Structural investigation of 2-naphthyl phenyl ether inhibitors bound to WT and Y181C reverse transcriptase highlights key features of the NNRTI binding site
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99 GENERAL AND MISCELLANEOUS↗
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Results for “binding modes”
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Structural mechanisms for binding and activation of a contact-quenched fluorophore by RhoBAST
The fluorescent light-up aptamer RhoBAST, which binds and activates the fluorophore–quencher conjugate tetramethylrhodamine-dinitroaniline with high affinity, super high brightness, remarkable photostability, and fast exchange kinetics, exhibits excellent performance in super-resolution RNA imaging. Here we determine the co-crystal structure of RhoBAST in complex with tetramethylrhodamine-dinitroaniline to elucidate the molecular basis for ligand binding and fluorescence activation. The structure exhibits an asymmetric “A”-like architecture for RhoBAST with a semi-open binding pocket harboring the xanthene of tetramethylrhodamine at the tip, while the dinitroaniline quencher stacks over the phenyl of tetramethylrhodamine instead of being fully released. Molecular dynamics simulations show highly heterogeneous conformational ensembles with the contact-but-unstacked fluorophore–quencher conformation for both free and bound tetramethylrhodamine-dinitroaniline being predominant. The simulations also show that, upon RNA binding, the fraction of xanthene-dinitroaniline stacked conformation significantly decreases in free tetramethylrhodamine-dinitroaniline. This highlights the importance of releasing dinitroaniline from xanthene tetramethylrhodamine to unquench the RhoBAST–tetramethylrhodamine-dinitroaniline complex. Using SAXS and ITC, we characterized the magnesium dependency of the folding and binding mode of RhoBAST in solution and indicated its strong structural robustness. The structures and binding modes of relevant fluorescent light-up aptamers are compared, providing mechanistic insights for rational design and optimization of this important fluorescent light-up aptamer-ligand system.
59 BASIC BIOLOGICAL SCIENCES↗
Design of protein-binding proteins from the target structure alone
The design of proteins that bind to a specific site on the surface of a target protein using no information other than the three-dimensional structure of the target remains a challenge. Here we describe a general solution to this problem that starts with a broad exploration of the vast space of possible binding modes to a selected region of a protein surface, and then intensifies the search in the vicinity of the most promising binding modes. We demonstrate the broad applicability of this approach through the de novo design of binding proteins to 12 diverse protein targets with different shapes and surface properties. Biophysical characterization shows that the binders, which are all smaller than 65 amino acids, are hyperstable and, following experimental optimization, bind their targets with nanomolar to picomolar affinities. We succeeded in solving crystal structures of five of the binder–target complexes, and all five closely match the corresponding computational design models. Experimental data on nearly half a million computational designs and hundreds of thousands of point mutants provide detailed feedback on the strengths and limitations of the method and of our current understanding of protein–protein interactions, and should guide improvements of both. Our approach enables the targeted design of binders to sites of interest on a wide variety of proteins for therapeutic and diagnostic applications.
59 BASIC BIOLOGICAL SCIENCES↗
Self-Assembly of Metallo-Supramolecules with Dissymmetrical Ligands and Characterization by Scanning Tunneling Microscopy
Asymmetrical and dissymmetrical structures are widespread and play a critical role in nature and life systems. In the field of metallo-supramolecular assemblies, it is still in its infancy for constructing artificial architectures using dissymmetrical building blocks. Herein, we report the self-assembly of supramolecular systems based on two dissymmetrical double-layered ligands. With the aid of ultra-high-vacuum, low-temperature scanning tunneling microscopy (UHV-LT-STM), we were able to investigate four isomeric structures corresponding to four types of binding modes of ligand LA with two major conformations complexes A. The distribution of isomers measured by STM and total binding energy of each isomer obtained by density functional theory (DFT) calculations suggested that the most abundant isomer could be the most stable one with highest total binding energy. Lastly, through shortening the linker between inner and outer layers and the length of arms, the arrangement of dissymmetrical ligand LB could be controlled within one binding mode corresponding to the single conformation for complexes B.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Enzyme-mediated aminoglycoside resistance without target mimicry
Abstract The primary mode of resistance to aminoglycoside antibiotics is through chemical modification catalyzed by aminoglycoside-modifying enzymes. Numerous structural studies of these enzymes have invariably shown that they bind aminoglycosides in the same lowest-energy conformation as the intended target for these antibiotics, the A site of the bacterial ribosome. Presumably, the binding mode mimicry enables these enzymes to compete successfully with the target, thus conferring effective resistance. Here we present the first structural and functional studies of two aminoglycoside-modifying enzymes that do not use target mimicry, AAC(3)-Ia and AAC(3)-XIa. X-ray diffraction studies reveal that these enzymes bind aminoglycoside antibiotics in a conformation where the central 2-deoxystreptamine ring is in boat conformation. The effect of this non-canonical binding mode on the enzymes’ ability to modify antibiotics is assessed in silico and in vitro, and its impact for conferring resistance is assessed in vivo. Overall, the results show that target mimicry, while advantageous, is not an essential strategy for aminoglycoside-modifying enzymes to be effective in conferring resistance.
Chemistry↗
Structures of drug-specific monoclonal antibodies bound to opioids and nicotine reveal a common mode of binding
Opioid-related fatal overdoses have reached epidemic proportions. Because existing treatments for opioid use disorders offer limited long-term protection, accelerating the development of newer approaches is critical. Monoclonal antibodies (mAbs) are an emerging treatment strategy that targets and sequesters selected opioids in the bloodstream, reducing drug distribution across the blood-brain barrier, thus preventing or reversing opioid toxicity. We previously identified a series of murine mAbs with high affinity and selectivity for oxycodone, morphine, fentanyl, and nicotine. To determine their binding mechanism, we used X-ray crystallography to solve the structures of mAbs bound to their respective targets, to 2.2 Å resolution or higher. Structural analysis showed a critical convergent hydrogen bonding mode that is dependent on a glutamic acid residue in the mAbs’ heavy chain and a tertiary amine of the ligand. Further, characterizing drug-mAb complexes represents a significant step toward rational antibody engineering and future manufacturing activities to support clinical evaluation.
60 APPLIED LIFE SCIENCES↗
Highly Structured Water Networks in Microhydrated Dodecaborate Clusters
Here, we report a combined photoelectron spectroscopy and theoretical investigation of a series of size-selected hydrated closo-dodecaborate clusters B 12 X 12 2– ·nH 2 O (X = H, F, or I; n = 1–6). Distinct structural arrangements of water clusters from monomer to hexamer can be achieved by using different B 12 X 12 2– bases, illustrating the evident solute specificity. Because B–H···H–O dihydrogen bonds are stronger than O···H–O hydrogen bonds in water, the added water molecules are arranged in a unified binding mode by forming highly structured water networks manipulated by B 12 H 12 2– . As a comparison, the hydrated B 12 F 12 2– clusters display similar water evolution for n values of 1 and 2 but different binding modes for larger clusters, while water networks in B 12 I 12 2– share similarities with the free water clusters. This finding provides a consistent picture of the structural diversity of hydrogen bonding networks in microhydrated dodecaborates and a molecular-level understanding of microsolvation dynamics in aqueous borate chemistry.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structural basis of a shared antibody response to SARS-CoV-2
Molecular understanding of neutralizing antibody responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could accelerate vaccine design and drug discovery. We analyzed 294 anti–SARS-CoV-2 antibodies and found that immunoglobulin G heavy-chain variable region 3-53 (IGHV3-53) is the most frequently used IGHV gene for targeting the receptor-binding domain (RBD) of the spike protein. Co-crystal structures of two IGHV3-53–neutralizing antibodies with RBD, with or without Fab CR3022, at 2.33- to 3.20-angstrom resolution revealed that the germline-encoded residues dominate recognition of the angiotensin I converting enzyme 2 (ACE2)–binding site. This binding mode limits the IGHV3-53 antibodies to short complementarity-determining region H3 loops but accommodates light-chain diversity. These IGHV3-53 antibodies show minimal affinity maturation and high potency, which is promising for vaccine design. Knowledge of these structural motifs and binding mode should facilitate the design of antigens that elicit this type of neutralizing response.
59 BASIC BIOLOGICAL SCIENCES↗
Engineering Organization of DNA Nano-Chambers through Dimensionally Controlled and Multi-Sequence Encoded Differentiated Bonds
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99 GENERAL AND MISCELLANEOUS↗
Y(III) Sorption at the Orthoclase (001) Surface Measured by X-ray Reflectivity
Interactions of heavy metals with charged mineral surfaces control their mobility in the environment. Here, we investigate the adsorption of Y(III) onto the orthoclase (001) basal plane, the former as a representative of rare earth elements and an analogue of trivalent actinides and the latter as a representative of naturally abundant K-feldspar minerals. In this study, we apply in situ high-resolution X-ray reflectivity to determine the sorption capacity and molecular distribution of adsorbed Y species as a function of the Y 3+ concentration, [Y 3+ ], at pH 7 and 5. With [Y 3+ ] ≥ 1 mM at pH 7, we observe an inner-sphere (IS) sorption complex at a distance of ~1.5 Å from the surface and an outer-sphere (OS) complex at 3–4 Å. Based on the adsorption height of the IS complex, a bidentate, binuclear binding mode, in which Y 3+ binds to two terminal oxygens, is proposed. In contrast, mostly OS sorption is observed at pH 5. The observed maximum Y coverage is ~1.3 Y 3+ /A UC (A UC : area of the unit cell = 111.4 Å 2 ) for all the investigated pH values and Y concentrations, which is in the expected range based on the estimated surface charge of orthoclase (001).
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
ModE Regulates Alternative Nitrogenase Expression in the Methanogen Methanosarcina acetivorans
ABSTRACT All methanogens that can fix nitrogen use molybdenum (Mo) nitrogenase. Some methanogens, including Methanosarcina acetivorans , also contain alternative vanadium‐ and iron‐nitrogenases, encoded by the vnf and anf operons, respectively. These nitrogenases are produced when there is insufficient Mo to support Mo‐nitrogenase activity. The factors that control the expression of the alternative nitrogenases in response to Mo availability are unknown in methanogens. Here we show that ModE is the regulator that represses transcription of the vnf and anf operons in M. acetivorans when cells are grown with Mo. CRISPRi repression of modE results in a significant increase in the transcription of the vnf and anf operons as well as the detection of Fe‐nitrogenase during nitrogen fixation in the presence of Mo. Gel shift assays with recombinant ModE demonstrated that ModE binds a specific sequence motif upstream of the vnf and anf operons, as well as other genes and operons related to nitrogen fixation and Mo transport. However, purified ModE does not contain Mo, and the addition of Mo does not alter the affinity of ModE for DNA, indicating M. acetivorans ModE may not directly bind Mo. This study shows that ModE is the primary Mo‐responsive regulator of alternative nitrogenase expression in M. acetivorans , but other factor(s) are likely involved in directly sensing Mo.
Chanderban, Melissa [Department of Biological Scie↗
Side-On N 2 Binding and Reduction by a Heterotetrametallic Zr 2 Co 2 Cluster
In multimetallic compounds, N 2 typically bridges late transition metals in an end-on (η 1 :η 1 ) fashion while early transition metals often bind N 2 side-on (η 2 ), with the latter resulting in more significant N–N bond elongation. In this work, N 2 fixation is accomplished by using a well-defined scaffold featuring a heterobimetallic combination of Zr and Co. We report a heterotetrametallic Zr 2 Co 2 cluster in which N 2 is bound side-on to the two Co centers and end-on to Zr in a μ 3 -η 1 :η 2 :η 2 binding mode that defies established paradigms for N 2 binding. The heterometallic approach is shown to facilitate catalytic reductive silylation of N 2 with turnover numbers far exceeding those of reported cobalt catalysts.
catalysts↗
Discovery of GuaB inhibitors with efficacy against Acinetobacter baumannii infection
ABSTRACT Guanine nucleotides are required for growth and viability of cells due to their structural role in DNA and RNA, and their regulatory roles in translation, signal transduction, and cell division. The natural antibiotic mycophenolic acid (MPA) targets the rate-limiting step inde novoguanine nucleotide biosynthesis executed by inosine-5´-monophosphate dehydrogenase (IMPDH). MPA is used clinically as an immunosuppressant, but whetherin vivoinhibition of bacterial IMPDH (GuaB) is a valid antibacterial strategy is controversial. Here, we describe the discovery of extremely potent small molecule GuaB inhibitors (GuaBi) specific to pathogenic bacteria with a low frequency of on-target spontaneous resistance and bactericidal efficacyin vivoagainstAcinetobacter baumanniimouse models of infection. The spectrum of GuaBi activity includes multidrug-resistant pathogens that are a critical priority of new antibiotic development. Co-crystal structures ofA. baumannii, Staphylococcus aureus, andEscherichia coliGuaB proteins bound to inhibitors show comparable binding modes of GuaBi across species and identifies key binding site residues that are predictive of whole-cell activity across both Gram-positive and Gram-negative clades of Bacteria. The clearin vivoefficacy of these small molecule GuaB inhibitors in a model ofA. baumanniiinfection validates GuaB as an essential antibiotic target. IMPORTANCE The emergence of multidrug-resistant bacteria worldwide has renewed interest in discovering antibiotics with novel mechanism of action. For the first time ever, we demonstrate that pharmacological inhibition ofde novoguanine biosynthesis is bactericidal in a mouse model ofAcinetobacter baumanniiinfection. Structural analyses of novel inhibitors explain differences in biochemical and whole-cell activity across bacterial clades and underscore why this discovery may have broad translational impact on treatment of the most recalcitrant bacterial infections.
Microbiology↗
Structural Characterization of Two CO Molecules Bound to the Nitrogenase Active Site
As an approach towards unraveling the nitrogenase mechanism, we have studied the binding of CO to the activesite FeMo-cofactor. CO is not only an inhibitor of nitrogenase, but it is also a substrate, undergoing reduction to hydrocarbons (Fischer–Tropsch-type chemistry). The CC bond forming capabilities of nitrogenase suggest that multiple CO or COderived ligands bind to the active site. Herein, we report a crystal structure with two CO ligands coordinated to the FeMo-cofactor of the molybdenum nitrogenase at 1.33 resolution. In addition to the previously observed bridging CO ligand between Fe2 and Fe6 of the FeMo-cofactor, a new ligand binding mode is revealed through a second CO ligand coordinated terminally to Fe6. While the relevance of this state to nitrogenase-catalyzed reactions remains to be established, it highlights the privileged roles for Fe2 and Fe6 in ligand binding, with multiple coordination modes available depending on the ligand and reaction conditions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Enzyme kinetics by GH7 cellobiohydrolases on chromogenic substrates is dictated by non‐productive binding: insights from crystal structures and MD simulation
Cellobiohydrolases (CBHs) in the glycoside hydrolase family 7 (GH7) ( EC3.2.1.176 ) are the major cellulose degrading enzymes both in industrial settings and in the context of carbon cycling in nature. Small carbohydrate conjugates such as p‐ nitrophenyl‐β‐ d ‐cellobioside (pNPC), p‐ nitrophenyl‐β‐ d ‐lactoside (pNPL) and methylumbelliferyl‐β‐ d ‐cellobioside have commonly been used in colorimetric and fluorometric assays for analysing activity of these enzymes. Despite the similar nature of these compounds the kinetics of their enzymatic hydrolysis vary greatly between the different compounds as well as among different enzymes within the GH7 family. Through enzyme kinetics, crystallographic structure determination, molecular dynamics simulations, and fluorometric binding studies using the closely related compound o‐nitrophenyl‐β‐ d ‐cellobioside (oNPC), in this work we examine the different hydrolysis characteristics of these compounds on two model enzymes of this class, TrCel7A from Trichoderma reesei and PcCel7D from Phanerochaete chrysosporium . Protein crystal structures of the E212Q mutant of TrCel7A with pNPC and pNPL, and the wildtype TrCel7A with oNPC, reveal that non‐productive binding at the product site is the dominating binding mode for these compounds. Enzyme kinetics results suggest the strength of non‐productive binding is a key determinant for the activity characteristics on these substrates, with PcCel7D consistently showing higher turnover rates ( k cat ) than TrCel7A, but higher Michaelis–Menten ( K M ) constants as well. Furthermore, oNPC turned out to be useful as an active‐site probe for fluorometric determination of the dissociation constant for cellobiose on TrCel7A but could not be utilized for the same purpose on PcCel7D, likely due to strong binding to an unknown site outside the active site.
59 BASIC BIOLOGICAL SCIENCES↗
Structural insights into the unique recognition module between α-synuclein peptide and nanobody
Nanobodies are single-domain fragments of antibodies with comparable specificity and affinity to antibodies. They are emerging as versatile tools in biology due to their relatively small size. Here, we report the crystal structure of a specific nanobody Nbα-syn01, bound to a 14 amino acid long peptide of α-synuclein (αSyn), a 140-residue protein whose aggregation is associated with Parkinson's disease. The complex structure exhibits a unique binding pattern where the αSyn peptide replaces the N-terminal region of nanobody. Recognition is mediated principally by extended main chain interaction of the αSyn peptide and specificity of the interaction lies in the central 48–52 region of αSyn peptide. Structure-guided truncation of Nbα-syn01 shows tighter binding to αSyn peptide and improved inhibition of α-synuclein aggregation. The structure of the truncated complex was subsequently determined and was indistinguishable to full length complex as the full-length form had no visible electron density for the N-terminal end. These findings reveal the molecular basis for a previously unobserved binding mode for nanobody recognition of α-synuclein, providing an explanation for the enhanced binding, and potential for an alternate framework for structure-based protein engineering of nanobodies to develop better diagnostic and therapeutic tools.
59 BASIC BIOLOGICAL SCIENCES↗
Green synthesis and characterization of nontoxic L-methionine capped silver and gold nanoparticles
The simple green method for synthesis of stable L-Methionine (L-Met) capped silver (Ag@LM NPs) and gold (Au@LM NPs) nanoparticles (NPs) without adding any additional reduction agent or stabilizer was developed. Colloidal dispersions were characterized by UV–Vis spectrophotometry. The size and spherical shape of NPs were evaluated by transmission electron microscopy. Their surface covering was confirmed by atomic force microscopy, Fourier transform infrared spectroscopy, dynamic light scattering, and zeta potential measurements. Density functional theory calculations pointed that the preferential adsorption mode of L-Met on both Ag and Au surfaces was a vertical binding geometry via –NH2 group, while horizontal binding mode via [sbnd]S[sbnd] and –NH2 groups is also possible. The genotoxicity (evaluated by the micronucleus assay) of NPs, as well as their effects on some oxidative stress parameters (catalase activity, malondialdehyde level), were assessed in vitro using human peripheral blood cells as a model system. The influence of NPs on the morphology of lymphocyte cells studied using atomic force microscopy revealed that the membrane of cells remained unaffected after the treatment with NPs. When considering the effects of NPs on catalase activity and malondialdehyde level, neither particle type promoted oxidative stress. However, the treatment of lymphocytes with Ag@LM NPs induced a concentration-dependent enhancement of the micronuclei incidence and suppression of the cell proliferation while Au@LM NPs promoted cell proliferation, with no significant effects on micronuclei formation. The Ag@LM NPs were more prone to induce DNA damage than Au@LM NPs, which makes the latter type more suitable for further studies in nano-medicine. © 2019.
60 APPLIED LIFE SCIENCES↗
DFT-based investigation of solvation of Nd(III)/Yb(III) cations in room-temperature ionic-liquid
We report a DFT study on the solvation of bare rare-earth (RE) cations [Nd(III) and Yb(III)] in the room-temperature ionic-liquid (RTIL) based on 1,3-dimethyl-imidazolium + , PF 6 - , [MMI][PF 6 ]. In the present article, we aim to investigate whether the chosen RTIL can preferentially solvate any of the RE cations under study. First, the RTIL binding to the RE cation is studied in the gas phase, and then explored with continuum solvation model employing RTIL parameters. First, we considered the formation of the first solvation shell, where the PF 6 - anions directly bond with the Ln(III) cation. We then further surrounded the first solvation shell with [MMI]+ cations to form the second solvation shell. The stability of PF 6 - coordinated complexes is studied by calculating the binding energy values. The number of PF 6 - anions for both Ln(III) cations starts with three ligands and goes until the maximum binding energy in the RTIL medium is reached. The coordination number and binding modes of PF 6 - depend on the size of the RE cation. Comparing the binding energy values between the RE cations for the first solvation shell complexes, it is noticed that Yb-complexes have relatively greater binding energy than Nd-complexes. We have further performed a Boltzmann population analysis to find out the most dominant conformer among each category of PF 6 - coordinated complexes. A study using Natural Population Analysis shows that after complexation with PF 6 - the charge on the Yb-centers lower to a greater extent than Nd-centers, implying stronger bonding between Yb and PF 6 - , which is in harmony with the binding energy analysis. Overall, the computational investigation provides an in-depth understanding of the complexation phenomena of RE cations in RTIL, which can be useful for the practical separation of RE cations using RTIL.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗