Publications by authors named "Monica Olvera de la Cruz"

172 Publications

Chemically controlled pattern formation in self-oscillating elastic shells.

Proc Natl Acad Sci U S A 2021 Mar;118(10)

Department of Materials Science and Engineering, Northwestern University, Evanston, IL 60208;

Patterns and morphology develop in living systems such as embryos in response to chemical signals. To understand and exploit the interplay of chemical reactions with mechanical transformations, chemomechanical polymer systems have been synthesized by attaching chemicals into hydrogels. In this work, we design autonomous responsive elastic shells that undergo morphological changes induced by chemical reactions. We couple the local mechanical response of the gel with the chemical processes on the shell. This causes swelling and deswelling of the gel, generating diverse morphological changes, including periodic oscillations. We further introduce a mechanical instability and observe buckling-unbuckling dynamics with a response time delay. Moreover, we investigate the mechanical feedback on the chemical reaction and demonstrate the dynamic patterns triggered by an initial deformation. We show the chemical characteristics that account for the shell morphology and discuss the future designs for autonomous responsive materials.
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http://dx.doi.org/10.1073/pnas.2025717118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7958227PMC
March 2021

A Perspective on the Design of Ion-Containing Polymers for Polymer Electrolyte Applications.

J Phys Chem B 2021 Apr 26;125(12):3015-3022. Epub 2021 Feb 26.

Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States.

Ion-containing polymers have numerous potential applications as energy storage and conversion devices, water purification membranes, and gas separation membranes, to name a few. Given the low dielectric constant of the media, ions and charges on polymers in a molten state interact strongly producing large effects on chain statistics, thermodynamics, and diffusion properties. Here, we discuss recent research accomplishments on the effects of ionic correlation and dielectric heterogeneity on the phase behavior of ion-containing polymers. Progress made in studying ion transport properties in these material systems is also highlighted. Charged block copolymers (BCPs), among all kinds of ion-containing polymers, have a particular advantage owing to their robust mechanical support and ion conducting paths provided by the segregation of the neutral and charged blocks. Coulombic interactions among the charges play a critical role in determining the phase segregation in charged BCPs and the domain size of charge-rich regions. We show that strongly charged BCPs display ordered phases as a result of electrostatic interactions alone. In addition, bulky charge-containing side groups attached to the charged block lead to the formation of morphologies that provide continuous channels and better dissociation for ion conduction purposes. Finally, a few avenues for designing ion-containing polymers for energy applications are discussed.
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http://dx.doi.org/10.1021/acs.jpcb.0c08707DOI Listing
April 2021

Polycrystalline Covalent Organic Framework Films Act as Adsorbents, Not Membranes.

J Am Chem Soc 2021 Jan 13;143(3):1466-1473. Epub 2021 Jan 13.

Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States.

Covalent organic framework (COF) membranes are of great promise for energy-efficient separations. Thick, polycrystalline COF films have been reported to separate dyes, salts, bacteria, and nanoparticles on the basis of size-selective transport through ordered pores. Here, we show that these materials function as adsorbents, not as size-sieving membranes. Binding isotherms of several dyes typical of the COF membrane literature to three COF powder samples illustrate that COFs are high-capacity adsorbents with affinities that span a range of 3 orders of magnitude, trends which map onto previously reported separation behavior. Computational results suggest that observed differences in adsorption can be correlated to variable entropic gains driving the adsorption process. Polycrystalline COF pellets show volume-dependent and flow-rate dependent "rejection" of dyes, consistent with an adsorption-based removal mechanism. Previous reports of thick, polycrystalline COF membranes used low flow rates and small dye volumes to probe rejection capabilities, where membrane and adsorbent behavior is not distinguishable. A mixed dye separation experiment in flow shows affinity-dependent performance. These results necessitate a careful reexamination of the COF membrane literature, as separations based on differential transport through 2D COF pores remain an important yet unrealized frontier.
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http://dx.doi.org/10.1021/jacs.0c11159DOI Listing
January 2021

Fast and programmable locomotion of hydrogel-metal hybrids under light and magnetic fields.

Sci Robot 2020 12;5(49)

Center for Bio-inspired Energy Science, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.

The design of soft matter in which internal fuels or an external energy input can generate locomotion and shape transformations observed in living organisms is a key challenge. Such materials could assist in productive functions that may range from robotics to smart management of chemical reactions and communication with cells. In this context, hydrated matter that can function in aqueous media would be of great interest. Here, we report the design of hydrogels containing a scaffold of high-aspect ratio ferromagnetic nanowires with nematic order dispersed in a polymer network that change shape in response to light and experience torques in rotating magnetic fields. The synergistic response enables fast walking motion of macroscopic objects in water on either flat or inclined surfaces and also guides delivery of cargo through rolling motion and light-driven shape changes. The theoretical description of the response to the external energy input allowed us to program specific trajectories of hydrogel objects that were verified experimentally.
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http://dx.doi.org/10.1126/scirobotics.abb9822DOI Listing
December 2020

Dynamics of a driven confined polyelectrolyte solution.

J Chem Phys 2020 Nov;153(18):184904

Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA.

The transport of polyelectrolytes confined by oppositely charged surfaces and driven by a constant electric field is of interest in studies of DNA separation according to size. Using molecular dynamics simulations that include the surface polarization effect, we find that the mobilities of the polyelectrolytes and their counterions change non-monotonically with the confinement surface charge density. For an optimum value of the confinement charge density, efficient separation of polyelectrolytes can be achieved over a wide range of polyelectrolyte charge due to the differential friction imparted by oppositely charged confinement on the polyelectrolyte chains. Furthermore, by altering the placement of the charged confinement counterions, enhanced polyelectrolyte separation can be achieved by utilizing the surface polarization effect due to dielectric mismatch between the media inside and outside the confinement.
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http://dx.doi.org/10.1063/5.0027049DOI Listing
November 2020

Insights into the Enhanced Catalytic Activity of Cytochrome c When Encapsulated in a Metal-Organic Framework.

J Am Chem Soc 2020 10 13;142(43):18576-18582. Epub 2020 Oct 13.

Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States.

The encapsulation of enzymes within porous materials has shown great promise, not only in protecting the enzymes from denaturation under nonbiological environments, but also, in some cases, in facilitating their enzymatic reaction rates at favorable reaction conditions. While a number of hypotheses have been developed to explain this phenomenon, the detailed structural changes of the enzymes upon encapsulation within the porous material, which are closely related to their activity, remain largely elusive. Herein, the structural change of cytochrome c (Cyt c) upon encapsulation within a hierarchical metal-organic framework, NU-1000, is investigated through a combination of experimental and computational methods, such as electron paramagnetic resonance, solid-state ultraviolet-visible spectroscopy, and all-atom explicit solvent molecular dynamics simulations. The enhanced catalytic performance of Cyt c after being encapsulated within NU-1000 is supported by the physical and in silico observations of a change around the heme ferric active center.
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http://dx.doi.org/10.1021/jacs.0c07870DOI Listing
October 2020

Homopolymer self-assembly of poly(propylene sulfone) hydrogels via dynamic noncovalent sulfone-sulfone bonding.

Nat Commun 2020 09 29;11(1):4896. Epub 2020 Sep 29.

Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.

Natural biomolecules such as peptides and DNA can dynamically self-organize into diverse hierarchical structures. Mimicry of this homopolymer self-assembly using synthetic systems has remained limited but would be advantageous for the design of adaptive bio/nanomaterials. Here, we report both experiments and simulations on the dynamic network self-assembly and subsequent collapse of the synthetic homopolymer poly(propylene sulfone). The assembly is directed by dynamic noncovalent sulfone-sulfone bonds that are susceptible to solvent polarity. The hydration history, specified by the stepwise increase in water ratio within lower polarity water-miscible solvents like dimethylsulfoxide, controls the homopolymer assembly into crystalline frameworks or uniform nanostructured hydrogels of spherical, vesicular, or cylindrical morphologies. These electrostatic hydrogels have a high affinity for a wide range of organic solutes, achieving >95% encapsulation efficiency for hydrophilic small molecules and biologics. This system validates sulfone-sulfone bonding for dynamic self-assembly, presenting a robust platform for controllable gelation, nanofabrication, and molecular encapsulation.
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http://dx.doi.org/10.1038/s41467-020-18657-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7525563PMC
September 2020

Protein Surface Printer for Exploring Protein Domains.

J Chem Inf Model 2020 10 16;60(10):5255-5264. Epub 2020 Sep 16.

Department of Chemical Engineering, Northwestern University, Evanston, Illinois 60201, United States.

The surface of proteins is vital in determining protein functions. Herein, a program, Protein Surface Printer (PSP), is built that performs multiple functions in quantifying protein surface domains. Two proteins, PETase and cytochrome P450, are used to validate that the program supports atomistic simulations with different combinations of programs and force fields. A case study is conducted on the structural analysis of the spike proteins of SARS-CoV-2 and SARS-CoV and the human cell receptor ACE2. Although the surface domains of both spike proteins are highly similar, their receptor-binding domains (RBDs) and the O-linked glycan domains are structurally different. The O-linked glycan domain of SARS-CoV-2 is highly positively charged, which may promote binding to negatively charged human cells.
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http://dx.doi.org/10.1021/acs.jcim.0c00582DOI Listing
October 2020

Enhanced Binding of SARS-CoV-2 Spike Protein to Receptor by Distal Polybasic Cleavage Sites.

ACS Nano 2020 08 4;14(8):10616-10623. Epub 2020 Aug 4.

The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein plays a crucial role in binding the human cell receptor ACE2 that is required for viral entry. Many studies have been conducted to target the structures of RBD-ACE2 binding and to design RBD-targeting vaccines and drugs. Nevertheless, mutations distal from the SARS-CoV-2 RBD also impact its transmissibility and antibody can target non-RBD regions, suggesting the incomplete role of the RBD region in the spike protein-ACE2 binding. Here, in order to elucidate distant binding mechanisms, we analyze complexes of ACE2 with the wild-type spike protein and with key mutants large-scale all-atom explicit solvent molecular dynamics simulations. We find that though distributed approximately 10 nm away from the RBD, the SARS-CoV-2 polybasic cleavage sites enhance, electrostatic interactions and hydration, the RBD-ACE2 binding affinity. A negatively charged tetrapeptide (GluGluLeuGlu) is then designed to neutralize the positively charged arginine on the polybasic cleavage sites. We find that the tetrapeptide GluGluLeuGlu binds to one of the three polybasic cleavage sites of the SARS-CoV-2 spike protein lessening by 34% the RBD-ACE2 binding strength. This significant binding energy reduction demonstrates the feasibility to neutralize RBD-ACE2 binding by targeting this specific polybasic cleavage site. Our work enhances understanding of the binding mechanism of SARS-CoV-2 to ACE2, which may aid the design of therapeutics for COVID-19 infection.
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http://dx.doi.org/10.1021/acsnano.0c04798DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7409923PMC
August 2020

Surface polarization effects in confined polyelectrolyte solutions.

Proc Natl Acad Sci U S A 2020 08 3;117(33):19677-19684. Epub 2020 Aug 3.

Department of Materials Science and Engineering, Northwestern University, Evanston, IL 60208;

Understanding nanoscale interactions at the interface between two media with different dielectric constants is crucial for controlling many environmental and biological processes, and for improving the efficiency of energy storage devices. In this contributed paper, we show that polarization effects due to such dielectric mismatch remarkably influence the double-layer structure of a polyelectrolyte solution confined between two charged surfaces. Surprisingly, the electrostatic potential across the adsorbed polyelectrolyte double layer at the confining surface is found to decrease with increasing surface charge density, indicative of a negative differential capacitance. Furthermore, in the presence of polarization effects, the electrostatic energy stored in the double-layer structure is enhanced with an increase in the charge amplification, which is the absorption of ions on a like-charged surface. We also find that all of the important double-layer properties, such as charge amplification, energy storage, and differential capacitance, strongly depend on the polyelectrolyte backbone flexibility and the solvent quality. These interesting behaviors are attributed to the interplay between the conformational entropy of the confined polyelectrolytes, the Coulombic interaction between the charged species, and the repulsion from the surfaces with lower dielectric constant.
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http://dx.doi.org/10.1073/pnas.2007545117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7443958PMC
August 2020

Controlling protein adsorption modes electrostatically.

Soft Matter 2020 Jun;16(22):5224-5232

Department of Material Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA. and Department of Chemistry, Northwestern University, Evanston, USA and Department of Physics and Astronomy, Northwestern University, Evanston, USA.

Protein adsorption on surfaces is ubiquitous in biology and in biotechnology. There are various forces required for controlling protein adsorption. Here, we introduce an explicit ion coarse-grained molecular dynamics simulation approach for studying the effects of electrostatics on protein adsorption, and 2D protein assembly on charged surfaces. Our model accounts for the spatial distribution of protein charges. We use catalase as our model protein. We find that the preferential adsorption mode of proteins at low protein concentration on a charged surface is "standing up". When the protein concentration in a solution increases to reach a critical density on the surface, the adsorption mode switches from "standing up" to a mixed state "flat on" and "standing up", which increases the lateral correlations among the adsorbed proteins. As such, the changes in the adsorption mode arise from the protein adsorption that cancel the surface charge and the protein-protein repulsion. This correlated surface structure melts as the salt concentration increases because the charged surface is cancelled by the salt ions and the proteins de-adsorb. For the case of strongly charged surfaces the "standing up" conformation remains more favorable even at high protein adsorption at low salt concentrations since in that conformation the surface charge is cancelled more effectively, generating an even more laterally correlated structure. We elucidate the effects of parameters such as surface charge density, salt concentration, and protein charges on the different adsorption modes and the structure and organization of proteins on the charged surfaces. This study provides a guide for controlling protein assembly on surfaces.
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http://dx.doi.org/10.1039/d0sm00632gDOI Listing
June 2020

Sublattice melting in binary superionic colloidal crystals.

Phys Rev E 2020 Mar;101(3-1):032603

Department of Chemistry, Department of Physics and Astronomy, and Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA.

In superionic compounds one component premelts, providing high ionic conductivity to solid-state electrolytes. Here we find sublattice melting in colloidal crystals of oppositely charged particles that are highly asymmetric in size and charge in salt solutions. The small particles in ionic compounds melt when the temperature increases, forming a superionic phase. These delocalized small particles in a crystal of large oppositely charged particles, in contrast to superionic phases in atomic systems, form crystals with nonelectroneutral stoichiometric ratios. This generates structures with multiple domains of ionic crystals in percolated superionic phases with adjustable stoichiometries.
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http://dx.doi.org/10.1103/PhysRevE.101.032603DOI Listing
March 2020

Assembly and Stability of Simian Virus 40 Polymorphs.

ACS Nano 2020 04 2;14(4):4430-4443. Epub 2020 Apr 2.

Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States.

Understanding viral assembly pathways is of critical importance to biology, medicine, and nanotechology. Here, we study the assembly path of a system with various structures, the simian vacuolating virus 40 (SV40) polymorphs. We simulate the templated assembly process of VP1 pentamers, which are the constituents of SV40, into icosahedal shells made of = 12 pentamers ( = 1). The simulations include connections formed between pentamers by C-terminal flexible lateral units, termed here "C-terminal ligands", which are shown to control assembly behavior and shell dynamics. The model also incorporates electrostatic attractions between the N-terminal peptide strands (ligands) and the negatively charged cargo, allowing for agreement with experiments of RNA templated assembly at various pH and ionic conditions. During viral assembly, pentamers bound to any template increase its effective size due to the length and flexibility of the C-terminal ligands, which can connect to other VP1 pentamers and recruit them to a partially completed capsid. All closed shells formed other than the = 1 feature the ability to dynamically rearrange and are thus termed "pseudo-closed". The = 13 shell can even spontaneously "self-correct" by losing a pentamer and become a = 1 capsid when the template size fluctuates. Bound pentamers recruiting additional pentamers to dynamically rearranging capsids allow closed shells to continue growing the pseudo-closed growth mechanism, for which experimental evidence already exists. Overall, we show that the C-terminal ligands control the dynamic assembly paths of SV40 polymorphs.
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http://dx.doi.org/10.1021/acsnano.9b10004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7232851PMC
April 2020

Multicanonical Monte Carlo ensemble growth algorithm.

Phys Rev E 2020 Feb;101(2-1):021301

Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA.

We present an ensemble Monte Carlo growth method to sample the equilibrium thermodynamic properties of random chains. The method is based on the multicanonical technique of computing the density of states in the energy space. Such a quantity is temperature independent, and therefore microcanonical and canonical thermodynamic quantities, including the free energy, entropy, and thermal averages, can be obtained by reweighting with a Boltzmann factor. The algorithm we present combines two approaches: The first is the Monte Carlo ensemble growth method, where a "population" of samples in the state space is considered, as opposed to traditional sampling by long random walks, or iterative single-chain growth. The second is the flat-histogram Monte Carlo, similar to the popular Wang-Landau sampling, or to multicanonical chain-growth sampling. We discuss the performance and relative simplicity of the proposed algorithm, and we apply it to known test cases.
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http://dx.doi.org/10.1103/PhysRevE.101.021301DOI Listing
February 2020

Strain-Dependent Nanowrinkle Confinement of Block Copolymers.

Nano Lett 2020 Feb 13;20(2):1433-1439. Epub 2020 Jan 13.

This paper describes an all-soft, templated assembly of block copolymers (BCPs) with programmable alignment. Using polymeric nanowrinkles as a confining scaffold, poly(styrene)--poly(dimethylsiloxane) (PS--PDMS) BCPs were assembled to be parallel or perpendicular to the wrinkle orientation by manipulating the substrate strain. Self-consistent field theory modeling revealed that wrinkle curvature and surface affinity govern the BCP structural formation. Furthermore, control of BCP alignment was demonstrated for complex wrinkle geometries, various copolymer molecular weights, and functional wrinkle skin layers. This integration of BCP patterning with flexible 3D architectures offers a promising nanolithography approach for next-generation soft electronics.
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http://dx.doi.org/10.1021/acs.nanolett.9b05189DOI Listing
February 2020

Single-chain heteropolymers transport protons selectively and rapidly.

Nature 2020 01 8;577(7789):216-220. Epub 2020 Jan 8.

Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, USA.

Precise protein sequencing and folding are believed to generate the structure and chemical diversity of natural channels, both of which are essential to synthetically achieve proton transport performance comparable to that seen in natural systems. Geometrically defined channels have been fabricated using peptides, DNAs, carbon nanotubes, sequence-defined polymers and organic frameworks. However, none of these channels rivals the performance observed in their natural counterparts. Here we show that without forming an atomically structured channel, four-monomer-based random heteropolymers (RHPs) can mimic membrane proteins and exhibit selective proton transport across lipid bilayers at a rate similar to those of natural proton channels. Statistical control over the monomer distribution in an RHP leads to segmental heterogeneity in hydrophobicity, which facilitates the insertion of single RHPs into the lipid bilayers. It also results in bilayer-spanning segments containing polar monomers that promote the formation of hydrogen-bonded chains for proton transport. Our study demonstrates the importance of the adaptability that is enabled by statistical similarity among RHP chains and of the modularity provided by the chemical diversity of monomers, to achieve uniform behaviour in heterogeneous systems. Our results also validate statistical randomness as an unexplored approach to realize protein-like behaviour at the single-polymer-chain level in a predictable manner.
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http://dx.doi.org/10.1038/s41586-019-1881-0DOI Listing
January 2020

DNA- and Field-Mediated Assembly of Magnetic Nanoparticles into High-Aspect Ratio Crystals.

Adv Mater 2020 Jan 9;32(4):e1906626. Epub 2019 Dec 9.

Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA.

Under an applied magnetic field, superparamagnetic Fe O nanoparticles with complementary DNA strands assemble into crystalline, pseudo-1D elongated superlattice structures. The assembly process is driven through a combination of DNA hybridization and particle dipolar coupling, a property dependent on particle composition, size, and interparticle distance. The DNA controls interparticle distance and crystal symmetry, while the magnetic field leads to anisotropic crystal growth. Increasing the dipole interaction between particles by increasing particle size or external field strength leads to a preference for a particular crystal morphology (e.g., rhombic dodecahedra, stacked clusters, and smooth rods). Molecular dynamics simulations show that an understanding of both DNA hybridization energetic and magnetic interactions is required to predict the resulting crystal morphology. Taken together, the data show that applied magnetic fields with magnetic nanoparticles can be deliberately used to access nanostructures beyond what is possible with DNA hybridization alone.
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http://dx.doi.org/10.1002/adma.201906626DOI Listing
January 2020

Control of Ionic Mobility via Charge Size Asymmetry in Random Ionomers.

Nano Lett 2020 Jan 3;20(1):43-49. Epub 2019 Dec 3.

Department of Materials Science and Engineering , Northwestern University , Evanston , Illinois 60208 , United States.

Solid polymer electrolytes are considered a promising alternative to traditional liquid electrolytes in energy storage applications because of their good mechanical properties, and excellent thermal and chemical stability. A gap, however, still exists in understanding ion transport mechanisms and improving ion transport in solid polymer electrolytes. Therefore, it is crucial to bridge composition-structure and structure-property relationships. Here, we demonstrate that size asymmetry, λ, represented by the ratio of counterion to charged monomer size, plays a key role both in the nanostructure and in the ionic dynamics. More specifically, when the nanostructure is modified by an external electric field such that the mobility cannot be described by linear response theory, two situations arise. The ionic mobility increases as λ decreases (small counterions) in the weak electrostatics (high dielectric constant) regime, whereas in systems with strong electrostatic interactions, ionomers with higher size symmetry (λ ≈ 1) display higher ionic mobility. Moreover, ion transport is found to be dominated by the hopping of the ions and not by moving ionic clusters (also known as "vehicular" charge transport). These results serve as a guide for designing ion-containing polymers for ion transport related applications.
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http://dx.doi.org/10.1021/acs.nanolett.9b02743DOI Listing
January 2020

Electrostatic shape control of a charged molecular membrane from ribbon to scroll.

Proc Natl Acad Sci U S A 2019 10 14;116(44):22030-22036. Epub 2019 Oct 14.

Department of Materials Science and Engineering, Northwestern University, Evanston, IL 60208;

Bilayers of amphiphiles can organize into spherical vesicles, nanotubes, planar, undulating, and helical nanoribbons, and scroll-like cochleates. These bilayer-related architectures interconvert under suitable conditions. Here, a charged, chiral amphiphile (palmitoyl-lysine, C-K) is used to elucidate the pathway for planar nanoribbon to cochleate transition induced by salt (NaCl) concentration. In situ small- and wide-angle X-ray scattering (SAXS/WAXS), atomic force and cryogenic transmission electron microscopies (AFM and cryo-TEM) tracked these transformations over angstrom to micrometer length scales. AFM reveals that the large length (L) to width (W) ratio nanoribbons (L/W > 10) convert to sheets (L/W → 1) before rolling into cochleates. A theoretical model based on electrostatic and surface energies shows that the nanoribbons convert to sheets via a first-order transition, at a critical Debye length, with 2 shallow minima of the order of thermal energy at L/W > 1 and at L/W = 1. SAXS shows that interbilayer spacing () in the cochleates scales linearly with the Debye length, and ranges from 13 to 35 nm for NaCl concentrations from 100 to 5 mM. Theoretical arguments that include electrostatic and elastic energies explain the membrane rolling and the bilayer separation-Debye length relationship. These models suggest that the salt-induced ribbon to cochleate transition should be common to all charged bilayers possessing an intrinsic curvature, which in the present case originates from molecular chirality. Our studies show how electrostatic interactions can be tuned to attain and control cochleate structures, which have potential for encapsulating, and releasing macromolecules in a size-selective manner.
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http://dx.doi.org/10.1073/pnas.1913632116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6825261PMC
October 2019

Enzymatic Degradation of DNA Probed by X-ray Scattering.

ACS Nano 2019 10 18;13(10):11382-11391. Epub 2019 Sep 18.

Label-free X-ray scattering from protein spherical nucleic acids (Pro-SNAs, consisting of protein cores densely functionalized with covalently bound DNA) was used to elucidate the enzymatic reaction pathway for the DNase I-induced degradation of DNA. Time-course small-angle X-ray scattering (SAXS) and gel electrophoresis reveal a two-state system with time-dependent populations of intact and fully degraded DNA in the Pro-SNAs. SAXS shows that in the fully degraded state, the DNA strands forming the outer shell of the Pro-SNA were completely digested. SAXS analysis of reactions with different Pro-SNA concentrations reveals a reaction pathway characterized by a slow, rate determining DNase I-Pro-SNA association, followed by rapid DNA hydrolysis. Molecular dynamics (MD) simulations provide the distributions of monovalent and divalent ions around the Pro-SNA, relevant to the activity of DNase I. Taken together, SAXS in conjunction with MD simulations yield key mechanistic and structural insights into the interaction of DNA with DNase I. The approach presented here should prove invaluable in probing other enzyme-catalyzed reactions on the nanoscale.
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http://dx.doi.org/10.1021/acsnano.9b04752DOI Listing
October 2019

Water follows polar and nonpolar protein surface domains.

Proc Natl Acad Sci U S A 2019 09 9;116(39):19274-19281. Epub 2019 Sep 9.

Department of Materials Science and Engineering, Northwestern University, Evanston, IL 60208;

The conformation of water around proteins is of paramount importance, as it determines protein interactions. Although the average water properties around the surface of proteins have been provided experimentally and computationally, protein surfaces are highly heterogeneous. Therefore, it is crucial to determine the correlations of water to the local distributions of polar and nonpolar protein surface domains to understand functions such as aggregation, mutations, and delivery. By using atomistic simulations, we investigate the orientation and dynamics of water molecules next to 4 types of protein surface domains: negatively charged, positively charged, and charge-neutral polar and nonpolar amino acids. The negatively charged amino acids orient around 98% of the neighboring water dipoles toward the protein surface, and such correlation persists up to around 16 Å from the protein surface. The positively charged amino acids orient around 94% of the nearest water dipoles against the protein surface, and the correlation persists up to around 12 Å. The charge-neutral polar and nonpolar amino acids are also orienting the water neighbors in a quantitatively weaker manner. A similar trend was observed in the residence time of the nearest water neighbors. These findings hold true for 3 technically important enzymes (PETase, cytochrome P450, and organophosphorus hydrolase). Our results demonstrate that the water-amino acid degree of correlation follows the same trend as the amino acid contribution in proteins solubility, namely, the negatively charged amino acids are the most beneficial for protein solubility, then the positively charged amino acids, and finally the charge-neutral amino acids.
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http://dx.doi.org/10.1073/pnas.1910225116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6765241PMC
September 2019

Crystalline membrane morphology beyond polyhedra.

Phys Rev E 2019 Jul;100(1-1):012610

Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA; Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA; and Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208, USA.

Elastic crystalline membranes exhibit a buckling transition from sphere to polyhedron. However, their morphologies are restricted to convex polyhedra and are difficult to externally control. Here we study morphological changes of closed crystalline membranes of superparamagnetic particles. The competition of magnetic dipole-dipole interactions with the elasticity of this magnetoelastic membrane leads to concave morphologies. Interestingly, as the magnetic field strength increases, the symmetry of the buckled membrane decreases from 5-fold to 3-fold, to 2-fold and, finally, to 1-fold rotational symmetry. This gives the ability to switch the membrane morphology between convex and concave shapes with specific symmetry and provides promising applications for membrane shape control in the design of actuatable microcontainers for targeted delivery systems.
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http://dx.doi.org/10.1103/PhysRevE.100.012610DOI Listing
July 2019

Manipulation of Confined Polyelectrolyte Conformations through Dielectric Mismatch.

ACS Nano 2019 08 15;13(8):9298-9305. Epub 2019 Aug 15.

Department of Chemical and Biological Engineering , Northwestern University , Evanston , Illinois 60208 , United States.

We demonstrate that a highly charged polyelectrolyte confined in a spherical cavity undergoes reversible transformations between amorphous conformations and a four-fold symmetry morphology as a function of dielectric mismatch between the media inside and outside the cavity. Surface polarization due to dielectric mismatch exhibits an extra "confinement" effect, which is most pronounced within a certain range of the cavity radius and the electrostatic strength between the monomers and counterions and multivalent counterions. For cavities with a charged surface, surface polarization leads to an increased amount of counterions adsorbed in the outer side, further compressing the confined polyelectrolyte into a four-fold symmetry morphology. The equilibrium conformation of the chain is dependent upon several key factors including the relative permittivities of the media inside and outside the cavity, multivalent counterion concentration, cavity radius relative to the chain length, and interface charge density. Our findings offer insights into the effects of dielectric mismatch in packaging and delivery of polyelectrolytes across media with different relative permittivities. Moreover, the reversible transformation of the polyelectrolyte conformations in response to environmental permittivity allows for potential applications in biosensing and medical monitoring.
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http://dx.doi.org/10.1021/acsnano.9b03900DOI Listing
August 2019

Impact of charge switching stimuli on supramolecular perylene monoimide assemblies.

Chem Sci 2019 Jun 14;10(22):5779-5786. Epub 2019 May 14.

Department of Materials Science and Engineering , 2220 Campus Drive , Evanston , IL 60208 , USA.

The development of stimuli-responsive amphiphilic supramolecular nanostructures is an attractive target for systems based on light-absorbing chromophores that can function as photosensitizers in water. We report here on a water soluble supramolecular carboxylated perylene monoimide system in which charge can be switched significantly by a change in pH. This was accomplished by substituting the perylene core with an ionizable hydroxyl group. In acidic environments, crystalline supramolecular nanoribbons with dimensions on the order of 500 × 50 × 2 nm form readily, while in basic solution the additional electrostatic repulsion of the ionized hydroxyl reduces assemblies to very small dimensions on the order of only several nanometers. The HOMO/LUMO levels were also found to be sensitive to pH; in acidic media the HOMO/LUMO levels are -5.65 and -3.70 eV respectively vacuum, whereas is in basic conditions they are -4.90 and -3.33 eV, respectively. Utilizing the assemblies as photosensitizers in photocatalytic production of hydrogen with [MoS] as a catalyst at a pH of 4, H was generated with a turnover number of 125 after 18 hours. Charge switching the assemblies at a pH of 9-10 and using an iron porphyrin catalyst, protons could again be reduced to hydrogen and CO was reduced to CO with a turnover number of 30. The system investigated offers an example of dynamic photosensitizing assemblies that can drive reactions in both acidic and basic media.
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http://dx.doi.org/10.1039/c8sc05595eDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6568310PMC
June 2019

Particle analogs of electrons in colloidal crystals.

Science 2019 06;364(6446):1174-1178

Department of Materials Science and Engineering, Northwestern University, Evanston, IL 60208, USA.

A versatile method for the design of colloidal crystals involves the use of DNA as a particle-directing ligand. With such systems, DNA-nanoparticle conjugates are considered programmable atom equivalents (PAEs), and design rules have been devised to engineer crystallization outcomes. This work shows that when reduced in size and DNA grafting density, PAEs behave as electron equivalents (EEs), roaming through and stabilizing the lattices defined by larger PAEs, as electrons do in metals in the classical picture. This discovery defines a new property of colloidal crystals-metallicity-that is characterized by the extent of EE delocalization and diffusion. As the number of strands increases or the temperature decreases, the EEs localize, which is structurally reminiscent of a metal-insulator transition. Colloidal crystal metallicity, therefore, provides new routes to metallic, intermetallic, and compound phases.
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http://dx.doi.org/10.1126/science.aaw8237DOI Listing
June 2019

Crystallizing protein assemblies via free and grafted linkers.

Soft Matter 2019 May;15(21):4311-4319

Department of Material Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA.

Porous protein superlattices have plausible catalytic applications in biotechnology and nanotechnology. They are solid yet open structures with the potential for preserving the activity of enzymes. However, there is still a lack of understanding of the design parameters that are required to arrange proteins in a periodic porous fashion. Here, we introduce a coarse-grained molecular dynamics (MD) simulation approach to study the effects of the lengths and geometries of linkers on the stability of 3D crystalline assemblies of metal ion anchored ferritin proteins. By simulating a system of proteins (eight metal ion anchored sites per protein) and linkers (two free ends per linker), we find that there is a range of optimal linker lengths for crystalline order. The optimal linker length is found to depend on the linker to protein concentration ratio and binding energy. We also examine the case of grafted flexible linkers on the protein surface as an alternative route for constructing highly porous crystalline structures. Our study demonstrates that the length of grafted linkers is a better tunable parameter than the length of free linkers to achieve high porosity protein superlattices. The computational study developed here provides guidelines to assemble biomolecules into crystals with high porosity.
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http://dx.doi.org/10.1039/c9sm00693aDOI Listing
May 2019

Self-Assembly of Charge-Containing Copolymers at the Liquid-Liquid Interface.

ACS Cent Sci 2019 Apr 25;5(4):688-699. Epub 2019 Mar 25.

Department of Materials Science and Engineering, Department of Chemistry, Department of Chemical and Biological Engineering, and Department of Physics, Northwestern University, Evanston, Illinois 60208, United States.

Quantitatively understanding the self-assembly of amphiphilic macromolecules at liquid-liquid interfaces is a fundamental scientific concern due to its relevance to a broad range of applications including bottom-up nanopatterning, protein encapsulation, oil recovery, drug delivery, and other technologies. Elucidating the mechanisms that drive assembly of amphiphilic macromolecules at liquid-liquid interfaces is challenging due to the combination of hydrophobic, hydrophilic, and Coulomb interactions, which require consideration of the dielectric mismatch, solvation effects, ionic correlations, and entropic factors. Here we investigate the self-assembly of a model block copolymer with various charge fractions at the chloroform-water interface. We analyze the adsorption and conformation of poly(styrene)--poly(2-vinylpyridine) (PS--P2VP) and of the homopolymer poly(2-vinylpyridine) (P2VP) with varying charge fraction, which is controlled via a quaternization reaction and distributed randomly along the backbone. Interfacial tension measurements show that the polymer adsorption increases only marginally at low charge fractions (<5%) but increases more significantly at higher charge fractions for the copolymer, while the corresponding randomly charged P2VP homopolymer analogues display much more sensitivity to the presence of charged groups. Molecular dynamics (MD) simulations of the experimental systems reveal that the diblock copolymer (PS--P2VP) interfacial activity could be mediated by the formation of a rich set of complex interfacial copolymer aggregates. Circular domains to elongated stripes are observed in the simulations at the water-chloroform interface as the charge fraction increases. These structures are shown to resemble the spherical and cylindrical helicoid structures observed in bulk chloroform as the charge fraction increases. The self-assembly of charge-containing copolymers is found to be driven by the association of the charged component in the hydrophilic block, with the hydrophobic segments extending away from the hydrophilic cores into the chloroform phase.
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http://dx.doi.org/10.1021/acscentsci.9b00084DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6487451PMC
April 2019

Receptor-Ligand Rebinding Kinetics in Confinement.

Biophys J 2019 05 5;116(9):1609-1624. Epub 2019 Apr 5.

Department of Physics and Astronomy, Northwestern University, Evanston, Illinois; Department of Molecular Biosciences, Northwestern University, Evanston, Illinois. Electronic address:

Rebinding kinetics of molecular ligands plays a key role in the operation of biomachinery, from regulatory networks to protein transcription, and is also a key factor in design of drugs and high-precision biosensors. In this study, we investigate initial release and rebinding of ligands to their binding sites grafted on a planar surface, a situation commonly observed in single-molecule experiments and that occurs in vivo, e.g., during exocytosis. Via scaling arguments and molecular dynamic simulations, we analyze the dependence of nonequilibrium rebinding kinetics on two intrinsic length scales: the average separation distance between the binding sites and the total diffusible volume (i.e., height of the experimental reservoir in which diffusion takes place or average distance between receptor-bearing surfaces). We obtain time-dependent scaling laws for on rates and for the cumulative number of rebinding events. For diffusion-limited binding, the (rebinding) on rate decreases with time via multiple power-law regimes before the terminal steady-state (constant on-rate) regime. At intermediate times, when particle density has not yet become uniform throughout the diffusible volume, the cumulative number of rebindings exhibits a novel, to our knowledge, plateau behavior because of the three-dimensional escape process of ligands from binding sites. The duration of the plateau regime depends on the average separation distance between binding sites. After the three-dimensional diffusive escape process, a one-dimensional diffusive regime describes on rates. In the reaction-limited scenario, ligands with higher affinity to their binding sites (e.g., longer residence times) delay entry to the power-law regimes. Our results will be useful for extracting hidden timescales in experiments such as kinetic rate measurements for ligand-receptor interactions in microchannels, as well as for cell signaling via diffusing molecules.
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http://dx.doi.org/10.1016/j.bpj.2019.02.033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6506716PMC
May 2019

"Mirror"-like Protein Dimers Stabilized by Local Heterogeneity at Protein Surfaces.

J Phys Chem B 2019 05 30;123(18):3907-3915. Epub 2019 Apr 30.

Protein aggregation has been observed inside cells and holds true for membraneless organelles. The precise understanding of protein dimerization is a prerequisite for manipulating protein aggregation, which is promising for elevating enzyme concentration to enhance their catalytic performance. Here, the dimerization of two industrially important enzymes of cytochrome P450 (P450) and organophosphorus hydrolase (OPH) is investigated using all-atom explicit solvent molecular dynamics simulations, umbrella sampling, and protein-protein docking calculations. The calculated potentials of mean force of dimer-monomer dissociation demonstrate that the dimeric forms are more stable with the free energy barrier of around 60 kJ/mol for P450 and 101 kJ/mol for OPH. The docking calculations on the OPH dimer evidence the uniqueness of the native orientation. The protein dimers form "mirror"-like orientations with some degree of rotation. Such signature orientations are interpreted based on the predominant polar amino acids in the contact regime. In the dimer conformations, the active sites are exposed. This work highlights the crucial roles of the polar and nonpolar protein surface domains to form enzymatically active protein dimer aggregates. Our work will potentially aid the design of molecules that can deliver and protect native protein function in various environments.
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http://dx.doi.org/10.1021/acs.jpcb.9b01394DOI Listing
May 2019

Electrostatic Origin of Element Selectivity during Rare Earth Adsorption.

Phys Rev Lett 2019 Feb;122(5):058001

Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208, USA.

Rare earths, which are fundamental components of modern technologies, are often extracted from aqueous solutions using surfactants at oil-water interfaces. Heavier lanthanides are more easily extracted, even though all lanthanides are chemically very similar. Using x-ray fluorescence measurements and theoretical arguments, we show that there is a sharp bulk-concentration-dependent transition in the interfacial adsorption of cations from aqueous solutions containing Er^{3+} or Nd^{3+} in contact with a floating monolayer. The threshold bulk concentration of erbium (Z=68) is an order of magnitude lower than that of neodymium (Z=60), and erbium is preferentially adsorbed when the solution contains both ions. This implies that elemental selectivity during separation originates at the surfactant interface. Electrostatic effects arising from the interface dielectric mismatch, ionic correlations, and sizes of the ions explain the sharp adsorption curve and selectivity.
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http://dx.doi.org/10.1103/PhysRevLett.122.058001DOI Listing
February 2019