Multifunctional Biomolecules Bridging a Buried Interface for Efficient Perovskite Solar Cells.

The inevitably positively and negatively charged defects on the SnO2/perovskite buried interface often lead to nonradiative recombination of carriers and unfavorable alignment of energy levels in perovskite solar cells (PSCs). Interface engineering is a reliable strategy to manage charged defects. Herein, the nicotinamide adenine dinucleotide (NAD) molecules with multiple active groups of ─P=O, ─P-O, and ─NH2 are introduced to bridge the SnO2/perovskite buried interface for achieving simultaneous elimination of positively and negatively charged defects. We demonstrate that the ─P=O and ─P-O groups in NAD not only fix the uncoordinated Pb2+ but also fill the oxygen vacancies (VO) on the SnO2 layer to eliminate positively charged defects. Meanwhile, ─NH2 groups form hydrogen bonds with PbI2 to reduce the number of negatively charged defects. In addition, the NAD biomolecules as a bridge induce high perovskite crystallization and accelerated electronic transfer along with favorable energy band alignment between SnO2 and perovskite. Finally, the PSCs with the ITO/SnO2/NAD/Cs0.15FA0.75MA0.1PbI3/Spiro-OMeTAD/Ag structure deliver an improvement in the power conversion efficiency from 20.49 to 23.18% with an excellent open-circuit voltage (Voc) of 1.175 V. This work demonstrates that interface engineering through multifunctional molecular bridges with various functional groups is an effective approach to improve the performance of PSCs by eliminating charged defects and simultaneously regulating energy level alignment.

Protein Allostery Study in Cells Using NMR Spectroscopy.

Protein allostery is commonly observed in vitro. But how protein allostery behaves in cells is unknown. In this work, a protein monomer-dimer equilibrium system was built with the allosteric effect on the binding characterized using NMR spectroscopy through mutations away from the dimer interface. A chemical shift linear fitting method was developed that enabled us to accurately determine the dissociation constant. A total of 28 allosteric mutations were prepared and grouped to negative allosteric, nonallosteric, and positive allosteric modulators. ∼ 50% of mutations displayed the allosteric-state changes when moving from a buffered solution into cells. For example, there were no positive allosteric modulators in the buffered solution but eight in cells. The change in protein allostery is correlated with the interactions between the protein and the cellular environment. These interactions presumably drive the surrounding macromolecules in cells to transiently bind to the monomer and dimer mutational sites and change the free energies of the two species differently which generate new allosteric effects. These surrounding macromolecules create a new protein allostery pathway that is only present in cells.

Synergistic Defect Passivation and Crystallization Modulation in Efficient Perovskite Solar Cells: The Case of Multifunctional 2-Anisidine-4-Sulfonic Acid.

With the continuous development of the performance of perovskite solar cells, the high-density defects on the perovskite film surface and grain boundaries as well as undesired perovskite crystallization are increasingly emerging as challenges to their commercial application. Herein, a dye intermediate 2-anisidine-4-sulfonic acid (2A4SA), containing sulfonic acid group (SO3-), amino group (-NH2), methoxy group (CH3O-), and benzene ring, which exhibit a synergistic effect in comprehensive defect passivation and crystallization modulation, is incorporated. Detailed investigations show that the SO3- of 2A4SA with high electronegativity firmly chelates with uncoordinated lead ions through the coordination interaction, while the -NH2 and the CH3O- of 2A4SA separately immobilize iodide ions and organic cations in the perovskite lattice through hydrogen bonds, enabling substantially decreased nonradiative recombination and trap state density. Meanwhile, 2A4SA molecules attached to the surface of perovskite nuclei can delay crystallization kinetics and promote preferred vertical growth orientation, thereby attaining the high-crystallinity and large-size-grain perovskite films. Consequently, the 2A4SA-doped device with the structure ITO/SnO2/Cs0.15FA0.75MA0.10PbI3 (2A4SA)/Spiro-OMeTAD/Ag presents a splendid power conversion efficiency (PCE) of 23.06% accompanied by increased open-circuit voltage (1.15 V) and fill factor (82.17%). Furthermore, the optimized film and device demonstrate enhanced long-term stability. The unencapsulated optimized device retains ≈80% of the original PCE after 1000 h upon exposure to ambient atmosphere (20-50% RH), whereas the control group is only 56.8%.

Intracellular environment can change protein conformational dynamics in cells through weak interactions.

Conformational dynamics is important for protein functions, many of which are performed in cells. How the intracellular environment may affect protein conformational dynamics is largely unknown. Here, loop conformational dynamics is studied for a model protein in Escherichia coli cells by using nuclear magnetic resonance (NMR) spectroscopy. The weak interactions between the protein and surrounding macromolecules in cells hinder the protein rotational diffusion, which extends the dynamic detection timescale up to microseconds by the NMR spin relaxation method. The loop picosecond to microsecond dynamics is confirmed by nanoparticle-assisted spin relaxation and residual dipolar coupling methods. The loop interactions with the intracellular environment are perturbed through point mutation of the loop sequence. For the sequence of the protein that interacts stronger with surrounding macromolecules, the loop becomes more rigid in cells. In contrast, the mutational effect on the loop dynamics in vitro is small. This study provides direct evidence that the intracellular environment can modify protein loop conformational dynamics through weak interactions.

Biomimetic Epigallocatechin Gallate-Cerium Assemblies for the Treatment of Rheumatoid Arthritis.

Rheumatoid arthritis (RA) is an autoimmune and inflammatory disease that is so far incurable with long-term health risks. The high doses and frequent administration for the available RA drug always lead to adverse side effects. Aiming at the obstacles to achieving effective RA treatment, we prepared macrophage cell membrane-camouflaged nanoparticles (M-EC), which were assembled from epigallocatechin gallate (EGCG) and cerium(IV) ions. Due to its geometrical similarity to the active metal sites of a natural antioxidant enzyme, the EC possessed a high scavenge efficiency to various types of reactive oxygen species (ROS) and reactive nitrogen species (RNS). The macrophage cell membrane assisted M-EC in escaping from the immune system, being uptaken by inflammatory cells, and specifically binding IL-1ß. After tail vein injection to the collagen-induced arthritis (CIA) mouse model, the M-EC accumulated at inflamed joints and effectively repaired the bone erosion and cartilage damage of rheumatoid arthritis by relieving synovial inflammation and cartilage erosion. It is expected that the M-EC can not only pave a new way for designing metal-phenolic networks with better biological activity but also provide a more biocompatible therapeutic strategy for effective treatment of RA.

Improving the Enzymatic Activity and Stability of a Lytic Polysaccharide Monooxygenase.

Lytic Polysaccharide Monooxygenases (LPMOs) are copper-dependent enzymes that play a pivotal role in the enzymatic conversion of the most recalcitrant polysaccharides, such as cellulose and chitin. Hence, protein engineering is highly required to enhance their catalytic efficiencies. To this effect, we optimized the protein sequence encoding for an LPMO from Bacillus amyloliquefaciens (BaLPMO10A) using the sequence consensus method. Enzyme activity was determined using the chromogenic substrate 2,6-Dimethoxyphenol (2,6-DMP). Compared with the wild type (WT), the variants exhibit up to a 93.7% increase in activity against 2,6-DMP. We also showed that BaLPMO10A can hydrolyze p-nitrophenyl-ß-D-cellobioside (PNPC), carboxymethylcellulose (CMC), and phosphoric acid-swollen cellulose (PASC). In addition to this, we investigated the degradation potential of BaLPMO10A against various substrates such as PASC, filter paper (FP), and Avicel, in synergy with the commercial cellulase, and it showed up to 2.7-, 2.0- and 1.9-fold increases in production with the substrates PASC, FP, and Avicel, respectively, compared to cellulase alone. Moreover, we examined the thermostability of BaLPMO10A. The mutants exhibited enhanced thermostability with an apparent melting temperature increase of up to 7.5 °C compared to the WT. The engineered BaLPMO10A with higher activity and thermal stability provides a better tool for cellulose depolymerization.

Magnetic Resonance Diagnosis of Early Triple-Negative Breast Cancer Based on the Ionic Covalent Organic Framework with High Relaxivity and Long Retention Time.

Patients with triple-negative breast cancer (TNBC) have dismal prognoses due to the lack of therapeutic targets and susceptibility to lymph node (LN) metastasis. Therefore, it is essential to develop more effective approaches to identify early TNBC tissues and LNs. In this work, a magnetic resonance imaging (MRI) contrast agent (Mn-iCOF) was constructed based on the Mn(II)-chelated ionic covalent organic framework (iCOF). Because of the porous structure and hydrophilicity, the Mn-iCOF has a high longitudinal relaxivity (r1) of 8.02 mM-1 s-1 at 3.0 T. For the tumor-bearing mice, a lower dose (0.02 mmol [Mn]/kg) of Mn-iCOF demonstrated a higher signal-to-noise ratio (SNR) value (1.8) and longer retention time (2 h) compared to a 10-fold dose of commercial Gd-DOTA (0.2 mmol [Gd]/kg). Moreover, the Mn-iCOF can provide continuous and significant MR contrast for the popliteal LNs within 24 h, allowing for accurate evaluation and dissection of LNs. These excellent MRI properties of the Mn-iCOF may open new avenues for designing more biocompatible MRI contrast agents with higher resolutions, particularly in the diagnosis of TNBC.

Intelligent Clinical Lab for the Diagnosis of Post-Neurosurgical Meningitis Based on Machine-Learning-Aided Cerebrospinal Fluid Analysis.

Post-neurosurgical meningitis (PNM) often leads to serious consequences; unfortunately, the commonly used clinical diagnostic methods of PNM are time-consuming or have low specificity. To realize the accurate and convenient diagnosis of PNM, herein, we propose a comprehensive strategy for cerebrospinal fluid (CSF) analysis based on a machine-learning-aided cross-reactive sensing array. The sensing array involves three Eu3+-doped metal-organic frameworks (MOFs), which can generate specific fluorescence responding patterns after reacting with potential targets in CSF. Then, the responding pattern is used as learning data to train the machine learning algorithms. The discrimination confidence for artificial CSF containing different components of molecules, proteins, and cells is from 81.3 to 100%. Furthermore, the machine-learning-aided sensing array was applied in the analysis of CSF samples from post-neurosurgical patients. Only 25 µL of CSF samples was needed, and the samples could be robustly classified into "normal," "mild," or "severe" groups within 40 min. It is believed that the combination of machine learning algorithms with robust data processing capability and a lanthanide luminescent sensor array will provide a reliable alternative for more comprehensive, convenient, and rapid diagnosis of PNM.

Quantifying Protein Electrostatic Interactions in Cells by Nuclear Magnetic Resonance Spectroscopy.

Most proteins perform their functions in cells. How the cellular environment modulates protein interactions is an important question. In this work, electrostatic interactions between protein charges were studied using in-cell nuclear magnetic resonance (NMR) spectroscopy. A total of eight charge pairs were introduced in protein GB3. Compared to the charge pair electrostatic interactions in a buffer, five charge pairs in cells displayed no apparent changes whereas three pairs had the interactions weakened by more than 70%. Further investigation suggests that the transfer free energy is responsible for the electrostatic interaction modulation. Both the transfer free energy of the folded state and that of the unfolded state can contribute to the cellular environmental effect on protein electrostatics, although the latter is generally larger (more negative) than the former. Our work highlights the importance of direct in-cell studies of protein interactions and thus protein function.

Osmolytes Can Destabilize Proteins in Cells by Modulating Electrostatics and Quinary Interactions.

Although numerous in vitro studies have shown that osmolytes are capable of stabilizing proteins, their effect on protein folding in vivo has been less understood. In this work, we investigated the effect of osmolytes, including glycerol, sorbitol, betaine, and taurine, on the folding of a protein GB3 variant in E. coli cells using NMR spectroscopy. 400 mM osmolytes were added to E. coli cells; only glycerol stabilizes the folded protein, whereas betaine and taurine considerably destabilize the protein through modulating folding and unfolding rates. Further investigation indicates that betaine and taurine can enhance the quinary interaction between the protein and cellular environment and manifestly weaken the electrostatic attraction in protein salt bridges. The combination of the two factors causes destabilization of the protein in E. coli cells. These factors counteract the preferential exclusion mechanism that is adopted by osmolytes to stabilize proteins.

Characterization of Residue Specific Protein Folding and Unfolding Dynamics in Cells.

In this work, we measured the millisecond residue specific protein folding and unfolding dynamics in E. coli cells for two protein GB3 mutants using NMR. The results show that the protein folding and unfolding dynamics in cells is different from that in buffer. Through a two-site exchange model, it is shown that both the population and the exchange rate are changed by the E. coli cellular environment. Further investigation suggests that the change is likely due to the quinary interaction with crowded molecules in the cell. Our work underlines the importance of cellular environment to protein folding kinetics and thermodynamics although this environmental effect may not be large enough to change the protein structure.

Entropy Drives the Formation of Salt Bridges in the Protein GB3.

Salt bridges are very common in proteins. But what drives the formation of protein salt bridges is not clear. In this work, we determined the strength of four salt bridges in the protein GB3 by measuring the ΔpKa values of the basic residues that constitute the salt bridges with a highly accurate NMR titration method at different temperatures. The results show that the ΔpKa values increase with temperature, thus indicating that the salt bridges are stronger at higher temperatures. Fitting of ΔpKa values to the van't Hoff equation yields positive ΔH and ΔS values, thus indicating that entropy drives salt-bridge formation. Molecular dynamics simulations show that the protein and solvent make opposite contributions to ΔH and ΔS. Specifically, the enthalpic gain contributed from the protein is more than offset by the enthalpic loss contributed from the solvent, whereas the entropic gain originates from the desolvation effect.

A kinetic study of Trichoderma reesei Cel7B catalyzed cellulose hydrolysis.

One prominent feature of Trichoderma reesei (Tr) endoglucanases catalyzed cellulose hydrolysis is that the reaction slows down quickly after it starts (within minutes). But the mechanism of the slowdown is not well understood. A structural model of Tr- Cel7B catalytic domain bound to cellulose was built computationally and the potentially important binding residues were identified and tested experimentally. The 13 tested mutants show different binding properties in the adsorption to phosphoric acid swollen cellulose and filter paper. Though the partitioning parameter to filter paper is about 10 times smaller than that to phosphoric acid swollen cellulose, a positive correlation is shown for two substrates. The kinetic studies show that the reactions slow down quickly for both substrates. This slowdown is not correlated to the binding constant but anticorrelated to the enzyme initial activity. The amount of reducing sugars released after 24h by Cel7B in phosphoric acid swollen cellulose, Avicel and filter paper cellulose hydrolysis is correlated with the enzyme activity against a soluble substrate p-nitrophenyl lactoside. Six of the 13 tested mutants, including N47A, N52D, S99A, N323D, S324A, and S346A, yield ∼15-35% more reducing sugars than the wild type (WT) Cel7B in phosphoric acid swollen cellulose and filter paper hydrolysis. This study reveals that the slowdown of the reaction is not due to the binding of the enzyme to cellulose. The activity of Tr- Cel7B against the insoluble substrate cellulose is determined by the enzyme's capability in hydrolyzing the soluble substrate.

Cellulose chain binding free energy drives the processive move of cellulases on the cellulose surface.

Processivity is essential for cellulases in their catalysis of cellulose hydrolysis. But what drives the processive move is not well understood. In this work, we use Trichoderma reesei Cel7B as a model system and show that its processivity is directly correlated to the binding free energy difference of a cellulose chain occupying the binding sites -7 to +2 and that occupying sites -7 to -1. Several mutants that have stronger interactions with glycosyl units in sites +1 and +2 than the wild type enzyme show higher processivity. The results suggest that after the release of the product cellobiose located in sites +1 and +2, the enzyme pulls the cellulose chain to fill the vacant sites, which propels its processive move on the cellulose surface. Biotechnol. Bioeng. 2016;113: 1873-1880. © 2016 Wiley Periodicals, Inc.

Improving the activity of Trichoderma reesei cel7B through stabilizing the transition state.

Trichoderma reesei (Tr.) cellulases, which convert cellulose to reducing sugars, are a promising catalyst used in the lignocellulosic biofuel production. Improving Tr. cellulases activity, though very difficult, is highly desired due to the recalcitrance of lignocellulose. Meanwhile, it is preferable to enhance the cellulase's promiscuity so that substrates other than cellulose can also be hydrolyzed. In this work, an attempt is made to improve the catalytic activity of a major endogluanase Tr. Cel7B against xylan which crosslinks with cellulose in lignocellulose. By using quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations, the transition state of the xylo-oligosaccharide hydrolysis is identified. Then, mutations are introduced and their effect on the transition state stabilization is ranked based on the free energy calculations. Seven top ranked mutants are evaluated experimentally. Three mutants A208Q, A222D, and G230R show a higher activity than the wild-type Tr. Cel7B in the hydrolysis of xylan (by up to 47%) as well as filter paper (by up to 50%). The combination of the single mutants can further improve the enzyme activity. Our work demonstrates that the free energy method is effective in engineering the Tr. Cel7B activity against xylan and cellulose, and thus may also be useful for improving the activity of other Tr. cellulases. Biotechnol. Bioeng. 2016;113: 1171-1177. © 2015 Wiley Periodicals, Inc.

Integration of bacterial expansin-like proteins into cellulosome promotes the cellulose degradation.

Cellulosomes are multi-enzyme complexes assembled by cellulases and hemicellulases through dockerin-cohesin interactions, which are the most efficient system for the degradation of lignocellulosic resources in nature. Recent genomic analysis of a cellulosome-producing anaerobe Clostridium clariflavum DSM 19732 revealed that two expansin-like proteins, Clocl_1298 and Clocl_1862, contain a dockerin module, which suggests that they are components of the cellulosome. Bacterial expansin-like proteins do not have hydrolytic activities, but can facilitate the degradation of cellulosic biomass via synergistic effects with cellulases. In this study, the synergistic effect of the expansin-like proteins with both native and designer cellulosomes was investigated. The free expansin-like proteins, including expansin-like domains of Clocl_1298 and Clocl_1862, as well as a well-studied bacterial expansin-like protein BsEXLX1 from Bacillus subtilis, promoted the cellulose degradation by native cellulosomes, indicating the cellulosomal expansin-like proteins have the synergistic function. When they were integrated into a trivalent designer cellulosome, the synergistic effect was further amplified. The sequence and structure analyses indicated that these cellulosomal expansin-like proteins share the conserved functional mechanism with other bacterial expansin-like proteins. These results indicated that non-catalytic expansin-like proteins in the cellulosome can enhance the activity of the cellulosome in lignocellulose degradation. The involvement of functional expansin-like proteins in the cellulosome also implies new physiological functions of bacterial expansin-like proteins and cellulosomes.

Characterization of the Dielectric Constant in the Trichoderma reesei Cel7B Active Site.

An attempt is made to evaluate the dielectric constant of the Trichoderma reesei Cel7B active site. Through kinetic measurements, the pKa value of the catalytic acid E201 is determined. Mutations (away from E201) with net charge changes are introduced to perturb the E201 pKa. It is shown that the mutation with a +1 charge change (including G225R, G230R, and A335R) decreases the pKa of E201, whereas the mutation with a -1 charge change (including Q149E, A222D, G225D, and G230D) increases the pKa. This effect is consistent with the electrostatic interaction between the changed charge and the E201 side chain. The fitting of the experimental data yields an apparent dielectric constant of 25-80. Molecular dynamics simulations with explicit water molecules indicate that the high solvent accessibility of the active site contributes largely to the high dielectric constant. ONIOM calculations show that high dielectric constant benefits the catalysis through decreasing the energy of the transition state relative to that of the enzyme substrate complex.

Improving Trichoderma reesei Cel7B thermostability by targeting the weak spots.

For proteins that denature irreversibly, the denaturation is typically triggered by a partial unfolding, followed by a permanent change (e.g., aggregation). The regions that initiate the partial unfolding are named "weak spots". In this work, a molecular dynamics (MD) simulation and data analysis protocol is developed to identify the weak spots of Trichoderma reesei Cel7B, an important endoglucanase in cellulose hydrolysis, through assigning the local melting temperature (Tmp) to individual residue pairs. To test the predicted weak spots, a total of eight disulfide bonds were designed in these regions and all enhanced the enzyme thermostability. The increased stability, quantified by ΔT50 (which is the T50 difference between the mutant and the wild type enzyme), is negatively correlated with the MD-predicted Tmp, demonstrating the effectiveness of the protocol and highlighting the importance of the weak spots. Strengthening interactions in these regions proves to be a useful strategy in improving the thermostability of Tr. Cel7B.

Engineering a more thermostable blue light photo receptor Bacillus subtilis YtvA LOV domain by a computer aided rational design method.

The ability to design thermostable proteins offers enormous potential for the development of novel protein bioreagents. In this work, a combined computational and experimental method was developed to increase the T m of the flavin mononucleotide based fluorescent protein Bacillus Subtilis YtvA LOV domain by 31 Celsius, thus extending its applicability in thermophilic systems. Briefly, the method includes five steps, the single mutant computer screening to identify thermostable mutant candidates, the experimental evaluation to confirm the positive selections, the computational redesign around the thermostable mutation regions, the experimental reevaluation and finally the multiple mutations combination. The adopted method is simple and effective, can be applied to other important proteins where other methods have difficulties, and therefore provides a new tool to improve protein thermostability.