Structural and functional analysis of EntV reveals a 12 amino acid fragment protective against funga
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Cruz, Melissa R.↗
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Fission fragment decay simulations with the CGMF code
The CGMF code implements the Hauser-Feshbach statistical nuclear reaction model to follow the de-excitation of fission fragments by successive emissions of prompt neutrons and γ rays. The Monte Carlo technique is used to facilitate the analysis of complex distributions and correlations among the prompt fission observables. Starting from initial configurations for the fission fragments in mass, charge, kinetic energy, excitation energy, spin, and parity, Y(A,Z,KE,U,J,π), CGMF samples neutron and γ-ray probability distributions at each stage of the decay process, conserving energy, spin and parity. Nuclear structure and reaction input data from the RIPL3 library are used to describe fission fragment properties and decay probabilities. Characteristics of prompt fission neutrons, prompt fission γ rays, and independent fission yields can be studied consistently. Correlations in energy, angle and multiplicity among the emitted neutrons and γ rays can be easily analyzed as a function of the emitting fragments. Finally, in its current version, CGMF is limited to certain spontaneous fission reactions on Pu and Cf isotopes, as well as neutron-induced fission reactions up to 20 MeV on U, Np, and Pu isotopes.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Strong-field induced fragmentation and isomerization of toluene probed by ultrafast femtosecond electron diffraction and mass spectrometry
We investigate the fragmentation and isomerization of toluene molecules induced by strong-field ionization with a femtosecond near-infrared laser pulse. Momentum-resolved coincidence time-of-flight ion mass spectrometry is used to determine the relative yield of different ionic products and fragmentation channels as a function of laser intensity. Ultrafast electron diffraction is used to capture the structure of the ions formed on a picosecond time scale by comparing the diffraction signal with theoretical predictions. Through the combination of the two measurements and theory, we are able to determine the main fragmentation channels and to distinguish between ions with identical mass but different structures. In addition, our diffraction measurements show that the independent atom model, which is widely used to analyze electron diffraction patterns, is not a good approximation for diffraction from ions. Here, we show that the diffraction data is in very good agreement with ab initio scattering calculations.
74 ATOMIC AND MOLECULAR PHYSICS↗
Fragmentation of jets containing a prompt J$/\psi$ meson in PbPb and pp collisions at $\sqrt{s_\mathrm{NN}} =$ 5.02 TeV
Jets containing a prompt J$/\psi$ meson are studied in lead-lead collisions at a nucleon-nucleon center-of-mass energy of 5.02 TeV, using the CMS detector at the LHC. Jets are selected to be in the transverse momentum range of 30 $\lt p_\mathrm{T} \lt$ 40 GeV. The J$/\psi$ yield in these jets is evaluated as a function of the jet fragmentation variable $z$, the ratio of the J$/\psi$$p_\mathrm{T} $ to the jet $p_\mathrm{T}$. The nuclear modification factor, $R_\mathrm{AA}$, is then derived by comparing the yield in lead-lead collisions to the corresponding expectation based on proton-proton data, at the same nucleon-nucleon center-of-mass energy. The suppression of the J$/\psi$ yield shows a dependence on $z$, indicating that the interaction of the J$/\psi$ with the quark-gluon plasma formed in heavy ion collisions depends on the fragmentation that gives rise to the J$/\psi$ meson.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Embedding Thiols into Choline Phosphate Polymer Zwitterions
Abstract The compositional scope of polymer zwitterions has grown significantly in recent years and now offers designer synthetic materials that are broadly applicable across numerous areas, including supracolloidal structures, electronic materials interfaces, and macromolecular therapeutics. Among recent developments in polymer zwitterion syntheses are those that allow insertion of reactive functionality directly into the zwitterionic moiety, yielding new monomer and polymer structures that hold potential for maximizing the impact of zwitterions on the macromolecular materials chemistry field. This manuscript describes the preparation of zwitterionic choline phosphate (CP) methacrylates containing either aromatic or aliphatic thiols embedded directly into the zwitterionic moiety. The polymerization of these functional CP methacrylates by reversible addition‐fragmentation chain‐transfer methodology yields polymeric zwitterionic thiols containing protected thiol functionality in the zwitterionic units. After polymerization, the protected thiols are liberated to yield thiol‐rich polymer zwitterions which serve as precursors to subsequent reactions that produce polymer networks as well as polymer‐protein bioconjugates.
Polymer Science↗
Fragmentation dynamics through geometrical distortion in low-energy electron attachment to carbon disulfide
The dissociation dynamics of dissociative electron attachment to carbon disulfide is studied using the velocity map imaging technique. Ion yields of the S− and CS− fragments are measured as a function of incident electron energy between 2 and 12 eV. Energy and angle-differential yields of the S− fragments are analyzed to investigate the dynamics of the CS2− anion around the 3.8-eV peak. The resonances involved in this fragmentation are identified and characterized in calculations using the well-known R-matrix method. Based on our measurements and the geometry dependence of the calculated resonances, we propose that a geometrical distortion of the transient negative-ion state of CS2 is necessary for S-CS bond dissociation to occur.
Paul, Anirban↗
Development of Human Carbonic Anhydrase II Heterobifunctional Degraders
Human carbonic anhydrase II (hCAII) is a metalloenzyme essential to critical physiological processes in the body. hCA inhibitors are used clinically for the treatment of indications ranging from glaucoma to epilepsy. Targeted protein degraders have emerged as a promising means of inducing the degradation of disease-implicated proteins by using the endogenous quality control mechanisms of a cell. Here, a series of heterobifunctional degrader candidates targeting hCAII were developed from a simple aryl sulfonamide fragment. Degrader candidates were functionalized to produce either cereblon E3 ubiquitin ligase (CRBN) recruiting proteolysis targeting chimeras (PROTACs) or adamantyl-based hydrophobic tags (HyTs). Screens in HEK293 cells identified two PROTAC small-molecule degraders of hCA. Optimization of linker length and composition yielded a degrader with sub-nanomolar potency and sustained depletion of hCAII over prolonged treatments. Mechanistic studies suggest that this optimized degrader depletes hCAII through the same mechanism as previously reported CRBN-recruiting heterobifunctional degraders.
60 APPLIED LIFE SCIENCES↗
Low-energy electron driven reactions in 2-bromo-5-nitrothiazole
Thiazole derivatives are biologically relevant molecules, used also in pharmaceutical applications. Herein, we report results for electron attachment to 2-bromo-5-nitrothiazole (BNT) in the gas phase. Employing two crossed electron–molecule beam experiments, we determined the efficiency curves of various fragment anions as a function of the initial electron energy between about 0 and 10 eV as well as the emission angle and kinetic energy distributions of Br− and NO2− ions formed from a resonance near 4 eV. The experiments were supported by quantum chemical calculations, exploring possible dissociation pathways along with their reaction energies. We also compared the electron attachment characteristics of BNT with those of the native thiazole molecule by performing electron attachment experiments and calculations for this molecule as well. Compared to thiazole, which is primarily degraded only by electrons with kinetic energies between about 5 and 10 eV, BNT is susceptible to low-energy electrons near 0 eV with enhanced cross section for (dissociative) electron attachment. However, although BNT offers two localization sites with high electron affinity (Br and NO2 moieties), we do not find the corresponding anions as the dominant negatively charged species formed upon electron attachment. Instead, the reaction channels with an abstraction of Br and NO2 as neutral radicals prevail, accompanied by the opening of the thiazole ring due to the relatively weak C–S bond.
Chen, Jiakuan (ORCID:0009000729608641)↗
Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER
Structure determination of novel biological macromolecules by X-ray crystallography can be facilitated by the use of small structural fragments, some of only a few residues in length, as effective search models for molecular replacement to overcome the phase problem. Independence from the need for a complete pre-existing model with sequence similarity to the crystallized molecule is the primary appeal of ARCIMBOLDO , a suite of programs which employs this ab initio algorithm for phase determination. Here, the use of ARCIMBOLDO is investigated to overcome the phase problem with the electron cryomicroscopy (cryoEM) method known as microcrystal electron diffraction (MicroED). The results support the use of the ARCIMBOLDO_SHREDDER pipeline to provide phasing solutions for a structure of proteinase K from 1.6 Å resolution data using model fragments derived from the structures of proteins sharing a sequence identity of as low as 20%. ARCIMBOLDO_SHREDDER identified the most accurate polyalanine fragments from a set of distantly related sequence homologues. Alternatively, such templates were extracted in spherical volumes and given internal degrees of freedom to refine towards the target structure. Both modes relied on the rotation function in Phaser to identify or refine fragment models and its translation function to place them. Model completion from the placed fragments proceeded through phase combination of partial solutions and/or density modification and main-chain autotracing using SHELXE . The combined set of fragments was sufficient to arrive at a solution that resembled that determined by conventional molecular replacement using the known target structure as a search model. This approach obviates the need for a single, complete and highly accurate search model when phasing MicroED data, and permits the evaluation of large fragment libraries for this purpose.
59 BASIC BIOLOGICAL SCIENCES↗
Bridging the gap between molecules and materials in quantum chemistry with localized active spaces
The number of materials that “bridge the gap” between single molecules and extended solids, such as metal-organic frameworks and organic semiconductors, has been increasing. Consequently, there is a growing need for modeling approaches that effectively integrate the real-space molecular perspective employed by computational chemists and the reciprocal-space dispersive perspective employed by computational physicists. Here, we propose the localized active space (LAS) approach as a promising method to successfully bridge this gap. The LAS approach extends the active space concept from multiconfigurational methods such as complete active space self-consistent field theory to multiple molecular fragments via a product-form wave function ansatz. Here, we apply this method to solid state phenomena by treating each unit cell as a fragment with different sets of local quantum numbers (e.g., charge and excitation number). State interaction between these LAS states (LASSI) thus provides a comprehensive basis for the study of charge and energy transfer, meeting and surpassing the capabilities of single-reference fragmentation approaches such as constrained density functional theory (cDFT). Most centrally, we show how combining this LASSI approach with multiconfigurational pair-density functional theory (MC-PDFT) provides an elegant and efficient method to compute band structures that capture multiconfigurational character. We apply the LASSI band structure approach to the computation of band gaps in stretched hydrogen chain, polyacetylene, and bulk nickel oxide (NiO), finding good or excellent quantitative agreement with reference values in all cases. Additionally, we use the LAS basis in one-dimensional model systems to demonstrate its ability to treat difficult solid-state phenomena such as exciton transfer and excitation at p-n junctions.
method development↗
Enhanced Optical Contrast and Switching in Near‐Infrared Electrochromic Devices by Optimizing Conjugated Polymer Oligo(Ethylene Glycol) Sidechain Content and Gel Electrolyte Composition
Abstract A detailed investigation addressing the effects of functionalizing conjugated polymers with oligo(ethylene glycol) (EG n ) sidechains on the performance and polymer‐electrolyte compatibility of electrochromic devices (ECDs) is reported. The electrochemistry for a series of donor‐acceptor copolymers having near‐infrared (NIR)‐optical absorption, where the donor fragment is 3,4‐ethylenedioxythiophene (EDOT) or an EG n functionalized bithiophene (g2T) and the acceptor fragment is diketopyrrolopyrrole (DPP) functionalized with branched alkyl or EG n sidechains, is extensively probed. ECDs are next fabricated and it is found that EG n sidechain incorporation must be finely balanced to promote polymer‐electrolyte compatibility and provide efficient ion exchange. Proper electrolyte‐cation pairing and polymer structural tuning affords a 2x increase in optical contrast (from 12% to 24%) and >60x reduction in switching time (from 20 to 0.3 s). Atomic force microscopy (AFM)/grazing incidence wide‐angle X‐ray scattering (GIWAXS) characterization of the polymer film morphology/microstructure reveals that an over‐abundance of EG n sidechains generates large polymer crystallites, which can suppress ion exchange. Lastly, time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) indicates sidechain/electrolyte identity does not influence the electrolyte penetration depth into the films, and EG n sidechain inclusion increases electrolyte cation uptake. The material structural design insight and guidelines regarding the polymer‐electrolyte ion insertion/expulsion dynamics reported here should be of significant utility for developing next‐generation mixed ionic‐electronic conducting materials.
Chemistry↗
Green’s function coupled cluster simulation of the near-valence ionizations of DNA-fragments
Accurate description of the ionization process in DNA is crucial to the understanding of the DNA damage under exposure to ionizing radiation and the exploration of the potential application of DNA strands in nanoelectronics. In this work, by employing our recently developed Green’s function coupled-cluster library on supercomputing facilities, we have studied the spectral functions of several guanine–cytosine (G–C) base pair structures ([G–C]n, n = 1–3) for the first time in a relatively broad near-valence regime ([−25.0, −5.0] eV) in the coupled-cluster with singles and doubles level. Our focus is to give a preliminary many-body coupled-cluster understanding and guideline of the vertical ionization energy (VIE), spectral profile, and ionization feature changes of these systems as the system size expands in this near-valence regime. The results show that, as the system size expands, even though the lowest VIEs keep decreasing, the changes of spectral function profile and the relative peak positions get unexpectedly smaller. Further analysis of the ionized states associated with the most intensive peak in the spectral functions reveals non-negligible |2h, 1p⟩’s in the ionized wave functions of the considered G–C base pair systems. The leading |2h, 1p⟩’s associated with the main ionizations from the cytosine part of the G–C base pairs feature a transition from the intra-base-pair cytosine π → π* excitation to the inter-base-pair electron excitation as the size of G–C base pairs expands, which also indicates the minimum quantum region in the many-body calculations of DNA systems.
Peng, Bo (ORCID:0000000242267294)↗
Engineering a new tripartite split-ccGFP system from Corynactis californica for detecting protein–protein interactions
Protein-protein interactions (PPIs) are critical to a range of biological processes and, consequently, aberrant interactions are implicated in many disorders. The study of the complex networks of PPIs promises to elucidate undiscovered roles in cellular processes and the mechanisms of disease. To accomplish this, tools to effectively sense PPIs are necessary. Effective PPI sensors must rapidly detect interactions in real-time with high sensitivity without perturbing the proteins of interest (POIs) under study. Split fluorescent proteins have previously been used to successfully monitor PPIs, in part due to the small size of the tags. Here, we developed an optimized tripartite split GFP system based on Corynactis californica GFP (ccGFP) to detect PPIs in vitro. In this sensor system, ccGFP fragments ccGFP10 and ccGFP11 are tagged to two POIs. PPIs can then be detected via fluorescence by complementation to the third fragment, ccGFP1-9, which reconstitutes functional ccGFP. The optimized ccGFP system shows improved detection kinetics and pH and temperature stability compared to a previous system. We then validated the sensor by monitoring PPIs in two model systems: attractive/repulsive coiled-coils and rapamycin-inducible FRB/FKBP heterodimerization. Finally, we developed an anti-tripartite ccGFP single-chain variable fragment (scFv), which could enable versatile detection of identified protein-protein complexes.
59 BASIC BIOLOGICAL SCIENCES↗
Therapeutic efficacy of a potent anti-Venezuelan equine encephalitis virus antibody is contingent on Fc effector function
The development of specific, safe, and potent monoclonal antibodies (Abs) has led to novel therapeutic options for infectious disease. In addition to preventing viral infection through neutralization, Abs can clear infected cells and induce immunomodulatory functions through engagement of their crystallizable fragment (Fc) with complement proteins and Fc receptors on immune cells. Little is known about the role of Fc effector functions of neutralizing Abs in the context of encephalitic alphavirus infection. To determine the role of Fc effector function in therapeutic efficacy against Venezuelan equine encephalitis virus (VEEV), we compared the potently neutralizing anti-VEEV human IgG F5 (hF5) Ab with intact Fc function (hF5-WT) or containing the loss of function Fc mutations L234A and L235A (hF5-LALA) in the context of VEEV infection. We observed significantly reduced binding to complement and Fc receptors, as well as differential in vitro kinetics of Fc-mediated cytotoxicity for hF5-LALA compared to hF5-WT. The in vivo efficacy of hF5-LALA was comparable to hF5-WT at -24 and + 24 h post infection, with both Abs providing high levels of protection. However, when hF5-WT and hF5-LALA were administered + 48 h post infection, there was a significant decrease in the therapeutic efficacy of hF5-LALA. Together these results demonstrate that optimal therapeutic Ab treatment of VEEV, and possibly other encephalitic alphaviruses, requires neutralization paired with engagement of immune effectors via the Fc region.
59 BASIC BIOLOGICAL SCIENCES↗
Porting Fragmentation Methods to Graphical Processing Units Using an OpenMP Application Programming Interface: Offloading the Fock Build for Low Angular Momentum Functions
Here, a framework to offload four-index two-electron repulsion integrals to graphical processing units (GPUs) using OpenMP is discussed. The method has been applied to the Fock build for low angular momentum s and p functions in both the restricted Hartree–Fock (RHF) and in the effective fragment molecular orbital (EFMO) framework. Benchmark calculations for the GPU code for the pure RHF method show an increasing speedup relative to the existing OpenMP CPU code in GAMESS from 1.04 to 52× for clusters of 70–569 water molecules. The parallel efficiency on 24 NVIDIA V100 GPU boards also increases when increasing the system size: from 75 to 94% for water clusters that contain 303–1120 molecules. In the EFMO framework, the GPU Fock build shows a high linear scalability up to 4608 V100s with a parallel efficiency of 96% for calculations on a solvated mesoporous silica nanoparticle system with ~67,000 basis functions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Surface Functionalization of Black Phosphorus with Nitrenes: Identification of P=N Bonds Using Isotopic Labeling
Abstract: Surface functionalization of two-dimensional crystals is a key path to tuning their intrinsic physical and chemical properties. However, synthetic protocols and experimental strategies to directly probe chemical bonding in modified surfaces are scarce. Introduced here is a mild, surface-specific protocol for the surface functionalization of few-layer black phosphorus nanosheets using a family of photolytically generated nitrenes (RN) from the corresponding azides. By embedding spectroscopic tags in the organic backbone, a multitude of characterization techniques are employed to investigate in detail the chemical structure of the modified nanosheets, including vibrational (infrared, Raman), Xray (emission, photoelectron), CPMAS NMR, and UV-vis spectroscopy. To directly probe the functional groups introduced on the surface, R fragments were selected such that in conjunction with vibrational spectroscopy, 15N-labeling experiments, and DFT methods, diagnostic P=N vibrational modes indicative of iminophosphorane units on the nanosheet surface could be conclusively identified.
Walz, Kendall↗
Generation, dynamics, and correlations of the fission fragments' angular momenta
The generation of angular momentum in fissioning nuclei is not well understood. The predictions of different models disagree, particularly concerning the correlation between the fragments' angular momenta. In this article, a time-dependent collective Hamiltonian model is proposed to treat the generation of the angular momentum in the fission fragments due to the quantum uncertainty principle as well as the dynamics of the collective wave function during and after scission. The model is constructed in the framework of the frozen Hartree-Fock approximation using a Skyrme energy functional to extract deformations of the fission fragments as well as the interactions in a derived collective Hamiltonian. The fission reactions studied are $^{240}$Pu $\rightarrow$ $^{132}$Sn+$^{108}$Ru and $^{240}$Pu $\rightarrow$ $^{144}$Ba+$^{96}$Sr. The model can account for a large part of the angular momentum found in experimental data. The orientation of the angular momentum of each fragment is found to be mainly in the plane perpendicular to the fission axis, in agreement with the experiment. The magnitudes of the angular momenta in the two fragments are nearly uncorrelated, in agreement with the recent experimental data of Wilson et al., Nature (London) 590, 566 (2021). Some of the conclusions of the traditional collective vibration model are supported by the present model but some are not. Surprisingly, it is found that the angular momenta of the fragments are slightly correlated positively as in a wriggling mode. As a result, it is also found that the presence of an octupole deformation in a fragment can significantly increase the generated angular momentum.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
An experimental and computational view of the photoionization of diol–water clusters
In the interstellar medium, diols and other prebiotic molecules adsorb onto icy mantles surrounding dust grains. Water in the ice may affect the reactivity and photoionization of these diols. Ethylene glycol (EG), 1,2-propylene glycol, and 1,3-propylene glycol clusters with water clusters were used as a proxy to study these interactions. The diol–water clusters were generated in a continuous supersonic molecular beam, photoionized by synchrotron-based vacuum ultraviolet light from the Advanced Light Source, and subsequently detected by reflectron time-of-flight mass spectrometry. The appearance energies for the detected clusters were determined from the mass spectra, collected at increasing photon energy. Clusters of both diol fragments and unfragmented diols with water were detected. The lowest energy geometry optimized conformers for the observed EG–water clusters and EG fragment–water clusters have been visualized using density functional theory (DFT), providing insight into hydrogen bonding networks and how these affect fragmentation and appearance energy. As the number of water molecules clustered around EG fragments (m/z 31 and 32) increased, the appearance energy for the cluster decreased, indicating a stabilization by water. This trend was supported by DFT calculations. Fragment clusters from 1,2-propylene glycol exhibited a similar trend, but with a smaller energy decrease, and no trend was observed from 1,3-propylene glycol. In conclusion, we discuss and suggest that the reactivity and photoionization of diols in the presence of water depend on the size of the diol, the location of the hydroxyl group, and the number of waters clustered around the diol.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗