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696 results on '"Olvera de la Cruz, Monica"'

53. Vertex protein PduN tunes encapsulated pathway performance by dictating bacterial metabolosome morphology

Author

Mills, Carolyn E, primary, Waltmann, Curt, additional, Archer, Andre G, additional, Kennedy, Nolan W, additional, Abrahamson, Charlotte H, additional, Jackson, Alexander D, additional, Roth, Eric W, additional, Shirman, Sasha, additional, Jewett, Michael C, additional, Mangan, Niall M, additional, Olvera de la Cruz, Monica, additional, and Tullman-Ercek, Danielle, additional

Published
2021
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56. Impact of charge switching stimuli on supramolecular perylene monoimide assemblies† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c8sc05595e

Author

Dannenhoffer, Adam, Sai, Hiroaki, Huang, Dongxu, Nagasing, Benjamin, Harutyunyan, Boris, Fairfield, Daniel J., Aytun, Taner, Chin, Stacey M., Bedzyk, Michael J., Olvera de la Cruz, Monica, and Stupp, Samuel I.

Subjects
Chemistry, sense organs, skin and connective tissue diseases
Abstract

A switchable perylene monoimide which undergoes reversible morphological and electronic changes controlled by the ionization state of the phenolic oxygen., 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 versus 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 [Mo3S13]2– as a catalyst at a pH of 4, H2 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 CO2 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.

Published
2019

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

Author

Qiao, Baofu and Olvera de la Cruz, Monica

Subjects
Arginine, Pneumonia, Viral, Protein domain, Binding energy, Mutant, General Physics and Astronomy, 02 engineering and technology, Molecular Dynamics Simulation, Peptidyl-Dipeptidase A, 010402 general chemistry, Cleavage (embryo), Antiviral Agents, 01 natural sciences, Article, Betacoronavirus, Protein Domains, Viral entry, Humans, General Materials Science, polybasic cleavage sites, Receptor, Pandemics, peptide inhibitor, Binding Sites, Host Microbial Interactions, Tetrapeptide, Chemistry, SARS-CoV-2, General Engineering, COVID-19, molecular dynamics simulations, Virus Internalization, 021001 nanoscience & nanotechnology, 0104 chemical sciences, Amino Acid Substitution, Drug Design, Mutation, Spike Glycoprotein, Coronavirus, Biophysics, Receptors, Virus, Angiotensin-Converting Enzyme 2, Coronavirus Infections, 0210 nano-technology, Oligopeptides, hormones, hormone substitutes, and hormone antagonists, Protein Binding
Abstract

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 via 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, via 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.

Published
2020

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

Author

Chen, Yijing, primary, Jiménez-Ángeles, Felipe, additional, Qiao, Baofu, additional, Krzyaniak, Matthew D., additional, Sha, Fanrui, additional, Kato, Satoshi, additional, Gong, Xinyi, additional, Buru, Cassandra T., additional, Chen, Zhijie, additional, Zhang, Xuan, additional, Gianneschi, Nathan C., additional, Wasielewski, Michael R., additional, Olvera de la Cruz, Monica, additional, and Farha, Omar K., additional

Published
2020
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69. Designing Biomimetic, Dissipative Material Systems

Author

Balazs, Anna C., primary, Whitesides, George M., additional, Brinker, C. Jeffrey, additional, Aranson, Igor S., additional, Chaikin, Paul, additional, Dogic, Zvonimir, additional, Glotzer, Sharon, additional, Hammer, Daniel, additional, Irvine, Darrell, additional, Little, Steven R., additional, Olvera de la Cruz, Monica, additional, Parikh, Atul N., additional, Stupp, Samuel, additional, and Szostak, Jack, additional

Published
2016
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88. Particle analogs of electrons in colloidal crystals

Author

Girard, Martin, primary, Wang, Shunzhi, additional, Du, Jingshan S., additional, Das, Anindita, additional, Huang, Ziyin, additional, Dravid, Vinayak P., additional, Lee, Byeongdu, additional, Mirkin, Chad A., additional, and Olvera de la Cruz, Monica, additional

Published
2019
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96. A variational formulation of electrostatics in a medium with spatially varying dielectric permittivity.

Author

Jadhao, Vikram, Solis, Francisco J., and Olvera de la Cruz, Monica

Subjects
ELECTROSTATICS, MOLECULAR dynamics, DIELECTRICS, PERMITTIVITY, POLARIZATION (Electricity), DENSITY functionals
Abstract

In biological and synthetic materials, many important processes involve charges that are present in a medium with spatially varying dielectric permittivity. To accurately understand the role of electrostatic interactions in such systems, it is important to take into account the spatial dependence of the permittivity of the medium. However, due to the ensuing theoretical and computational challenges, this inhomogeneous dielectric response of the medium is often ignored or excessively simplified. We develop a variational formulation of electrostatics to accurately investigate systems that exhibit this inhomogeneous dielectric response. Our formulation is based on a true energy functional of the polarization charge density. The defining characteristic of a true energy functional is that at its minimum it evaluates to the actual value of the energy; this is a feature not found in many commonly used electrostatic functionals. We explore in detail the charged systems that exhibit sharp discontinuous change in dielectric permittivity, and we show that for this case our functional reduces to a functional of only the surface polarization charge density. We apply this reduced functional to study model problems for which analytical solutions are well known. We demonstrate, in addition, that the functional has many properties that make it ideal for use in molecular dynamics simulations. [ABSTRACT FROM AUTHOR]

Published
2013
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97. Large Counterions Boost the Solubility and Renormalized Charge of Suspended Nanoparticles

Author

Guerrero-García, Guillermo Iván, González-Mozuelos, Pedro, and Olvera de la Cruz, Monica

Abstract

Colloidal particles are ubiquitous in biology and in everyday products such as milk, cosmetics, lubricants, paints, or drugs. The stability and aggregation of colloidal suspensions are of paramount importance in nature and in diverse nanotechnological applications, including the fabrication of photonic materials and scaffolds for biological assemblies, gene therapy, diagnostics, targeted drug delivery, and molecular labeling. Electrolyte solutions have been extensively used to stabilize and direct the assembly of colloidal particles. In electrolytes, the effective electrostatic interactions among the suspended colloids can be changed over various length scales by tuning the ionic concentration. However, a major limitation is gelation or flocculation at high salt concentrations. This is explained by classical theories, which show that the electrostatic repulsion among charged colloids is significantly reduced at high electrolyte concentrations. As a result, these screened colloidal particles are expected to aggregate due to short-range attractive interactions or dispersion forces as the salt concentration increases. We discuss here a robust, tunable mechanism for colloidal stability by which large counterions prevent highly charged nanoparticles from aggregating in salt solutions with concentrations up to 1 M. Large counterions are shown to generate a thicker ionic cloud in the proximity of each charged colloid, which strengthens short-range repulsions among colloidal particles and also increases the corresponding renormalized colloidal charge perceived at larger separation distances. These effects thus provide a reliable stabilization mechanism in a broad range of biological and synthetic colloidal suspensions.

Published
2024
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98. Driving Force for Crystallization of Anionic Lipid Membranes Revealed by Atomistic Simulations

Author

Qiao, Bao Fu and Olvera de la Cruz, Monica

Abstract

Crystalline vesicles are promising nanomaterials due to their mechanical stability in various environments. To control their fabrication, it is essential to understand the effects of different experimental conditions on crystallization. Here we perform atomistic molecular dynamics simulations of anionic lipid membranes of 1,2-dilauroyl-sn-glycero-3-phosphol-l-serine. In the presence of Na+monovalent counterions, we access the phase transition from the liquid-like disordered liquid-crystalline phase to the ordered gel phase by lowering the temperature of the system. The phase transition is conclusivelyevidenced by the scattering structure factor. Quantitativecalculations show that the enhancement of the intertail van der Waals interaction (about −6 kBT) plays a dominant role in driving the phase transition rather than the increase in the cohesive interaction (−0.5 kBT) between lipids and counterions. Meanwhile, in the presence of multivalent counterions of Zn2+or La3+the gel phase is found throughout the temperature range investigated. Moreover, the van der Waals interaction per hydrocarbon group is ∼20% stronger in the gel phase (∼ −1.8 kBTregardless of the counterions) than in the liquid-crystalline phase (−1.5 kBT).

Published
2024
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99. Liquid Crystal Phase Transition in Epitaxial Monolayers of DNA-Functionalized Nanoparticle Superlattices

Author

Pan, Saijie, Boon, Niels, and Olvera de la Cruz, Monica

Abstract

Epitaxial growth of DNA-functionalized nanoparticles is used to grow extended superlattices with a preferred orientation for optimizing the physical properties of metamaterials for real applications. Like any solid in nature, superlattices can contain different kinds of structural defects, which significantly alter their physical properties. Further development of these materials requires a deeper understanding of, as well as precise control over, structural defect formation. Here we use Monte Carlo simulations to conduct a systematic study of the equilibrium structures of the adsorbed nanoparticle monolayers by changing the binding energies of different attachment sites. The simulations show two main results. First, the structural defects form one-dimensional clusters with an exponential length distribution. Second, these linear defects exhibit spontaneous symmetry breaking and undergo a liquid crystal phase transition. Subsequently, a mean-field approach is introduced to provide theoretical descriptions for the system. Our theory matches with the simulation results. We anticipate that this theoretical framework will be highly applicable to other two-dimensional assemblies. Our work demonstrates that defects can be engineered to design two-dimensional superlattices with interesting physical properties.

Published
2024
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