Open conformation of tetraspanins shapes interaction partner networks on cell membranes.

Tetraspanins, including CD53 and CD81, regulate a multitude of cellular processes through organizing an interaction network on cell membranes. Here, we report the crystal structure of CD53 in an open conformation poised for partner interaction. The large extracellular domain (EC2) of CD53 protrudes away from the membrane surface and exposes a variable region, which is identified by hydrogen-deuterium exchange as the common interface for CD53 and CD81 to bind partners. The EC2 orientation in CD53 is supported by an extracellular loop (EC1). At the closed conformation of CD81, however, EC2 disengages from EC1 and rotates toward the membrane, thereby preventing partner interaction. Structural simulation shows that EC1-EC2 interaction also supports the open conformation of CD81. Disrupting this interaction in CD81 impairs the accurate glycosylation of its CD19 partner, the target for leukemia immunotherapies. Moreover, EC1 mutations in CD53 prevent the chemotaxis of pre-B cells toward a chemokine that supports B-cell trafficking and homing within the bone marrow, a major CD53 function identified here. Overall, an open conformation is required for tetraspanin-partner interactions to support myriad cellular processes.

Footprinting Mass Spectrometry of Membrane Proteins: Ferroportin Reconstituted in Saposin A Picodiscs.

Membrane proteins participate in a broad range of cellular processes and represent more than 60% of drug targets. One approach to their structural analyses is mass spectrometry (MS)-based footprinting including hydrogen/deuterium exchange (HDX), fast photochemical oxidation of proteins (FPOP), and residue-specific chemical modification. Studying membrane proteins usually requires their isolation from the native lipid environment, after which they often become unstable. To overcome this problem, we are pursuing a novel methodology of incorporating membrane proteins into saposin A picodiscs for MS footprinting. We apply different footprinting approaches to a model membrane protein, mouse ferroportin, in picodiscs and achieve high coverage that enables the analysis of the ferroportin structure. FPOP footprinting shows extensive labeling of the extramembrane regions of ferroportin and protection at its transmembrane regions, suggesting that the membrane folding of ferroportin is maintained throughout the labeling process. In contrast, an amphipathic reagent, N-ethylmaleimide (NEM), efficiently labels cysteine residues in both extramembrane and transmembrane regions, thereby affording complementary footprinting coverage. Finally, optimization of sample treatment gives a peptic-map of ferroportin in picodiscs with 92% sequence coverage, setting the stage for HDX. These results, taken together, show that picodiscs are a new platform broadly applicable to mass spectrometry studies of membrane proteins.

Missense VKOR mutants exhibit severe warfarin resistance but lack VKCFD via shifting to an aberrantly reduced state.

Missense vitamin K epoxide reductase (VKOR) mutations in patients cause resistance to warfarin treatment but not abnormal bleeding due to defective VKOR activity. The underlying mechanism of these phenotypes remains unknown. Here we show that the redox state of these mutants is essential to their activity and warfarin resistance. Using a mass spectrometry-based footprinting method, we found that severe warfarin-resistant mutations change the VKOR active site to an aberrantly reduced state in cells. Molecular dynamics simulation based on our recent crystal structures of VKOR reveals that these mutations induce an artificial opening of the protein conformation that increases access of small molecules, enabling them to reduce the active site and generating constitutive activity uninhibited by warfarin. Increased activity also compensates for the weakened substrate binding caused by these mutations, thereby maintaining normal VKOR function. The uninhibited nature of severe resistance mutations suggests that patients showing signs of such mutations should be treated by alternative anticoagulation strategies.

Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps.

The SARS-CoV-2 Omicron variant, with 15 mutations in Spike receptor-binding domain (Spike-RBD), renders virtually all clinical monoclonal antibodies against WT SARS-CoV-2 ineffective. We recently engineered the SARS-CoV-2 host entry receptor, ACE2, to tightly bind WT-RBD and prevent viral entry into host cells ("receptor traps"). Here we determine cryo-EM structures of our receptor traps in complex with stabilized Spike ectodomain. We develop a multi-model pipeline combining Rosetta protein modeling software and cryo-EM to allow interface energy calculations even at limited resolution and identify interface side chains that allow for high-affinity interactions between our ACE2 receptor traps and Spike-RBD. Our structural analysis provides a mechanistic rationale for the high-affinity (0.53-4.2 nM) binding of our ACE2 receptor traps to Omicron-RBD confirmed with biolayer interferometry measurements. Finally, we show that ACE2 receptor traps potently neutralize Omicron and Delta pseudotyped viruses, providing alternative therapeutic routes to combat this evolving virus.

A Characteristic Interval Modeling Method for Simultaneous Detection of Multiple Metal Ions.

Aiming at the problems of low accuracy and large prediction errors caused by the serious overlap of multi-metal spectral signals in zinc smelting industrial wastewater, a characteristic interval modeling method is proposed. First, according to the absorption spectra of mixed solution, the characteristic intervals of copper and nickel are preliminarily screened by using different partition lengths. Second, take the smallest root mean squares error of cross validation and the largest correlation coefficient as the evaluation indicators, compare the full-spectral model and each local model, and select the optimal feature sub-intervals of copper and nickel. Last, the partial least squares method is used to model the combined wavelengths of the optimal sub-intervals to realize the simultaneous detection of copper and nickel. The linear determination ranges are 0.3-3.0 mg/L for copper and nickel. the correlation coefficients of copper and nickel are 0.9974 and 0.9966, respectively. The results show that the method reduces the complexity of the wavelength variable screening process, improves the accuracy of the model, and lays the foundation for the accurate analysis of polymetallic ions in zinc smelting industrial wastewater.

Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps.

The SARS-CoV-2 Omicron variant, with 15 mutations in Spike receptor binding domain (Spike-RBD), renders virtually all clinical monoclonal antibodies against WT SARS-CoV-2 ineffective. We recently engineered the SARS-CoV-2 host entry receptor, ACE2, to tightly bind WT-Spike-RBD and prevent viral entry into host cells ("receptor traps"). Here we determine cryo-EM structures of our receptor traps in complex with full length Spike. We develop a multi-model pipeline combining Rosetta protein modeling software and cryo-EM to allow interface energy calculations even at limited resolution and identify interface side chains that allow for high affinity interactions between our ACE2 receptor traps and Spike-RBD. Our structural analysis provides a mechanistic rationale for the high affinity (0.53 - 4.2nM) binding of our ACE2 receptor traps to Omicron-RBD confirmed with biolayer interferometry measurements. Finally, we show that ACE2 receptor traps potently neutralize Omicron- and Delta-pseudotyped viruses, providing alternative therapeutic routes to combat this evolving virus.

A Nonlinear Integrated Modeling Method of Extended Kalman Filter Based on Adaboost Algorithm.

In the zinc hydrometallurgical purification process, the concentration ratio of zinc ion to trace nickel ion is as high as 105, so that the nickel spectral signal is completely covered by high concentration zinc signal, resulting in low sensitivity and nonlinear characteristics of nickel spectral signal. Aiming at the problem that it is difficult to detect nickel in zinc sulfate solution, this paper proposes a nonlinear integrated modeling method of extended Kalman filter based on Adaboost algorithm. First, a non-linear nickel model is established based on nickel standard solution. Second, an extended Kalman filter wavelength optimization method based on correlation coefficient is proposed to select wavelength variables with high signal sensitivity, large amount of information and strong nonlinear correlation. Finally, a nonlinear integrated modeling method based on Adaboost algorithm is proposed, which uses extended Kalman filter as a basic submodel, and realizes the stable detection of trace nickel through the weighted combination of multiple basic models. The results show that the average relative error of this method for detecting nickel is 4.56%, which achieves accurate detection of trace nickel in zinc sulfate solution.

Sentinel cells enable genetic detection of SARS-CoV-2 Spike protein.

The COVID-19 pandemic has demonstrated the need for exploring different diagnostic and therapeutic modalities to tackle future viral threats. In this vein, we propose the idea of sentinel cells, cellular biosensors capable of detecting viral antigens and responding to them with customizable responses. Using SARS-CoV-2 as a test case, we developed a live cell sensor (SARSNotch) using a de novo-designed protein binder against the SARS-CoV-2 Spike protein. SARSNotch is capable of driving custom genetically-encoded payloads in immortalized cell lines or in primary T lymphocytes in response to purified SARS-CoV-2 Spike or in the presence of Spike-expressing cells. Furthermore, SARSNotch is functional in a cellular system used in directed evolution platforms for development of better binders or therapeutics. In keeping with the rapid dissemination of scientific knowledge that has characterized the incredible scientific response to the ongoing pandemic, we extend an open invitation for others to make use of and improve SARSNotch sentinel cells in the hopes of unlocking the potential of the next generation of smart antiviral therapeutics.

A spectrophotometric method for simultaneous determination of trace ions of copper, cobalt, and nickel in the zinc sulfate solution by ultraviolet-visible spectrometry.

In the zinc sulfate solution, the concentration ratio of zinc to metal ion impurities can be up to 105, which causes impurity ion signals to be severely masked by the zinc signal. In particular, nickel exhibits a strong nonlinearity. Conventional spectroscopic methods are commonly used to detect multi-component analytes with similar concentrations and require the detection component to be linear to satisfy Beer-Lambert law. In order to solve high concentration ratio and nonlinear problems, a spectrophotometric method combining the extended Kalman filter and derivative methods is proposed to simultaneously determine copper, cobalt and nickel in the zinc sulfate solution by ultraviolet-visible spectroscopy. The derivative method developed by using continuous wavelet transform with a Haar wavelet function was applied to detect copper and cobalt in regions with wavelengths greater than 500nm, in which the absorbance of zinc and nickel changed to a fixed value, where linear regression graphs for copper and cobalt were established at zero-crossing wavelengths. Extended Kalman filter spectrophotometry is a filtering algorithm for nonlinear systems, so it was proposed to iteratively detect nickel concentration. The detection range was found to be 0.5-5mg/L for copper, 0.3-3mg/L for cobalt, and 0.6-6mg/L. The predicted root mean square error was 0.097 for copper, 0.049 for cobalt, and 0.206 for nickel. The average relative deviations of copper, cobalt, and nickel in 10 sets of mixed solutions were 3.19%, 2.23%, and 4.56%, respectively. The spectrophotometric method studied is suitable for real-time detection and control of trace amounts of copper, cobalt, and nickel in purification process of zinc hydrometallurgy, and can be applied to more fields.

Warfarin traps human vitamin K epoxide reductase in an intermediate state during electron transfer.

Although warfarin is the most widely used anticoagulant worldwide, the mechanism by which warfarin inhibits its target, human vitamin K epoxide reductase (hVKOR), remains unclear. Here we show that warfarin blocks a dynamic electron-transfer process in hVKOR. A major fraction of cellular hVKOR is in an intermediate redox state containing a Cys51-Cys132 disulfide, a characteristic accommodated by a four-transmembrane-helix structure of hVKOR. Warfarin selectively inhibits this major cellular form of hVKOR, whereas disruption of the Cys51-Cys132 disulfide impairs warfarin binding and causes warfarin resistance. Relying on binding interactions identified by cysteine alkylation footprinting and mass spectrometry coupled with mutagenesis analysis, we conducted structure simulations, which revealed a closed warfarin-binding pocket stabilized by the Cys51-Cys132 linkage. Understanding the selective warfarin inhibition of a specific redox state of hVKOR should enable the rational design of drugs that exploit the redox chemistry and associated conformational changes in hVKOR.

Single-exposure optical focusing inside scattering media using binarized time-reversed adapted perturbation.

Light scattering inhibits high-resolution optical imaging, manipulation and therapy deep inside biological tissue by preventing focusing. To form deep foci, wavefront shaping techniques that break the optical diffusion limit have been developed. For in vivo applications, such focusing must provide high gain, high speed, and a high focal peak-to-background ratio. However, none of the previous techniques meet these requirements simultaneously. Here, we overcome this challenge by rapidly measuring the perturbed optical field within a single camera exposure followed by adaptively time-reversing the phase-binarized perturbation. Consequently, a phase-conjugated wavefront is synthesized within a millisecond, two orders of magnitude shorter than the digitally achieved record. We demonstrated real-time focusing in dynamic scattering media, and extended laser speckle contrast imaging to new depths. The unprecedented combination of fast response, high gain, and high focusing contrast makes this work a major stride toward in vivo deep tissue optical imaging, manipulation, and therapy.