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At least 649 records · Page 36
All sourcesNASA NTRSDOE OSTI
NASA NTRSDate not supplied

Application of OpenFOAM to Plume Impingement in Space Environments

After 30 years of continuous human presence in low-earth orbit, NASA is returning to the moon and eventually will go to Mars. Travelling beyond low earth orbit requires NASA to learn how humans can live in Deep Space environments – beyond the protection of Earth’s magnetosphere and at distances from Earth that prevent a quick return in case of trouble. To this end, NASA is constructing the Lunar Gateway, an ISS-like space station to be put in orbit around the moon to act as a home base for Lunar exploration for NASA astronauts. The Gateway Lunar outpost will be built incrementally, via modules which will arrive at separate times and dock to the existing structure. The incremental addition of Gateway modules, and the docking of visiting vehicles, is achieved via a sequence of firings from the approaching body’s onboard reaction control system (RCS) thrusters to achieve the required approach trajectory. The typical hypergolic chemical RCS thrusters work by firing hot gases to produce adverse thrust and the needed change in velocity to safely finish the docking process. The exhaust gas from the RCS thrusters form plumes that expand into the vacuum of space and can impinge onto the outer surfaces of the Lunar Gateway, causing unwanted forces and moments, heat loads, sediment deposition, and in extreme cases, even surface erosion - all mechanisms that can damage the Lunar Gateway and must be minimized. Both permanent and visiting modules will have this RCS thruster exhaust impingement problem. This research aims to establish existing OpenFOAM solvers as a methodology for improving simulation techniques of rocket exhaust plume impingement in space environments. The flow structure of a plume in a space environment is complex; a plume that originates from a hypergolic chemical RCS thruster and expands into a vacuum will experience several regimes of rarefication. This range includes the continuum flow in the rocket nozzle through the fully rarefied free molecular flow further from the nozzle. The flow physics is different at these two extremes, and as such, the simulation approach for plumes is generally divided into a traditional computational fluid dynamics (CFD) simulation in and near the nozzle which is coupled to a subsequent direct simulation Monte Carlo (DSMC) simulation. At this time, the scope of this research is developing, verifying, and validating a method using existing solvers in the OpenFOAM framework for performing coupled CFD/DSMC calculations to determine the extent of plume impingement loading on generic space structures. This presentation will detail code-to-code comparisons between the hyStrath dsmcFoam+ solver, developed using OpenFOAM and available as open-source, and NASA’s in-house DSMC Analysis Code (DAC). Comparisons to several open-source publication findings using DAC [3,4] are presented, and advantages of using an OpenFOAM based solver are also discussed. The presentation concludes with a discussion of future work, and a plan for coupling the dsmcFoam+ solver with CFD simulations of chemical rocket engines for unified coupled plume simulation.

DSMC↗
NASA NTRSDate not supplied

Effects of Ambient Alcohol Levels on the Real-time Monitoring of the Atmosphere of the International Space Station

Monitoring of the spacecraft environment is required to ensure the health of the crew and the vehicle systems. For the ISS atmosphere, routine volatile organic compound (VOC) monitoring has been performed for almost a decade by Air Quality Monitors (AQMs). The target compounds measured by the AQMs include three types of chemicals: 1) those compounds that would be harmful to crew, 2) those compounds that have been detected regularly in archival samples, and 3) compounds that, while not necessarily harmful to crew health, could present problems for Environmental Control and Life Support Systems (ECLSS). Following the docking of SpaceX-Demo1 (SpX-DM1), the AQMs began to report high levels of isopropanol (IPA). While elevated IPA is routinely observed with visiting vehicles, the level measured by the AQM, and its continued presence following multiple days of scrubbing, caused concerns regarding the U.S. Water Recovery System. Following the departure of SpX-DM1, the IPA levels decreased to nominal levels, allowing the team to investigate the cause of the elevated measurements. Based on the changes in the shape of the gas chromatograph (GC) traces in the IPA region during docked operations, it appeared that an unknown coeluting species was causing problems with quantification. However, with the docking of Northrup-Grumman-11 (NG-11), the elevated IPA returned, as well as the changes in GC traces. In contrast to the SpX-DM1 results, the AQM IPA results did not return to nominal levels following the departure of NG-11, suggesting that the changes could not be tied directly to the visiting vehicle. In this paper, we will discuss a number of potential causes for both the genuine (measured in archival samples) increases in IPA as well as the much higher levels measured by the AQM. Additionally, we will discuss methods being explored to decrease the potential for a reoccurrence in the future.

William T. Wallace↗
NASA NTRSDate not supplied

Options for Offloading a 90-Ton Common Habitat from its Lander on the Surface of Mars

The Common Habitat is a large, long-duration habitat being explored as part of a conceptual study (not an active NASA program) that uses an SLS core stage liquid oxygen (LOX) tank as its primary structure. Measuring 8.4 meters in diameter and 15.6 meters in length, it is manufactured as a habitat and launched as such into space. It is intended for use on the Moon as part of a permanently occupied outpost, on Mars as part of an outpost that will be occupied for hundreds of days at a time, and in deep space as part of the Deep Space Exploration Vehicle where it will support crewed missions up to 1200 days in duration. A study of internal orientation and crew size resulted in a Common Habitat configuration sized for a crew of eight with a three-deck horizontal orientation. There are obvious challenges associated with the delivery of such a large habitat, which may mass as much as 90-tons when initially deployed. The Mars destination in particular imposes extreme challenges due to Martian gravity. This paper identifies initial options for the offloading of a 90-ton Common Habitat from a lander spacecraft on the surface of Mars. On Mars, the Common Habitat is part of a surface outpost where a Habitation Zone includes the Common Habitat docked to a two-chamber airlock node, up to two logistics modules, and up to two pressurized rovers. It is connected by underground conduit to a radiator farm and communications tower assembly. These elements and other surface infrastructure, including robotic systems for surface preparation, are landed prior to the Common Habitat. In the baseline Common Habitat Architecture, the Common Habitat is delivered on the third heavy cargo flight. The Habitation Zone configuration dictates that the Common Habitat needs to be offloaded from the lander. All of the docked elements require direct access to the surface and the Common Habitat must actually be placed in a trench to lower its docking ports to be level with those of the mated elements. Additionally, the habitat must be emplaced in a horizontal configuration, while for any conceivable Earth launch system it must be launched in a vertical configuration. It is true that the Common Habitat must be offloaded from its lander on both the Moon and Mars and a common offloading system must therefore work in both destinations. Mars, however, is considered the driving case for offloading in most, but not all, aspects. A four-day internal study in 2021 recommended that a modified Starship be used to land the Common Habitat on Mars and considered multiple approaches to offload the Common Habitat from the payload section and lower it to the surface. The topic was presented at a public hackathon organized by the Johnson Space Center’s Emerge Employee Resource Group. One team took on the challenge and proposed a concept in some ways similar to the previously considered jib crane. Despite the excellent innovation in the team’s work, a number of study refinements are necessary to truly establish feasibility. These and other future work needed to mature the concept are discussed in this work.

Lander Offloading↗
NASA NTRSDate not supplied

Towards Plume Impingement Modeling in Space Environments

After 30 years human presence in low-earth orbit, NASA is returning to the moon and eventually will go to Mars. To this end, NASA is constructing the Lunar Gateway, an ISS-like space station to act as a home base for Lunar exploration. A large space station must be assembled while in orbit, using a “piecemeal” approach. In this context, it means that the different modules will arrive at different times and attach to what is already in service. The ISS provides an excellent example of this approach, and the proposed Lunar Gateway will undergo a similar assembly process. This assembly is achieved via “docking” maneuvers between modules, which are made possible by sequential firings of the onboard reaction control system (RCS) thrusters. They work by firing hot gases to produce adverse thrust and the needed change in velocity to safely finish the docking approach. The issue is that the gas from these thrusters' forms flow structures described as “plumes” and can impinge onto the outer surfaces of the space station, causing unwanted forces and moments, heat loads, sediment deposition, and in extreme cases, even surface erosion. All mechanisms that can damage the space station and must be avoided. Both permanent and visiting modules will have these RCS thruster exhaust impingement problems. Accurately and efficiently modeling these plume is an involved multi-physics calculation but also an important tool when designing the control algorithms of approaching modules. This poster presents progress towards this simulation on two fronts. First is the verification of OpenFOAM for rarefied plume impingement calculations by direct comparison to published DAC cases. Second is the estimation of plume impingement strikes over the time scale of an entire docking event. This is done by using a simple plume source flow model and a prescribed motion visualizer—coded in Python. Together these tools help push NASA's capabilities for simulating these plume impingement effects.

Rarefied Flows↗
DOE OSTI2019

Identification of Ebola Virus Inhibitors Targeting GP2 Using Principles of Molecular Mimicry

A key step in the Ebola virus (EBOV) replication cycle involves conformational changes in viral glycoprotein 2 (GP2) which facilitate host-viral membrane fusion and subsequent release of the viral genome. Ebola GP2 plays a critical role in virus entry and has similarities in mechanism and structure to the HIV gp41 protein for which inhibitors have been successfully developed. In this work, a putative binding pocket for the C-terminal heptad repeat in the N-terminal heptad repeat trimer was targeted for identification of small molecules that arrest EBOV-host membrane fusion. Two computational structure-based virtual screens of ~1.7 M compounds were performed (DOCK program) against a GP2 five-helix bundle, resulting in 165 commercially available compounds purchased for experimental testing. Based on assessment of inhibitory activity, cytotoxicity, and target specificity, four promising candidates emerged with 50% inhibitory concentration values in the 3 to 26 μM range. Molecular dynamics simulations of the two most potent candidates in their DOCK-predicted binding poses indicate that the majority of favorable interactions involve seven highly conserved residues that can be used to guide further inhibitor development and refinement targeting EBOV. The most recent Ebola virus disease outbreak, from 2014 to 2016, resulted in approximately 28,000 individuals becoming infected, which led to over 12,000 causalities worldwide. The particularly high pathogenicity of the virus makes paramount the identification and development of promising lead compounds to serve as inhibitors of Ebola infection. To limit viral load, the virus-host membrane fusion event can be targeted through the inhibition of the class I fusion glycoprotein of. In the current work, several promising small-molecule inhibitors that target the glycoprotein GP2 were identified through systematic application of structure-based computational and experimental drug design procedures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A goldilocks computational protocol for inhibitor discovery targeting DNA damage responses including replication-repair functions

While many researchers can design knockdown and knockout methodologies to remove a gene product, this is mainly untrue for new chemical inhibitor designs that empower multifunctional DNA Damage Response (DDR) networks. Here, we present a robust Goldilocks (GL) computational discovery protocol to efficiently innovate inhibitor tools and preclinical drug candidates for cellular and structural biologists without requiring extensive virtual screen (VS) and chemical synthesis expertise. By computationally targeting DDR replication and repair proteins, we exemplify the identification of DDR target sites and compounds to probe cancer biology. Our GL pipeline integrates experimental and predicted structures to efficiently discover leads, allowing early-structure and early-testing (ESET) experiments by many laboratories. By employing an efficient VS protocol to examine protein-protein interfaces (PPIs) and allosteric interactions, we identify ligand binding sites beyond active sites, leveraging in silico advances for molecular docking and modeling to screen PPIs and multiple targets. A diverse 3,174 compound ESET library combines Diamond Light Source DSI-poised, Protein Data Bank fragments, and FDA-approved drugs to span relevant chemotypes and facilitate downstream hit evaluation efficiency for academic laboratories. Two VS per library and multiple ranked ligand binding poses enable target testing for several DDR targets. This GL library and protocol can thus strategically probe multiple DDR network targets and identify readily available compounds for early structural and activity testing to overcome bottlenecks that can limit timely breakthrough drug discoveries. By testing accessible compounds to dissect multi-functional DDRs and suggesting inhibitor mechanisms from initial docking, the GL approach may enable more groups to help accelerate discovery, suggest new sites and compounds for challenging targets including emerging biothreats and advance cancer biology for future precision medicine clinical trials.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Structure-Based Design of Small-Molecule Inhibitors of Human Interleukin-6

Human Interleukin-6 (hIL-6) is a pro inflammatory cytokine that binds to its receptor, IL-6Rα followed by binding to gp130 and subsequent dimerization to form a hexamer signaling complex. As a critical inflammation mediator, hIL-6 is associated with a diverse range of diseases and monoclonal antibodies in clinical use that either target IL-6Rα or hIL-6 to inhibit signaling. Here, we perform high-throughput structure-based computational screening using ensemble docking for small-molecule antagonists for which the target conformations were taken from 600 ns long molecular dynamics simulations of the apo protein. Prior knowledge of the contact sites from binary complex studies and experimental work was incorporated into the docking studies. The top 20 scoring ligands from the in silico studies after post analysis were subjected to in vitro functional assays. Among these compounds, the ligand with the second-highest calculated binding affinity experimentally showed an ~84% inhibitory effect on IL6-induced STAT3 reporter activity at 10 μM concentration. This finding may pave the way for designing small-molecule inhibitors of hIL-6 of therapeutic significance.

Human Interleukin-6↗
NASA NTRS2016

Navigation and Alignment Aids Concept of Operations and Supplemental Design Information

The IDSS Navigation and Alignment Aids Concept of Operations and Supplemental Design Information document provides supplemental information to the IDSS IDD. The guide provides insight into the navigation and alignment aids design, and how those aids can be utilized by incoming vehicles for proximity operations and docking. The navigation aids are paramount to successful docking.

International Docking Standard Target↗
NASA NTRS2020

Electric Six Degree of Freedom Installation Timelapse (Six Degree of Freedom Dynamic Test System)

The Six-degree-of-freedom Dynamic Test System (SDTS) is a short-range real-time motion based testing platform. Its primary use at NASA/JSC has been for development and qualification testing of docking systems, robotic assisted berthing mechanisms, and dynamic attachment systems. The SDTS is a closed-loop force feedback system that can simulate on-orbit contact dynamics between two vehicles utilizing the actual mechanical interfaces for testing. The facility is controlled by interconnected computers running real-time simulation software that takes measured contact forces, integrates the equations of motion in real time, and provide those states back into the motion table. This infrastructure can also be used for non-mating applications such as relative position sensor testing/evaluations. The SDTS facility provides a superstructure for mounting test articles, multiple test sensors, an intercom network for voice communications, and a synchronized timing system for data acquisition that includes HD video. This time-lapse video shows the buildup and testing of a modern electric actuation system created by Mikrolar, Inc. at the Johnson Space Center. This motion base will replace the current hydraulic actuator system, which is been in use since the 1970s, for all-future NASA testing. Once the system goes through customization to provide JSC’s unique closed-loop environment, the facility will help certify docking system and attach mechanisms on the ground before we send the first woman and the next man to the lunar surface

hexapod↗
NASA NTRSDate not supplied

Design, Development, and Test of the Advanced Apollo Orbital Assembly System

As spaceflight moves toward commercial solutions for Crew Vehicles and Space Stations, opportunity exists to lower costs with novel designs. Probe and cone docking systems provide a lightweight, low cost, and high-performance docking solution. This work revisits the Apollo probe and cone design and modifies it for the requirements of today’s computer-controlled spacecraft. This new system is called the Advanced Apollo Orbital Assembly (APOA) system, and is intended to support satellite, cargo, and space station assembly missions. A simulation of the APOA was programmed, components were sized, and a design was created by scaling the probe to the size of an EELV Secondary Payload Adapter (ESPA) tunnel. Prototype test hardware was 3D printed using Fused Deposition Modeling (FDM) methods with Polylactic Acid (PLA) material. Testing of the APOA-ESPA was conducted at Marshall Space Flight Center’s (MSFC) Flat Floor, and a test-correlated simulation is used to evaluate a Monte-Carlo of Initial Contact Conditions (ICC’s) to establish baseline performance. The successful development, test, and correlation of the APOA-ESPA proves the design validity and increases Technology Readiness Level (TRL) from 2 to 4. This work opens the door to construction of an APOA-ESPA from flight like materials, and to develop a larger scale prototype APOA. When the full scale APOA is incorporated with the Common Berthing Mechanism (CBM), becomes the Hybrid Berthing System (HBS), which allows for berthing without a robotic arm.

Berthing↗
DOE OSTI2025

An evolutionarily conserved tryptophan cage promotes folding of the extended RNA recognition motif in the hnRNPR ‐like protein family

Abstract The heterogeneous nuclear ribonucleoprotein (hnRNP) R‐like family is a class of RNA binding proteins in the hnRNP superfamily with diverse functions in RNA processing. Here, we present the 1.90 Å X‐ray crystal structure and solution NMR studies of the first RNA recognition motif (RRM) of human hnRNPR. We find that this domain adopts an extended RRM (eRRM1) featuring a canonical RRM with a structured N‐terminal extension (N ext ) motif that docks against the RRM and extends the β‐sheet surface. The adjoining loop is structured and forms a tryptophan cage motif to position the N ext motif for docking to the RRM. Combining mutagenesis, solution NMR spectroscopy, and thermal denaturation studies, we evaluate the importance of residues in the N ext –RRM interface and adjoining loop on eRRM folding and conformational dynamics. We find that these sites are essential for protein solubility, conformational ordering, and thermal stability. Consistent with their importance, mutations in the N ext –RRM interface and loop are associated with several cancers in a survey of somatic mutations in cancer studies. Sequence and structure comparison of the human hnRNPR eRRM1 to experimentally verified and predicted hnRNPR‐like proteins reveals conserved features in the eRRM.

Biochemistry & Molecular Biology↗
DOE OSTI2020

Machine learning-based prediction of enzyme substrate scope: Application to bacterial nitrilases

Predicting the range of substrates accepted by an enzyme from its amino acid sequence is challenging. Although sequenc- and structure-based annotation approaches are often accurate for predicting broad categories of substrate specificity, they generally cannot predict which specific molecules will be accepted as substrates for a given enzyme, particularly within a class of closely related molecules. Combining targeted experimental activity data with structural modeling, ligand docking, and physicochemical properties of proteins and ligands with various machine learning models provides complementary information that can lead to accurate predictions of substrate scope for related enzymes. Here we describe such an approach that can predict the substrate scope of bacterial nitrilases, which catalyze the hydrolysis of nitrile compounds to the corresponding carboxylic acids and ammonia. Each of the four machine learning models (logistic regression, random forest, gradient-boosted decision trees, and support vector machines) performed similarly (average ROC = 0.9, average accuracy = ~82%) for predicting substrate scope for this dataset, although random forest offers some advantages. Finally, this approach is intended to be highly modular with respect to physicochemical property calculations and software used for structural modeling and docking.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Sublethal doses of neonicotinoid imidacloprid can interact with honey bee chemosensory protein 1 (CSP1) and inhibit its function

As a frequently used neonicotinoid insecticide, imidacloprid can impair the chemoreceptive behavior of honey bees even at sublethal doses, while the physiochemical mechanism has not been further revealed. Here, multiple fluorescence spectra, thermodynamic method, and molecular docking were used to study the interaction and the functional inhibition of imidacloprid to the recombinant CSP1 protein in Asian honey bee, Apis cerana. The results showed that the fluorescence intensity (λ{sub em} = 332 nm) of CSP1 could be significantly quenched by imidacloprid in a dynamic mode. During the quenching process, ΔH > 0, ΔS > 0, indicating that the acting forces of imidacloprid with CSP1 are mainly hydrophobic interactions. Synchronous fluorescence showed that the fluorescence of CSP1 was mainly derived from tryptophan, and the hydrophobicity of tryptophan decreased with the increase of imidacloprid concentration. Molecular docking predicted the optimal pose and the amino acid composition of the binding process. Circular dichroism (CD) spectra showed that imidacloprid reduced the α-helix of CSP1 and caused the extension of the CSP1 peptide chain. In addition, the binding of CSP1 to floral scent β-ionone was inhibited by nearly 50% of the apparent association constant (K{sub A}) in the presence of 0.28–2.53 ng/bee of imidacloprid, and the inhibition rate of nearly 95% at 3.75 ng/bee of imidacloprid at sublethal dose level. This study initially revealed the molecular physiochemical mechanism that sublethal doses of neonicotinoid still interact and inhibit the physiological function of the honey bees' chemoreceptive system. - Highlights: • Sublethal doses of imidacloprid can directly interact with CSP1 in Apis cerana. • Sublethal imidacloprid can inhibit the function of CSP1 binding to semiochemicals. • The fluorescence intensity of CSP1 quenched by imidacloprid in a dynamic mode. • The binding between CSP1 and imidacloprid are driven by hydrophobic interactions. • Imidacloprid caused the extension of the CSP1 peptide chain.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

DOK1/PPARgamma pathway mediates anti-tumor ability of all-trans retinoic acid in breast cancer MCF-7 cells

Previous studies have showed the anticancer effect of the all-trans retinoic acid (ATRA) in many tumors including breast cancer; however, the underlying molecular mechanism is still poorly understood. This study experimentally revealed that ATRA treatment inhibited MCF-7 cell proliferation and promoted its apoptosis, along with an enhanced expression of docking protein 1 (DOK1). ATRA's effects on cell proliferation and apoptosis were prevented by DOK1 knockdown. In addition, the genetic silence of DOK1 can inhibit PPARγ expression and its activity. Moreover, inactivation of PPARγ by its specific inhibitor GW9662 reversed the impacts of ATRA on cell proliferation and apoptosis. Taken together, these results indicate that ATRA-enhanced expression of DOK1 activates PPARγ leading to inhibition of cell proliferation and enhancement of cell apoptosis in MCF-7 cell. - Highlights: • ATRA treatment inhibited MCF-7 cell proliferation, along with an enhanced expression of docking protein 1 (DOK1). • The genetic silence of DOK1 can inhibit PPARγ expression and its activity. • Inactivation of PPARγ by its specific inhibitor GW9662 reversed the impacts of ATRA on cell proliferation. • ATRA-enhanced expression of DOK1 activates PPARγ leading to inhibition of cell proliferation in MCF-7 cells.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Functional and structural characterization of a β-glucosidase involved in saponin metabolism from intestinal bacteria

Highlights: • Bifidobacterium longum are involved in the metabolism of saponins. • BlBG3 shows higher efficiency to saponins than known bacterial β-glucosidases. • First structure of β-glucosidase from intestinal bacteria to hydrolyze saponins. • A special binding pocket differs to other structural available GH3 β-glucosidases. • Molecular docking revealed the binding interactions of substrate with BlBG3. Saponins are natural glycosides widely used in medicine and the food industry. Although saponin metabolism in human is dependent on intestinal microbes, few involving bacteria enzymes have been identified. We cloned BlBG3, a GH3 β-glucosidase from Bifidobacterium longum, from human stool. We found that BlBG3 catalyzes the hydrolysis of glycoside furostanol and ginsenoside Rb1 at higher efficiency than other microbial β-glucosidases. Structural analysis of BlBG3 in complex with d-glucose revealed its three unique loops, which form a deep pocket and participate in substrate binding. To understand how substrate is bound to the pocket, molecular docking was performed and the binding interactions of protobioside with BlBG3 were revealed. Mutational study suggested that R484 and H642 are critical for enzymatic activity. Our study presents the first structural and functional analysis of a saponin-processing enzyme from human microbiota.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Structural basis of the cystein protease inhibitor Clonorchis sinensis Stefin-1

Highlights: • Clonorchis sinensis Stefin-1 has known as a host immune modulator. • The first crystal structure of CsStefin-1 was determined by the MAD method. • CsStefin-1 inhibited CsCF-8 cysteine protease activity. • A molecular docking model of CsStefin-1 and CsCF-8 was developed. • The CsStefin-1 was physically bound to CsCF-8 with an apparent K{sub D} value. Cystein protease plays a critical role as a virulence factor in the development and progression of various diseases. Cystatin is a superfamily of cysteine protease inhibitors that participates in various physiological and pathological processes. The cysteine protease inhibitor CsStein-1 isolated from Clonorchis sinensis belongs to the type 1 stefin of cystatins. This inhibitor regulates the activity and processing of CsCF (Cathepsin F of Clonorchis sienesis), which plays an important role in parasite nutrition and host-parasite interaction. CsStefin-1 has also been proposed as a host immune modulator and a participant in the mechanism associated with anti-inflammatory ability. Here, we report the first crystal structure of CsStefin-1 determined by the multi-wavelength anomalous diffraction (MAD) method to 2.3 Å. There are six molecules of CsStefin-1 per asymmetric unit, with a solvent content of 36.5%. The structure of CsStefin-1 is composed of twisted four-stranded antiparallel β-sheets, a central α-helix, and a short α-helix. We also demonstrate that CsStefin-1 binds to CsCF-8 cysteine protease and inhibits its activity. In addition, a molecular docking model of CsStefin-1 and CsCF-8 was developed using homology modeling based on their structures. The structural information regarding CsStefin-1 and molecular insight into its interaction with CsCF-8 are important to understanding their biological function and to design of inhibitors that modulate cysteine protease activity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Ascorbic acid as DNase I inhibitor in prevention of male infertility

Highlights: • As a known dietary antioxidant ascorbic acid protects sperm DNA. • Another possible mechanism of sperm DNA protection by ascorbic acid was evaluated. • Ascorbic acid was investigated on DNase I inhibiton in vitro. • Molecular docking study was performed. • By inhibiting DNase I ascorbic acid could prevent sperm DNA fragmentation. Apoptotic and/or ROS-induced DNA fragmentation in sperm cells may contribute to the development of male infertility. As the known dietary antioxidant, ascorbic acid prevents ROS production and protects sperm cells from DNA damage. Here, we found that ascorbic acid has the ability to inhibit DNase I, one of the main endonucleases involved in DNA fragmentation during apoptosis. Site Finder and Molecular docking defined the ascorbic acid interactions with the most important residues of DNase I, including H-donor interactions with Asp 168 and Asn 170, and H-acceptor interaction with Asn 170. As a furan derivative, ascorbic acid could be considered a pioneer of substrate-based DNase I inhibitors. The results indicate to another possible mechanism for prevention of male infertility by ascorbic acid.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Molecular characterization of single-chain antibody variable fragments (scFv) specific to Pep27 from Streptococcus pneumoniae

Highlights: • Two antibody fragments specific to pneumococcal autolysis factor Pep27 are selected. • The antibody fragments show sub-micromolar affinity with good selectivity. • Molecular docking supports epitope on Pep27 identified by alanine scanning. Pep27 from Streptococcus pneumoniae is reported to initiate pneumococcal autolysis, thereby constituting a major virulence factor. Although a few antisera recognizing Pep27 have been reported, no monoclonal, well-characterized antibody for Pep27 has been developed. Here we screened two single-chain antibody variable fragments (scFv) using a phage display from a large human synthetic scFv library to select clones E2 and F9. Dissociation constants (K{sub d}) of E2 and F9 were 1.1 μM and 0.50 μM, respectively. E2 and F9 did not cross-react with other pneumococcal and unrelated proteins. The epitopes of Pep27 were localized to residues 24, 26 and 27 by alanine scanning. Molecular docking analysis supported the experimentally investigated epitope. The E2 and F9 clones specifically detected Pep27 in an environment mimicking in vivo conditions, demonstrated in human serum. The scFv clones characterized here represent molecular tools for the detection of pneumococcal diseases with potential for further improvement in affinity.

60 APPLIED LIFE SCIENCES↗