1D diffusion of the protein along the DNA molecule, leading to the so-called “speed-stability paradox,” wherein fast diffusion along the DNA molecule is seemingly incompatible with stable targeting of the reaction site.
We develop diffusion-reaction models that use discrete and continuous Gaussian random 1D diffusion landscapes with or without a high-energy cut-off, and two-state models with a transition to and from a “searching” mode in which the protein diffuses rapidly without recognizing the target. In general, we find that a rough landscape is compatible with a fast search if the highest energy barriers can be avoided by “hopping” or by the protein transitioning to a lower-energy “searching” mode. We validate these predictions with the results of Brownian dynamics, kinetic Metropolis, and kinetic Monte Carlo simulations of the diffusion and targeting process, and apply these concepts to the case of T7 RNA polymerase searching for its target site on T7 DNA.