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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Protein-Nanoparticle Interactions Govern the Interfacial Behavior of Polymeric Nanogels: Study of Protein Corona Formation at the Air/Water Interface

Biomedical applications of nanoparticles require a fundamental understanding of their interactions and behavior with biological interfaces. Protein corona formation can alter the morphology and properties of nanomaterials, and knowledge of the interfacial behavior of the complexes, using in situ analytical techniques, will impact the development of nanocarriers to maximize uptake and permeability at cellular interfaces. In this study we evaluate the interactions of acrylamide-based nanogels, with neutral, positive, and negative charges, with serum-abundant proteins albumin, fibrinogen, and immunoglobulin G. The formation of a protein corona complex between positively charged nanoparticles and albumin is characterized by dynamic light scattering, circular dichroism, and surface tensiometry; we use neutron reflectometry to resolve the complex structure at the air/water interface and demonstrate the effect of increased protein concentration on the interface. Surface tensiometry data suggest that the structure of the proteins can impact the interfacial properties of the complex formed. These results contribute to the understanding of the factors that influence the bio-nano interface, which will help to design nanomaterials with improved properties for applications in drug delivery.

Traldi, Federico (ORCID:0000000161251012)↗
NASA NTRS1982

Protein folding, protein structure and the origin of life: Theoretical methods and solutions of dynamical problems

Theoretical methods and solutions of the dynamics of protein folding, protein aggregation, protein structure, and the origin of life are discussed. The elements of a dynamic model representing the initial stages of protein folding are presented. The calculation and experimental determination of the model parameters are discussed. The use of computer simulation for modeling protein folding is considered.

Weaver, D. L.↗
NASA NTRS1986

Meal composition and plasma amino acid ratios: Effect of various proteins or carbohydrates, and of various protein concentrations

The effects of meals containing various proteins and carbohydrates, and of those containing various proportions of protein (0 percent to 20 percent of a meal, by weight) or of carbohydrate (0 percent to 75 percent), on plasma levels of certain large neutral amino acids (LNAA) in rats previously fasted for 19 hours were examined. Also the plasma tryptophan ratios (the ratio of the plasma trytophan concentration to the summed concentrations of the other large neutral amino acids) and other plasma amino acid ratios were calculated. (The plasma tryptophan ratio has been shown to determine brain tryptophan levels and, thereby, to affect the synthesis and release of the neurotransmitter serotonin). A meal containing 70 percent to 75 percent of an insulin-secreting carbohydrate (dextrose or dextrin) increased plasma insulin levels and the tryptophan ratio; those containing 0 percent or 25 percent carbohydrate failed to do so. Addition of as little as 5 percent casein to a 70 percent carbohydrate meal fully blocked the increase in the plasma tryptophan ratio without affecting the secretion of insulin - probably by contributing much larger quantities of the other LNAA than of tryptophan to the blood. Dietary proteins differed in their ability to suppress the carbohydrate-induced rise in the plasma tryptophan ratio. Addition of 10 percent casein, peanut meal, or gelatin fully blocked this increase, but lactalbumin failed to do so, and egg white did so only partially. (Consumption of the 10 percent gelatin meal also produced a major reduction in the plasma tyrosine ratio, and may thereby have affected brain tyrosine levels and catecholamine synthesis.) These observations suggest that serotonin-releasing neurons in brains of fasted rats are capable of distinguishing (by their metabolic effects) between meals poor in protein but rich in carbohydrates that elicit insulin secretion, and all other meals. The changes in brain serotonin caused by carbohydrate-rich, protein-poor meals may affect subsequent food choice and various serotonin-mediated behaviors.

Yokogoshi, Hidehiko↗
NASA NTRS1998

Biologically active protein fragments containing specific binding regions of serum albumin or related proteins

In accordance with the present invention, biologically active protein fragments can be constructed which contain only those specific portions of the serum albumin family of proteins such as regions known as subdomains IIA and IIIA which are primarily responsible for the binding properties of the serum albumins. The artificial serums that can be prepared from these biologically active protein fragments are advantageous in that they can be produced much more easily than serums containing the whole albumin, yet still retain all or most of the original binding potential of the full albumin proteins. In addition, since the protein fragment serums of the present invention can be made from non-natural sources using conventional recombinant DNA techniques, they are far safer than serums containing natural albumin because they do not carry the potentially harmful viruses and other contaminants that will be found in the natural substances.

Carter, Daniel C.↗
DOE OSTI2023

Announcing the launch of Protein Data Bank China as an Associate Member of the Worldwide Protein Data Bank Partnership

The Protein Data Bank (PDB) is the single global archive of atomic-level, three-dimensional structures of biological macromolecules experimentally determined by macromolecular crystallography, nuclear magnetic resonance spectroscopy or three-dimensional cryo-electron microscopy. The PDB is growing continuously, with a recent rapid increase in new structure depositions from Asia. In 2022, the Worldwide Protein Data Bank (wwPDB; https://www.wwpdb.org/) partners welcomed Protein Data Bank China (PDBc; https://www.pdbc.org.cn) to the organization as an Associate Member. PDBc is based in the National Facility for Protein Science in Shanghai which is associated with the Shanghai Advanced Research Institute of Chinese Academy of Sciences, the Shanghai Institute for Advanced Immunochemical Studies and the iHuman Institute of ShanghaiTech University. This letter describes the history of the wwPDB, recently established mechanisms for adding new wwPDB data centers and the processes developed to bring PDBc into the partnership.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Mesoscale fractal whey protein particles derived from microscale linear-shaped protein assemblies (Part 1): Manufacturing method and particle characteristics

Whey protein isolates (WPI) are widely used in processed foods for their versatile functional properties. Modifying the structural properties of proteins by assembling them into mesoscale or microscale particles may improve their functionality and broaden their applications. This study aims to manufacture and characterize mesoscale whey protein particles (WPP) derived from WPI. Two types of WPP, WPP1 (0.05 mL/min) and WPP2 (0.25 mL/min), were prepared through a multistep approach involving liquid antisolvent (LAS) precipitation, heat treatment, and microfluidization. Liquid antisolvent precipitation was performed by injecting a 20% (wt/vol) WPI dispersion (pH 7) into an ethanol-glycerol mixture (75:25, vol/vol) under laminar flow, followed by heat treatment at 80°C for 20 min as a particle hardening step. This process produced stable fiber- and ribbon-shaped whey protein assemblies (WPA), which served as precursors to WPP. Subsequent microfluidization (150 MPa, 6 passages) reduced the size of WPA, yielding mesoscale WPP with irregular morphologies and a more uniform size distribution, as revealed by microscopy and dynamic light scattering. ζ-Potential and fluorescence labeling indicated higher surface charge and surface hydrophobicity of WPP compared with untreated WPI. The WPP showed internal mass fractal and surface fractal structures at larger length scales, analyzed using small-angle X-ray scattering. Fourier transform infrared spectroscopy demonstrated an increased fraction of intermolecular β-sheets in WPP, suggesting that hydrogen bonding contributed to their formation. Gel electrophoresis confirmed that disulfide bonds served as the primary cross-links stabilizing the WPP structure. Furthermore, turbidity measurements showed that WPP exhibited superior colloidal phase stability compared with untreated WPI and maintained high colloidal stability under both acidic and neutral pH conditions.

Antisolvent precipitation↗
DOE OSTI2024

Watching a signaling protein function: What has been learned over four decades of time-resolved studies of photoactive yellow protein

Photoactive yellow protein (PYP) is a signaling protein whose internal p-coumaric acid chromophore undergoes reversible, light-induced trans-to-cis isomerization, which triggers a sequence of structural changes that ultimately lead to a signaling state. Since its discovery nearly 40 years ago, PYP has attracted much interest and has become one of the most extensively studied proteins found in nature. The method of time-resolved crystallography, pioneered by Keith Moffat, has successfully characterized intermediates in the PYP photocycle at near atomic resolution over 12 decades of time down to the sub-picosecond time scale, allowing one to stitch together a movie and literally watch a protein as it functions. But how close to reality is this movie? To address this question, results from numerous complementary time-resolved techniques including x-ray crystallography, x-ray scattering, and spectroscopy are discussed. Emerging from spectroscopic studies is a general consensus that three time constants are required to model the excited state relaxation, with a highly strained ground-state cis intermediate formed in less than 2.4 ps. Persistent strain drives the sequence of structural transitions that ultimately produce the signaling state. Crystal packing forces produce a restoring force that slows somewhat the rates of interconversion between the intermediates. Moreover, the solvent composition surrounding PYP can influence the number and structures of intermediates as well as the rates at which they interconvert. When chloride is present, the PYP photocycle in a crystal closely tracks that in solution, which suggests the epic movie of the PYP photocycle is indeed based in reality.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1993

Evolution of EF-hand calcium-modulated proteins. III. Exon sequences confirm most dendrograms based on protein sequences: calmodulin dendrograms show significant lack of parallelism

In the first report in this series we presented dendrograms based on 152 individual proteins of the EF-hand family. In the second we used sequences from 228 proteins, containing 835 domains, and showed that eight of the 29 subfamilies are congruent and that the EF-hand domains of the remaining 21 subfamilies have diverse evolutionary histories. In this study we have computed dendrograms within and among the EF-hand subfamilies using the encoding DNA sequences. In most instances the dendrograms based on protein and on DNA sequences are very similar. Significant differences between protein and DNA trees for calmodulin remain unexplained. In our fourth report we evaluate the sequences and the distribution of introns within the EF-hand family and conclude that exon shuffling did not play a significant role in its evolution.

Non-NASA Center↗
DOE OSTI2023

Calculated vibrational properties of pigments in protein binding sites 2: Semiquinones in photosynthetic proteins

[Q A – – Q A ] Fourier transform infrared difference spectra have previously been obtained using purple bacterial reaction centers from Rhodobacter sphaeroides with unlabeled, 18 O and 13 C isotope labeled phylloquinone (PhQ, also known as vitamin K 1 ) incorporated into the QA protein binding site (Breton, (1997), Proc. Natl. Acad. Sci. USA 94 11318–11323). The nature of the bands in these spectra and the isotope induced band shifts are poorly understood, especially for the phyllosemiquinone anion (PhQ – ) state. Here, to aid in the interpretation of the bands in these experimental spectra, ONIOM type QM/MM vibrational frequency calculations were undertaken. Calculations were also undertaken for PhQ – in solution. Surprisingly, both sets of calculated spectra are similar and agree well with the experimental spectra. This similarity suggests pigment-protein interactions do not perturb the electronic structure of the semiquinone in the Q A binding site. This is not found to be the case for the neutral PhQ species in the same protein binding site. PhQ also occupies the A 1 protein binding site in photosystem I, and the vibrational properties of PhQ – in the Q A and A 1 binding sites are compared and shown to exhibit considerable differences. These differences probably arise because of changes in the degree of asymmetry of hydrogen bonding of PhQ – in the A 1 and Q A binding sites.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1992

Growing protein crystals in microgravity - The NASA Microgravity Science and Applications Division (MSAD) Protein Crystal Growth (PCG) program

In collaboration with a medical researcher at the University of Alabama at Birmingham, NASA's Marshall Space Flight Center in Huntsville, Alabama, under the sponsorship of the Microgravity Science and Applications Division (MSAD) at NASA Headquarters, is continuing a series of space experiments in protein crystal growth which could lead to innovative new drugs as well as basic science data on protein molecular structures. From 1985 through 1992, Protein Crystal Growth (PCG) experiments will have been flown on the Space Shuttle a total of 14 times. The first four hand-held experiments were used to test hardware concepts; later flights incorporated these concepts for vapor diffusion protein crystal growth with temperature control. This article provides an overview of the PCG program: its evolution, objectives, and plans for future experiments on NASA's Space Shuttle and Space Station Freedom.

Herren, B.↗
DOE OSTI2023

Identification of small-molecule protein–protein interaction inhibitors for NKG2D

NKG2D (natural-killer group 2, member D) is a homodimeric transmembrane receptor that plays an important role in NK, γδ + , and CD8 + T cell-mediated immune responses to environmental stressors such as viral or bacterial infections and oxidative stress. However, aberrant NKG2D signaling has also been associated with chronic inflammatory and autoimmune diseases, and as such NKG2D is thought to be an attractive target for immune intervention. Here, in this study, we describe a comprehensive small-molecule hit identification strategy and two distinct series of protein–protein interaction inhibitors of NKG2D. Although the hits are chemically distinct, they share a unique allosteric mechanism of disrupting ligand binding by accessing a cryptic pocket and causing the two monomers of the NKG2D dimer to open apart and twist relative to one another. Leveraging a suite of biochemical and cell-based assays coupled with structure-based drug design, we established tractable structure–activity relationships with one of the chemical series and successfully improved both the potency and physicochemical properties. Together, we demonstrate that it is possible, albeit challenging, to disrupt the interaction between NKG2D and multiple protein ligands with a single molecule through allosteric modulation of the NKG2D receptor dimer/ligand interface.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Lassa virus protein–protein interactions as mediators of Lassa fever pathogenesis

Viral hemorrhagic Lassa fever (LF), caused by Lassa virus (LASV), is a significant public health concern endemic in West Africa with high morbidity and mortality rates, limited treatment options, and potential for international spread. Despite advances in interrogating its epidemiology and clinical manifestations, the molecular mechanisms driving pathogenesis of LASV and other arenaviruses remain incompletely understood. This review synthesizes current knowledge regarding the role of LASV host-virus interactions in mediating the pathogenesis of LF, with emphasis on interactions between viral and host proteins. Through investigation of these critical protein–protein interactions, we identify potential therapeutic targets and discuss their implications for development of medical countermeasures including antiviral drugs. This review provides an update in recent literature of significant LASV host-virus interactions important in informing the development of targeted therapies and improving clinical outcomes for LF patients. Knowledge gaps are highlighted as opportunities for future research efforts that would advance the field of LASV and arenavirus pathogenesis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins

Recent advances in Artificial Intelligence and Machine Learning (e.g., AlphaFold, RosettaFold, and ESMFold) enable prediction of three-dimensional (3D) protein structures from amino acid sequences alone at accuracies comparable to lower-resolution experimental methods. These tools have been employed to predict structures across entire proteomes and the results of large-scale metagenomic sequence studies, yielding an exponential increase in available biomolecular 3D structural information. Given the enormous volume of this newly computed biostructure data, there is an urgent need for robust tools to manage, search, cluster, and visualize large collections of structures. Equally important is the capability to efficiently summarize and visualize metadata, biological/biochemical annotations, and structural features, particularly when working with vast numbers of protein structures of both experimental origin from the Protein Data Bank (PDB) and computationally-predicted models. Moreover, researchers require advanced visualization techniques that support interactive exploration of multiple sequences and structural alignments. This paper introduces a suite of tools provided on the RCSB PDB research-focused web portal RCSB. org, tailor-made for efficient management, search, organization, and visualization of this burgeoning corpus of 3D macromolecular structure data.

3D visualization↗
DOE OSTI2026

ProtNHF: Neural Hamiltonian Flows for Controllable Protein Sequence Generation

This dataset accompanies the publication "ProtNHF: Neural Hamiltonian Flows for Controllable Protein Sequence Generation". This paper introduces a new AI model for protein sequence generation. This dataset contains data related to experiments discussed in the publication. This includes generated sequences and evaluation metrics supporting all unconditional and bias-controlled experiments in the ProtNHF paper.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

The Polymorphic Membrane Protein G Has a Neutral Effect and the Plasmid Glycoprotein 3 an Antagonistic Effect on the Ability of the Major Outer Membrane Protein to Elicit Protective Immune Responses against a Chlamydia muridarum Respiratory Challenge

Chlamydia trachomatis is the most common bacterial sexually transmitted pathogen. The number of chlamydial infections continuous to increase and there is an urgent need for a safe and efficacious vaccine. To assess the ability of the Chlamydia muridarum polymorphic membrane protein G (PmpG) and the plasmid glycoprotein 3 (Pgp3) as single antigens, and in combination with the major outer-membrane protein (MOMP) to induce protection, BALB/c mice were immunized utilizing CpG-1826 and Montanide ISA 720 VG as adjuvants. Following vaccination with MOMP, significant humoral and cell-mediated immune responses were observed, while immunization with PmpG, or Pgp3, elicited weaker immune responses. Weaker immune responses were induced with MOMP+Pgp3 compared with MOMP alone. Following the intranasal challenge with C. muridarum, mice vaccinated with MOMP showed robust protection against body-weight loss, inflammatory responses in the lungs and number of Chlamydia recovered from the lungs. PmpG and Pgp3 elicited weaker protective responses. Mice immunized with MOMP+PmpG, were no better protected than animals vaccinated with MOMP only, while Pgp3 antagonized the protection elicited by MOMP. In conclusion, PmpG and Pgp3 elicited limited protective immune responses in mice against a respiratory challenge with C. muridarum and failed to enhance the protection induced by MOMP alone. The virulence of Pgp3 may result from its antagonistic effect on the immune protection induced by MOMP.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1992

Protein changes associated with reprotonation of the Schiff base in the photocycle of Asp96-->Asn bacteriorhodopsin. The MN intermediate with unprotonated Schiff base but N-like protein structure

The difference Fourier transform infrared spectrum for the N intermediate in the photoreaction of the light-adapted form of bacteriorhodopsin can be recorded at pH 10 at 274 K (Pfefferle, J.-M., Maeda, A., Sasaki, J., and Yoshizawa, T. (1991) Biochemistry 30, 6548-6556). Under these conditions, Asp96-->Asn bacteriorhodopsin gives a photoproduct which shows changes in protein structure similar to those observed in N of wild-type bacteriorhodopsin. However, decreased intensity of the chromophore bands and the single absorbance maximum at about 400 nm indicate that the Schiff base is unprotonated, as in the M intermediate. This photoproduct was named MN. At pH 7, where the supply of proton is not as restricted as at pH 10, Asp96-->Asn bacteriorhodopsin yields N with a protonated Schiff base. The Asn96 residue, which cannot deprotonate as Asp96 in wild-type bacteriorhodopsin, is perturbed upon formation of both MN at pH 10 and N at pH 7. We suggest that the reprotonation of the Schiff base is preceded by a large change in the protein structure including perturbation of the residue at position 96.

Non-NASA Center↗
DOE OSTI2024

Protein–Protein Interaction Networks Derived from Classical and Machine Learning-Based Natural Language Processing Tools

The study of protein-protein interactions (PPIs) provides insight into various biological mechanisms, including the binding of antibodies to antigens, enzymes to inhibitors or promoters, and receptors to ligands. Recent studies of PPIs have led to significant biological breakthroughs. For example, the study of PPIs involved in the human:SARS-CoV-2 viral infection mechanism aided in the development of the SARS-CoV-2 vaccines. Though several databases exist for the manual curation of PPI networks, text mining methods have been routinely demonstrated as useful alternatives for newly studied or understudied species where databases are incomplete. Here, the relationship extraction (RE) performance of several open-source classical text processing, machine learning (ML)-based natural language processing (NLP), and large language model (LLM)-based NLP tools were compared. Overall, our results indicated that networks derived from classical methods tend to have high true positive rates at the expense of having overconnected-networks, ML-based NLP methods have lower true positive rates but networks with the closest structures to the target network, and LLM-based NLP methods tend to exist in-between the two other approaches, with variable performances. Finally, the selection of a specific NLP approach should be tied to the needs of a study and text availability, as models varied in performance due to the amount of text provided.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

NGPINT V3: a containerized orchestration Python software for discovery of next-generation protein–protein interactions

Abstract Summary Batch yeast two-hybrid (Y2H) assays, leveraged with next-generation sequencing, have afforded successful innovations for the analysis of protein–protein interactions. NGPINT is a Conda-based software designed to process the millions of raw sequencing reads resulting from Y2H–next-generation interaction screens. Over time, increasing compatibility and dependency issues have prevented clean NGPINT installation and operation. A system-wide update was essential to continue effective use with its companion software, Y2H-SCORES. We present NGPINT V3, a containerized implementation built with both Singularity and Docker, allowing accessibility across virtually any operating system and computing environment. Availability and implementation This update includes streamlined dependencies and container images hosted on Sylabs (https://cloud.sylabs.io/library/schuyler/ngpint/ngpint) and Dockerhub (https://hub.docker.com/r/schuylerds/ngpint), facilitating easier adoption and integration into high-throughput and cloud-computing workflows. Full instructions and software can be also found in the GitHub repository https://github.com/Wiselab2/NGPINT_V3 and Zenodo https://doi.org/10.5281/zenodo.15256036.

Biochemistry & Molecular Biology↗