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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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Drugging the entire human proteome: Are we there yet?

Each of the ~20 000 proteins in the human proteome is a potential target for compounds that bind to it and modify its function. The 3D structures of most of these proteins are now available. Here, we discuss the prospects for using these structures to perform proteome-wide virtual HTS (VHTS). Furthermore, we compare physics-based (docking) and AI VHTS approaches, some of which are now being applied with large databases of compounds to thousands of targets. Although preliminary proteome-wide screens are now within our grasp, further methodological developments are expected to improve the accuracy of the results.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Crystal structure of dihydrofolate reductase from the filarial nematode W. bancrofti in complex with NADPH and folate

Lymphatic filariasis is a debilitating illness with an estimated 50 million cases as of 2018. The majority of cases are caused by the parasitic worm W. bancrofti and additional cases by the worms B. malayi and B. timori. Dihydrofolate reductase (DHFR) is an established target in the treatment of cancer, bacterial, and protozoal infections and may be a potential target for drugs targeting parasitic worm infections, including filariasis. Recent studies have shown that known antifolate compounds, including methotrexate, inhibit the activity of W. bancrofti DHFR (WbDHFR). However, the absence of structural information for filarial DHFRs has limited the study of more in-depth structure-function relationships. We report the structure of WbDHFR complexed with NADPH and folate using X-ray diffraction data measured to 2.47 Å resolution. The structure of WbDHFR reveals the usual DHFR fold and is currently only the second nematode DHFR structure in the Protein Data Bank. The equilibrium dissociation constants for NADPH (90 ± 29 nM) and folate (23 ± 4 nM) were determined by equilibrium titrations. The interactions of known antifolates with WbDHFR were analyzed using molecular docking programs and molecular dynamics simulations. Antifolates with a hydrophobic core and extended linker formed favorable interactions with WbDHFR. These combined data should now facilitate the rational design of filarial DHFR inhibitors, which in turn can be used to determine whether DHFR is a viable drug target for filariasis and whether existing antifolates may be repurposed for its treatment.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Structure-Based Identification of Novel Histone Deacetylase 4 (HDAC4) Inhibitors

Histone deacetylases (HDACs) are important cancer drug targets. Existing FDA-approved drugs target the catalytic pocket of HDACs, which is conserved across subfamilies (classes) of HDAC. However, engineering specificity is an important goal. Herein, we use molecular modeling approaches to identify and target potential novel pockets specific to Class IIA HDAC-HDAC4 at the interface between HDAC4 and the transcriptional corepressor component protein NCoR. These pockets were screened using an ensemble docking approach combined with consensus scoring to identify compounds with a different binding mechanism than the currently known HDAC modulators. Binding was compared in experimental assays between HDAC4 and HDAC3, which belong to a different family of HDACs. HDAC4 was significantly inhibited by compound 88402 but not HDAC3. Two other compounds (67436 and 134199) had IC50 values in the low micromolar range for both HDACs, which is comparable to the known inhibitor of HDAC4, SAHA (Vorinostat). However, both of these compounds were significantly weaker inhibitors of HDAC3 than SAHA and thus more selective, albeit to a limited extent. Five compounds exhibited activity on human breast carcinoma and/or urothelial carcinoma cell lines. The present result suggests potential mechanistic and chemical approaches for developing selective HDAC4 modulators.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Nematic Colloidal Micro‐Robots as Physically Intelligent Systems

Abstract Physically intelligent micro‐robotic systems exploit information embedded in micro‐robots, their colloidal cargo, and their milieu to interact, assemble, and form functional structures. Nonlinear anisotropic fluids such as nematic liquid crystals (NLCs) provide untapped opportunities to embed interactions via their topological defects, complex elastic responses, and ability to dramatically restructure in dynamic settings. Here a four‐armed ferromagnetic micro‐robot is designed and fabricated to embed and dynamically reconfigure information in the nematic director field, generating a suite of physical interactions for cargo manipulation. The micro‐robot shape and surface chemistry are designed to generate a nemato‐elastic energy landscape in the domain that defines multiple modes of emergent, bottom‐up interactions with passive colloids. Micro‐robot rotation expands the ability to sculpt interactions; the energy landscape around a rotating micro‐robot is dynamically reconfigured by complex far‐from‐equilibrium dynamics of the micro‐robot's companion topological defect. These defect dynamics allow transient information to be programmed into the domain and exploited. Robust micro‐robotic manipulation strategies are demonstrated that exploit these diverse modes of nemato‐elastic interaction to achieve cargo docking, transport, release, and assembly of complex reconfigurable structures at multi‐stable sites. Such structures are of great interest to future developments of LC‐based advanced optical device and micro‐manufacturing in anisotropic environments.

Yao, Tianyi↗
DOE OSTI2024

Carbonic Anhydrase Variants Catalyze the Reduction of Dialkyl Ketones with High Enantioselectivity

Abstract Human carbonic anhydrase II (hCAII) naturally catalyzes the reaction between two achiral molecules—water and carbon dioxide—to yield the achiral product carbonic acid through a zinc hydroxide intermediate. We have previously shown that a zinc hydride, instead of a hydroxide, can be generated in this enzyme to create a catalyst for the reduction of aryl ketones. Dialkyl ketones are more challenging to reduce, and the enantioselective reduction of dialkyl ketones with two alkyl groups that are similar in size and electronic properties, is a particularly challenging transformation to achieve with high activity and selectivity. Here, we show that hCAII, as well as a double mutant of it, catalyzes the enantioselective reduction of dialkyl ketones with high yields and enantioselectivities, even when the two alkyl groups are similar in size. We also show that variants of hCAII catalyze the site‐selective reduction of one ketone over the other in an unsymmetrical aliphatic diketone. Computational docking of a dialkyl ketone to variants of hCAII containing the zinc hydride provides insights into the origins of the reactivity of various substrates and the high enantioselectivity of the transformations and show how a confined environment can control the enantioselectivity of an abiological intermediate.

Chen, Reichi↗
DOE OSTI2021

Identification and analysis of sugar transporters capable of co–transporting glucose and xylose simultaneously

Simultaneous co-fermentation of glucose and xylose is a key desired trait of engineered Saccharomyces cerevisiae for efficient and rapid production of biofuels and chemicals. However, glucose strongly inhibits xylose transport by endogenous hexose transporters of S. cerevisiae. We identified structurally distant sugar transporters (Lipomyces starkeyi LST1_205437 and Arabidopsis thaliana AtSWEET7) capable of co-transporting glucose and xylose from previously unexplored oleaginous yeasts and plants. Kinetic analysis showed that LST1_205437 had lenient glucose inhibition on xylose transport and AtSWEET7 transported glucose and xylose simultaneously with no inhibition. Modelling studies of LST1_205437 revealed that Ala335 residue at sugar binding site can accommodates both glucose and xylose. Docking studies with AtSWEET7 revealed that Trp59, Trp183, Asn145, and Asn179 residues stabilized the interactions with sugars, allowing both xylose and glucose to be co-transported. In addition, we altered sugar preference of LST1_205437 by single amino acid mutation at Asn365. Furthermore, our findings provide a new mechanistic insight on glucose and xylose transport mechanism of sugar transporters and the identified sugar transporters can be employed to develop engineered yeast strains for producing cellulosic biofuels and chemicals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers

Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. In this study, we aim to develop a reliable methodology for a rational aptamer in silico et vitro design. The new approach combines multiple steps: (1) Molecular design, based on screening in a DNA aptamer library and directed mutagenesis to fit the protein tertiary structure; (2) 3D molecular modeling of the target; (3) Molecular docking of an aptamer with the protein; (4) Molecular dynamics (MD) simulations of the complexes; (5) Quantum-mechanical (QM) evaluation of the interactions between aptamer and target with further analysis; (6) Experimental verification at each cycle for structure and binding affinity by using small-angle X-ray scattering, cytometry, and fluorescence polarization. By using a new iterative design procedure, structure- and interaction-based drug design (SIBDD), a highly specific aptamer to the receptor-binding domain of the SARS-CoV-2 spike protein, was developed and validated. The SIBDD approach enhances speed of the high-affinity aptamers development from scratch, using a target protein structure. The method could be used to improve existing aptamers for stronger binding. This approach brings to an advanced level the development of novel affinity probes, functional nucleic acids. It offers a blueprint for the straightforward design of targeting molecules for new pathogen agents and emerging variants.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Antihypertensive effect of quinoa protein under simulated gastrointestinal digestion and peptide characterization

Abstract BACKGROUND Quinoa protein is a potential source of bioactive peptides. Although some studies have demonstrated its angiotensin converting enzyme (ACE) inhibitory properties, research into its in vivo effect on blood‐pressure regulation and peptide characterization remains limited. RESULTS Quinoa protein hydrolyzate (QPH) was prepared by simulated gastrointestinal digestion. QPH lowered the systolic blood pressure (SBP) and diastolic blood pressure (DBP) in spontaneously hypertensive model rats (SHRs) from 2 h to10 h after oral administration, effectively controlling blood pressure in these SHRs. An in vitro study showed that QPH is capable of inhibiting ACE activity. This was attributed to the activity of a number of low‐molecular‐weight peptides. With relatively high scores predicted by PeptideRanker, three promising bioactive peptides, FHPFPR, NWFPLPR, and NIFRPF, were further studied and their ACE‐inhibition effects were confirmed with IC 50 values of 34.92, 16.77, and 32.40 μM, respectively. A molecular docking study provided insights into the binding of ACE with peptides, and revealed that the presence of specific amino acids in the peptide sequence (Pro, Phe, and Arg at the C‐terminal, and Asn at the N‐terminal) could contribute to the interaction between ACE and peptides. CONCLUSION These results demonstrated the potential of QPH for the management of hypertension, which indicates that it could be a good candidate for inclusion in functional foods to control high blood pressure. © 2020 Society of Chemical Industry

Guo, Huimin↗
DOE OSTI2023

Specificity determinants revealed by the structure of glycosyltransferase Campylobacter concisus PglA

Abstract In selected Campylobacter species, the biosynthesis of N‐linked glycoconjugates via the pgl pathway is essential for pathogenicity and survival. However, most of the membrane‐associated GT‐B fold glycosyltransferases responsible for diversifying glycans in this pathway have not been structurally characterized which hinders the understanding of the structural factors that govern substrate specificity and prediction of resulting glycan composition. Herein, we report the 1.8 Å resolution structure of Campylobacter concisus PglA, the glycosyltransferase responsible for the transfer of N ‐acetylgalatosamine (GalNAc) from uridine 5′‐diphospho‐ N ‐acetylgalactosamine (UDP‐GalNAc) to undecaprenyl‐diphospho‐ N , N ′‐diacetylbacillosamine (UndPP‐diNAcBac) in complex with the sugar donor GalNAc. This study identifies distinguishing characteristics that set PglA apart within the GT4 enzyme family. Computational docking of the structure in the membrane in comparison to homologs points to differences in interactions with the membrane‐embedded acceptor and the structural analysis of the complex together with bioinformatics and site‐directed mutagenesis identifies donor sugar binding motifs. Notably, E113, conserved solely among PglA enzymes, forms a hydrogen bond with the GalNAc C6″‐OH. Mutagenesis of E113 reveals activity consistent with this role in substrate binding, rather than stabilization of the oxocarbenium ion transition state, a function sometimes ascribed to the corresponding residue in GT4 homologs. The bioinformatic analyses reveal a substrate‐specificity motif, showing that Pro281 in a substrate binding loop of PglA directs configurational preference for GalNAc over GlcNAc. This proline is replaced by a conformationally flexible glycine, even in distant homologs, which favor substrates with the same stereochemistry at C4, such as glucose. The signature loop is conserved across all Campylobacter PglA enzymes, emphasizing its importance in substrate specificity.

Vuksanovic, Nemanja↗
DOE OSTI2025

The structural basis for the broad aldehyde specificity of the aminoaldehyde dehydrogenase PauC from the human pathogen Pseudomonas aeruginosa

Abstract Despite significant differences in size and formal charge, the aldehyde dehydrogenasePaPauC (PA5312) fromPseudomonas aeruginosaPAO1 efficiently catalyzes the NAD + ‐dependent oxidation of the aminoaldehydes formed in polyamines degradation. We report here thatPaPauC also oxidizes 4‐guanidinebutyraldehyde, formed in one arginine degradation pathway, trimethylaminobutyraldehyde, of unknown metabolic origin, and indole‐3‐acetaldehyde, a precursor of the plant growth‐promoting hormone indoleacetic acid.PaPauC has been proposed as a potential target for combatingP. aeruginosa. However, understanding its structure–function relationships, crucial for developing specific inhibitors, is lacking. Using X‐ray crystallography, we identified the structural characteristics that determinePaPauC broad aldehyde specificity: a spacious aldehyde‐entrance tunnel and six active‐site residues. Docking simulations, site‐directed mutagenesis, and kinetic analyses support the interactions of Lys479 with glutamylated aminoaldehydes; Phe169, Trp176, and Phe467 with amino and guanidinium groups through cation–π interactions and with the indole group via NH–π and CH–π interactions; Asp459 with amino and indole groups; and Thr303 with amide and guanidinium groups. Exploiting the distinctive structural features of thePaPauC active site could aid in developing specific inhibitors to combatP. aeruginosainfections in humans and animals, as well as in preventing its colonization of plants, which are abundantP. aeruginosareservoirs and, therefore, a significant source of human infections.

Biochemistry & Molecular Biology↗
DOE OSTI2026

Molecular basis and biological relevance of bacterial and plant pinoresinol/lariciresinol reductase specificities

A bacterial pinoresinol/lariciresinol reductase (PLR) homolog named NrPinZ was obtained from a Novosphingobium rhizosphaerae sp. LY bacterial strain, with NrPinZ being part of its 5-step biochemical system catabolizing pinoresinol into coniferyl aldehyde and vanillin. Recombinant NrPinZ reduces racemic 8–8′ furanofuran lignans [(±)-pinoresinols, medioresinols, and syringaresinols] with similar overall catalytic efficiencies. In those reductions, only one of the two furan ring systems is reduced. Two other bacterial PLR homologs, NaPinZ and SlPinZ, from N. aromaticivorans F199 and Sphingobium lignivorans SYK-6, respectively, had comparable substrate versatilities and catalytic efficacies. Plant PLR homologs, by comparison, are either enantiospecific, enantioselective, or variants thereof, being able to reduce either one or both furan rings. For example, a recombinant enantioselective PLR (PLR_Tp2) from western red cedar (Thuja plicata) preferentially reduces both (+)-pinoresinol furan rings to afford (−)-secoisolariciresinol. BoltZ-2 modeling of NrPinZ and PLR_Tp2, together with substrate docking of (+)- and (−)-pinoresinols, medioresinols, and syringaresinols, was very instructive. The NrPinZ active site P1/P2 sub-pockets allow for both racemic forms to be catabolized. Conversely, the smaller P1 pocket in PLR_Tp2 preferentially positions (+)-pinoresinol for downstream metabolism into (−)-secoisolariciresinol, thereby providing a biochemical explanation for the different stereochemical outcomes. NrPinZ, NaPinZ, and SlPinZ, catalyzing substrate versatile catabolism of both racemic forms, may have important ramifications for gymnosperm and angiosperm lignin and lignan biodegradation, including its evolutionary significance and potential in enzyme engineering.

Boltz-2 molecular modeling↗
DOE OSTI2026

Predicting compatibility between ferredoxins and the Fe protein of nitrogenase using in silico protein modeling

Biological nitrogen fixation is the process by which certain bacteria and archaea use the enzyme nitrogenase to reduce atmospheric nitrogen into bioavailable ammonium. Engineering non‐nitrogen‐fixing organisms, like plants, to use nitrogenase could reduce dependency on synthetic fertilizer and mitigate the environmental impacts of industrial fertilizer production. However, nitrogenase activity requires delivery of reducing power by small electron carrying proteins known as ferredoxins and flavodoxins, and successfully engineering nitrogenase into new systems will require a mechanistic understanding of electron delivery by these proteins. Most organisms often have multiple ferredoxins, raising the question of which ferredoxin can support nitrogenase activity. The purpose of this study is to gain insight into how we can predict which ferredoxin is compatible with the Fe protein, the component of nitrogenase that interacts with ferredoxin or flavodoxin. Our in silico protein–protein docking simulations reveal that most ferredoxins and flavodoxins involved in nitrogen fixation have the shortest distance (≤10 Å) between their redox cofactor and the [4Fe‐4S] cluster of the Fe protein. We found shorter cofactor distance contributes to faster intermolecular electron tunneling rates. Bacterial ferredoxins that play a role in nitrogen fixation also exhibit more complementary interactions with the Fe protein than bacterial and plant ferredoxins not involved in this process. Heterologous expression of a set of ferredoxins from both nitrogen‐fixing and non‐nitrogen‐fixing bacteria in the diazotroph Rhodopseudomonas palustris supports our model‐derived prediction that shorter distances between the electron‐carrying cofactors favor nitrogenase compatibility. These findings offer a framework to predict and potentially enhance ferredoxin–nitrogenase compatibility, which will help to improve our ability to engineer nitrogen fixation into non‐nitrogen‐fixing organisms like plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

De novo design and Rosetta-based assessment of high-affinity antibody variable regions (Fv) against the SARS-CoV -2 spike receptor binding domain ( RBD )

The continued emergence of new SARS-CoV-2 variants has accentuated the growing need for fast and reliable methods for the design of potentially neutralizing antibodies (Abs) to counter immune evasion by the virus. Here, we report on the de novo computational design of high-affinity Ab variable regions (Fv) through the recombination of VDJ genes targeting the most solvent-exposed hACE2-binding residues of the SARS-CoV-2 spike receptor binding domain (RBD) protein using the software tool OptMAVEn-2.0. Subsequently, we carried out computational affinity maturation of the designed variable regions through amino acid substitutions for improved binding with the target epitope. Immunogenicity of designs was restricted by preferring designs that match sequences from a 9-mer library of “human Abs” based on a human string content score. We generated 106 different antibody designs and reported in detail on the top five that trade-off the greatest computational binding affinity for the RBD with human string content scores. We further describe computational evaluation of the top five designs produced by OptMAVEn-2.0 using a Rosetta-based approach. We used Rosetta SnugDock for local docking of the designs to evaluate their potential to bind the spike RBD and performed “forward folding” with DeepAb to assess their potential to fold into the designed structures. Ultimately, our results identified one designed Ab variable region, P1.D1, as a particularly promising candidate for experimental testing. This effort puts forth a computational workflow for the de novo design and evaluation of Abs that can quickly be adapted to target spike epitopes of emerging SARS-CoV-2 variants or other antigenic targets.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Zeolite Nanosheets Stabilize Catalyst Particles to Promote the Growth of Thermodynamically Unfavorable, Small–Diameter Carbon Nanotubes

A challenge in the synthesis of single–wall carbon nanotubes (SWCNTs) is the lack of control over the formation and evolution of catalyst nanoparticles and the lack of control over their size or chirality. Here, zeolite MFI nanosheets (MFI–Ns) are used to keep cobalt (Co) nanoparticles stable during prolonged annealing conditions. Environmental transmission electron microscopy (ETEM) shows that the MFI–Ns can influence the size and shape of nanoparticles via particle/support registry, which leads to the preferential docking of nanoparticles to four or fewer pores and to the regulation of the SWCNT synthesis products. The resulting SWCNT population exhibits a narrow diameter distribution and SWCNTs of nearly all chiral angles, including sub–nm zigzag (ZZ) and near–ZZ tubes. Theoretical simulations reveal that the growth of these unfavorable tubes from unsupported catalysts leads to the rapid encapsulation of catalyst nanoparticles bearing them; their presence in the growth products suggests that the MFI–Ns prevent nanoparticle encapsulation and prologue ZZ and near–ZZ SWCNT growth. Furthermore, these results thus present a path forward for controlling nanoparticle formation and evolution, for achieving size– and shape–selectivity at high temperature, and for controlling SWCNT synthesis.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Synthesis and in silico and in vitro evaluation of trimethoxy-benzamides designed as anti-prion derivatives

Transmissible spongiform encephalopathies (TSEs), also known as prion diseases, are neurodegenerative disorders which affect mammals, including the human species, and arise after the conversion of the monomeric cellular prion protein (PrP{sup C}) into the aggregated scrapie form (PrP{sup Sc}). There is no therapy to treat TSEs and the identification of compounds that bind PrP{sup C}, preventing its conversion into PrP{sup Sc}, is a viable therapeutic strategy. We designed and synthesized six novel trimethoxy-benzamide compounds as anti-prion drug candidates. Molecular docking analyses predicted that all the derivatives bind to a hotspot region located in the PrP globular domain with very similar spatial orientation and interaction mode. Although none of the analogs inhibited in vitro-aggregation of recombinant PrP (rPrP) in a cell-free conversion assay, the RT-QuIC, compound 8a accelerated rPrP conversion into PrP{sup Sc}-like species. STD-NMR and ITC analyses indicated that both 8a and 8b bind to rPrP{sup 90–231}. These analogs were toxic to PrP{sup Sc}-infected cell lines, hence we could not assess their anti-prion activity by using this cellular approach, although this toxicity was cell line-dependent. These results point out that the 4-amino-quinoline trimethoxy-benzamide scaffold described herein represents a novel chemical pattern useful as a starting point for future structural optimization in the design of PrP ligands with improved affinity and safety profiles.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Structure and enzymatic characterization of CelD endoglucanase from the anaerobic fungus Piromyces finnis

Anaerobic fungi found in the guts of large herbivores are prolific biomass degraders whose genomes harbor a wealth of carbohydrate-active enzymes (CAZymes), of which only a handful are structurally or biochemically characterized. Here, we report the structure and kinetic rate parameters for a glycoside hydrolase (GH) family 5 subfamily 4 enzyme (CelD) from Piromyces finnis, a modular, cellulosome-incorporated endoglucanase that possesses three GH5 domains followed by two C-terminal fungal dockerin domains (double dockerin). We present the crystal structures of an apo wild-type CelD GH5 catalytic domain and its inactive E154A mutant in complex with cellotriose at 2.5 and 1.8 Å resolution, respectively, finding the CelD GH5 catalytic domain adopts the (β/α) 8 -barrel fold common to many GH5 enzymes. Structural superimposition of the apo wild-type structure with the E154A mutant-cellotriose complex supports a catalytic mechanism in which the E154 carboxylate side chain acts as an acid/base and E278 acts as a complementary nucleophile. Further analysis of the cellotriose binding pocket highlights a binding groove lined with conserved aromatic amino acids that when docked with larger cellulose oligomers is capable of binding seven glucose units and accommodating branched glucan substrates. Activity analyses confirm P. finnis CelD can hydrolyze mixed linkage glucan and xyloglucan, as well as carboxymethylcellulose (CMC). Measured kinetic parameters show the P. finnis CelD GH5 catalytic domain has CMC endoglucanase activity comparable to other fungal endoglucanases with k cat = 6.0 ± 0.6 s –1 and K m = 7.6 ± 2.1 g/L CMC. Enzyme kinetics were unperturbed by the addition or removal of the native C-terminal dockerin domains as well as the addition of a non-native N-terminal dockerin, suggesting strict modularity among the domains of CelD.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Correlated conformational dynamics of the human GluN1-GluN2A type N-methyl-D-aspartate (NMDA) receptor

N-Methyl-D-aspartate receptors (NMDARs) are glutamate-gated ion channels found in the nerve cell membranes. As a result of overexcitation of NMDARs, neuronal death occurs and may lead to diseases such as epilepsy, stroke, Alzheimer’s disease, and Parkinson’s disease. In this study, human GluN1- GluN2A type NMDAR structure is modeled based on the X-ray structure of the Xenopus laevis template and missing loops are added by ab-initio loop modeling. The final structure is chosen according to two different model assessment scores. To be able to observe the structural changes upon ligand binding, glycine and glutamate molecules are docked into the corresponding binding sites of the receptor. Subsequently, molecular dynamics simulations of 1.3 μs are performed for both apo and ligand-bound structures. Structural parameters, which have been considered to show functionally important changes in previous NMDAR studies, are monitored as conformational rulers to understand the dynamics of the conformational changes. Moreover, principal component analysis (PCA) is performed for the equilibrated part of the simulations. Additionally, from these analyses, the differences in between apo and ligand-bound simulations can be summarized as the following: The girdle right at the beginning of the pore loop, which connects M2 and M3 helices of the ion channel, partially opens. Ligands act like an adhesive for the ligand-binding domain (LBD) by keeping the bi-lobed structure together and consequently this is reflected to the overall dynamics of the protein as an increased correlation of the LBD with especially the amino-terminal domain (ATD) of the protein.

59 BASIC BIOLOGICAL SCIENCES↗