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At least 1,495 records · Page 83
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Coupling Kinesin Spindle Protein and Aurora B Inhibition with Apoptosis Induction Enhances Oral Cancer Cell Killing

Many proteins regulating mitosis have emerged as targets for cancer therapy, including the kinesin spindle protein (KSP) and Aurora kinase B (AurB). KSP is crucial for proper spindle pole separation during mitosis, while AurB plays roles in chromosome segregation and cytokinesis. Agents targeting KSP and AurB selectively affect dividing cells and have shown significant activity in vitro. However, these drugs, despite advancing to clinical trials, often yield unsatisfactory outcomes as monotherapy, likely due to variable responses driven by cyclin B degradation and apoptosis signal accumulation networks. Accumulated data suggest that combining emerging antimitotics with various cytostatic drugs can enhance tumor-killing effects compared to monotherapy. Here, we investigated the impact of inhibiting anti-apoptotic signals with the BH3-mimetic Navitoclax in oral cancer cells treated with the selective KSP inhibitor, Ispinesib, or AurB inhibitor, Barasertib, aiming to potentiate cell death. The combination of BH3-mimetics with both KSP and AurB inhibitors synergistically induced substantial cell death, primarily through apoptosis. A mechanistic analysis underlying this synergistic activity, undertaken by live-cell imaging, is presented. Our data underscore the importance of combining BH3-mimetics with antimitotics in clinical trials to maximize their effectiveness.

Silva, João P. N. (ORCID:0000000344554286)↗
DOE OSTI2021

Synthesis and Advanced Characterization of Polymer–Protein Core–Shell Nanoparticles

Enzyme immobilization techniques are widely researched due to their wide range of applications. Polymer–protein core–shell nanoparticles (CSNPs) have emerged as a promising technique for enzyme/protein immobilization via a self-assembly process. Based on the desired application, different sizes and distribution of the polymer–protein CSNPs may be required. This work systematically studies the assembly process of poly(4-vinyl pyridine) and bovine serum albumin CSNPs. Average particle size was controlled by varying the concentrations of each reagent. Particle size and size distributions were monitored by dynamic light scattering, ultra-small-angle X-ray scattering, small-angle X-ray scattering and transmission electron microscopy. Results showed a wide range of CSNPs could be assembled ranging from an average radius as small as 52.3 nm, to particles above 1 µm by adjusting reagent concentrations. In situ X-ray scattering techniques monitored particle assembly as a function of time showing the initial particle growth followed by a decrease in particle size as they reach equilibrium. The results outline a general strategy that can be applied to other CSNP systems to better control particle size and distribution for various applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Protein Conformational States—A First Principles Bayesian Method

Automated identification of protein conformational states from simulation of an ensemble of structures is a hard problem because it requires teaching a computer to recognize shapes. We adapt the naïve Bayes classifier from the machine learning community for use on atom-to-atom pairwise contacts. The result is an unsupervised learning algorithm that samples a ‘distribution’ over potential classification schemes. We apply the classifier to a series of test structures and one real protein, showing that it identifies the conformational transition with >95% accuracy in most cases. A nontrivial feature of our adaptation is a new connection to information entropy that allows us to vary the level of structural detail without spoiling the categorization. This is confirmed by comparing results as the number of atoms and time-samples are varied over 1.5 orders of magnitude. Further, the method’s derivation from Bayesian analysis on the set of inter-atomic contacts makes it easy to understand and extend to more complex cases.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Removal of Non-Specifically Bound Proteins Using Rayleigh Waves Generated on ST-Quartz Substrates

Label-free biosensors are plagued by the issue of non-specific protein binding which negatively affects sensing parameters such as sensitivity, selectivity, and limit-of-detection. In the current work, we explore the possibility of using the Rayleigh waves in ST-Quartz devices to efficiently remove non-specifically bound proteins via acoustic streaming. A coupled-field finite element (FE) fluid structure interaction (FSI) model of a surface acoustic wave (SAW) device based on ST-Quartz substrate in contact with a liquid loading was first used to predict trends in forces related to SAW-induced acoustic streaming. Based on model predictions, it is found that the computed SAW body force is sufficient to overcome adhesive forces between particles and a surface while lift and drag forces prevent reattachment for a range of SAW frequencies. We further performed experiments to validate the model predictions and observe that the excitation of Rayleigh SAWs removed non-specifically bound (NSB) antigens and antibodies from sensing and non-sensing regions, while rinsing and blocking agents were ineffective. An amplified RF signal applied to the device input disrupted the specific interactions between antigens and their capture antibody as well. ST-quartz allows propagation of Rayleigh and leaky SH-SAW waves in orthogonal directions. Thus, the results reported here could allow integration of three important biosensor functions on a single chip, i.e., removal of non-specific binding, mixing, and sensing in the liquid phase.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Evaluation of the Function of the ASFV KP177R Gene, Encoding for Structural Protein p22, in the Process of Virus Replication and in Swine Virulence

African swine fever virus (ASFV) causes a devastating disease of swine that has caused outbreaks in Central Europe since 2007, spreading into Asia in 2018. ASFV is a large, structurally complex virus with a large dsDNA genome encoding for more than 160 genes, most of them still uncharacterized. p22, encoded by the ASFV gene KP177R, is an early transcribed, structural virus protein located in the ASFV particle. Although its exact function is unknown, p22 has recently been identified as an interacting partner of several host proteins. Here, we describe the development of a recombinant ASFV (ASFV-G-ΔKP177R) lacking the KP177R gene as a tool to evaluate the role of p22 in virus replication and virulence in swine. The recombinant ASFV-G-ΔKP177R demonstrated that the KP177R gene is non-essential for ASFV replication in primary swine macrophages, with virus yields similar to those of the parental, highly virulent field isolate Georgia2010 (ASFV-G). In addition, experimental infection of domestic pigs with ASFV-G-ΔKP177R produced a clinical disease similar to that caused by the parental ASFV-G. Therefore, and surprisingly, p22 does not seem to be involved in virus replication or virulence in swine.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Light-Controlled Fermentations for Microbial Chemical and Protein Production

Microbial cell factories offer a sustainable alternative for producing chemicals and recombinant proteins from renewable feedstocks. However, overburdening a microorganism with genetic modifications can reduce host fitness and productivity. This problem can be overcome by using dynamic control: inducible expression of enzymes and pathways, typically using chemical- or nutrient-based additives, to balance cellular growth and production. Optogenetics offers a non-invasive, highly tunable, and reversible method of dynamically regulating gene expression. Here, we describe how to set up light-controlled fermentations of engineered Escherichia coli and Saccharomyces cerevisiae for the production of chemicals or recombinant proteins. We discuss how to apply light at selected times and dosages to decouple microbial growth and production for improved fermentation control and productivity, as well as the key optimization considerations for best results. Additionally, we describe how to implement light controls for lab-scale bioreactor experiments. As a result, these protocols facilitate the adoption of optogenetic controls in engineered microorganisms for improved fermentation performance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Tailored design of protein nanoparticle scaffolds for multivalent presentation of viral glycoprotein antigens

Multivalent presentation of viral glycoproteins can substantially increase the elicitation of antigen-specific antibodies. To enable a new generation of anti-viral vaccines, we designed self-assembling protein nanoparticles with geometries tailored to present the ectodomains of influenza, HIV, and RSV viral glycoprotein trimers. We first de novo designed trimers tailored for antigen fusion, featuring N-terminal helices positioned to match the C termini of the viral glycoproteins. Trimers that experimentally adopted their designed configurations were incorporated as components of tetrahedral, octahedral, and icosahedral nanoparticles, which were characterized by cryo-electron microscopy and assessed for their ability to present viral glycoproteins. Electron microscopy and antibody binding experiments demonstrated that the designed nanoparticles presented antigenically intact prefusion HIV-1 Env, influenza hemagglutinin, and RSV F trimers in the predicted geometries. This work demonstrates that antigen-displaying protein nanoparticles can be designed from scratch, and provides a systematic way to investigate the influence of antigen presentation geometry on the immune response to vaccination.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

An auto-inhibited state of protein kinase G and implications for selective activation

Cyclic GMP-dependent protein kinases (PKGs) are key mediators of the nitric oxide/cyclic guanosine monophosphate (cGMP) signaling pathway that regulates biological functions as diverse as smooth muscle contraction, cardiac function, and axon guidance. Understanding how cGMP differentially triggers mammalian PKG isoforms could lead to new therapeutics that inhibit or activate PKGs, complementing drugs that target nitric oxide synthases and cyclic nucleotide phosphodiesterases in this signaling axis. Alternate splicing of PRKG1 transcripts confers distinct leucine zippers, linkers, and auto-inhibitory (AI) pseudo-substrate sequences to PKG Iα and Iβ that result in isoform-specific activation properties, but the mechanism of enzyme auto-inhibition and its alleviation by cGMP is not well understood. Here, we present a crystal structure of PKG Iβ in which the AI sequence and the cyclic nucleotide-binding (CNB) domains are bound to the catalytic domain, providing a snapshot of the auto-inhibited state. Specific contacts between the PKG Iβ AI sequence and the enzyme active site help explain isoform-specific activation constants and the effects of phosphorylation in the linker. We also present a crystal structure of a PKG I CNB domain with an activating mutation linked to Thoracic Aortic Aneurysms and Dissections. Similarity of this structure to wildtype cGMP-bound domains and differences with the auto-inhibited enzyme provide a mechanistic basis for constitutive activation. We show that PKG Iβ auto-inhibition is mediated by contacts within each monomer of the native full-length dimeric protein, and using the available structural and biochemical data we develop a model for the regulation and cooperative activation of PKGs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Targeted protein degradation systems to enhance Wnt signaling

Molecules that facilitate targeted protein degradation (TPD) offer great promise as novel therapeutics. The human hepatic lectin asialoglycoprotein receptor (ASGR) is selectively expressed on hepatocytes. We have previously engineered an anti-ASGR1 antibody-mutant RSPO2 (RSPO2RA) fusion protein (called SWEETS) to drive tissue-specific degradation of ZNRF3/RNF43 E3 ubiquitin ligases, which achieved hepatocyte-specific enhanced Wnt signaling, proliferation, and restored liver function in mouse models, and an antibody–RSPO2RA fusion molecule is currently in human clinical trials. In the current study, we identified two new ASGR1- and ASGR1/2-specific antibodies, 8M24 and 8G8. High-resolution crystal structures of ASGR1:8M24 and ASGR2:8G8 complexes revealed that these antibodies bind to distinct epitopes on opposing sides of ASGR, away from the substrate-binding site. Both antibodies enhanced Wnt activity when assembled as SWEETS molecules with RSPO2RA through specific effects sequestering E3 ligases. In addition, 8M24-RSPO2RA and 8G8-RSPO2RA efficiently downregulate ASGR1 through TPD mechanisms. These results demonstrate the possibility of combining different therapeutic effects and degradation mechanisms in a single molecule.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1968

Rate constants measured for hydrated electron reactions with peptides and proteins

Effects of ionizing radiation on the amino acids of proteins and the reactivity of the protonated amino group depends upon the pK subscript a of the group. Estimates of the rate constants for reactions involving the amino acid side chains are presented. These rate constants gave an approximate rate constant for three different protein molecules.

Braams, R.↗
NASA NTRS1971

Mechanisms and kinetics of cellulose fermentation for protein production

The development of a process (and ancillary processing and analytical techniques) to produce bacterial single-cell protein of good nutritional quality from waste cellulose is discussed. A fermentation pilot plant and laboratory were developed and have been in operation for about two years. Single-cell protein (SCP) can be produced from sugarcane bagasse--a typical agricultural cellulosic waste. The optimization and understanding of this process and its controlling variables are examined. Both batch and continuous fermentation runs have been made under controlled conditions in the 535 liter pilot plant vessel and in the laboratory 14-liter fermenters.

Dunlap, C. A.↗
NASA NTRS1973

Single-cell protein from waste cellulose

The recycle, reuse, or reclamation of single cell protein from liquid and solid agricultural waste fibers by a fermentation process is reported. It is shown that cellulose comprises the bulk of the fibers at 50% to 55% of the dry weight of the refuse and that its biodegradability is of prime importance in the choice of a substrate. The application of sodium hydroxide followed by heat and pressure serves to de-polymerize and disrupt lignin structure while swelling the cellulose to increase water uptake and pore volume. Some of the lignin, hemi-celluloses, ash, and cellulose of the material is hydrolized and solubilized. Introduction of microorganisms to the substrate fibers mixed with nutrients produces continuous fermentation of cellulose for further protein extraction and purification.

Dunlap, C. E.↗
NASA NTRS1973

Changes in total plasma content of electrolytes and proteins with maximal exercise.

To determine to what extent the increases in concentration of plasma proteins and electrolytes with short maximal work were a result of hemoconcentration, the changes in plasma volume and total content of the plasma constituents were simultaneously evaluated. The results obtained from six human subjects indicated that in comparison to preexercise values there was a net decrease in total content of plasma protein, sodium, and chloride in the first 2 min of the postexercise period, due primarily to a significant loss (13-15%) of plasma fluid. The total plasma potassium content was increased immediately after exercise but was significantly below the preexercise plasma content after 2 min of recovery.

Van Beaumont, W.↗
NASA NTRS1975

Investigation of carbohydrate and protein metabolism in the digestive organs of the rabbit under the combined influence of vibration, acceleration and irradiation

During spaceflight, the organism is subjected to the influence of various extremal factors such as acceleration, vibration, irradiation, etc. The study of the influence of these factors on metabolism, especially carbohydrate and protein metabolism, in young rabbits is of great significance in simulation experiments. Dynamic factors and irradiation, depending on dose and duration, lead to reduced RNA and protein metabolism.

Yuy, R. I.↗
NASA NTRS1974

Salt-dependent properties of proteins from extremely halophilic bacteria

Based on information concerning the interaction of salts and macromolecules the literature of the enzymes of halophilic bacteria and their constituents is examined. Although in halophilic systems the salt requirement of enzyme activity is variable the enzymes investigated show a time-dependent inactivation at lower salt concentrations especially in the absence of salt. The studies described show that in some halophilic systems the effect of salt may be restricted to a small region on the protein molecule. The concept of the hydrophobic bond to consider certain solvent-dependent phenomena is introduced. It is shown that some halophilic enzymes are unable to maintain their structure without the involvement of hydrophobic interactions that are usually not supported by water. A table lists indices of hydrophobicity and polarity for various halophilic and nonhalophilic proteins.

Lanyi, J. K.↗
NASA NTRS1975

Tables of critical values for examining compositional non-randomness in proteins and nucleic acids

A binomially distributed statistic is defined to show whether or not the proportion of a particular amino acid in a protein deviates from random expectation. An analogous statistic is derived for nucleotides in nucleic acids. These new statistics are simply related to the classical chi-squared test. They explicitly account for the compositional fluctuations imposed by the finite length of proteins, and they are more accurate than previous tables.

Laird, M.↗