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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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At least 379 records · Page 21
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Assessment of software methods for estimating protein-protein relative binding affinities

A growing number of computational tools have been developed to accurately and rapidly predict the impact of amino acid mutations on protein-protein relative binding affinities. Such tools have many applications, for example, designing new drugs and studying evolutionary mechanisms. In the search for accuracy, many of these methods employ expensive yet rigorous molecular dynamics simulations. By contrast, non-rigorous methods use less exhaustive statistical mechanics, allowing for more efficient calculations. However, it is unclear if such methods retain enough accuracy to replace rigorous methods in binding affinity calculations. This trade-off between accuracy and computational expense makes it difficult to determine the best method for a particular system or study. Here, eight non-rigorous computational methods were assessed using eight antibody-antigen and eight non-antibody-antigen complexes for their ability to accurately predict relative binding affinities (ΔΔG) for 654 single mutations. In addition to assessing accuracy, we analyzed the CPU cost and performance for each method using a variety of physico-chemical structural features. This allowed us to posit scenarios in which each method may be best utilized. Most methods performed worse when applied to antibody-antigen complexes compared to non-antibody-antigen complexes. Rosetta-based JayZ and EasyE methods classified mutations as destabilizing (ΔΔG < -0.5 kcal/mol) with high (83–98%) accuracy and a relatively low computational cost for non-antibody-antigen complexes. Some of the most accurate results for antibody-antigen systems came from combining molecular dynamics with FoldX with a correlation coefficient (r) of 0.46, but this was also the most computationally expensive method. Overall, our results suggest these methods can be used to quickly and accurately predict stabilizing versus destabilizing mutations but are less accurate at predicting actual binding affinities. This study highlights the need for continued development of reliable, accessible, and reproducible methods for predicting binding affinities in antibody-antigen proteins and provides a recipe for using current methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural Insights into Mechanisms Underlying Mitochondrial and Bacterial Cytochrome c Synthases

Mitochondrial holocytochrome c synthase (HCCS) is an essential protein in assembling cytochrome c (cyt c) of the electron transport system. HCCS binds heme and covalently attaches the two vinyls of heme to two cysteine thiols of the cyt c CXXCH motif. Human HCCS recognizes both cyt c and cytochrome c1 of complex III (cytochrome bc1). HCCS is mutated in some human diseases and it has been investigated recombinantly by mutational, biochemical, and reconstitution studies in the past decade. Here, we employ structural prediction programs (e.g., AlphaFold 3) on HCCS and its two substrates, heme and cytochrome c. The results, when combined with spectroscopic and functional analyses of HCCS and variants, provide insights into the structural basis for heme binding, apocyt c binding, covalent attachment, and release of the holocyt c product. Results from in vitro reconstitution of purified human HCCS using cyt c and cyt c1 peptides as acceptors are consistent with the structural modeling of substrate binding. Reconstitution of HCCS and cyt c1 provides an approach to studying cyt c1 assembly, which has been refractile to recombinant in vivo reconstitution (unlike HCCS and cyt c). We propose a structural basis for release of the holocyt c product from HCCS based on in vitro studies and on cryoEM structures of the bacterial cyt c synthase (CcsBA) active site. We analyze the kinetoplastid mitochondrial synthase (KCCS), and hypothesize a molecular evolutionary path from mitochondrial endosymbiosis to the current HCCS.

Biochemistry & Molecular Biology↗
DOE OSTI2024

Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires

Borgs are huge extrachromosomal elements (ECE) of anaerobic methane-consuming “Candidatus Methanoperedens” archaea. Here, we used nanopore sequencing to validate published complete genomes curated from short reads and to reconstruct new genomes. 13 complete and four near-complete linear genomes share 40 genes that define a largely syntenous genome backbone. We use these conserved genes to identify new Borgs from peatland soil and to delineate Borg phylogeny, revealing two major clades. Remarkably, Borg genes encoding nanowire-like electron-transferring cytochromes and cell surface proteins are more highly expressed than those of host Methanoperedens, indicating that Borgs augment the Methanoperedens activity in situ. We reconstructed the first complete 4.00 Mbp genome for a Methanoperedens that is inferred to be a Borg host and predicted its methylation motifs, which differ from pervasive TC and CC methylation motifs of the Borgs. Thus, methylation may enable Methanoperedens to distinguish their genomes from those of Borgs. Very high Borg to Methanoperedens ratios and structural predictions suggest that Borgs may be capable of encapsulation. The findings clearly define Borgs as a distinct class of ECE with shared genomic signatures, establish their diversification from a common ancestor with genetic inheritance, and raise the possibility of periodic existence outside of host cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Uncovering Sequence and Structural Characteristics of Fungal Expansin‐Related Proteins With Potential to Drive Substrate Targeting

Expansins loosen plant cell wall networks through disrupting non-covalent bonds between cellulose microfibrils and matrix polysaccharides. Whereas expansins were first discovered in plants, expansin-related proteins have since been identified in bacteria and fungi. The biological function of microbial expansins remains unclear; however, several studies have shown distinct binding preferences toward different structural polysaccharides. Earlier studies of bacterial expansin-related proteins uncovered sequence and structural features that correlate to substrate binding. Herein, 20 fungal expansin-related sequences were recombinantly produced in Komagataella phaffii, and the purified proteins were compared in terms of substrate binding to cellulosic and chitinous substrates. The impact of pH on the zeta potential of prioritized substrates was also measured, and Principal Component Analysis was performed to uncover correlations between protein characteristics (e.g., pI, hydrophobicity, surface charge distribution) and measured substrate binding preferences. Whereas acidic proteins with a predicted pI less than 5.0 preferentially bound to chitin, basic proteins with pI greater than 8.0 preferentially bound to xylan and xylan-containing fiber. Similar to many cellulases, binding to cellulose was correlated to relatively high aromatic amino acid content in the protein sequence and presence of a carbohydrate binding module (CBM), which in the case of expansins is a C-terminal CBM63. Whereas overall sequence characteristics could be correlated to substrate binding preference, the identity of amino acids occupying conserved positions that impact protein activity was better correlated with loosenin versus expansin classifications.

chitin↗
DOE OSTI2023

Hydrodynamics of thermally driven chiral suspensions

Considerable effort has been directed towards the characterization of chiral mesoscale structures, as shown in chiral protein assemblies and carbon nanotubes. Here, we establish a thermally driven hydrodynamic description for the actuation and separation of mesoscale chiral structures in a fluid medium. Cross-flow of a Newtonian liquid with a thermal gradient gives rise to an effective torque that propels each particle of a chiral suspension according to its handedness. In turn, the chiral suspension alters the liquid flow, which thus acquires a transverse (chiral) velocity component. Since observation of the predicted effects requires a low degree of sophistication, our work provides an efficient and inexpensive approach to test and calibrate chiral particle propulsion and separation strategies.

Mechanics↗
DOE OSTI2021

The genotype-phenotype landscape of an allosteric protein

Allostery is a fundamental biophysical mechanism that underlies cellular sensing, signaling, and metabolism. Yet a quantitative understanding of allosteric genotype-phenotype relationships remains elusive. Here, we report the large-scale measurement of the genotype-phenotype landscape for an allosteric protein: the lac repressor from Escherichia coli , LacI. Using a method that combines long-read and short-read DNA sequencing, we quantitatively measure the dose-response curves for nearly 10 5 variants of the LacI genetic sensor. The resulting data provide a quantitative map of the effect of amino acid substitutions on LacI allostery and reveal systematic sequence-structure-function relationships. We find that in many cases, allosteric phenotypes can be quantitatively predicted with additive or neural-network models, but unpredictable changes also occur. For example, we were surprised to discover a new band-stop phenotype that challenges conventional models of allostery and that emerges from combinations of nearly silent amino acid substitutions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Rational Design of Novel Biomimetic Sequence-Defined Polymers for Mineralization Applications

Silica biomineralization is a naturally occurring process, wherein organisms use proteins and other biological structures to direct the formation of complex, hierarchical nanostructures. Discovery and characterization of such proteins and their underlying mechanisms spurred significant efforts to identify routes for biomimetic mineralization that reproduce the exquisite shapes and size selectivities found in nature. A common strategy has been the use of short peptide sequences with chemistry mimicking those found in natural systems, such as the use of the silaffin-derived R5 peptide. While progress has been made using this approach, there are many limitations that have prevented breakthroughs in biomimicry. To advance our ability to use charged macromolecules for silica formation, we propose to use sequence-defined synthetic polymers known as peptoids, or N-substituted polyglycines, which present significant capability for the precise tuning of sequence and structure beyond what can often be achieved with peptides alone. This study presents a computationally predicted design of these polymers that leads to the controlled formation of silica nanomaterials. We investigate surface adsorption and the mineralization process through analysis of binding mechanisms and energetics of the R5 system. Next, we synthesized two R5-inspired peptoids and validated our prediction in the design of mineralization polymers through characterization using surface plasmon resonance and electron microscopy. Here, this computationally guided study holds great promise for designing new sequences with unprecedented control of the placement of chemical functional groups, thus allowing for further unraveling of silicification mechanisms and the eventual design of sequence-defined synthetic polymers leading to the predictive synthesis of nanostructured functional materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Mechanism and dynamics of fatty acid photodecarboxylase

Photoenzymes are rare biocatalysts driven by absorption of a photon at each catalytic cycle; they inspire development of artificial photoenzymes with valuable activities. Fatty acid photodecarboxylase (FAP) is a natural photoenzyme that has potential applications in the bio-based production of hydrocarbons, yet its mechanism is far from fully understood. RATIONALE To elucidate the mechanism of FAP, we studied the wild-type (WT) enzyme from Chlorella variabilis (CvFAP) and variants with altered active-site residues using a wealth of techniques, including static and time-resolved crystallography and spectroscopy, as well as biochemical and computational approaches. RESULTS A 1.8-Å-resolution CvFAP x-ray crystal structure revealed a dense hydrogen-bonding network positioning the fatty acid carboxyl group in the vicinity of the flavin adenine dinucleotide (FAD) cofactor. Structures solved from free electron laser and low-dose synchrotron x-ray crystal data further highlighted an unusual bent shape of the oxidized flavin chromophore, and showed that the bending angle (14°) did not change upon photon absorption (step 1) or throughout the photocycle. Calculations showed that bending substantially affected the energy levels of the flavin. Structural and spectroscopic analysis of WT and mutant proteins targeting two conserved active-site residues, R451 and C432, demonstrated that both residues were crucial for proper positioning of the substrate and water molecules and for oxidation of the fatty acid carboxylate by 1 FAD* (~300 ps in WT FAP) to form FAD ∙– (step 2). Time-resolved infrared spectroscopy demonstrated that decarboxylation occured quasi-instantaneously upon this forward electron transfer, consistent with barrierless bond cleavage predicted by quantum chemistry calculations and with snapshots obtained by time-resolved crystallography. Transient absorption spectroscopy in H 2 O and D 2 O buffers indicated that back electron transfer from FAD ∙– was coupled to and limited by transfer of an exchangeable proton or hydrogen atom (step 3). Unexpectedly, concomitant with FAD ∙– reoxidation (to a red-shifted form FAD RS ) in 100 ns, most of the CO 2 product was converted, most likely into bicarbonate (as inferred from FTIR spectra of the cryotrapped FAD RS intermediate). Calculations indicated that this catalytic transformation involved an active-site water molecule. Cryo-Fourier transform infrared spectroscopy studies suggested that bicarbonate formation (step 4) was preceded by deprotonation of an arginine residue (step 3). At room temperature, the remaining CO 2 left the protein in 1.5 μs (step 4'). The observation of residual electron density close to C432 in electron density maps derived from time-resolved and cryocrystallography data suggests that this residue may play a role in stabilizing CO 2 and/or bicarbonate. Three routes for alkane formation were identified by quantum chemistry calculations; the one shown in the figure is favored by the ensemble of experimental data. CONCLUSION Finally, we provide a detailed and comprehensive characterization of light-driven hydrocarbon formation by FAP, which uses a remarkably complex mechanism including unique catalytic steps. We anticipate that our results will help to expand the green chemistry toolkit.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Structural and Dynamical Design Principles for Iron-Sulfur Clusters in Sequence Defined Polymers

This integrated synthetic and computational effort uses sequence defined polymers such as peptoids, and triazines, capable of mimicking a flexible protein environment to control the positioning of side chains around redox cofactors. This strategy will allow modulation of redox properties through both direct and indirect mechanisms. To this end the aim is defined to test the underlying hypothesis: that principles and critical functionalities governing the binding and tuning of naturally occurring electron carrier co-factors can be identified and used to predictably design and synthesize maquettes based on non-natural polymers resulting in new modular biomimetic scaffolds for Electron Transfer Materials. This will be achieved through design and synthesis of ligands that can stabilize iron-sulfur clusters and tune the redox potential based on sequence.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Bipartite chromatin recognition by Hop1 from two diverged Holozoa

In meiosis, ploidy reduction is driven by a complex series of DNA breakage and recombination events between homologous chromosomes, orchestrated by meiotic HORMA domain proteins (HORMADs). Meiotic HORMADs possess a central chromatin binding region (CBR) whose architecture varies across eukaryotic groups. Here, we determine high-resolution crystal structures of the meiotic HORMAD CBR from two diverged aquatic Holozoa,Schistosoma mansoniandPatiria miniata, which reveal tightly associated plant homeodomain (PHD) and winged helix-turn-helix (wHTH) domains. We show that PHD–wHTH CBRs bind duplex DNA through their wHTH domains, and identify key residues that disrupt this interaction. Combining experimental and predicted structures, we show that the CBRs’ PHDs likely interact with the tail of histone H3, and may discriminate between unmethylated and trimethylated H3 lysine 4. Finally, we show that Holozoa Hop1 CBRs bind nucleosomes in vitro in a bipartite manner involving both the PHD and wHTH domain. Our data reveal how meiotic HORMADs with PHD–wHTH CBRs can bind chromatin and potentially discriminate between chromatin states to drive meiotic recombination to specific chromosomal regions.

Life Sciences & Biomedicine - Other Topics↗
NASA NTRS2003

Mechanosensitive Ion Channels in Bacteria: Functional Domains and Mechanisms of Gating

The past funding period was productive for the group. The progress in the mechanosensitive channel field was critically affected in the end of 1998 by the solution of the crystal structure of the mycobacterial homolog of MscL by our colleagues from Caltech. Having the structure of TbMscL in the closed state, we developed a detailed homology model of EcoMscL, and related the structural model with the wealth of functional phenomenology available for the E. coli version of the channel (EcoMscL). The biophysical properties of the open MscL helped to model the open conformation and infer the pathway for the entire gating transition. The following experiments provided strong support to the atomic model of the gating process, and allowed to make further predictions. The work has advanced our understanding of tension-driven conformational transitions in membrane-embedded mechanosensory proteins, determine major energetic contributions and set the stage for further exploration of the whole family of mechanosensitive channels. The results have been published in seven experimental and theoretical papers, with three other papers currently in press or in preparation.

Sukharev, Sergei↗
DOE OSTI2024

Influence of pump laser fluence on ultrafast myoglobin structural dynamics

High-intensity femtosecond pulses from an X-ray free-electron laser enable pump–probe experiments for the investigation of electronic and nuclear changes during light-induced reactions. On timescales ranging from femtoseconds to milliseconds and for a variety of biological systems, time-resolved serial femtosecond crystallography (TR-SFX) has provided detailed structural data for light-induced isomerization, breakage or formation of chemical bonds and electron transfer. However, all ultrafast TR-SFX studies to date have employed such high pump laser energies that nominally several photons were absorbed per chromophore. As multiphoton absorption may force the protein response into non-physiological pathways, it is of great concern whether this experimental approach allows valid conclusions to be drawn vis-à-vis biologically relevant single-photon-induced reactions. Here we describe ultrafast pump–probe SFX experiments on the photodissociation of carboxymyoglobin, showing that different pump laser fluences yield markedly different results. In particular, the dynamics of structural changes and observed indicators of the mechanistically important coherent oscillations of the Fe–CO bond distance (predicted by recent quantum wavepacket dynamics) are seen to depend strongly on pump laser energy, in line with quantum chemical analysis. Our results confirm both the feasibility and necessity of performing ultrafast TR-SFX pump–probe experiments in the linear photoexcitation regime. We consider this to be a starting point for reassessing both the design and the interpretation of ultrafast TR-SFX pump–probe experiments such that mechanistically relevant insight emerges.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Host cell and viral protease targets of human SERPINs identified by in silico docking

Serine protease inhibitors (SERPINs) are involved in various physiological processes and diseases, such as inflammation, cancer metastasis, and neurodegeneration. Their role in viral infections is poorly understood, as their expression patterns during infection and the range of proteases they target have yet to be fully characterized. Here, we show widespread expression of human SERPINs in response to respiratory virus infections, both in bronchioalveolar lavages from COVID-19 patients and in polarized human airway epithelial cultures. Using in silico docking of 10 SERPINs to 48 host proteases, we confirm known targets and predict new interactions. Protease activity assays validated selected interactions, confirming the newly predicted host targets for PAI-1 (SERPINE1) and PAI-2 (SERPINB2). PAI-1 inhibits cathepsin L, essential for SARS-CoV-2 maturation, and suppresses multi-cycle replication of both ancestral SARS-CoV-2 WA-1 and its variant Omicron BA.1. In addition, we identify PAI-2 as an antiviral SERPIN that reduces infectivity of human adenovirus 5 by directly inhibiting the adenoviral protease. Our study leverages in silico docking using full-length 3D protein structures to uncover new SERPIN targets, offering a range of candidate targets for therapeutic interventions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Do Molecular Fingerprints Identify Diverse Active Drugs in Large-Scale Virtual Screening? (No)

Computational approaches for small-molecule drug discovery now regularly scale to the consideration of libraries containing billions of candidate small molecules. One promising approach to increased the speed of evaluating billion-molecule libraries is to develop succinct representations of each molecule that enable the rapid identification of molecules with similar properties. Molecular fingerprints are thought to provide a mechanism for producing such representations. Here, we explore the utility of commonly used fingerprints in the context of predicting similar molecular activity. We show that fingerprint similarity provides little discriminative power between active and inactive molecules for a target protein based on a known active—while they may sometimes provide some enrichment for active molecules in a drug screen, a screened data set will still be dominated by inactive molecules. We also demonstrate that high-similarity actives appear to share a scaffold with the query active, meaning that they could more easily be identified by structural enumeration. Furthermore, even when limited to only active molecules, fingerprint similarity values do not correlate with compound potency. In sum, these results highlight the need for a new wave of molecular representations that will improve the capacity to detect biologically active molecules based on their similarity to other such molecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Chemical manipulation of an activation/inhibition switch in the nuclear receptor PXR

Nuclear receptors are ligand-activated transcription factors that can often be useful drug targets. Unfortunately, ligand promiscuity leads to two-thirds of receptors remaining clinically untargeted. PXR is a nuclear receptor that can be activated by diverse compounds to elevate metabolism, negatively impacting drug efficacy and safety. This presents a barrier to drug development because compounds designed to target other proteins must avoid PXR activation while retaining potency for the desired target. This problem could be avoided by using PXR antagonists, but these compounds are rare, and their molecular mechanisms remain unknown. Here, we report structurally related PXR-selective agonists and antagonists and their corresponding co-crystal structures to describe mechanisms of antagonism and selectivity. Structural and computational approaches show that antagonists induce PXR conformational changes incompatible with transcriptional coactivator recruitment. These results guide the design of compounds with predictable agonist/antagonist activities and bolster efforts to generate antagonists to prevent PXR activation interfering with other drugs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Leveraging structure-informed machine learning for fast steric zipper propensity prediction across whole proteomes

Predicting the amyloid fold and the propensity of peptide segments to adopt amyloid-like structures remain a challenge. However, recent progress has facilitated structure-based prediction of steric zipper propensity and the use of machine learning to accelerate the calculation of predictive models across many scientific areas. Leveraging these advances, we have developed a new approach for rapid proteome-wide assessment of zipper profiles that is informed by four million steric zipper predictions collected over ten years. This collection is used to build a machine learning model capable of rapidly predicting steric zipper propensity, and allowing for the assessment of zippers at both the protein and proteome level. Our predictions show enrichment for zipper forming segments in proteins involved in cell wall reorganization in yeast, highlighting a potential category of interest for experimental characterization. Overall, our predictive model allows for the exploration of amyloid formation across the tree of life and provides a tool for assessment of both novel and designed sequences for zipper density.

Biochemistry & Molecular Biology↗
DOE OSTI2022

Mutations of Omicron Variant at the Interface of the Receptor Domain Motif and Human Angiotensin-Converting Enzyme-2

The most recent Omicron variant of SARS-CoV-2 has caused global concern and anxiety. The only thing certain about this strain, with a large number of mutations in the spike protein, is that it spreads quickly, seems to evade immune defense, and mitigates the benefits of existing vaccines. Based on the ultra-large-scale ab initio computational modeling of the receptor binding motif (RBM) and the human angiotensin-converting enzyme-2 (ACE2) interface, we provide the details of the effect of Omicron mutations at the fundamental atomic scale level. In-depth analysis anchored in the novel concept of amino acid-amino acid bond pair units (AABPU) indicates that mutations in the Omicron variant are connected with (i) significant changes in the shape and structure of AABPU components, together with (ii) significant increase in the positive partial charge, which facilitates the interaction with ACE2. We have identified changes in bonding due to mutations in the RBM. The calculated bond order, based on AABPU, reveals that the Omicron mutations increase the binding strength of RBM to ACE2. Our findings correlate with and are instrumental to explain the current observations and can contribute to the prediction of next potential new variant of concern.

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

Predicting Dexter Energy Transfer Interactions from Molecular Orbital Overlaps

Dexter energy transfer (DET), also known as spin forbidden energy transfer (e.g., 3 D 1 A → 1 D 3 A), is undergoing renewed interest because of its utility in energy science, photocatalysis, and biomedical imaging. The DET reactions enable exciton fission and fusion and have been recently used to facilitate nanoscale imaging of protein assemblies on cell surfaces. While DET and Förster energy transfer rates are often well described using Fermi’s golden rule, the donor–acceptor couplings for DET may be bridge-state-mediated and depend on the electronic structure of and interactions among the donor, bridge, and acceptor. We provide a simple approach to approximate DET couplings using a product of molecular orbital overlap factors. This approach may be used to guide the design of DET systems with targeted energy-transfer kinetics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗