Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “dimer”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 613 records · Page 34
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Scanning tunneling microscopy of ferrocenecarboxylic acid assemblies on Ag(111): a comparison to Au(111)

Scanning tunneling microscopy was used to investigate the arrangement of ferrocenecarboxylic acid (FcCOOH) monolayers on the Ag(111) surface. Four distinct structures were observed, none of which had previously been observed on other surfaces. Structural analysis indicates that these assemblies are primarily composed of dimers. VASP calculations support the molecular assignments of the monolayer structures, while ESI-MS experiments confirm that dimers are the predominant species in solution. Of particular note, the cyclic pentamers and aperiodic packing observed for FcCOOH on Au(111) were not observed, despite (1) the similarity of the Ag(111) and Au(111) surfaces in reactivity, flatness, and lattice constant, and (2) prior explanation of the Au(111) monolayer in terms of molecule–molecule interactions alone. It is clear that while the surface does not have a template structure, it has a significant influence on which structures are formed.

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

AP-Net: An atomic-pairwise neural network for smooth and transferable interaction potentials

Intermolecular interactions are critical to many chemical phenomena, but their accurate computation using ab initio methods is often limited by computational cost. The recent emergence of machine learning (ML) potentials may be a promising alternative. Useful ML models should not only estimate accurate interaction energies but also predict smooth and asymptotically correct potential energy surfaces. However, existing ML models are not guaranteed to obey these constraints. Indeed, systemic deficiencies are apparent in the predictions of our previous hydrogen-bond model as well as the popular ANI-1X model, which we attribute to the use of an atomic energy partition. As a solution, we propose an alternative atomic-pairwise framework specifically for intermolecular ML potentials, and we introduce AP-Net—a neural network model for interaction energies. The AP-Net model is developed using this physically motivated atomic-pairwise paradigm and also exploits the interpretability of symmetry adapted perturbation theory (SAPT). We show that in contrast to other models, AP-Net produces smooth, physically meaningful intermolecular potentials exhibiting correct asymptotic behavior. Initially trained on only a limited number of mostly hydrogen-bonded dimers, AP-Net makes accurate predictions across the chemically diverse S66x8 dataset, demonstrating significant transferability. On a test set including experimental hydrogen-bonded dimers, AP-Net predicts total interaction energies with a mean absolute error of 0.37 kcal mol−1, reducing errors by a factor of 2–5 across SAPT components from previous neural network potentials. The pairwise interaction energies of the model are physically interpretable, and an investigation of predicted electrostatic energies suggests that the model “learns” the physics of hydrogen-bonded interactions.

Glick, Zachary L. (ORCID:0000000309002849)↗
DOE OSTI2022

Hydrogen bond arrangements in (H 2 O) 20, 24, 28 clathrate hydrate cages: Optimization and many-body analysis

Here we provide a detailed study of hydrogen bonding arrangements, relative stability, residual entropy, and an analysis of the many-body effects in the (H 2 O) 20 (D-cage), (H 2 O) 24 (T-cage), and (H 2 O) 28 (H-cage) hollow cages making up structures I (sI) and II (sII) of clathrate hydrate lattices. Based on the enumeration of the possible hydrogen bonding networks for a fixed oxygen atom scaffold, the residual entropy (S 0 ) of these three gas phase cages was estimated at 0.754 82, 0.754 44, and 0.754 17 · Nk b , where N is the number of molecules and k b is Boltzmann’s constant. A previously identified descriptor of enhanced stability based on the relative arrangement and connectivity of nearest-neighbor fragments on the polyhedral water cluster [strong-weak-effective-bond model] also applies to the larger hollow cages. The three cages contain a maximum of 7, 9, and 11 such preferable arrangements of trans nearest dimer pairs with one “free” OH bond on the donor molecule (t1d dimers). The Many-Body Expansion (MBE) up to the 4-body suggests that the many-body terms vary nearly linearly with the cluster binding energy. Using a hierarchical approach of screening the relative stability of networks starting from optimizations with the TIP4P, TTM2.1-F, and MB-pol classical potentials, subsequently refining at more accurate levels of electronic structure theory (DFT and MP2), and finally correcting for zero-point energy, we were able to identify a group of four low-lying isomers of the (H 2 O) 24 T-cage, two of which are antisymmetric and the other two form a pair of antipode configurations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Electronic structure theory on modeling short-range noncovalent interactions between amino acids

While short-range noncovalent interactions (NCIs) are proving to be of importance in many chemical and biological systems, these atypical bindings happen within the so-called van der Waals envelope and pose an enormous challenge for current computational methods. We introduce SNCIAA, a database of 723 benchmark interaction energies of short-range noncovalent interactions between neutral/charged amino acids originated from protein x-ray crystal structures at the “gold standard” coupled-cluster with singles, doubles, and perturbative triples/complete basis set [CCSD(T)/CBS] level of theory with a mean absolute binding uncertainty less than 0.1 kcal/mol. Subsequently, a systematic assessment of commonly used computational methods, such as the second-order Møller−Plesset theory (MP2), density functional theory (DFT), symmetry-adapted perturbation theory (SAPT), composite electronic-structure methods, semiempirical approaches, and the physical-based potentials with machine learning (IPML) on SNCIAA is carried out. It is shown that the inclusion of dispersion corrections is essential even though these dimers are dominated by electrostatics, such as hydrogen bondings and salt bridges. Overall, MP2, ωB97M-V, and B3LYP+D4 turned out to be the most reliable methods for the description of short-range NCIs even in strongly attractive/repulsive complexes. SAPT is also recommended in describing short-range NCIs only if the δMP2 correction has been included. The good performance of IPML for dimers at close-equilibrium and long-range conditions is not transferable to the short-range. We expect that SNCIAA will assist the development/improvement/validation of computational methods, such as DFT, force-fields, and ML models, in describing NCIs across entire potential energy surfaces (short-, intermediate-, and long-range NCIs) on the same footing.

Chemistry↗
DOE OSTI2024

Molecular dynamics simulations of uranyl and plutonyl cations in a task-specific ionic liquid

Ionic liquids (ILs) are a unique class of solvents with potential applications in advanced separation technologies relevant to the nuclear industry. ILs are salts with low melting points and a wide range of tunable physical properties, such as viscosity, hydrophobiciy, conductivity, and liquidus range. ILs have negligible vapor pressure, are often non-flammable, and can have high thermal stability and a wide electrochemical window, making them attractive for use in separations processes relevant to the nuclear industry. Metal salts generally have a low solubility in ILs; however, by incorporating new functional groups into the IL cation or anion that promote complexation with the metal, the solubility can be greatly increased. One such task-specific ionic liquid (TSIL) is 1-carboxy-N, N, N-trimethylglycine bis(trifluoromethylsulfonyl)imide ([Hbet][Tf 2 N]). Water, which is detrimental for electrochemical separations, is a common impurity in ILs and can coordinate with actinyl cations, particularly in ILs containing only weakly coordinating components. Understanding the behavior of actinides in TSIL/water mixtures on a molecular level is vital for designing improved separations processes. Classical molecular dynamics simulations of uranyl(VI) and plutonyl(VI) in 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([EMIM][Tf 2 N]) with deprotonated Hbet (betaine) and water have been performed to understand the coordination and dynamics of the actinyl cations. We find that betaine is a much stronger ligand than water and prefers to coordinate the metal in a bidentate manner. Potential of mean force simulations yield a relative free energy for betaine coordination of approximately -120 to -90 kJ/mol in mixtures with water. As the amount of betaine coordinated to the actinide increases, the diffusion coefficient of the actinyl cation decreases. Moreover, the betaine ligand is able to bridge between two metal centers, resulting in dimeric complexes with actinide–actinide distances of ~5 Å. Potential of mean force simulations show that these structures are stable, with relative free energies of up to -40 kJ/mol. The crystal structure for [(UO 2 ) 2 (bet) 6 (H 2 O) 2 ][Tf 2 N] 4 shows that the betaine bridges between two uranium atoms to form dimeric complexes similar to those found in our simulations.

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

Structure of SARS-CoV-2 ORF8, a rapidly evolving immune evasion protein

The molecular basis for the severity and rapid spread of the COVID-19 disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is largely unknown. ORF8 is a rapidly evolving accessory protein that has been proposed to interfere with immune responses. The crystal structure of SARS-CoV-2 ORF8 was determined at 2.04-Å resolution by X-ray crystallography. The structure reveals a ~60-residue core similar to SARS-CoV-2 ORF7a, with the addition of two dimerization interfaces unique to SARS-CoV-2 ORF8. A covalent disulfide-linked dimer is formed through an N-terminal sequence specific to SARS-CoV-2, while a separate noncovalent interface is formed by another SARS-CoV-2-specific sequence, 73 YIDI 76 . Together, the presence of these interfaces shows how SARS-CoV-2 ORF8 can form unique large-scale assemblies not possible for SARS-CoV, potentially mediating unique immune suppression and evasion activities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Unifying the order and disorder dynamics in photoexcited VO 2

Photoinduced phase transition (PIPT) is always treated as a coherent process, but ultrafast disordering in PIPT is observed in recent experiments. Utilizing the real-time time-dependent density functional theory method, here we track the motion of individual vanadium (V) ions during PIPT in VO 2 and uncover that their coherent or disordered dynamics can be manipulated by tuning the laser fluence. We find that the photoexcited holes generate a force on each V–V dimer to drive their collective coherent motion, in competing with the thermal-induced vibrations. If the laser fluence is so weak that the photoexcited hole density is too low to drive the phase transition alone, the PIPT is a disordered process due to the interference of thermal phonons. Finally, we also reveal that the photoexcited holes populated by the V–V dimerized bonding states will become saturated if the laser fluence is too strong, limiting the timescale of photoinduced phase transition.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Triplet-pair spin signatures from macroscopically aligned heteroacenes in an oriented single crystal

The photo-driven process of singlet fission generates coupled triplet pairs (TT) with fundamentally intriguing and potentially useful properties. The quintet 5 TT 0 sublevel is particularly interesting for quantum information because it is highly entangled, is addressable with microwave pulses, and could be detected using optical techniques. Previous theoretical work on a model Hamiltonian and nonadiabatic transition theory, called the JDE model, has determined that this sublevel can be selectively populated if certain conditions are met. Among the most challenging, the molecules within the dimer undergoing singlet fission must have their principal magnetic axes parallel to one another and to an applied Zeeman field. Here, we present time-resolved electron paramagnetic resonance (TR-EPR) spectroscopy of a single crystal sample of a tetracenethiophene compound featuring arrays of dimers aligned in this manner, which were mounted so that the orientation of the field relative to the molecular axes could be controlled. The observed spin sublevel populations in the paired TT and unpaired (T+T) triplets are consistent with predictions from the JDE model, including preferential 5 TT 0 formation at z ‖ B 0 , with one caveat—two 5 TT spin sublevels have little to no population. This may be due to crossings between the 5 TT and 3 TT manifolds in the field range investigated by TR-EPR, consistent with the intertriplet exchange energy determined by monitoring photoluminescence at varying magnetic fields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Structure of metallochaperone in complex with the cobalamin-binding domain of its target mutase provides insight into cofactor delivery

G-protein metallochaperone MeaB in bacteria [methylmalonic aciduria type A (MMAA) in humans] is responsible for facilitating the delivery of adenosylcobalamin (AdoCbl) to methylmalonyl-CoA mutase (MCM), the only AdoCbl-dependent enzyme in humans. Genetic defects in the switch III region of MMAA lead to the genetic disorder methylmalonic aciduria in which the body is unable to process certain lipids. Here, we present a crystal structure of Methylobacterium extorquens MeaB bound to a nonhydrolyzable guanosine triphosphate (GTP) analog guanosine-5'-[(β,γ)-methyleno]triphosphate (GMPPCP) with the Cbl-binding domain of its target mutase enzyme (MeMCM cbl ). This structure provides an explanation for the stimulation of the GTP hydrolyase activity of MeaB afforded by target protein binding. We find that upon MCM cbl association, one protomer of the MeaB dimer rotates ~180°, such that the inactive state of MeaB is converted to an active state in which the nucleotide substrate is now surrounded by catalytic residues. Importantly, it is the switch III region that undergoes the largest change, rearranging to make direct contacts with the terminal phosphate of GMPPCP. These structural data additionally provide insights into the molecular basis by which this metallochaperone contributes to AdoCbl delivery without directly binding the cofactor. Our data suggest a model in which GTP-bound MeaB stabilizes a conformation of MCM that is open for AdoCbl insertion, and GTP hydrolysis, as signaled by switch III residues, allows MCM to close and trap its cofactor. Substitutions of switch III residues destabilize the active state of MeaB through loss of protein:nucleotide and protein:protein interactions at the dimer interface, thus uncoupling GTP hydrolysis from AdoCbl delivery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Genetic switching by the Lac repressor is based on two-state Monod–Wyman–Changeux allostery

High-resolution NMR spectroscopy enabled us to characterize allosteric transitions between various functional states of the dimeric Escherichia coli Lac repressor. In the absence of ligands, the dimer exists in a dynamic equilibrium between DNA-bound and inducer-bound conformations. Binding of either effector shifts this equilibrium toward either bound state. Analysis of the ternary complex between repressor, operator DNA, and inducer shows how adding the inducer results in allosteric changes that disrupt the interdomain contacts between the inducer binding and DNA binding domains and how this in turn leads to destabilization of the hinge helices and release of the Lac repressor from the operator. Based on our data, the allosteric mechanism of the induction process is in full agreement with the well-known Monod–Wyman–Changeux model.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

An in vitro BRAF activation assay elucidates molecular mechanisms driving disassembly of the autoinhibited BRAF state

The RAF kinases (ARAF, BRAF, and CRAF) are essential components of the RAS-ERK signaling pathway, which controls vital cellular processes and is frequently dysregulated in human disease. Notably, mutations that alter BRAF function are prominent drivers of human cancer and certain RASopathy disorders, making BRAF an important target for therapeutic intervention. Despite extensive research, several aspects of BRAF regulation remain unclear. In this study, we developed an in vitro BRAF activation assay using purified autoinhibited BRAF:14-3-3 2 :MEK complexes. Our results show that fully processed, active-state KRAS alone can promote dimer-dependent BRAF activation. Moreover, we found that phosphatidylserine (PS)-containing liposomes synergized with KRAS to promote BRAF activation, achieving activity levels comparable to those observed with BRAF proteins that constitutively dimerize. In contrast, the SMP phosphatase complex had only a minimal effect on BRAF catalytic activity in this system but mediated the dephosphorylation of the negative regulatory pS365 14-3-3 binding site in a manner that was accelerated by the presence of KRAS alone or KRAS and 30% PS liposomes. Finally, we show that inhibitors blocking the BRAF RBD:KRAS interaction were able to suppress the in vitro activation of BRAF, underscoring the critical role of RAS binding in initiating the disassembly of the BRAF autoinhibited state. Thus, this assay provides valuable insights into the steps required for BRAF activation and can serve as an effective screening tool for identifying compounds that may inhibit this process and have therapeutic potential.

BRAF↗
DOE OSTI2020

Structural basis for allosteric regulation of pyruvate kinase M2 by phosphorylation and acetylation

Pyruvate kinase muscle isoform 2 (PKM2) is a key glycolytic enzyme and transcriptional coactivator and is critical for tumor metabolism. In cancer cells, native tetrameric PKM2 is phosphorylated or acetylated, which initiates a switch to a dimeric/monomeric form that translocates into the nucleus, causing oncogene transcription. However, it is not known how these post-translational modifications (PTMs) disrupt the oligomeric state of PKM2. We explored this question via crystallographic and biophysical analyses of PKM2 mutants containing residues that mimic phosphorylation and acetylation. We find that the PTMs elicit major structural reorganization of the fructose 1,6-bisphosphate (FBP), an allosteric activator, binding site, impacting the interaction with FBP and causing a disruption in oligomerization. To gain insight into how these modifications might cause unique outcomes in cancer cells, we examined the impact of increasing the intracellular pH (pHi) from ~7.1 (in normal cells) to ~7.5 (in cancer cells). Biochemical studies of WT PKM2 (wtPKM2) and the two mimetic variants demonstrated that the activity decreases as the pH is increased from 7.0 to 8.0, and wtPKM2 is optimally active and amenable to FBP-mediated allosteric regulation at pHi 7.5. However, the PTM mimetics exist as a mixture of tetramer and dimer, indicating that physiologically dimeric fraction is important and might be necessary for the modified PKM2 to translocate into the nucleus. Thus, our findings provide insight into how PTMs and pH regulate PKM2 and offer a broader understanding of its intricate allosteric regulation mechanism by phosphorylation or acetylation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Sliding dynamics of skyrmion molecular crystals

Using both atomistic and particle-based simulations, we investigate the current-driven dynamics of skyrmions on two-dimensional periodic substrates when there are multiple skyrmions per substrate minimum. At zero drive, the system forms pinned skyrmion molecular crystal states consisting of dimers, trimers, or dimer-trimer mixtures that have both positional and orientational order. On a square substrate lattice, the motion above depinning occurs via a running soliton that travels completely transverse to the applied current. This motion is generated by a torque from the Magnus force, which rotates the n-mer states perpendicular to the applied current. At higher drives, the flow becomes disordered while the Hall angle diminishes and gradually approaches the intrinsic value. In some cases, we also find directional locking where the Hall angle becomes locked to certain symmetry directions of the substrate over a range of currents. The transitions into and out of directionally locked states are accompanied by negative differential mobility in which the net velocity decreases as the drive increases. In conclusion, on a triangular substrate, we find no transverse mobility effects, but still observe directionally locked motion.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Sneaking in SpyCatcher using cell penetrating peptides for in vivo imaging

Abstract In vivo imaging of protein complexes is a powerful method for understanding the underlying biological function of these key biomolecules. Though the engineering of small, high affinity nanobodies have become more prevalent, the off-rates of these tags may result in incomplete or partial labeling of proteins in live cells. The SpyCatcher003 and SpyTag split protein system allow for irreversible, covalent binding to a short target peptide unlike nanobody-affinity based probes. However, delivering these tags into a cell without disrupting its normal function is a key challenge. Cell penetrating peptides (CPPs) are short peptide sequences that facilitate the transduction of otherwise membrane-impermeable ‘cargo’ , such as proteins, into cells. Here we report on our efforts to engineer and characterize CPP-SpyCatcher003 fusions as modular imaging probes. We selected three CPPs, CUPID, Pentratin, and pVEC, to engineer fusion protein probes for superresolution microscopy, with the aim to eliminate prior permeabilization treatments that could introduce imaging artifacts. We find that fusing the CPP sequences to SpyCatcher003 resulted in dimer and multimer formation as determined by size exclusion chromatography, dynamic light scattering, and SDS resistant dimers on SDS-PAGE gels. By isolating and labeling the monomeric forms of the engineered protein, we show these constructs retained their ability to bind SpyTag and all three CPP sequences remain membrane active, as assessed by CD spectroscopy in the presence of SDS detergent. Using fluorescence and super resolution Lattice structured illumination microscopy (Lattice SIM) imaging we show that the CPPs did not enhance uptake of SpyCatcher by E. coli, however with Caulobacter crescentus cells, we show that Penetratin, and to a lesser degree CUPID, does enhance uptake. Our results demonstrate the ability of the CPP-SpyCatcher003 to label targets within living cells, providing the groundwork for using split protein systems for targeted in vivo imaging.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Gapless spin liquid and pair density wave of the Hubbard model on three-leg triangular cylinders

We study the ground state properties of the Hubbard model on three-leg triangular cylinders using large-scale density-matrix renormalization group simulations. At half-filling, we identify an intermediate gapless spin liquid phase, which has one gapless spin mode and algebraic spin–spin correlations but exponential decay scalar chiral–chiral correlations, between a metallic phase at weak coupling and Mott insulating dimer phase at strong interaction. Upon light doping the gapless spin liquid, the system exhibits power-law charge-density-wave (CDW) correlations but short-range single-particle, spin–spin, and chiral–chiral correlations. Similar to CDW correlations, the superconducting correlations also decay in power-law but oscillate in sign as a function of distance, which is consistent with the striped pair-density wave. When further doping the gapless spin liquid phase or doping the dimer order phase, another phase takes over, which has similar CDW correlations but all other correlations decay exponentially.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Reversible to irreversible transitions for ac driven skyrmions on periodic substrates

Abstract Using atomistic simulations, we investigate the dynamical behavior of magnetic skyrmions in dimer and trimer molecular crystal arrangements, as well as bipartite lattices at 3/2 and 5/2 fillings, under ac driving over a square array of anisotropy defects. For low ac amplitudes, at all fillings reversible motion appears in which the skyrmions return to their original positions at the end of each ac drive cycle and the diffusion is zero. We also identify two distinct irreversible regimes. The first is a translating regime in which the skyrmions form channels of flow in opposing directions and translate by one substrate lattice constant per ac drive cycle. The translating state appears in the dimer and trimer arrangements, and produces pronounced peaks in the diffusivity in the direction perpendicular to the external drive. For larger ac amplitudes, we find chaotic irreversible motion in which the skyrmions can randomly exchange places with each other over time, producing long-time diffusive behavior both parallel and perpendicular to the ac driving direction.

36 MATERIALS SCIENCE↗
DOE OSTI2023

The structure of the high-affinity nickel-binding site in the Ni,Zn-HypA•UreE2 complex

Abstract The maturation pathway for the nickel-dependent enzyme urease utilizes the protein UreE as a metallochaperone to supply Ni(II) ions. In Helicobacter pylori urease maturation also requires HypA and HypB, accessory proteins that are commonly associated with hydrogenase maturation. Herein we report on the characterization of a protein complex formed between HypA and the UreE2 dimer. Nuclear magnetic resonance (NMR) coupled with molecular modelling show that the protein complex apo, Zn-HypA•UreE2, forms between the rigorously conserved Met-His-Glu (MHE motif) Ni-binding N-terminal sequence of HypA and the two conserved His102A and His102B located at the dimer interface of UreE2. This complex forms in the absence of Ni(II) and is supported by extensive protein contacts that include the use of the C-terminal sequences of UreE2 to form additional strands of β-sheet with the Ni-binding domain of HypA. The Ni-binding properties of apo, Zn-HypA•UreE2 and the component proteins were investigated by isothermal titration calorimetry using a global fitting strategy that included all of the relevant equilibria, and show that the Ni,Zn-HypA•UreE2 complex contains a single Ni(II)-binding site with a sub-nanomolar KD. The structural features of this novel Ni(II) site were elucidated using proteins produced with specifically deuterated amino acids, protein point mutations, and the analyses of X-ray absorption spectroscopy, hyperfine shifted NMR features, as well as molecular modeling coupled with quantum-mechanical calculations. The results show that the complex contains a six-coordinate, high-spin Ni(II) site with ligands provided by both component proteins.

Zambelli, Barbara (ORCID:0000000238760051)↗
DOE OSTI2023

Structure, substrate binding and activity of a unique AAA+ protein: the BrxL phage restriction factor

Abstract Bacteriophage exclusion (‘BREX’) systems are multi-protein complexes encoded by a variety of bacteria and archaea that restrict phage by an unknown mechanism. One BREX factor, termed BrxL, has been noted to display sequence similarity to various AAA+ protein factors including Lon protease. In this study we describe multiple CryoEM structures of BrxL that demonstrate it to be a chambered, ATP-dependent DNA binding protein. The largest BrxL assemblage corresponds to a dimer of heptamers in the absence of bound DNA, versus a dimer of hexamers when DNA is bound in its central pore. The protein displays DNA-dependent ATPase activity, and ATP binding promotes assembly of the complex on DNA. Point mutations within several regions of the protein-DNA complex alter one or more in vitro behaviors and activities, including ATPase activity and ATP-dependent association with DNA. However, only the disruption of the ATPase active site fully eliminates phage restriction, indicating that other mutations can still complement BrxL function within the context of an otherwise intact BREX system. BrxL displays significant structural homology to MCM subunits (the replicative helicase in archaea and eukaryotes), implying that it and other BREX factors may collaborate to disrupt initiation of phage DNA replication.

59 BASIC BIOLOGICAL SCIENCES↗