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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Localization and functional exploration of leiomodin-2’s C-terminal binding sites

Striated muscle contraction occurs through interactions between overlapping myosin-based thick and actin-based thin filaments within the sarcomere. For effective contraction to occur, the length of the thin filament must be maintained to allow for sufficient overlap with the thick filament. The proteins leiomodin and tropomodulin compete for binding at the pointed end of thin filaments to regulate their length, utilizing their homologous N-terminal actin and tropomyosin binding sites. Leiomodin also has a region called the C-terminal extension, absent in tropomodulin. In this region, the cardiac isoform (leiomodin-2) contains additional actin-binding sites that enable it to bind along the sides of thin filaments in a Ca2+-dependent manner. Here, using nuclear magnetic resonance spectroscopy, we localize the regions of the C-terminal extension that contain residues involved in thin filament side-binding. Using co-sedimentation assays, we reveal that these regions can independently bind thin filaments and discover that the poly-proline region plays a role as a linker, maintaining an adequate distance between two of the regions required for effective interaction to occur. In addition to its role in side-binding, we provide direct evidence that the poly-proline region interacts with profilin and propose a new mechanism by which leiomodin-2 may assist in the polymerization of profilin-bound actin at thin filament pointed ends.

ACTIN-BINDING PROTEINS↗
DOE OSTI2025

The Many-Body Expansion for Metals: II. Nonadditive Terms in Clusters Composed of Metals with n s 1 , n s 2 , and n s 2 p 1 Configurations

The many-body expansion (MBE) was applied to homometallic and heterometallic trimers of metals with ns 1 , ns 2 , and ns 2 p 1 configurations to investigate its convergence, the magnitude and nature (stabilizing/destabilizing) of the individual terms and seek an understanding of their variation across the different families of clusters. In particular, we examined the series of alkali metals (Li 3 , Na 3 , K 3 , Li 2 Na, LiNa 2 ), alkali metal borides (Li 2 B and LiB 2 ), and alkaline earth metals (Be 3 , Be 2 Mg, BeMg 3 , and Mg 3 ) trimers, as well as sodium clusters Na n , n = 2–5. Here, we found that there is no uniform contribution (stabilizing or destabilizing) across the series in the different families of trimers. For instance, the 2-B term stabilizes the ground states of the Na 3 (doublet), Na 4 (singlet), and Na 5 (doublet) clusters, and the 3-B term destabilizes them; however, the opposite holds for the quartet state of the Li 3 , Li 2 Na, LiNa 2 , and Na 3 clusters (destabilizing 2-B, stabilizing 3-B). Substituting Li with B in the quartet state of Li 3 results in a significant reduction of the 3-B term amounting to 16% (Li 2 B) and 5% (LiB 3 ) of the binding energy. On the contrary, the ground states of the alkaline earth metal clusters (Be 3 , Be 2 Mg, BeMg 3 , and Mg 3 ) are stabilized by the 3-B term, while the 2-B term destabilizes them. Overall, we find that the 3-B terms significantly stabilize the high-spin multiplicity states of the ns 1 configurations and the low-spin states of the ns 2 configurations. Finally, as the size of the metal increases, the contribution of the 3-B term to the binding energy decreases due to the longer metal–metal bond distances.

Alkali metals↗
DOE OSTI2026

Energy-Screened Many-Body Expansion for Protein–Ligand Interactions: Examining Convergence for Metalloenzymes Through Seven–Body Interactions

Fragment-based quantum chemistry is a powerful strategy for calculating protein−ligand interaction energies using quantum chemistry methods. Rigorous convergence often requires hundreds of atoms in the protein binding-site model, especially if that model is constructed using distance-based criteria to select amino acid residues, while three- and four-body calculations exhibit instability related to combinatorial proliferation in the number of subsystem calculations. Here, we report an energy-based screening protocol for the many-body expansion applied to protein−ligand interactions, implemented in the open-source FRAGME∩T code. Using a combination of aggressive screening based on semiempirical quantum chemistry, with an improved graph-theoretical algorithm to eliminate unimportant subsystems, we are able to perform n-body calculations up to n = 7 using density functional theory in triple-ζ basis sets. Distance cutoffs further reduce the cost without compromising accuracy. Rapid and stable convergence of the many-body expansion is obtained by n = 4, for a pair of metalloenzymes in which a divalent ion coordinates directly to the ligand. As compared to previous results that relied solely on distance cutoffs, oscillations in the n-body corrections are reduced or eliminated, although residual errors remain in one case. This work demonstrates that benchmark-quality protein−ligand interaction energies can be systematically converged using a method with excellent parallel efficiency and scalability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Single-molecule tracking reveals dual front door/back door inhibition of Cel7A cellulase by its product cellobiose

Degrading cellulose is a key step in the processing of lignocellulosic biomass into bioethanol. Cellobiose, the disaccharide product of cellulose degradation, has been shown to inhibit cellulase activity, but the mechanisms underlying product inhibition are not clear. We combined single-molecule imaging and biochemical investigations with the goal of revealing the mechanism by which cellobiose inhibits the activity of Trichoderma reesei Cel7A, a well-characterized exo-cellulase. We find that cellobiose slows the processive velocity of Cel7A and shortens the distance moved per encounter; effects that can be explained by cellobiose binding to the product release site of the enzyme. Cellobiose also strongly inhibits the binding of Cel7A to immobilized cellulose, with a K i of 2.1 mM. The isolated catalytic domain (CD) of Cel7A was also inhibited to a similar degree by cellobiose, and binding of an isolated carbohydrate-binding module to cellulose was not inhibited by cellobiose, suggesting that cellobiose acts on the CD alone. Finally, cellopentaose inhibited Cel7A binding at micromolar concentrations without affecting the enzyme’s velocity of movement along cellulose. Together, these results suggest that cellobiose inhibits Cel7A activity both by binding to the “back door” product release site to slow activity and to the “front door” substrate-binding tunnel to inhibit interaction with cellulose. These findings point to strategies for engineering cellulases to reduce product inhibition and enhance cellulose degradation, supporting the growth of a sustainable bioeconomy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Density functional modeling of the binding energies between aluminosilicate oligomers and different metal cations

Interactions between negatively charged aluminosilicate species and positively charged metal cations are critical to many important engineering processes and applications, including sustainable cements and aluminosilicate glasses. In an effort to probe these interactions, here we have calculated the pair-wise interaction energies (i.e., binding energies) between aluminosilicate dimer/trimer and 17 different metal cations M n+ (M n+ = Li + , Na + , K + , Cu + , Cu 2+ , Co 2+ , Zn 2+ , Ni 2+ , Mg 2+ , Ca 2+ , Ti 2+ , Fe 2+ , Fe 3+ , Co 3+ , Cr 3+ , Ti 4+ and Cr 6+ ) using a density functional theory (DFT) approach. Analysis of the DFT-optimized structural representations for the clusters (dimer/trimer + M n+ ) shows that their structural attributes (e.g., interatomic distances) are generally consistent with literature observations on aluminosilicate glasses. The DFT-derived binding energies are seen to vary considerably depending on the type of cations (i.e., charge and ionic radii) and aluminosilicate species (i.e., dimer or trimer). A survey of the literature reveals that the difference in the calculated binding energies between different M n+ can be used to explain many literature observations associated with the impact of metal cations on materials properties (e.g., glass corrosion, mineral dissolution, and ionic transport). Analysis of all the DFT-derived binding energies reveals that the correlation between these energy values and the ionic potential and field strength of the metal cations are well captured by 2nd order polynomial functions ( R 2 values of 0.99–1.00 are achieved for regressions). Given that the ionic potential and field strength of a given metal cation can be readily estimated using well-tabulated ionic radii available in the literature, these simple polynomial functions would enable rapid estimation of the binding energies of a much wider range of cations with the aluminosilicate dimer/trimer, providing guidance on the design and optimization of sustainable cements and aluminosilicate glasses and their associated applications. Finally, the limitations associated with using these simple model systems to model complex interactions are also discussed.

Gong, Kai↗
DOE OSTI2022

Amyloid-like amelogenin nanoribbons template mineralization via a low-energy interface of ion binding sites

Protein scaffolds direct the organization of amorphous precursors that transform into mineralized tissues, but the templating mechanism remains elusive. Motivated by models for the biomineralization of tooth enamel, wherein amyloid-like amelogenin nanoribbons guide the mineralization of apatite filaments, we investigated the impact of nanoribbon structure, sequence, and chemistry on amorphous calcium phosphate (ACP) nucleation. Using full-length human amelogenin and peptide analogs with an amyloid-like domain, films of β-sheet nanoribbons were self-assembled on graphite and characterized by in situ atomic force microscopy and molecular dynamics simulations. All sequences substantially reduce nucleation barriers for ACP by creating low-energy interfaces, while phosphoserines along the length of the nanoribbons dramatically enhance kinetic factors associated with ion binding. Furthermore, the distribution of negatively charged residues along the nanoribbons presents a potential match to the Ca–Ca distances of the multi-ion complexes that constitute ACP. These findings show that amyloid-like amelogenin nanoribbons provide potent scaffolds for ACP mineralization by presenting energetically and stereochemically favorable templates of calcium phosphate ion binding and suggest enhanced surface wetting toward calcium phosphates in general.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Understanding How Ligand Functionalization Influences CO2 and N2 Adsorption in a Sodalite Metal–Organic Framework

In this work, a detailed study is conducted to understand how ligand substitution influences the CO2 and N2 adsorption properties of two highly crystalline sodalite metal–organic frameworks (MOFs) known as Cu–BTT (BTT–3 = 1,3,5-benzenetristetrazolate) and Cu–BTTri (BTTri–3 = 1,3,5-benzenetristriazolate). The enthalpy of adsorption and observed adsorption capacities at a given pressure are significantly lower for Cu–BTTri compared to its tetrazole counterpart, Cu–BTT. In situ X-ray and neutron diffraction, which allow visualization of the CO2 and N2 binding sites on the internal surface of Cu–BTTri, provide insights into understanding the subtle differences. As expected, slightly elongated distances between the open Cu2+ sites and surface-bound CO2 in Cu–BTTri can be explained by the fact that the triazolate ligand is a better electron donor than the tetrazolate. The more pronounced Jahn–Teller effect in Cu–BTTri leads to weaker guest binding. The results of the aforementioned structural analysis were complemented by the prediction of the binding energies at each CO2 and N2 adsorption site by density functional theory calculations. In addition, variable temperature in situ diffraction measurements shed light on the fine structural changes of the framework and CO2 occupancies at different adsorption sites as a function of temperature. Finally, simulated breakthrough curves obtained for both sodalite MOFs demonstrate the materials’ potential performance in dry postcombustion CO2 capture. The simulation, which considers both framework uptake capacity and selectivity, predicts better separation performance for Cu–BTT. The information obtained in this work highlights how ligand substitution can influence adsorption properties and hence provides further insights into the material optimization for important separations.

adsorption capacities↗
DOE OSTI2024

Structural basis of DNA recognition of the Campylobacter jejuni CosR regulator

Campylobacter jejuni is a foodborne pathogen commonly found in the intestinal tracts of animals. This pathogen is a leading cause of gastroenteritis in humans. Besides its highly infectious nature, C. jejuni is increasingly resistant to a number of clinically administrated antibiotics. As a consequence, the Centers for Disease Control and Prevention has designated antibiotic-resistant Campylobacter as a serious antibiotic resistance threat in the United States. The C. jejuni CosR regulator is essential to the viability of this bacterium and is responsible for regulating the expression of a number of oxidative stress defense enzymes. Importantly, it also modulates the expression of the CmeABC multidrug efflux system, the most predominant and clinically important system in C. jejuni that mediates resistance to multiple antimicrobials. Here, we report structures of apo-CosR and CosR bound with a 21 bp DNA sequence located at the cmeABC promotor region using both single-particle cryo-electron microscopy and X-ray crystallography. These structures allow us to propose a novel mechanism for CosR regulation that involves a long-distance conformational coupling and rearrangement of the secondary structural elements of the regulator to bind target DNA.

CosR-DNA complex↗
DOE OSTI2023

Evaluation of 6-OxP-CD, an Oxime-based cyclodextrin as a viable medical countermeasure against nerve agent poisoning: Experimental and molecular dynamic simulation studies on its inclusion complexes with cyclosarin, soman and VX

The ability of the cyclodextrin-oxime construct 6-OxP-CD to bind and degrade the nerve agents Cyclosarin (GF), Soman (GD) and S -[2-[Di(propan-2-yl)amino]ethyl] O -ethyl methylphosphonothioate (VX) has been studied using 31 P-nuclear magnetic resonance (NMR) under physiological conditions. While 6-OxP-CD was found to degrade GF instantaneously under these conditions, it was found to form an inclusion complex with GD and significantly improve its degradation (t 1/2 ~ 2 hrs) relative over background (t 1/2 ~ 22 hrs). Consequently, effective formation of the 6-OxP-CD:GD inclusion complex results in the immediate neutralization of GD and thus preventing it from inhibiting its biological target. In contrast, NMR experiments did not find evidence for an inclusion complex between 6-OxP-CD and VX, and the agent’s degradation profile was identical to that of background degradation (t 1/2 ~ 24 hrs). As a complement to this experimental work, molecular dynamics (MD) simulations coupled with Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) calculations have been applied to the study of inclusion complexes between 6-OxP-CD and the three nerve agents. These studies provide data that informs the understanding of the different degradative interactions exhibited by 6-OxP-CD with each nerve agent as it is introduced in the CD cavity in two different orientations (up and down). For its complex with GF, it was found that the oxime in 6-OxP-CD lies in very close proximity (P GF …O Oxime ~ 4–5 Å) to the phosphorus center of GF in the ‘down GF ’ orientation for most of the simulation accurately describing the ability of 6-OxP-CD to degrade this nerve agent rapidly and efficiently. Further computational studies involving the center of masses (COMs) for both components (GF and 6-OxP-CD) also provided some insight on the nature of this inclusion complex. Distances between the COMs (ΔCOM) lie closer in space in the ‘down GF ’ orientation than in the ‘up GF ’ orientation; a correlation that seems to hold true not only for GF but also for its congener, GD. In the case of GD, calculations for the ‘down GD ’ orientation showed that the oxime functional group in 6-OxP-CD although lying in close proximity (P GD …O Oxime ~ 4–5 Å) to the phosphorus center of the nerve agent for most of the simulation, adopts another stable conformation that increase this distance to ~ 12–14 Å, thus explaining the ability of 6-OxP-CD to bind and degrade GD but with less efficiency as observed experimentally (t 1/2 ~ 4 hr. vs. immediate). Lastly, studies on the VX:6-OxP-CD system demonstrated that VX does not form a stable inclusion complex with the oxime-bearing cyclodextrin and as such does not interact in a way that is conducive to an accelerated degradation scenario. Collectively, these studies serve as a basic platform from which the development of new cyclodextrin scaffolds based on 6-OxP-CD can be designed in the development of medical countermeasures against these highly toxic chemical warfare agents.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Conformational rearrangement of the NMDA receptor amino-terminal domain during activation and allosteric modulation

N-Methyl-D-aspartate receptors (NMDARs) are ionotropic glutamate receptors essential for synaptic plasticity and memory. Receptor activation involves glycine- and glutamate-stabilized closure of the GluN1 and GluN2 subunit ligand binding domains that is allosterically regulated by the amino-terminal domain (ATD). Using single molecule fluorescence resonance energy transfer (smFRET) to monitor subunit rearrangements in real-time, we observe a stable ATD inter-dimer distance in the Apo state and test the effects of agonists and antagonists. We find that GluN1 and GluN2 have distinct gating functions. Glutamate binding to GluN2 subunits elicits two identical, sequential steps of ATD dimer separation. Glycine binding to GluN1 has no detectable effect, but unlocks the receptor for activation so that glycine and glutamate together drive an altered activation trajectory that is consistent with ATD dimer separation and rotation. We find that protons exert allosteric inhibition by suppressing the glutamate-driven ATD separation steps, and that greater ATD separation translates into greater rotation and higher open probability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Optical recognition of constructs using hyperspectral imaging and detection (ORCHID)

Abstract Challenges to deep sample imaging have necessitated the development of special techniques such as spatially offset optical spectroscopy to collect signals that have travelled through several layers of tissue. However, these techniques provide only spectral information in one dimension (i.e., depth). Here, we describe a general and practical method, referred to as Optical Recognition of Constructs Using Hyperspectral Imaging and Detection (ORCHID). The sensing strategy integrates (1) the spatial offset detection concept by computationally binning 2D optical data associated with digital offsets based on selected radial pixel distances from the excitation source; (2) hyperspectral imaging using tunable filter; and (3) digital image binding and collation. ORCHID is a versatile modality that is designed to collect optical signals deep inside samples across three spatial (X, Y, Z) as well as spectral dimensions. The ORCHID method is applicable to various optical techniques that exhibit narrow-band structures, from Raman scattering to quantum dot luminescence. Samples containing surface-enhanced Raman scattering (SERS)-active gold nanostar probes and quantum dots embedded in gel were used to show a proof of principle for the ORCHID concept. The resulting hyperspectral data cube is shown to spatially locate target emitting nanoparticle volumes and provide spectral information for in-depth 3D imaging.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Tunable tunnel barriers in a semiconductor via ionization of individual atoms

individual adatoms deposited on an InSb(110) surface. The adatoms can be reproducibly dropped off from the STM tip by voltage pulses, and impact tunneling into the surface by up to ~100×. The spatial extent and magnitude of the tunneling effect are widely tunable by imaging conditions such as bias voltage, set current and photoillumination. We attribute the effect to occupation of a (+/0) charge transition level, and switching of the associated adatom-induced band bending. The effect in STM topographic images is well reproduced by transport modeling of filling and emptying rates as a function of the tip position. STM atomic contrast and tunneling spectra are in good agreement with density functional theory calculations for In adatoms. The adatom ionization effect can extend to distances greater than 50 nm away, which we attribute to the low concentration and low binding energy of the residual donors in the undoped InSb crystal. These studies demonstrate how individual atoms can be used to sensitively control current flow in nanoscale devices.

Physics↗
DOE OSTI2024

Lignin impairs Cel7A degradation of in vitro lignified cellulose by impeding enzyme movement and not by acting as a sink

Abstract Background Cellulose degradation by cellulases has been studied for decades due to the potential of using lignocellulosic biomass as a sustainable source of bioethanol. In plant cell walls, cellulose is bonded together and strengthened by the polyphenolic polymer, lignin. Because lignin is tightly linked to cellulose and is not digestible by cellulases, is thought to play a dominant role in limiting the efficient enzymatic degradation of plant biomass. Removal of lignin via pretreatments currently limits the cost-efficient production of ethanol from cellulose, motivating the need for a better understanding of how lignin inhibits cellulase-catalyzed degradation of lignocellulose. Work to date using bulk assays has suggested three possible inhibition mechanisms: lignin blocks access of the enzyme to cellulose, lignin impedes progress of the enzyme along cellulose, or lignin binds cellulases directly and acts as a sink. Results We used single-molecule fluorescence microscopy to investigate the nanoscale dynamics of Cel7A from Trichoderma reesei , as it binds to and moves along purified bacterial cellulose in vitro. Lignified cellulose was generated by polymerizing coniferyl alcohol onto purified bacterial cellulose, and the degree of lignin incorporation into the cellulose meshwork was analyzed by optical and electron microscopy. We found that Cel7A preferentially bound to regions of cellulose where lignin was absent, and that in regions of high lignin density, Cel7A binding was inhibited. With increasing degrees of lignification, there was a decrease in the fraction of Cel7A that moved along cellulose rather than statically binding. Furthermore, with increasing lignification, the velocity of processive Cel7A movement decreased, as did the distance that individual Cel7A molecules moved during processive runs. Conclusions In an in vitro system that mimics lignified cellulose in plant cell walls, lignin did not act as a sink to sequester Cel7A and prevent it from interacting with cellulose. Instead, lignin both blocked access of Cel7A to cellulose and impeded the processive movement of Cel7A along cellulose. This work implies that strategies for improving biofuel production efficiency should target weakening interactions between lignin and cellulose surface, and further suggest that nonspecific adsorption of Cel7A to lignin is likely not a dominant mechanism of inhibition.

09 BIOMASS FUELS↗
DOE OSTI2023

A density functional theory analysis of the adsorption and surface chemistry of inorganic iodine species on graphitea

In the event of a nuclear accident, fission products may be released into the environment. The release of 131 I is of particular concern to human health. Iodine can be captured using a number of materials and frequently, this is accomplished with activated carbon impregnated with organic bases. Previous studies have used DFT and the graphite (0001) surface as a surrogate for adsorption, those studies focus on the species I • , I 2 , and CH 3 I. In this work we perform an ab initio study of the adsorption onto the surface of a graphite sheet of I 2 , CH 3 I, and inorganic acidic iodine species (HI, HOI, HIO 2 , and HIO 3 ), which were selected to examine the possible effect of oxidation state on adsorption. The PBE exchange-correlation functional with D3 dispersion was employed. It was found that for molecular iodine, the iodine atoms tended to either situate above the center of a hexagonal site on the graphite or directly atop a carbon atom with the lighter components resting closer to the graphite. For each species the relative binding energies spanned the range of 21–33 kJ mol -1 and graphite-iodine distance was in the range of 3.52–3.93 Å. In all cases we found no significant charge transfer between the iodine species and the graphite, thus we conclude that all the iodine species studied undergo strong physisorption to the graphite.

Ritzmann, Andrew M.↗
DOE OSTI2021

Selectivity of enzymes involved in the formation of opposite enantiomeric series of p -menthane monoterpenoids in peppermint and Japanese catnip

Peppermint (Mentha x piperita L.) and Japanese catnip (Schizonepeta tenuifolia (Benth.) Briq.) accumulate p-menthane monoterpenoids with identical functionalization patterns but opposite stereochemistry. In the present study, we investigate the enantioselectivity of multiple enzymes involved in monoterpenoid biosynthesis in these species. Based on kinetic assays, mint limonene synthase, limonene 3-hydroxylase, isopiperitenol dehydrogenase, isopiperitenone reductase, and menthone reductase exhibited significant enantioselectivity toward intermediates of the pathway that proceeds through (-)-4S-limonene. Limonene synthase, isopiperitenol dehydrogenase and isopiperitenone reductase of Japanese catnip preferred intermediates of the pathway that involves (+)-4R-limonene, whereas limonene 3-hydroxylase was not enantioselective, and the activities of pulegone reductase and menthone reductase were too low to acquire meaningful kinetic data. Molecular modeling studies with docked ligands generally supported the experimental data obtained with peppermint enzymes, indicating that the preferred enantiomer was aligned well with the requisite cofactor and amino acid residues implicated in catalysis. A striking example for enantioselectivity was peppermint (-)-menthone reductase, which binds (-)-menthone with exquisite affinity but was predicted to bind (+)-menthone in a non-productive orientation that positions its carbonyl functional group at considerable distance to the NADPH cofactor. Here, the work presented here lays the groundwork for structure-function studies aimed at unraveling how enantioselectivity evolved in closely related species of the Lamiaceae and beyond.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Monte Carlo MP2-F12 for Noncovalent Interactions: The C 60 Dimer

A scalable stochastic algorithm is presented that can evaluate explicitly correlated (F12) second-order many-body perturbation (MP2) energies of weak, noncovalent, intermolecular interactions. It first transforms the formulas of the MP2 and F12 energy differences into a short sum of high-dimensional integrals of Green’s functions in real space and imaginary time. Furthermore, these integrals are then evaluated by the Monte Carlo method augmented by parallel execution, redundant-walker convergence acceleration, direct-sampling autocorrelation elimination, and control-variate error reduction. By sharing electron-pair walkers across the supermolecule and its subsystems spanned by the joint basis set, the statistical uncertainty is reduced by one to 2 orders of magnitude in the MP2 binding energy corrected for the basis-set incompleteness and superposition errors. The method predicts the MP2-F12/aug-cc-pVDZ binding energy of 19.1 ± 4.0 kcal mol –1 for the C 60 dimer at the center distance of 9.748 Å.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗