Micro-electron diffraction structure of the aggregation-driving N terminus of Drosophila neuronal protein Orb2A reveals amyloid-like β-sheets
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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
SEARCH · Engineering Papers
Results for “proteins binding”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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ATCUN-like Copper Site in βB2-Crystallin Plays a Protective Role in Cataract-Associated Aggregation
Cataract is the leading cause of blindness worldwide, and it is caused by crystallin damage and aggregation. Senile cataractous lenses have relatively high levels of metals, while some metal ions can directly induce the aggregation of human γ-crystallins. Here, for this work, we evaluated the impact of divalent metal ions in the aggregation of human βB2-crystallin, one of the most abundant crystallins in the lens. Turbidity assays showed that Pb 2+ , Hg 2+ , Cu 2+ , and Zn 2+ ions induce the aggregation of βB2-crystallin. Metal-induced aggregation is partially reverted by a chelating agent, indicating the formation of metal-bridged species. Our study focused on the mechanism of copper-induced aggregation of βB2-crystallin, finding that it involves metal-bridging, disulfide-bridging, and loss of protein stability. Circular dichroism and electron paramagnetic resonance (EPR) revealed the presence of at least three Cu 2+ binding sites in βB2-crystallin, one of them with spectroscopic features typical for Cu 2+ bound to an amino-terminal copper and nickel (ATCUN) binding motif, which is found in Cu transport proteins. The ATCUN-like Cu binding site is located at the unstructured N-terminus of βB2-crystallin, and it could be modeled by a peptide with the first six residues in the protein sequence (NH 2 -ASDHQF-). Isothermal titration calorimetry indicates a nanomolar Cu 2+ binding affinity for the ATCUN-like site. An N-truncated form of βB2-crystallin is more susceptible to Cu-induced aggregation and is less thermally stable, indicating a protective role for the ATCUN-like site. EPR and X-ray absorption spectroscopy studies reveal the presence of a copper redox active site in βB2-crystallin that is associated with metal-induced aggregation and formation of disulfide-bridged oligomers. Our study demonstrates metal-induced aggregation of βB2-crystallin and the presence of putative copper binding sites in the protein. Whether the copper-transport ATCUN-like site in βB2-crystallin plays a functional/protective role or constitutes a vestige from its evolution as a lens structural protein remains to be elucidated.
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Membrane Proteins Have Distinct Fast Internal Motion and Residual Conformational Entropy
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99 GENERAL AND MISCELLANEOUS↗
Behavior of Water Near Multimodal Chromatography Ligands and Its Consequences for Modulating Protein–Ligand Interactions
Multimodal chromatography is a powerful approach for purifying proteins that uses ligands containing multiple modes of interaction. Recent studies have shown that selectivity in multimodal chromatographic separations is a function of the ligand structure and geometry. Here, we performed molecular dynamics simulations to explore how the ligand structure and geometry affect ligand–water interactions and how these differences in solution affect the nature of protein–ligand interactions. Our investigation focused on three chromatography ligands: Capto MMC, Nuvia cPrime, and Prototype 4, a structural variant of Nuvia cPrime. First, the solvation characteristics of each ligand were quantified via three metrics: average water density, fluctuations, and residence time. We then explored how solvation was perturbed when the ligand was bound to the protein surface and found that the probability of the phenyl ring dewetting followed the order: Capto MMC > Prototype 4 > Nuvia cPrime. To explore how these differences in dewetting affect protein–ligand interactions, we calculated the probability of each ligand binding to different types of residues on the protein surface and found that the probability of binding to a hydrophobic residue followed the same order as the dewetting behavior. This study illustrates the role that wetting and dewetting play in modulating protein–ligand interactions.
59 BASIC BIOLOGICAL SCIENCES↗
Rare, convergent antibodies targeting the stem helix broadly neutralize diverse betacoronaviruses
Humanity has faced three recent outbreaks of novel betacoronaviruses, emphasizing the need to develop approaches that broadly target coronaviruses. Here, we identify 55 monoclonal antibodies from COVID-19 convalescent donors that bind diverse betacoronavirus spike proteins. Most antibodies targeted an S2 epitope that included the K814 residue and were non-neutralizing. However, 11 antibodies targeting the stem helix neutralized betacoronaviruses from different lineages. Eight antibodies in this group, including the six broadest and most potent neutralizers, were encoded by IGHV1-46 and IGKV3-20. Crystal structures of three antibodies of this class at 1.5–1.75-Å resolution revealed a conserved mode of binding. COV89-22 neutralized SARS-CoV-2 variants of concern including Omicron BA.4/5 and limited disease in Syrian hamsters. Collectively, these findings identify a class of IGHV1-46/IGKV3-20 antibodies that broadly neutralize betacoronaviruses by targeting the stem helix but indicate these antibodies constitute a small fraction of the broadly reactive antibody response to betacoronaviruses after SARS-CoV-2 infection.
60 APPLIED LIFE SCIENCES↗
Binding Free Energy Analysis of Colicin D, E3 and E8 to Their Respective Cognate Immunity Proteins Using Computational Simulations
Colicins are antimicrobial proteins produced by bacteria for the purpose of destroying neighboring bacteria. Colicin activity is neutralized by a specific cognate immunity protein in order to protect the host. This study investigates the structural and binding mechanisms underlying the interaction of colicin-D, -E3 and -E8 to their respective immunity proteins (ImD, Im3 and Im8) using structure prediction, molecular dynamics (MD) simulations and MM-PBSA approach of free energy calculations. High-confidence colicin-immunity (Col-Im) complex structures predicted using AlphaFold2 were subjected to MD simulations of 150 ns with GROMACS and were analyzed for the binding free energy calculation using gmx_MMPBSA. Results showed that the complex of Col_E3-Im3 exhibited the most favorable binding free energy, driven by strong van der Waals and electrostatic interactions. Col_D-ImD and Col_E8-Im8 also showed the favorable binding. Electrostatics and hydrogen bonding emerged as a key factor driving binding and stability, while polar solvation acted as a destabilizing factor across all systems. These outcomes provide an understanding of the molecular mechanisms of Col-Im systems, with potential applications for developing natural antimicrobials for food safety.
Biochemistry & Molecular Biology↗
Ancient origins of allosteric activation in a Ser-Thr kinase
A myriad of cellular events are regulated by allostery; therefore, evolution of this process is of fundamental interest. Here, we use ancestral sequence reconstruction to resurrect ancestors of two colocalizing proteins, Aurora A kinase and its allosteric activator TPX2 (targeting protein for Xklp2), to experimentally characterize the evolutionary path of allosteric activation. Autophosphorylation of the activation loop is the most ancient activation mechanism; it is fully developed in the oldest kinase ancestor and has remained stable over 1 billion years of evolution. As the microtubule-associated protein TPX2 appeared, efficient kinase binding to TPX2 evolved, likely owing to increased fitness by virtue of colocalization. Subsequently, TPX2-mediated allosteric kinase regulation gradually evolved. Surprisingly, evolution of this regulation is encoded in the kinase and did not arise by a dominating mechanism of coevolution.
Science & Technology - Other Topics↗
Protein conformational switch discerned via network centrality properties
Network analysis has emerged as a powerful tool for examining structural biology systems. The spatial organization of the components of a biomolecular structure has been rendered as a graph representation and analyses have been performed to deduce the biophysical and mechanistic properties of these components. For proteins, the analysis of protein structure networks (PSNs), especially via network centrality measurements and cluster coefficients, has led to identifying amino acid residues that play key functional roles and classifying amino acid residues in general. Whether these network properties examined in various studies are sensitive to subtle (yet biologically significant) conformational changes remained to be addressed. Here, we focused on four types of network centrality properties (betweenness, closeness, degree, and eigenvector centralities) for conformational changes upon ligand binding of a sensor protein (constitutive androstane receptor) and an allosteric enzyme (ribonucleotide reductase). We found that eigenvector centrality is sensitive and can distinguish salient structural features between protein conformational states while other centrality measures, especially closeness centrality, are less sensitive and rather generic with respect to the structural specificity. We also demonstrated that an ensembleinformed, modified PSN with static edges removed (which we term PSN*) has enhanced sensitivity at discerning structural changes.
59 BASIC BIOLOGICAL SCIENCES↗
SAA1 is transcriptionally activated by STAT3 and accelerates renal interstitial fibrosis by inducing endoplasmic reticulum stress
Renal interstitial fibrosis (RIF) is the common irreversible pathway by which chronic kidney disease (CKD) progresses to the end stage. The transforming growth factor-β (TGF-β)/signal transducer and activator of transcription 3 (STAT3) signaling pathway is a common factor leading to inflammation-mediated RIF, but its downstream regulatory mechanism is still unclear. Bioinformatics analysis predicted that serum amyloid A protein 1 (SAA1) was one of the target genes for transcriptional activation of STAT3 signaling. As an acute phase reaction protein, SAA1 plays an important role in many inflammatory reactions, and research has suggested that SAA1 is significantly elevated in the serum of patients with CKD. In this research, multiple experiments were performed to investigate the role of SAA1 in the process of RIF. SAA1 was abnormally highly expressed in kidney tissue from individuals who underwent unilateral ureteral obstruction (UUO) and TGF-β-induced HK2 cells, and the abnormal expression was directly related to the transcriptional activation of STAT3. Additionally, SAA1 can directly target and bind valosin-containing protein (VCP)-interacting membrane selenoprotein (VIMP) to inhibit the function of the Derlin-1/VCP/VIMP complex, preventing the transportation and degradation of the misfolded protein, resulting in endoplasmic reticulum (ER) stress characterized by an increase in glucose-regulated protein 78 (GRP78) levels and ultimately promoting the occurrence and development of RIF.
60 APPLIED LIFE SCIENCES↗
Models of the Protocellular Structures, Functions and Evolution
In the absence of extinct or extant record of protocells, the most direct way to test our understanding of the origin of cellular life is to construct laboratory models that capture important features of protocellular systems. Such efforts are currently underway in a collaborative project between NASA-Ames, Harvard medical School and University of California. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures. The centerpiece of this project is a method for the in vitro evolution of protein enzymes toward arbitrary catalytic targets. A similar approach has already been developed for nucleic acids: First, a very large population of candidate molecules is generated using a random synthetic approach. Next, the small numbers of molecules that can accomplish the desired task are selected. These molecules are next vastly multiplied using the polymerase chain reaction. A mutagenic approach, in which the sequences of selected molecules are randomly altered, can yield further improvements in performance or alterations of specificities. Unfortunately, the catalytic potential of nucleic acids is rather limited. Proteins are more catalytically capable but cannot be directly amplified. In the new technique, this problem is circumvented by covalently linking each protein of the initial, diverse, pool to the RNA sequence that codes for it. Then, selection is performed on the proteins, but the nucleic acids are replicated. To date, we have obtained "a proof of concept" by evolving simple, novel proteins capable of selectively binding adenosine tri-phosphate (ATP). Our next goal is to create an enzyme that can phosphorylate amino acids and another to catalyze the formation of peptide bonds in the absence of nucleic acid templates. This latter reaction does not take place in contemporary cells. once developed, these enzymes will be encapsulated in liposomes so that they will function in a simulated cellular environment. To provide a continuous energy supply, usually needed to activate the substrates, an energy transduction complex which generates ATP from adenosine diphosphate, inorganic phosphate and light will be used. This system, consisting of two modern proteins, ATP synthase and bacteriorhodopsin, has already been built and shown to work efficiently. By coupling chemical synthesis to such a system, it will be possible to drive chemical reactions by light if only the substrates for these reactions are supplied.
Pohorille, Andrew↗
Development of a universal nanobody-binding Fab module for fiducial-assisted cryo-EM studies of membrane proteins
Structural studies of membrane proteins by cryogenic electron microscopy (cryo-EM) often require antibody fragments (Fabs) to facilitate particle alignments and achieve high resolution. While conformational nanobodies have been developed to lock specific states of many membrane proteins, they only add 15 kDa of mass to the complex. We developed a synthetic Fab (NabFab) that rigidly binds the conserved scaffold of nanobodies, providing a universally applicable fiducial for cryo-EM studies of protein–nanobody complexes. Additionally, we demonstrate the concept by determining two high-resolution structures of membrane proteins bound to specific nanobodies and NabFab. As the structural epitope for NabFab can be incorporated into the scaffold of virtually any nanobody, this raises the prospect of facile structure determination of many nanobody–protein complexes.
59 BASIC BIOLOGICAL SCIENCES↗
Inhibitor Mimetic Mutations in the Pseudomonas aeruginosa PqsE Enzyme Reveal a Protein-Protein Interaction with the Quorum-Sensing Receptor RhlR That Is Vital for Virulence Factor Production
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99 GENERAL AND MISCELLANEOUS↗
Aspartate Residues in a Forisome-Forming SEO Protein Are Critical for Protein Body Assembly and Ca 2+ Responsiveness
Forisomes are protein bodies known exclusively from sieve elements of legumes. Forisomes contribute to the regulation of phloem transport due to their unique Ca 2+ -controlled, reversible swelling. The assembly of forisomes from sieve element occlusion (SEO) protein monomers in developing sieve elements and the mechanism(s) of Ca 2+ -dependent forisome contractility are poorly understood because the amino acid sequences of SEO proteins lack conventional protein–protein interaction and Ca 2+ -binding motifs. Here we selected amino acids potentially responsible for forisome-specific functions by analyzing SEO protein sequences in comparison to those of the widely distributed SEO-related (SEOR), or SEOR proteins. SEOR proteins resemble SEO proteins closely but lack any Ca 2+ responsiveness. We exchanged identified candidate residues by directed mutagenesis of the Medicago truncatula SEO1 gene, expressed the mutated genes in yeast ( Saccharomyces cerevisiae ) and studied the structural and functional phenotypes of the forisome-like bodies that formed in the transgenic cells. We identified three aspartate residues critical for Ca 2+ responsiveness and two more that were required for forisome-like bodies to assemble. The phenotypes observed further suggested that Ca 2+ -controlled and pH-inducible swelling effects in forisome-like bodies proceeded by different yet interacting mechanisms. Finally, we observed a previously unknown surface striation in native forisomes and in recombinant forisome-like bodies that could serve as an indicator of successful forisome assembly. To conclude, this study defines a promising path to the elucidation of the so-far elusive molecular mechanisms of forisome assembly and Ca 2+ -dependent contractility.
59 BASIC BIOLOGICAL SCIENCES↗
The J-elongated conformation of β 2 -glycoprotein I predominates in solution: Implications for our understanding of antiphospholipid syndrome
β 2 -Glycoprotein I (β 2 GPI) is an abundant plasma protein displaying phospholipid-binding properties. Because it binds phospholipids, it is a target of antiphospholipid antibodies (aPLs) in antiphospholipid syndrome (APS), a life-threatening autoimmune thrombotic disease. Indeed, aPLs prefer membrane-bound β 2 GPI to that in solution. β 2 GPI exists in two almost equally populated redox states: oxidized, in which all the disulfide bonds are formed, and reduced, in which one or more disulfide bonds are broken. Furthermore, β 2 GPI can adopt multiple conformations (i.e. J-elongated, S-twisted, and O-circular). While strong evidence indicates that the J-form is the structure bound to aPLs, which conformation exists and predominates in solution remains controversial, and so is the conformational pathway leading to the bound state. Here, we report that human recombinant β 2 GPI purified under native conditions is oxidized. Moreover, under physiological pH and salt concentrations, this oxidized form adopts a J-elongated, flexible conformation, not circular or twisted, in which the N-terminal domain I (DI) and the C-terminal domain V (DV) are exposed to the solvent. Consistent with this model, binding kinetics and mutagenesis experiments revealed that in solution the J-form interacts with negatively charged liposomes and with MBB2, a monoclonal anti-DI antibody that recapitulates most of the features of pathogenic aPLs. We conclude that the preferential binding of aPLs to phospholipid-bound β 2 GPI arises from the ability of its preexisting J-form to accumulate on the membranes, thereby offering an ideal environment for aPL binding. We propose that targeting the J-form of β 2 GPI provides a strategy to block pathogenic aPLs in APS.
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Covalent Drug Binding in Live Cells Monitored by Mid-Infrared Quantum Cascade Laser Spectroscopy: Photoactive Yellow Protein as a Model System
The detection of drug-target interactions in live cells enables analysis of therapeutic compounds in a native cellular environment. Recent advances in spectroscopy and molecular biology have facilitated the development of genetically encoded vibrational probes like nitriles that can sensitively report on molecular interactions. Nitriles are powerful tools for measuring electrostatic environments within condensed media like proteins, but such measurements in live cells have been hindered by low signal-to-noise ratios. In this study, we design a spectrometer based on a double-beam quantum cascade laser (QCL)-based transmission infrared (IR) source with balanced detection that can significantly enhance sensitivity to nitrile vibrational probes embedded in proteins within cells compared to a conventional FTIR spectrometer. Here, using this approach, we detect small-molecule binding in Escherichia coli, with particular focus on the interaction between para-Coumaric acid (pCA) and nitrile-incorporated photoactive yellow protein (PYP). This system effectively serves as a model for investigating covalent drug binding in a cellular environment. Notably, we observe large spectral shifts of up to 15 cm –1 for nitriles embedded in PYP between the unbound and drug-bound states directly within bacteria, in agreement with observations for purified proteins. Such large spectral shifts are ascribed to the changes in the hydrogen-bonding environment around the local environment of nitriles, accurately modeled through high-level molecular dynamics simulations using the AMOEBA force field. Our findings underscore the QCL spectrometer’s ability to enhance sensitivity for monitoring drug–protein interactions, offering new opportunities for advanced methodologies in drug development and biochemical research.
chromophores↗
SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 2 (Lowest Temperature Extracted Protein Coordinate Trajectories)
Protein-only trajectories of the lowest-temperature window (310K) extracted from temperature replica-exchange molecular dynamics simulations of 23 different SARS CoV-2 systems, including S Protein ACE2-receptor binding-domain, MPro, PLPro, NSP3 ADRP (X-domain/macrodomain/phosphatase), NSP15 (endoribonuclease), NSP9, NSP10, NSP16, and N-protein N-terminus. Systems were prepared with charmm-gui and simulated using the GROMACS simulation software suite. Trajectories are provided in compressed dcd format with accompanying coordinate/topology files in pdb and psf formats. This data supplements the data release, DOI: 10.13139/OLCF/1650650 ('SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 1 (Simulation Initial Conditions and Parameters)')
59 BASIC BIOLOGICAL SCIENCES↗
SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 3 (Raw Temperature Replica Exchange Molecular Dynamics Trajectories)
Raw temperature replica-exchange molecular dyanmics trajectories of 23 different SARS CoV-2 Systems including S Protein ACE2-receptor binding-domain, MPro, PLPro, NSP3 ADRP (X-domain/macrodomain/phosphatase), NSP15 (endoribonuclease), NSP9, NSP10, NSP16, and N-protein N-terminus. Systems were prepared with charmm-gui and simulated using the GROMACS simulation software suite. Non-demuxed, i.e. discontinuous/constant temperature window, trajectories are provided in compressed GROMACS xtc and full trr formats. This data supplements the data releases DOI: 10.13139/OLCF/160650 'SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 1 (Simulation Initial Conditions and Parameters)' and DOI: 10.13139/OLCF/1657844 'SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 2 (Extracted Protein Coordinate Trajectories)'
59 BASIC BIOLOGICAL SCIENCES↗
Rapid Computational Identification of Therapeutic Targets for Pathogens
Biological threats continue to persist and evolve as an important challenge to national security. There are multiple ways in which novel viral pathogens could emerge to pose a serious threat to human health. This project developed a pathogen target identification tool that can rapidly respond to a novel or emerging viral biological threat. A set of computational tools were developed that provide detailed information on the newly sequenced genes, their protein products and the drug target sites for the proteins that are best suited for biological countermeasure development. Three key innovations were developed in the project. 1) Development of a new extensive database of protein pocket structures with structure-based search algorithms to rapidly link novel protein targets with the complete collection of previously experimentally solved protein structures. 2) A novel clustering pipeline was introduced to group matching structures and associated small-molecule binding ligands into a consensus protein pocket with the associated small-molecule chemotypes predicted to fit in the pocket site. The matching experimentally solved structures were used to inform the value of different target sites. 3) Where there are viral protein targets with pockets structurally matched to similar human proteins, a biological knowledge graph, which links molecular interactions with human disease, was used to further assess the potential negative impact of a viral protein target with similarities to human proteins that could have important off target side effects. In total, the project produced a new resource for rapid and detailed assessment of promising targets for countermeasures, reflecting the ongoing wet lab, clinical, and computational data being collected. These capabilities will improve the ability to respond to a biological threat in multiple domains.
59 BASIC BIOLOGICAL SCIENCES↗