skip to main content

Title: In situ monitoring of protein transfer into nanoscale channels
Protein transfer into nanoscale compartments is critical for many cellular/life processes, yet there are few reports on how compartment properties impact the protein orientation during a transfer. Such a knowledge gap limits a deeper understanding of the protein transfer mechanism, which could be bridged using nanoporous materials. Here, we use a mesoporous silica, a covalent organic framework, and a metal-organic framework with charged, hydrophobic, and neutral surfaces, respectively, to elucidate the impact of channel properties on the transfer of a model protein, lysozyme. Using site-directed spin labeling and time-resolved electron paramagnetic resonance spectroscopy, we reveal that the transfer can be a multi-step process depending on channel properties and depict the relative orientation changes of lysozyme upon transfer into each channel. To the best of our knowledge, this is the first structural insight into protein orientation upon transfer into different compartments, meaningful for the rational design of synthetic materials to host enzymes or mimic the cellular compartments.  more » « less
Award ID(s):
Author(s) / Creator(s):
; ; ; ; ; ; ; ; ; ;
Date Published:
Journal Name:
Cell reports physical science
Page Range / eLocation ID:
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Confining proteins in synthetic nanoscale spatial compartments has offered a cell-free avenue to understand enzyme structure–function relationships and complex cellular processes near the physiological conditions, an important branch of fundamental protein biophysics studies. Enzyme confinement has also provided advancement in biocatalysis by offering enhanced enzyme reusability, cost-efficiency, and substrate selectivity in certain cases for research and industrial applications. However, the primary research efforts in this area have been focused on the development of novel confinement materials and investigating protein adsorption/interaction with various surfaces, leaving a fundamental knowledge gap, namely, the lack of understanding of the confined enzymes (note that enzyme adsorption to or interactions with surfaces differs from enzyme confinement as the latter offers an enhanced extent of restriction to enzyme movement and/or conformational flexibility). In particular, there is limited understanding of enzymes' structure, dynamics, translocation (into biological pores), folding, and aggregation in extreme cases upon confinement, and how confinement properties such as the size, shape, and rigidity affect these details. The first barrier to bridge this gap is the difficulty in “penetrating” the “shielding” of the confinement walls experimentally; confinement could also lead to high heterogeneity and dynamics in the entrapped enzymes, challenging most protein-probing experimental techniques. The complexity is raised by the variety in the possible confinement environments that enzymes may encounter in nature or on lab benches, which can be categorized to rigid confinement with regular shapes, rigid restriction without regular shapes, and flexible/dynamic confinement which also introduces crowding effects. Thus, to bridge such a knowledge gap, it is critical to combine advanced materials and cutting-edge techniques to re-create the various confinement conditions and understand enzymes therein. We have spearheaded in this challenging area by creating various confinement conditions to restrict enzymes while exploring experimental techniques to understand enzyme behaviors upon confinement at the molecular/residue level. This review is to summarize our key findings on the molecular level details of enzymes confined in (i) rigid compartments with regular shapes based on pre-formed, mesoporous nanoparticles and Metal–Organic Frameworks/Covalent-Organic Frameworks (MOFs/COFs), (ii) rigid confinement with irregular crystal defects with shapes close to the outline of the confined enzymes via co-crystallization of enzymes with certain metal ions and ligands in the aqueous phase (biomineralization), and (iii) flexible, dynamic confinement created by protein-friendly polymeric materials and assemblies. Under each case, we will focus our discussion on (a) the way to load enzymes into the confined spaces, (b) the structural basis of the function and behavior of enzymes within each compartment environments, and (c) technical advances of our methodology to probe the needed structural information. The purposes are to depict the chemical physics details of enzymes at the challenging interface of natural molecules and synthetic compartment materials, guide the selection of enzyme confinement platforms for various applications, and generate excitement in the community on combining cutting-edge technologies and synthetic materials to better understand enzyme performance in biophysics, biocatalysis, and biomedical applications.

    more » « less
  2. Developing protein confinement platforms is an attractive research area that not only promotes protein delivery but also can result in artificial environment mimicking of the cellular one, impacting both the controlled release of proteins and the fundamental protein biophysics. Polymeric nanoparticles (PNPs) are attractive platforms to confine proteins due to their superior biocompatibility, low cytotoxicity, and controllable release under external stimuli. However, loading proteins into PNPs can be challenging due to the potential protein structural perturbation upon contacting the interior of PNPs. In this work, we developed a novel approach to encapsulate proteins in PNPs with the assistance of the zeolitic imidazolate framework (ZIF). Here, ZIF offers an additional protection layer to the target protein by forming the protein@ZIF composite via aqueous-phase cocrystallization. We demonstrated our platform using a model protein, lysozyme, and a widely studied PNP composed of poly(ethylene glycol)-poly(lactic-co-glycolic acid) (PEG–PLGA). A comprehensive study via standard loading and release tests as well as various spectroscopic techniques was carried out on lysozyme loaded onto PEG–PLGA with and without ZIF protection. As compared with the direct protein encapsulation, an additional layer with ZIF prior to loading offered enhanced loading capacity, reduced leaching, especially in the initial stage, led to slower release kinetics, and reduced secondary structural perturbation. Meanwhile, the function, cytotoxicity, and cellular uptake of proteins encapsulated within the ZIF-bound systems are decent. Our results demonstrated the use of ZIF in assisting in protein encapsulation in PNPs and established the basis for developing more sophisticated protein encapsulation platforms using a combination of materials of diverse molecular architectures and disciplines. As such, we anticipate that the protein-encapsulated ZIF systems will serve as future polymer protein confinement and delivery platforms for both fundamental biophysics and biochemistry research and biomedical applications where protein delivery is needed to support therapeutics and/or nutrients. 
    more » « less
  3. Diamine-appended variants of the metal–organic framework M2(dobpdc) (M = Mg, Mn, Fe, Co, Zn; dobpdc4– = 4,4′-dioxidobiphenyl-3,3′-dicarboxylate) exhibit exceptional CO2 capture properties owing to a unique cooperative adsorption mechanism, and thus hold promise for use in the development of energy- and cost-efficient CO2 separations. Understanding the nature of thermal transport in these materials is essential for such practical applications, however, as temperature rises resulting from exothermic CO2 uptake could potentially offset the energy savings offered by such cooperative adsorbents. Here, molecular dynamics (MD) simulations are employed in investigating thermal transport in bare and e-2-appended Zn2(dobpdc) (e-2 = N-ethylethylenediamine), both with and without CO2 as a guest. In the absence of CO2, the appended diamines function to enhance thermal conductivity in the ab-plane of e-2–Zn2(dobpdc) relative to the bare framework, as a result of noncovalent interactions between adjacent diamines that provide additional heat transfer pathways across the pore channel. Upon introduction of CO2, the thermal conductivity along the pore channel (the c-axis) increases due to the cooperative formation of metal-bound ammonium carbamates, which serve to create additional heat transfer pathways. In contrast, the thermal conductivity of the bare framework remains unchanged in the presence of zinc-bound CO2 but decreases in the presence of additional adsorbed CO2. 
    more » « less
  4. Abstract

    The properties of foams, an important class of cellular solids, are most sensitive to the volume fraction and openness of its elementary compartments; size, shape, orientation, and the interconnectedness of the cells are other important design attributes. Control of these morphological traits would allow the tailored fabrication of useful materials. While approaches like ice templating have produced foams with elongated cells, there is a need for rapid, versatile, and energy‐efficient methods that also control the local order and macroscopic alignment of cellular elements. Here, a fast and convenient method is described to obtain anisotropic structural foams using frontal polymerization. Foams are fabricated by curing mixtures of dicyclopentadiene and a blowing agent via frontal ring‐opening metathesis polymerization (FROMP). The materials are characterized using microcomputed tomography (micro‐CT) and an image analysis protocol to quantify the morphological characteristics. The cellular structure, porosity, and hardness of the foams change with blowing agent, concentration, and resin viscosity. Moreover, a full factorial combination of variables is used to correlate each parameter with the structure of the obtained foams. The results demonstrate the controlled production of foams with specific morphologies using the simple and efficient method of frontal polymerization.

    more » « less
  5. Abstract

    Poly(dimethylsiloxane) (PDMS) is likely the most popular material for microfluidic devices in lab-on-a-chip and other biomedical applications. However, the hydrophobicity of PDMS leads to non-specific adsorption of proteins and other molecules such as therapeutic drugs, limiting its broader use. Here, we introduce a simple method for preparing PDMS materials to improve hydrophilicity and decrease non-specific protein adsorption while retaining cellular biocompatibility, transparency, and good mechanical properties without the need for any post-cure surface treatment. This approach utilizes smart copolymers comprised of poly(ethylene glycol) (PEG) and PDMS segments (PDMS-PEG) that, when blended with PDMS during device manufacture, spontaneously segregate to surfaces in contact with aqueous solutions and reduce the hydrophobicity without any added manufacturing steps. PDMS-PEG-modified PDMS samples showed contact angles as low as 23.6° ± 1° and retained this hydrophilicity for at least twenty months. Their improved wettability was confirmed using capillary flow experiments. Modified devices exhibited considerably reduced non-specific adsorption of albumin, lysozyme, and immunoglobulin G. The modified PDMS was biocompatible, displaying no adverse effects when used in a simple liver-on-a-chip model using primary rat hepatocytes. This PDMS modification method can be further applied in analytical separations, biosensing, cell studies, and drug-related studies.

    more » « less