Integrative structural dynamics probing of the conformational heterogeneity in synaptosomal-associated protein 25
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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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Nanoscopic lipid domains determined by microscopy and neutron scattering
Biological membranes are highly complex supramolecular assemblies, which play central roles in biology. However, their complexity makes them challenging to study their nanoscale structures. To overcome this challenge, model membranes assembled using reduced sets of membrane-associated biomolecules have been found to be both excellent and tractable proxies for biological membranes. Due to their relative simplicity, they have been studied using a range of biophysical characterization techniques. Here, in this review article, we will briefly detail the use of fluorescence and electron microscopies, and X-ray and neutron scattering techniques used over the past few decades to study the nanostructure of biological membranes.
59 BASIC BIOLOGICAL SCIENCES↗
Detection and Quantification of Biologically Active Botulinum Neurotoxin Serotypes A and B Using a Förster Resonance Energy Transfer-Based Quantum Dot Nanobiosensor
Botulinum neurotoxin (BoNT) is the most potent toxin known. The ingestion of food contaminated with biologically active BoNT causes foodborne botulism, which can lead to respiratory paralysis, coma, and death after ingestion of as little as 70 mu g for a 70 kg human. Because of its lethality and challenges associated with current detection methods, there is an urgent need for highly sensitive rapid screening techniques capable of detecting biologically active BoNT. Here, we describe a Forster resonance energy transfer-based nanobiosensor that uses quantum dots (QDs) and two specific quencher-labeled peptide probes to detect and differentiate two biologically active forms of BoNT, serotypes A and B, which were responsible for 80% of human foodborne botulism cases in the U.S. from 2012 to 2015. Each peptide probe contains an enzymatic cleavage site specific to only one serotype. QDs were selected based on the spectral overlap with the quenchers. In the presence of the target BoNT serotype, the peptide probe is cleaved and the quenching of QD photoluminescence (PL) is reduced, giving a signal that is easily detected by a PL spectrophotometer. This sensor performance was evaluated with light chains of BoNT/A and BoNT/B (LcA and LcB), catalytic domains of the respective serotypes. LcA and LcB were detected in 3 h with limits of detection of 0.2 and 2 ng/mL, respectively. The specificity of the sensor was evaluated, and no cross-reactivity from nontarget serotypes was observed with 2 h of incubation. Because each serotype-specific peptide is conjugated to a QD with a unique emission wavelength, multiple biologically active BoNT serotypes could be detected in one PL spectrum. The sensor was also shown to be responsive to BoNT/A and BoNT/B holotoxins. Good performance of this sensor implies its potential application as a rapid screening method for biologically active BoNT/A and BoNT/B in the laboratory and in the field.
botulinum neurotoxin↗
Ion-Switchable Quantum Dot Förster Resonance Energy Transfer Rates in Ratiometric Potassium Sensors
The tools for optically imaging cellular potassium concentrations in real-time are currently limited to a small set of molecular indicator dyes. Quantum dot-based nanosensors are more photostable and tunable than organic indicators, but previous designs have fallen short in size, sensitivity, and selectivity. In this paper, we introduce a small, sensitive, and selective nanosensor for potassium measurements. A dynamic quencher modulates the fluorescence emitted by two different quantum dot species to produce a ratiometric signal. We characterized the potassium-modulated sensor properties and investigated the photonic interactions within the sensors. The quencher’s protonation changes in response to potassium, which modulates its Förster radiative energy transfer rate and the corresponding interaction radii with each quantum dot species. Finally, the nanosensors respond to changes in potassium concentrations typical of the cellular environment and thus provide a promising tool for imaging potassium fluxes during biological events.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Toward Imaging Defect-Mediated Energy Transfer between Single Nanocrystal Donors and Single Molecule Acceptors
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Single-Molecule Fluorescence Microscopy Reveals Energy Transfer Active versus Inactive Nanocrystal/Dye Conjugate Pairs
Defect-mediated energy transfer (EnT) is a radiative process that occurs between donor defect states in the forbidden bandgap of semiconductor nanocrystals (NCs) and dye molecules bound to their surfaces. The EnT efficiency depends on the number of dye molecules attached to each NC, the donor–acceptor distance, and the dipole orientation factor between the donor and acceptor, all of which vary across all individual NCs in a sample. While ensemble-level fluorescence spectroscopy measurements have provided average values for donor–acceptor distances, dye-to-NC ratios, and EnT rate constants, questions remain about the impact of donor/acceptor heterogeneity on observed EnT efficiencies. Notably, ensemble-level measurements cannot distinguish between bare NCs and EnT-active versus inactive NC/dye pairs in the same sample batch, limiting the ability to design systems with 100% EnT efficiency. To address this, we studied defect-mediated EnT between AlexaFluor 555 dye acceptors chemically bound to ZnO NC donors at the level of single molecules and single NCs. Interestingly, 20% of bound NC/dye pairs are EnT-inactive, likely contributing to residual defect photoluminescence (PL) observed in ensemble-level measurements and reducing overall EnT efficiency. Single particle-level ZnO defect PL and acceptor fluorescence trajectories exhibited distinct microfluctuations, which are absent in bare ZnO NCs. We hypothesized that our observations can be explained with a competitive dye fluorescence quenching pathway, possibly due to charge transfer between the excited state dye and the ZnO NC. Numerical simulations of single-molecule PL traces for this scenario produced microfluctuations consistent with the experimental results. These findings highlight the impact of sample heterogeneity on EnT processes and provide insights for designing light-harvesting systems with optimized EnT efficiency.
25 ENERGY STORAGE↗
Structure of an EIIC sugar transporter trapped in an inward-facing conformation
The phosphoenolpyruvate-dependent phosphotransferase system (PTS) transports sugar into bacteria and phosphorylates the sugar for metabolic consumption. The PTS is important for the survival of bacteria and thus a potential target for antibiotics, but its mechanism of sugar uptake and phosphorylation remains unclear. The PTS is composed of multiple proteins, and the membrane-embedded Enzyme IIC (EIIC) component transports sugars across the membrane. Crystal structures of two members of the glucose superfamily of EIICs, bcChbC and bcMalT, were solved in the inward-facing and outward-facing conformations, and the structures suggest that sugar translocation could be achieved by movement of a structured domain that contains the sugar-binding site. However, different conformations have not been captured on the same transporter to allow precise description of the conformational changes. Here we present a crystal structure of bcMalT trapped in an inward-facing conformation by a mercury ion that bridges two strategically placed cysteine residues. The structure allows direct comparison of the outward- and inward-facing conformations and reveals a large rigid-body motion of the sugar-binding domain and other conformational changes that accompany the rigid-body motion. All-atom molecular dynamics simulations show that the inward-facing structure is stable with or without the cross-linking. Here, the conformational changes were further validated by single-molecule Föster resonance energy transfer (smFRET). Combined, these results establish the elevator-type mechanism of transport in the glucose superfamily of EIIC transporters.
59 BASIC BIOLOGICAL SCIENCES↗
Glutamine-rich regions of the disordered CREB transactivation domain mediate dynamic intra- and intermolecular interactions
The cyclic AMP response element (CRE) binding protein (CREB) is a transcription factor that contains a 280-residue N-terminal transactivation domain and a basic leucine zipper that mediates interaction with DNA. The transactivation domain comprises three subdomains, the glutamine-rich domains Q1 and Q2 and the kinase inducible activation domain (KID). NMR chemical shifts show that the isolated subdomains are intrinsically disordered but have a propensity to populate local elements of secondary structure. The Q1 and Q2 domains exhibit a propensity for formation of short β-hairpin motifs that function as binding sites for glutamine-rich sequences. These motifs mediate intramolecular interactions between the CREB Q1 and Q2 domains as well as intermolecular interactions with the glutamine-rich Q1 domain of the TATA-box binding protein associated factor 4 (TAF4) subunit of transcription factor IID (TFIID). Using small-angle X-ray scattering, NMR, and single-molecule Förster resonance energy transfer, we show that the Q1, Q2, and KID regions remain dynamically disordered in a full-length CREB transactivation domain (CREB TAD ) construct. The CREB TAD polypeptide chain is largely extended although some compaction is evident in the KID and Q2 domains. Paramagnetic relaxation enhancement reveals transient long-range contacts both within and between the Q1 and Q2 domains while the intervening KID domain is largely devoid of intramolecular interactions. Phosphorylation results in expansion of the KID domain, presumably making it more accessible for binding the CBP/p300 transcriptional coactivators. In conclusion, our study reveals the complex nature of the interactions within the intrinsically disordered transactivation domain of CREB and provides molecular-level insights into dynamic and transient interactions mediated by the glutamine-rich domains.
59 BASIC BIOLOGICAL SCIENCES↗
Interaction between the PH and START domains of ceramide transfer protein competes with phosphatidylinositol 4-phosphate binding by the PH domain
De novo synthesis of the sphingolipid sphingomyelin requires non-vesicular transport of ceramide from the endoplasmic reticulum to the Golgi by the multidomain protein ceramide transfer protein (CERT). CERT's N-terminal pleckstrin homology (PH) domain targets it to the Golgi by binding to phosphatidylinositol 4-phosphate (PtdIns(4)P) in the Golgi membrane, whereas its C-terminal StAR-related lipid transfer domain (START) carries out ceramide transfer. Hyperphosphorylation of a serine-rich motif immediately after the PH domain decreases both PtdIns(4)P binding and ceramide transfer by CERT. This down-regulation requires both the PH and START domains, suggesting a possible inhibitory interaction between the two domains. In this study we show that isolated PH and START domains interact with each other. The crystal structure of a PH–START complex revealed that the START domain binds to the PH domain at the same site for PtdIns(4)P-binding, suggesting that the START domain competes with PtdIns(4)P for association with the PH domain. We further report that mutations disrupting the PH–START interaction increase both PtdIns(4)P-binding affinity and ceramide transfer activity of a CERT-serine–rich phosphorylation mimic. We also found that these mutations increase the Golgi localization of CERT inside the cell, consistent with enhanced PtdIns(4)P binding of the mutant. Collectively, our structural, biochemical, and cellular investigations provide important structural insight into the regulation of CERT function and localization.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Synthesis of two fluorescent GTP$\gamma$S molecules and their biological relevance
Fluorescent GTP analogues are utilized for an assortment of nucleic acid and protein characterization studies. Non-hydrolysable analogues such as GTPγS offer the advantage of keeping proteins in a GTP-bound conformation due to their resistance to hydrolysis into GDP. Two novel fluorescent GTPγS molecules were developed by linking fluorescein and tetramethylrhodamine to the γ-thiophosphate of GTPγS. Chemical and biological analysis of these two compounds revealed their successful synthesis and ability to bind to the nucleotide-binding site of tubulin. These two new fluorescent non-hydrolysable nucleotides offer new possibilities for biophysical and biochemical characterization of GTP-binding proteins.
59 BASIC BIOLOGICAL SCIENCES↗
Model-free analysis of time-dependent single-molecule spectroscopy: Dynamics of biological macromolecules
Rigorous and unbiased statistical analysis of single molecule data is now recognized as a crucial component to substantiate any discovery made through such experiments. Here, this presentation summarizes many such tools, and ventures some future directions in the context of the dynamics of biological macromolecules.
59 BASIC BIOLOGICAL SCIENCES↗
SU-E-T-502: Biometrically Accepted Patient Records
Purpose: To implement a clinically useful palm vein pattern recognition biometric system to treat the correct treatment plan to the correct patient each and every time and to check-in the patient into the department to access the correct medical record. Methods: A commercially available hand vein scanning system was paired to Aria and utilized an ADT interface from the hospital electronic health system. Integration at two points in Aria, version 11 MR2, first at the appointment tracker screen for the front desk medical record access and second at the queue screen on the 4D treatment console took place for patient daily time-out. A test patient was utilized to check accuracy of identification as well as to check that no unintended interactions take place between the 4D treatment console and the hand vein scanning system. This system has been in clinical use since December 2013. Results: Since implementation, 445 patients have been enrolled into our biometric system. 95% of patients learn the correct methodology of hand placement on the scanner in the first try. We have had two instances of patient not found because of a bad initial scan. We simply erased the scanned metric and the patient enrolled again in those cases. The accuracy of the match is 100% for each patient, we have not had one patient misidentified. We can state this because we still use patient photo and date of birth as identifiers. A QA test patient is run monthly to check the integrity of the system. Conclusion: By utilizing palm vein scans along with the date of birth and patient photo, another means of patient identification now exits. This work indicates the successful implementation of technology in the area of patient safety by closing the gap of treating the wrong plan to a patient in radiation oncology. FOJP Service Corporation covered some of the costs of the hardware and software of the palm vein pattern recognition biometric system.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Programmable two-dimensional nanocrystals assembled from POSS-containing peptoids as efficient artificial light-harvesting systems
A class of POSS-containing 2D nanocrystals was developed to offer high stability, biocompatibility, and programmability.
2D nanomaterials↗
Identification of Inhibitors of the Association of ZAP-70 with the T Cell Receptor by High-Throughput Screen
ZAP-70 is a critical molecule in the transduction of T cell antigen receptor signaling and the activation of T cells. Upon activation of the T cell antigen receptor, ZAP-70 is recruited to the intracellular ζ-chains of the T cell receptor, where ZAP-70 is activated and colocalized with its substrates. Inhibitors of ZAP-70 could potentially function as treatments for autoimmune diseases or organ transplantation. In this work, we present the design, optimization, and implementation of a screen for inhibitors that would disrupt the interaction between ZAP-70 and the T cell antigen receptor. Finally, the screen is based on a fluorescence polarization assay for peptide binding to ZAP-70.
60 APPLIED LIFE SCIENCES↗
Electromagnetic Field in Hybrid Quantum Plasmonic-Photonic Systems
We study excitations and quantum optical properties of hybrid networks made up of metal nanoparticles, semiconductor quantum dots and molecules. Such processes can be used for the localization and the guiding of the electromagnetic field. Localized modes occurring in these networks and the generation of confined fields are also connected to the enhancement of Raman-scattering occurring in these systems. We review some recent theoretical and computational studies of optical properties in hybrid nano-systems to gain control of light–matter interactions at the quantum level for efficient energy transport and sensing applications.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Nanoporous silica-based protocells at multiple scales for designs of life and nanomedicine
In this study, various protocell models have been constructed de novo with the bottom-up approach. Here we describe a silica-based protocell composed of a nanoporous amorphous silica core encapsulated within a lipid bilayer built by self-assembly that provides for independent definition of cell interior and the surface membrane. In this review, we will first describe the essential features of this architecture and then summarize the current development of silica-based protocells at both micro- and nanoscale with diverse functionalities. As the structure of the silica is relatively static, silica-core protocells do not have the ability to change shape, but their interior structure provides a highly crowded and, in some cases, authentic scaffold upon which biomolecular components and systems could be reconstituted. In basic research, the larger protocells based on precise silica replicas of cells could be developed into geometrically realistic bioreactor platforms to enable cellular functions like coupled biochemical reactions, while in translational research smaller protocells based on mesoporous silica nanoparticles are being developed for targeted nanomedicine. Ultimately we see two different motivations for protocell research and development: (1) to emulate life in order to understand it; and (2) to use biomimicry to engineer desired cellular interactions.
59 BASIC BIOLOGICAL SCIENCES↗
Förster Resonance Energy Transfer and Enhanced Emission in Cs 4 PbBr 6 Nanocrystals Encapsulated in Silicon Nano-Sheets for Perovskite Light Emitting Diode Applications
Encapsulating Cs 4 PbBr 6 quantum dots in silicon nano-sheets not only stabilizes the halide perovskite, but also takes advantage of the nano-sheet for a compatible integration with the traditional silicon semiconductor. Here, we report the preparation of un-passivated Cs 4 PbBr 6 ellipsoidal nanocrystals and pseudo-spherical quantum dots in silicon nano-sheets and their enhanced photoluminescence (PL). For a sample with low concentrations of quantum dots in silicon nano-sheets, the emission from Cs 4 PbBr 6 pseudo-spherical quantum dots is quenched and is dominated with Pb 2+ ion/silicene emission, which is very stable during the whole measurement period. For a high concentration of Cs 4 PbBr 6 ellipsoidal nanocrystals in silicon nano-sheets, we have observed Förster resonance energy transfer with up to 87% efficiency through the oscillation of two PL peaks when UV excitation switches between on and off, using recorded video and PL lifetime measurements. In an area of a non-uniform sample containing both ellipsoidal nanocrystals and pseudo-spherical quantum dots, where Pb 2+ ion/silicene emissions, broadband emissions from quantum dots, and bandgap edge emissions (515 nm) appear, the 515 nm peak intensity increases five times over 30 min of UV excitation, probably due to a photon recycling effect. This irradiated sample has been stable for one year of ambient storage. Cs 4 PbBr 6 quantum dots encapsulated in silicon nano-sheets can lead to applications of halide perovskite light emitting diodes (PeLEDs) and integration with traditional semiconductor materials.
36 MATERIALS SCIENCE↗
Microslips between contacting paraboloids.
Hertz and Mindlin problems for fourth order paraboloids in contact generalized, minimizing microslips and annulus of slip
OPTIMIZATION↗