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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 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Regulatory helix plays a key role in genetic ON-OFF switching for the 2’-deoxyguanosine sensing mRNA element

Transcriptional riboswitches, noncoding mRNA elements that operate in cis to regulate gene expression, have a promising potential in medicine, synthetic biology and directed evolution. They bind to cellular metabolites or metal ions with high specificity, leading to conformational rearrangements that facilitate the activation or premature termination of transcription for downstream genes. This elegant mechanism for feedback regulation of metabolic pathways has been identified in prokaryotes and a few in eukaryotes. Our chemical probing of the 2’-deoxyguanosine (2’-dG)-sensing riboswitch demonstrates that the overall conformational state of the full-length riboswitch (dGsw-fl) is unresponsive to the 2’-dG. Although binding proceeds as expected, dGsw-fl exclusively populates an OFF state of transcriptional inhibition. We chemically probed the structure of a known dGsw transcriptional intermediate (dGsw-int) to evaluate the possibility of a cotranscriptional regulatory role. Interestingly, apo dGsw-int adopts an alternative conformation in which a stable anti-terminator helix is formed, leading to an ON state where transcription can proceed. In the presence of 2’-dG, this anti-terminator helix is destabilized to produce a conformation reminiscent of the full-length, OFF-state dGsw. Using a fluorescence quenching assay, we demonstrate that binding 2’-dG to early transcriptional intermediates can inhibit the formation of the anti-terminator helix, locking dGsw in an OFF state. These data suggest that metabolite sensing occurs during a brief window of time between the synthesis of two transcriptional intermediates. Our studies indicate that dGsw does not function as a binary ON−OFF switch, but instead fine-tunes the transcription of downstream genes during RNA synthesis using key intermediates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Recognition of a Key Anchor Residue by a Conserved Hydrophobic Pocket Ensures Subunit Interface Integrity in DNA Clamps

Sliding clamp proteins encircle duplex DNA and are involved in processive DNA replication and the DNA damage response. Clamp proteins are ring-shaped oligomers (dimers or trimers) and are loaded onto DNA by an ATP-dependent clamp loader complex that ruptures the interface between two adjacent subunits. Here we measured the solution dynamics of the human clamp protein, proliferating cell nuclear antigen, by monitoring the change in the fluorescence of a site-specifically labeled. To unravel the origins of clamp subunit interface stability, we carried out comprehensive comparative analysis of the interfaces of seven sliding clamps. Here, we used computational modeling (molecular dynamic simulations and MM/GBSA binding energy decomposition analyses) to identify conserved networks of hydrophobic residues critical for clamp stability and ring-opening dynamics. The hydrophobic network is shared among clamp proteins and exhibits a “key in a keyhole” pattern where a bulky aromatic residue from one clamp subunit is anchored into a hydrophobic pocket of the opposing subunit. Bioinformatics and dynamic network analyses showed that this oligomeric latch is conserved across DNA sliding clamps from all domains of life and dictates the dynamics of clamp opening and closing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

An analysis of key characteristics of the Frank-Read source process in FCC metals

A well-known intragranular dislocation source, the Frank-Read (FR) source plays an important role in size-dependent dislocation multiplication in crystalline materials. Despite a number of studies in this topic, a systematic investigation of multiple aspects of the FR source in different materials is lacking. Here, in this paper, we employ large scale quasistatic concurrent atomistic-continuum (CAC) simulations to model an edge dislocation bowing out from an FR source in Cu, Ni, and Al. First, a number of quantities that are important for the FR source process are quantified in the coarse-grained domain. Then, two key characteristics of the FR source, including the critical shear stress and critical dislocation configuration, are investigated. In all crystalline materials, the critical stresses and the aspect ratio of the dislocation half-loop height to the FR source length scale well with respect to the FR source length. In Al, the critical stress calculated by CAC simulations for a given FR source length agrees reasonably well with a continuum model that explicitly includes the dislocation core energy. Nevertheless, the predictions of the isotropic elastic theory do not accurately capture the FR source responses in Cu and Ni, which have a relatively large stacking fault width and elastic anisotropy. Our results highlight the significance of directly simulating the FR source activities using fully 3D models and shed light on developing more accurate continuum models.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Key aspects of numerical analysis of gas hydrate reservoir performance: Alaska North Slope Prudhoe Bay Unit “L-Pad” hydrate accumulation

In previous work, we reported the development of the 3D geostatistical hydrate reservoir model of "L-Pad" (Myshakin et al., 2016). Here, gas production sensitivity on key reservoir parameters are studied. Hydraulic communication with an aquifer and optimal depressurization strategies are subjects of investigation. Uncertainty in initial in situ permeability within 0.1–10 mD range leads to 2.0 × 10 8 –3.5 × 10 8 ST m 3 of gas produced over 10 years. Accounting for reservoir quality and irreducible water saturation leads to noticeable change in productivity. Lastly, sequential depressurization of hydrate-bearing units was found to be more attractive versus simultaneous depressurization.

03 NATURAL GAS↗
DOE OSTI2017

Electron beam test of key elements of the laser-based calibration system for the muon g - 2 experiment

We report the test of many of the key elements of the laser-based calibration system for muon g - 2 experiment E989 at Fermilab. The test was performed at the Laboratori Nazionali di Frascati's Beam Test Facility using a 450 MeV electron beam impinging on a small subset of the final g - 2 lead-fluoride crystal calorimeter system. The calibration system was configured as planned for the E989 experiment and uses the same type of laser and most of the final optical elements. We show results regarding the calorimeter's response calibration, the maximum equivalent electron energy which can be provided by the laser and the stability of the calibration system components.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Accident event progression, gaps, and key performance indicators for steam generator tube rupture events in water-cooled SMRs: A review

According to historical records of reactor-related incidents, a steam generator tube rupture (SGTR) is one of the most common occurrences at operating pressurized water reactors (PWRs). Such design-basis accidents (DBAs) could lead to a direct path for radionuclides to be released to the atmosphere via the safety and relief valves, making assessments of radionuclide discharge from operating nuclear power plants (NPPs) into the environment crucial for ensuring safety. In such analyses, the primary focus has been on the extent of radioactive release, not the potential damage to the core. Moreover, significant and timely intervention by operators is needed during the initial stages of SGTRs in order to avert overfilling of the SGs, as well as to restrict the dissemination of radioactive materials. Determining the event sequence and phases that occur during an SGTR incident in an advanced passive (e.g., AP1000) water-cooled nuclear reactor is crucial for implementing effective passive safety systems (PSSs) for a specific water-cooled small modular reactor (SMR) design. Here this study provides a comprehensive review of the accident event progression, associated physical phenomena, knowledge gaps, and key performance indicators that must be evaluated and assessed in thermal-hydraulics models, based on relevant test data, respectively.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2025

The water use of data center workloads: A review and assessment of key determinants

The global importance of data center water use is increasing with the rapid growth of digitalization and artificial intelligence. This study analyzes the factors influencing workload-level water use, measured in liters consumed per workload, to guide water-saving strategies in data centers. Our findings reveal workload-level water use variations exceeding 10,000-fold, driven by over 1000-fold differences in water consumption per kilowatt hour of server electricity consumed and approximately 10-fold differences in server workload efficiency. Key determinants are ranked as server efficiency, electrical grid water consumption factors, server utilization, cooling system type, infrastructure efficiency, climate zone, inactive server percentage, and server refresh cycle. Notably, there is no single recipe for minimizing water use; instead, optimal outcomes depend on tailored combinations of these factors. This analysis addresses critical knowledge gaps by identifying the determinants of data center water use and exploring their achievable minima under diverse site-specific constraints.

Data centers↗
DOE OSTI2014

A systems toxicology approach identifies Lyn as a key signaling phosphoprotein modulated by mercury in a B lymphocyte cell model

Network and protein–protein interaction analyses of proteins undergoing Hg{sup 2+}-induced phosphorylation and dephosphorylation in Hg{sup 2+}-intoxicated mouse WEHI-231 B cells identified Lyn as the most interconnected node. Lyn is a Src family protein tyrosine kinase known to be intimately involved in the B cell receptor (BCR) signaling pathway. Under normal signaling conditions the tyrosine kinase activity of Lyn is controlled by phosphorylation, primarily of two well known canonical regulatory tyrosine sites, Y-397 and Y-508. However, Lyn has several tyrosine residues that have not yet been determined to play a major role under normal signaling conditions, but are potentially important sites for phosphorylation following mercury exposure. In order to determine how Hg{sup 2+} exposure modulates the phosphorylation of additional residues in Lyn, a targeted MS assay was developed. Initial mass spectrometric surveys of purified Lyn identified 7 phosphorylated tyrosine residues. A quantitative assay was developed from these results using the multiple reaction monitoring (MRM) strategy. WEHI-231 cells were treated with Hg{sup 2+}, pervanadate (a phosphatase inhibitor), or anti-Ig antibody (to stimulate the BCR). Results from these studies showed that the phosphoproteomic profile of Lyn after exposure of the WEHI-231 cells to a low concentration of Hg{sup 2+} closely resembled that of anti-Ig antibody stimulation, whereas exposure to higher concentrations of Hg{sup 2+} led to increases in the phosphorylation of Y-193/Y-194, Y-501 and Y-508 residues. These data indicate that mercury can disrupt a key regulatory signal transduction pathway in B cells and point to phospho-Lyn as a potential biomarker for mercury exposure. - Highlights: • Inorganic mercury (Hg{sup 2+}) induces changes in the WEHI-231 B cell phosphoproteome. • The B cell receptor (BCR) signaling pathway was the pathway most affected by Hg{sup 2+}. • The Src family phosphoprotein kinase Lyn was the most interconnected node. • Lyn is likely central to the immunotoxic potential of Hg{sup 2+}. • Lyn phosphorylation profiles may be biomarkers for Hg{sup 2+} intoxication of B cells.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Antioxidant role of glutathione S-transferases: 4-Hydroxynonenal, a key molecule in stress-mediated signaling

4-Hydroxy-2-trans-nonenal (4HNE), one of the major end products of lipid peroxidation (LPO), has been shown to induce apoptosis in a variety of cell lines. It appears to modulate signaling processes in more than one way because it has been suggested to have a role in signaling for differentiation and proliferation. It has been known that glutathione S-transferases (GSTs) can reduce lipid hydroperoxides through their Se-independent glutathione-peroxidase activity and that these enzymes can also detoxify LPO end-products such as 4HNE. Available evidence from earlier studies together with results of recent studies in our laboratories strongly suggests that LPO products, particularly hydroperoxides and 4HNE, are involved in the mechanisms of stress-mediated signaling and that it can be modulated by the alpha-class GSTs through the regulation of the intracellular concentrations of 4HNE. We demonstrate that 4HNE induced apoptosis in various cell lines is accompanied with c-Jun-N-terminal kinase (JNK) and caspase-3 activation. Cells exposed to mild, transient heat or oxidative stress acquire the capacity to exclude intracellular 4HNE at a faster rate by inducing GSTA4-4 which conjugates 4HNE to glutathione (GSH), and RLIP76 which mediates the ATP-dependent transport of the GSH-conjugate of 4HNE (GS-HNE). The balance between formation and exclusion promotes different cellular processes — higher concentrations of 4HNE promote apoptosis; whereas, lower concentrations promote proliferation. In this article, we provide a brief summary of the cellular effects of 4HNE, followed by a review of its GST-catalyzed detoxification, with an emphasis on the structural attributes that play an important role in the interactions with alpha-class GSTA4-4. Taken together, 4HNE is a key signaling molecule and that GSTs being determinants of its intracellular concentrations, can regulate stress-mediated signaling, are reviewed in this article. - Highlights: • GSTs are the major determinants of the intracellular concentration of 4HNE. • Higher concentrations of 4HNE promote apoptosis whereas lower promote proliferation. • Stress-mediated signaling can be modulated by the α-class glutathione S-transferase. • Genotoxic effect of 4HNE may be ameliorated by modulating the cellular GSH levels. • RLIP76 (RalBP1) mediates ATP-dependent transport of GSH-conjugate of 4HNE (GSHNE).

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

IL-1β is a key inflammatory cytokine that weakens lactation-specific tight junctions of mammary epithelial cells

Highlights: • TNF-α, IL-1β, and IL-6 directly affect tight junctions of MECs in different ways. • IL-1β rapidly disrupts tight junctions at tricellular contacts between MECs. • IL-1β decreases the amount of tight junction proteins and weaken the TJ barrier. • Activation of p38 by IL-1β triggers disruption of tight junctions. In lactating mammary glands, alveolar mammary epithelial cells (MECs) produce milk and form less-permeable tight junctions (TJs). However, alveolar TJs are weakened with a reduction in milk production in mammary glands due to mastitis or weaning in the presence of high levels of IL-1β, IL-6, or TNF-α. In this study, using in vitro cultured model of MECs with milk-producing ability and lactation-specific TJs, we investigated whether the aforementioned cytokines affect MEC TJs. The results showed that TNF-α, IL-1β, and IL-6 affected lactation-specific TJs in different ways. In particular, upon activation of p38 and JNK signalling, IL-1β caused rapid disruption of TJs at tricellular contact points. IL-1β treatment led to decreased CLDN3, CLDN4, and OCLN levels and a weakened TJ barrier. The adverse effects of IL-1β on TJs were mimicked by anisomycin, which is an activator of p38 and JNK signalling, and were blocked by MEC pretreatment with a p38 inhibitor but not a JNK inhibitor. The mislocalization of tricellulin at tricellular contact areas was confirmed in MECs treated with IL-1β or anisomycin. These results indicate that IL-1β is a key cytokine that adversely affects the TJs between MECs by activating p38.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Key role of the REC lobe during CRISPR–Cas9 activation by ‘sensing’, ‘regulating’, and ‘locking’ the catalytic HNH domain

Understanding the conformational dynamics of CRISPR (clustered regularly interspaced short palindromic repeat)–Cas9 is of the utmost importance for improving its genome editing capability. Here, molecular dynamics simulations performed using Anton-2 – a specialized supercomputer capturing micro-to-millisecond biophysical events in real time and at atomic-level resolution – reveal the activation process of the endonuclease Cas9 toward DNA cleavage. Over the unbiased simulation, we observe that the spontaneous approach of the catalytic domain HNH to the DNA cleavage site is accompanied by a remarkable structural remodeling of the recognition (REC) lobe, which exerts a key role for DNA cleavage. Specifically, the significant conformational changes and the collective conformational dynamics of the REC lobe indicate a mechanism by which the REC1–3 regions ‘sense’ nucleic acids, ‘regulate’ the HNH conformational transition, and ultimately ‘lock’ the HNH domain at the cleavage site, contributing to its catalytic competence. By integrating additional independent simulations and existing experimental data, we provide a solid validation of the activated HNH conformation, which had been so far poorly characterized, and we deliver a comprehensive understanding of the role of REC1–3 in the activation process. Considering the importance of the REC lobe in the specificity of Cas9, this study poses the basis for fully understanding how the REC components control the cleavage of off-target sequences, laying the foundation for future engineering efforts toward improved genome editing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Structure-Guided Analyses of a Key Enzyme Involved in the Biosynthesis of an Antivitamin

RosB catalyzes the formation of 8-aminoriboflavin 5'-phosphate (AFP), the key intermediate in roseoflavin biosynthesis, from the metabolic precursors riboflavin 5'-phosphate (RP, also known as FMN) and glutamate. Here, the conversion of the aromatic methyl group at position 8 in RP into the aromatic amine in AFP occurs via two intermediates, namely, the aldehyde 8-formyl-RP and the acid 8-carboxy-RP. To gain insights into the mechanism for this chemically challenging transformation, we utilized a structure-based approach to identify active site variants of RosB that stall the reaction at various points along the reaction coordinate. Crystal structures of individual variants in complex with different reaction intermediates, identified via mass spectroscopic analysis, illuminate conformational changes that occur at the active site during multistep conversion. These studies provide a plausible route for the progression of the reaction and a molecular rationale for the mechanism of this unusual biocatalyst.

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

Probing Surface/Bulk Structural Chemistry of Key Components of Solid Oxide Electrochemical Cells with In Situ / Operando Raman Spectroscopy

The remarkable attributes of solid oxide electrochemical cell technology (e.g., energy efficiency, low cost, scalability, low emissions, and operational flexibility, etc.) drive the wider adoption of electrochemical conversion routes for sustainability. It is critical for the codevelopment of solid oxide cell materials and processes to establish the mechanistic understanding of the underlying chemical phenomena at the molecular level. Herein, we summarize the advancements in Raman spectroscopy that provide structural/molecular information on electrode/electrolyte materials typically used in solid oxide cells for energy conversion. In particular, we discuss the multifactorial environment induced chemical processes that govern the performance and longevity of solid oxide electrochemical devices. The in situ/operando Raman spectroscopic investigations on the electrode/electrolyte materials reported in the literature are summarized with the emphasis on identification of key material properties that control the functional aspects of the solid oxide cells. The molecular level understanding of the electrochemical processes will allow advancement of the rational design of electrochemical materials for process level deployment of solid oxide cell technology.

Electrodes↗
DOE OSTI2024

Quantifying and Modeling the Impact of Phase State on the Ice Nucleation Abilities of 2-Methyltetrols as a Key Component of Secondary Organic Aerosol Derived from Isoprene Epoxydiols

Organic aerosols (OAs) may serve as ice-nucleating particles (INPs), impacting the formation and properties of cirrus clouds when their phase state and viscosity are in the semisolid to glassy range. However, there is a lack of direct parameterization between aerosol viscosity and their ice nucleation capabilities. In this study, we experimentally measured the ice nucleation rate of 2-methyltetrols (2-MT) aerosols, a key component of isoprene-epoxydiol-derived secondary organic aerosols (IEPOX-SOA), at different viscosities. These results demonstrate that the phase state has a significant impact on the ice nucleation abilities of OA under typical cirrus cloud conditions, with the ice nucleation rate increasing by 2 to 3 orders of magnitude when the phase state changes from liquid to semisolid. An innovative parametric model based on classical nucleation theory was developed to directly quantify the impact of viscosity on the heterogeneous nucleation rate. This model accurately represents our laboratory measurement and can be implemented into climate models due to its simple, equation-based form. Based on data collected from the ACRIDICON-CHUVA field campaign, our model predicts that the INP concentration from IEPOX-SOA can reach the magnitude of 1 to tens per liter in the cirrus cloud region impacted by the Amazon rainforest, consistent with recent field observations and estimations. This novel parameterization framework can also be applied in regional and global climate models to further improve representations of cirrus cloud formation and associated climate impacts.

2-methyltetrol↗
DOE OSTI2020

Consistency-Enhanced Evolution for Variable Selection Can Identify Key Chemical Information from Spectroscopic Data

In the last few decades, spectroscopic techniques such as near-infrared (NIR) spectroscopy have gained wide applications in several industries, such as the pharmaceutical, agricultural, oil, and gas industries. As a result, various soft sensors have been developed to predict sample properties from spectroscopic readings. Because the spectroscopic readings at different wavelengths, especially at the adjacent wavelengths, are highly correlated, it has been shown that variable selection could significantly improve a soft sensor’s prediction performance while reducing the model complexity. To improve the prediction performance, most variable selection methods focus on identifying the variables (i.e., wavelengths or wavelength segments) that are strongly correlated with the dependent variable. Although many successful applications have been reported, these variable selection methods do have their limitations. Specifically, the selected wavelengths sometimes show little connection to the chemical bounds or functional groups presenting in the sample. In addition, the selected variables can be quite sensitive to the choice of the training samples. In this work, we address these limitations from a different perspective: if a variable selection algorithm can identify the truly relevant input variables, it should consistently identify the same subset of variables regardless of the choice of the training samples. Therefore, we propose a variable selection method that aims to improve the consistency of variable selection resulting from different training samples. Furthermore, the new algorithm is termed consistency-enhanced evolution for variable selection (CEEVS). To demonstrate the performance and robustness of CEEVS, we compare the proposed method with three representative variable selection methods using five published NIR data sets. These case studies clearly demonstrate that by improving the variable selection consistency, we can not only achieve improved prediction performance, but also identify key chemical information from spectroscopic data.

42 ENGINEERING↗
DOE OSTI2019

Synthetic Model Complex of the Key Intermediate in Cytochrome P450 Nitric Oxide Reductase

Fungal denitrification plays a crucial role in the nitrogen cycle and contributes to the total N 2 O emission from agricultural soils. Here, cytochrome P450 NO reductase (P450nor) reduces two NO to N 2 O using a single heme site. Despite much research, the exact nature of the critical "Intermediate I" responsible for the key N-N coupling step in P450nor is unknown. This species likely corresponds to a Fe-NHOH-type intermediate with an unknown electronic structure. Here we report a new strategy to generate a model system for this intermediate, starting from the iron(III) methylhydroxylamide complex [Fe(3,5-Me-BAFP)(NHOMe)] (1), which was fully characterized by 1 H NMR, UV-vis, electron paramagnetic resonance, and vibrational spectroscopy (rRaman and NRVS). Our data show that 1 is a high-spin ferric complex with an N-bound hydroxylamide ligand that is strongly coordinated (Fe–N distance, 1.918 Å; Fe-NHOMe stretch, 558 cm –1 ). Simple one-electron oxidation of 1 at –80 °C then cleanly generates the first model system for Intermediate I, [Fe(3,5-Me-BAFP)(NHOMe)] + (1 + ). UV–vis, resonance Raman, and Mössbauer spectroscopies, in comparison to the chloro analogue [Fe(3,5-Me-BAFP)(Cl)] + , demonstrate that 1 + is best described as an Fe III -(NHOMe)• complex with a bound NHOMe radical. Further reactivity studies show that 1 + is highly reactive toward NO, a reaction that likely proceeds via N–N bond formation, following a radical–radical-type coupling mechanism. Here our results therefore provide experimental evidence, for the first time, that an Fe III -(NHOMe)• electronic structure is indeed a reasonable electronic description for Intermediate I and that this electronic structure is advantageous for P450nor catalysis because it can greatly facilitate N–N bond formation and, ultimately, N 2 O generation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Structure Based Design of a Grp94-Selective Inhibitor: Exploiting a Key Residue in Grp94 To Optimize Paralog-Selective Binding

Grp94 and Hsp90, the ER and cytoplasmic hsp90 paralogs, share a conserved ATP-binding pocket that has been targeted for therapeutics. Paralog-selective inhibitors may lead to drugs with fewer side effects. In this work, we analyzed 1 (BnIm), a benzyl imidazole resorcinylic inhibitor, for its mode of binding. The structures of 1 bound to Hsp90 and Grp94 reveal large conformational changes in Grp94 but not Hsp90 that expose site 2, a binding pocket adjacent to the central ATP cavity that is ordinarily blocked. The Grp94:1 structure reveals a flipped pose of the resorcinylic scaffold that inserts into the exposed site 2. We exploited this flipped binding pose to develop a Grp94-selective derivative of 1. Our structural analysis shows that the ability of the ligand to insert its benzyl imidazole substituent into site 1, a different side pocket off the ATP binding cavity, is the key to exposing site 2 in Grp94.

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

Hotspot Coevolution Is a Key Identifier of Near-Native Protein Complexes

Protein–protein interactions play a key role in mediating numerous biological functions, with more than half the proteins in living organisms existing as either homo- or hetero-oligomeric assemblies. Protein subunits that form oligomers minimize the free energy of the complex, but exhaustive computational search-based docking methods have not comprehensively addressed the challenge of distinguishing a natively bound complex from non-native forms. Current protein docking approaches address this problem by sampling multiple binding modes in proteins and scoring each mode, with the lowest-energy (or highest scoring) binding mode being regarded as a near-native complex. However, high-scoring modes often match poorly with the true bound form, suggesting a need for improvement of the scoring function. Here in this study, we propose a scoring function, KFC-E, that accounts for both conservation and coevolution of putative binding hotspot residues at protein–protein interfaces. We tested KFC-E on four benchmark sets of unbound examples and two benchmark sets of bound examples, with the results demonstrating a clear improvement over scores that examine conservation and coevolution across the entire interface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗