The performance of organic photovoltaic (OPV) material systems are hypothesized to depend strongly on the intermolecular arrangements at the donor:fullerene interfaces. A review of some of the most ...efficient polymers utilized in polymer:fullerene PV devices, combined with an analysis of reported polymer donor materials wherein the same conjugated backbone was used with varying alkyl substituents, supports this hypothesis. Specifically, the literature shows that higher-performing donor–acceptor type polymers generally have acceptor moieties that are sterically accessible for interactions with the fullerene derivative, whereas the corresponding donor moieties tend to have branched alkyl substituents that sterically hinder interactions with the fullerene. To further explore the idea that the most beneficial polymer:fullerene arrangement involves the fullerene docking with the acceptor moiety, a family of benzo1,2-b:4,5-b′dithiophene–thieno3,4-cpyrrole-4,6-dione polymers (PBDTTPD derivatives) was synthesized and tested in a variety of PV device types with vastly different aggregation states of the polymer. In agreement with our hypothesis, the PBDTTPD derivative with a more sterically accessible acceptor moiety and a more sterically hindered donor moiety shows the highest performance in bulk-heterojunction, bilayer, and low-polymer concentration PV devices where fullerene derivatives serve as the electron-accepting materials. Furthermore, external quantum efficiency measurements of the charge-transfer state and solid-state two-dimensional (2D) 13C{1H} heteronuclear correlation (HETCOR) NMR analyses support that a specific polymer:fullerene arrangement is present for the highest performing PBDTTPD derivative, in which the fullerene is in closer proximity to the acceptor moiety of the polymer. This work demonstrates that the polymer:fullerene arrangement and resulting intermolecular interactions may be key factors in determining the performance of OPV material systems.
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The structures and properties of membrane proteins in lipid bilayers are expected to closely resemble those in native cell-membrane environments, although they have been difficult to elucidate. By ...performing solid-state NMR measurements at very fast (100 kHz) magic-angle spinning rates and at high (23.5 T) magnetic field, severe sensitivity and resolution challenges are overcome, enabling the atomic-level characterization of membrane proteins in lipid environments. This is demonstrated by extensive 1H-based resonance assignments of the fully protonated heptahelical membrane protein proteorhodopsin, and the efficient identification of numerous 1H–1H dipolar interactions, which provide distance constraints, inter-residue proximities, relative orientations of secondary structural elements, and protein–cofactor interactions in the hydrophobic transmembrane regions. These results establish a general approach for high-resolution structural studies of membrane proteins in lipid environments via solid-state NMR.
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The diverse functionalities of membrane proteins (MPs) have garnered much interest in leveraging these biomolecules for technological applications. One challenge of studying MPs in artificial ...micellar surfactant environments is that many factors modulate their structures and functionalities, including the surfactants that interact with the MP or their assembly into oligomers. As oligomerization offers a means by which MPs could selectively interact among the copious environmental factors in biological environments, we hypothesized that MP function is predominantly modified by oligomerization rather than interactions with local surfactants that, by comparison, largely interact with MPs nonspecifically. To test this, we study the light-activated proton pump proteorhodopsin (PR) in micellar surfactant solutions because it is functionally active in monomeric and oligomeric forms, the light-activated functionalities of which can be assessed in detail. The surfactant composition and oligomerization are correlated with PR function, as measured by the protonation behaviors of aspartic acid residue 97, which mediates light-activated proton transport, and the associated photocycle kinetics. The results demonstrate that oligomerization dominantly mediates PR function in different surfactant environments, whereas some surfactants can subtly modulate proton-pumping kinetics. This work underscores the importance of understanding and controlling oligomerization of MPs to study and exploit their function.
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4.
Protein-Catalyzed Capture Agents Agnew, Heather D; Coppock, Matthew B; Idso, Matthew N ...
Chemical reviews,
09/2019, Volume:
119, Issue:
17
Journal Article
Peer reviewed
Open access
Protein-catalyzed capture agents (PCCs) are synthetic and modular peptide-based affinity agents that are developed through the use of single-generation in situ click chemistry screens against large ...peptide libraries. In such screens, the target protein, or a synthetic epitope fragment of that protein, provides a template for selectively promoting the noncopper catalyzed azide–alkyne dipolar cycloaddition click reaction between either a library peptide and a known ligand or a library peptide and the synthetic epitope. The development of epitope-targeted PCCs was motivated by the desire to fully generalize pioneering work from the Sharpless and Finn groups in which in situ click screens were used to develop potent, divalent enzymatic inhibitors. In fact, a large degree of generality has now been achieved. Various PCCs have demonstrated utility for selective protein detection, as allosteric or direct inhibitors, as modulators of protein folding, and as tools for in vivo tumor imaging. We provide a historical context for PCCs and place them within the broader scope of biological and synthetic aptamers. The development of PCCs is presented as (i) Generation I PCCs, which are branched ligands engineered through an iterative, nonepitope-targeted process, and (ii) Generation II PCCs, which are typically developed from macrocyclic peptide libraries and are precisely epitope-targeted. We provide statistical comparisons of Generation II PCCs relative to monoclonal antibodies in which the protein target is the same. Finally, we discuss current challenges and future opportunities of PCCs.
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The protein catalyzed capture agent (PCC) method is a powerful combinatorial screening strategy for discovering synthetic macrocyclic peptide ligands, called PCCs, to designated protein epitopes. The ...foundational concept of the PCC method is the use of in situ click chemistry to survey large combinatorial libraries of peptides for ligands to designated biological targets. State-of-the-art PCC screens integrate synthetic libraries of constrained macrocyclic peptides with epitope-specific targeting strategies to identify high-affinity (<100 nM) binders de novo. Automated instrumentation can accelerate PCC discovery to a rapid 2-week timeframe. Here, we describe methods to perform combinatorial screens that yield epitope-targeted PCCs.
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•Integrate PDMS chip with Q3D-PNAs SERS substrates into an optofluidic microsystem.•Enable real-time monitoring because of a short switch-off time.•Improve detection efficiency and ...lower the limit of detection via increasing the flow rate.•Offer a simple approach for online, label-free chemical and biological analysis.
Practical applications of chemical and biological detections through surface-enhanced Raman scattering (SERS) require high reproducibility, sensitivity, and efficiency, along with low-cost, straightforward fabrication. In this work, we integrated a poly-(dimethylsiloxane) (PDMS) chip with quasi-3D gold plasmonic nanostructure arrays (Q3D-PNAs), which serve as SERS-active substrates, into an optofluidic microsystem for online sensitive and reproducible SERS detections. The Q3D-PNA PDMS chip was fabricated through soft lithography to ensure both precision and low-cost fabrication. The optimal dimension of the Q3D-PNA in PDMS was designed using finite-difference time-domain (FDTD) electromagnetic simulations with a simulated enhancement factor (EF) of 1.6×106. The real-time monitoring capability of the SERS-based optofluidic microsystem was investigated by kinetic on/off experiments through alternatively flowing Rhodamine 6G (R6G) and ethanol in the microfluidic channel. A switch-off time of ∼2min at a flow rate of 0.3mLmin−1 was demonstrated. When applied to the detection of low concentration malathion, the SERS-based optofluidic microsystem with Q3D-PNAs showed high reproducibility, significantly improved efficiency and higher detection sensitivity via increasing the flow rate. The optofluidic microsystem presented in this paper offers a simple and low-cost approach for online, label-free chemical and biological analysis and sensing with high sensitivity, reproducibility, efficiency, and molecular specificity.
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The functional properties of proteorhodopsin (PR) have been found to be strongly modulated by oligomeric distributions and lipid membrane mimetics. This study aims to distinguish and explain their ...effects by investigating how oligomer formation impacts PR’s function of proton transport in lipid-based membrane mimetic environments. We find that PR forms stable hexamers and pentamers in both E. coli membranes and synthetic liposomes. Compared with the monomers, the photocycle kinetics of PR oligomers is ∼2 and ∼4.5 times slower for transitions between the K and M and the M and N photointermediates, respectively, indicating that oligomerization significantly slows PR’s rate of proton transport in liposomes. In contrast, the apparent pKa of the key proton acceptor residue D97 (pKaD97) of liposome-embedded PR persists at 6.2–6.6, regardless of cross-protomer modulation of D97, suggesting that the liposome environment helps maintain PR’s functional activity at neutral pH. By comparison, when extracted directly from E. coli membranes into styrene-maleic acid lipid particles, the pKaD97 of monomer-enriched E50Q PR drastically increases to 8.9, implying that there is a very low active PR population at neutral pH to engage in PR’s photocycle. These findings demonstrate that oligomerization impacts PR’s photocycle kinetics, while lipid-based membrane mimetics strongly affect PR’s active population via different mechanisms.
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We present here a detailed molecular-level understanding of the interactions among surface-functionalized mesoporous SBA-15 silica and pharmaceutical guests that influence macroscopic adsorption and ...release behaviors. A model drug species, methylprednisolone sodium succinate, was adsorbed on the surfaces of functionalized mesoporous SBA-15 silica materials with different aminoalkyl species and without or with C60 fullerene moieties. Zeta potential measurements show that the electrostatic interactions among methylprednisolone species and modified silica surfaces are important for the adsorption and release of the methylprednisolone molecules. Complementary one and two-dimensional (2D) solid-state 13C{1H} NMR measurements provide evidence for specific intermolecular interactions between adsorbed methylprednisolone species and different types of functionalized silica surfaces. In particular, correlated 13C and 1H signal intensities from the methylprednisolone alkyl moieties and the aminoalkyl groups of the functionalized silica surfaces unambiguously establish their close (<1 nm) molecular proximities and strong interactions. The molecular-level insights are correlated with macroscopic adsorption and release behaviors of methylprednisolone, providing detailed new understanding of the interactions responsible for the high loadings and slow release of this important pharmaceutical agent from surface-functionalized mesoporous materials.
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Antibiotic resistant infections are projected to cause over 10 million deaths by 2050, yet the development of new antibiotics has slowed. This points to an urgent need for methodologies for the rapid ...development of antibiotics against emerging drug resistant pathogens. We report on a generalizable combined computational and synthetic approach, called antibody-recruiting protein-catalyzed capture agents (AR-PCCs), to address this challenge. We applied the combinatorial protein catalyzed capture agent (PCC) technology to identify macrocyclic peptide ligands against highly conserved surface protein epitopes of carbapenem-resistant
Klebsiella pneumoniae
, an opportunistic Gram-negative pathogen with drug resistant strains. Multi-omic data combined with bioinformatic analyses identified epitopes of the highly expressed MrkA surface protein of
K. pneumoniae
for targeting in PCC screens. The top-performing ligand exhibited high-affinity (EC
50
∼50 nM) to full-length MrkA, and selectively bound to MrkA-expressing
K. pneumoniae
, but not to other pathogenic bacterial species. AR-PCCs that bear a hapten moiety promoted antibody recruitment to
K. pneumoniae
, leading to enhanced phagocytosis and phagocytic killing by macrophages. The rapid development of this highly targeted antibiotic implies that the integrated computational and synthetic toolkit described here can be used for the accelerated production of antibiotics against drug resistant bacteria.
Antibody-recruiting protein-catalyzed capture agent (AR-PCCs) are a new class of all-synthetic and highly targeted antibiotics that recruit endogenous immune responses to eliminate drug-resistant microbes.
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A versatile synthetic protocol is reported that allows high concentrations of functionally active membrane proteins to be incorporated in mesostructured silica materials. Judicious selections of ...solvent, surfactant, silica precursor species, and synthesis conditions enable membrane proteins to be stabilized in solution and during subsequent coassembly into silica–surfactant composites with nano- and mesoscale order. This was demonstrated by using a combination of nonionic (n-dodecyl-β-d-maltoside or Pluronic P123), lipid-like (1,2-diheptanoyl-s n-glycero-3-phosphocholine), and perfluoro-octanoate surfactants under mild acidic conditions to coassemble the light-responsive transmembrane protein proteorhodopsin at concentrations up to 15 wt % into the hydrophobic regions of worm-like mesostructured silica materials in films. Small-angle X-ray scattering, electron paramagnetic resonance spectroscopy, and transient UV–visible spectroscopy analyses established that proteorhodopsin molecules in mesostructured silica films exhibited native-like function, as well as enhanced thermal stability compared to surfactant or lipid environments. The light absorbance properties and light-activated conformational changes of proteorhodopsin guests in mesostructured silica films are consistent with those associated with the native H+-pumping mechanism of these biomolecules. The synthetic protocol is expected to be general, as demonstrated also for the incorporation of functionally active cytochrome c, a peripheral membrane protein enzyme involved in electron transport, into mesostructured silica–cationic surfactant films.
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