Solution NMR Studies Research Articles

Promiscuous binding by Hsp70 results in conformational heterogeneity and fuzzy chaperone-substrate ensembles.

The Hsp70 chaperone system is integrated into a myriad of biochemical processes that are critical for cellular proteostasis. Although detailed pictures of Hsp70 bound with peptides have emerged, correspondingly detailed structural information on complexes with folding-competent substrates remains lacking. Here we report a methyl-TROSY based solution NMR study showing that the Escherichia coli version of Hsp70, DnaK, binds to as many as four distinct sites on a small 53-residue client protein, hTRF1. A fraction of hTRF1 chains are also bound to two DnaK molecules simultaneously, resulting in a mixture of DnaK-substrate sub-ensembles that are structurally heterogeneous. The interactions of Hsp70 with a client protein at different sites results in a fuzzy chaperone-substrate ensemble and suggests a mechanism for Hsp70 function whereby the structural heterogeneity of released substrate molecules enables them to circumvent kinetic traps in their conformational free energy landscape and fold efficiently to the native state.

Spectrally Undiscerned Isomers Might Lead to Erroneous Determination of Water Exchange Rates of paraCEST Eu(III) Agents.

We report a detailed study of the solution structure and water exchange rate of a Eu(III) complex with the cyclen-based ligand L1, containing (S)-2-(2-acetamido)-3-(4-(trifluoromethyl)phenyl)propanoate pendant arms at positions 1 and 7 of the cyclen ring and acetylglycinate pendants at positions 4 and 10. The EuL1 complex was characterized by a combination of NMR and luminescence spectroscopy and density functional theory (DFT) calculations. The chemical exchange saturation transfer (CEST) spectra obtained at different temperatures and saturation powers present a CEST signal attributed to the coordinated water molecule. However, the spectra recorded at low temperatures (10 °C) and low saturation powers revealed the presence of two different species with coordinated water molecules having very similar chemical shifts. Determination of the water exchange rates of the coordinated water molecules was carried out by using the Bloch four-pool model that accounts for the presence of these isomers, and this model was compared to conventional methods for CEST quantification, namely the Omega plot and QUESP (quantification of exchange rate as a function of saturation power), which assume the presence of a single CEST active species. The results indicated that only the four-pool Bloch equations provide reasonable water exchange rates and activation parameters. Solution NMR studies and DFT calculations indicated that the two isomers present in solution correspond to the SS-Δ(λλλλ) and SS-Λ(δδδδ) isomers, which present capped square-antiprismatic (SAP) coordination environments. Additional NMR studies on the EuL2 and EuL3 complexes, which present four (S)-2-(2-acetamido)-3-(4-(trifluoromethyl)phenyl)propanoate or acetylglycinate pendant arms, respectively, confirm the results obtained for EuL1.

Preparation and Chemical/Microstructural Characterization of Azacrown Ether-Crosslinked Chitosan Films

Chemically stable porous azacrown ether-crosslinked chitosan films were prepared by reacting varying molar amounts of N,N-diallyl-7,16-diaza-1,4,10,13-tetraoxa-dibenzo-18-crown-6 (molar equivalents ranging from 0, 0.125, 0.167, 0.25 and 0.5) with chitosan. Their chemical and structural properties were characterized by solid state-nuclear magnetic resonance (NMR), elemental, Fourier transform infrared (FTIR), microscopy, and X-ray analyses, as well as gel content. NMR and FTIR analyses of the reaction products suggested that new –CH2– crosslink bridges were produced between the amine groups of chitosan (Ch) and the allyl groups of the azacrown (DAC). The crosslinking chemistry between allyl and amine groups of the reactants was further evidenced with solution NMR studies on model compound of glucosamine with the azacrown. X-ray diffraction analysis of the Ch/azacrown films using wide angle X-ray scattering (WAXS), including synchrotron-WAXS, revealed that the crystalline arrangement of chitosan (Ch) was partially destroyed with increasing grafting of azacrown ether proportion on the Ch polymer chain. Solubility and gel content determination confirmed network formation with a gel content as high as 84–95 wt %. Microstructural analysis revealed microporous morphology with high surface area. The morphology and structure of the azacrown ether-crosslinked chitosan films could be tailored by stoichiometry of the reacting species.

Organocatalysts Fold To Generate an Active Site Pocket for the Mannich Reaction

Catalysts containing urea, thiourea, and tertiary amine groups fold into a three-dimensional organized structure in solution both in the absence as well as in the presence of substrates or substrate analogues, as indicated by solution NMR and computational studies. These foldamer catalysts promote Mannich reactions with both aliphatic and aromatic imines and malonate esters. Hammett plot and secondary kinetic isotope effects provide evidence for the C–C bond forming event as the turnover-limiting step of the Mannich reaction. Computational studies suggest two viable pathways for the C–C bond formation step, differing in the activation modes of the malonate and imine substrates. The results show that the foldamer catalysts may promote C–C bond formation with an aliphatic substrate bearing a cyclohexyl group by enhanced binding of the substrates by dispersion interactions, but these interactions are largely absent with a simpler catalyst. Additional control experiments demonstrate the ability of simple thio...

PARASHIFT Probes: Solution NMR and X-ray Structural Studies of Macrocyclic Ytterbium and Yttrium Complexes.

Ytterbium and yttrium complexes of octadentate ligands based on 1,4,7,10-tetraazacyclododecane with a coordinated pyridyl group and either tricarboxylate (L1) or triphosphinate (L2) donors form twisted-square-antiprismatic structures. The former crystallizes in the centrosymmetric group P21/c, with the two molecules related by an inversion center, whereas the latter was found as an unusual kryptoracemate in the chiral space group P21. Pure shift NMR and EXSY spectroscopy allowed the dynamic exchange between the (RRR)-Δ-(δδδδ) and (RRR)-Λ-(λλλλ) TSAP diastereomers of the [Y.L2] complex to be detected. The rate-limiting step in the exchange between Δ and Λ isomers involves cooperative ligand arm rotation, which is much faster for [Ln.L1] than for [Ln.L2]. Detailed analysis of NOESY, COSY, HSQC, and HMBC spectra confirms that the major conformer in solution is (RRR)-Λ-(λλλλ), consistent with crystal structure analysis and DFT calculations. The magnetic susceptibility tensors for [Yb.L1] and [Yb.L2], obtained from a full pseudocontact chemical shift analysis, are very different, in agreement with a CASSCF calculation. The remarkably different pseudocontact shift behavior is explained by the change in the orientation of the pseudocontact shift field, as defined by the Euler angles of the susceptibility tensor.

Backbone resonance assignment of an insect arylalkylamine N-acetyltransferase from Bombyx mori reveals conformational heterogeneity.

Arylalkylamine N-acetyltransferases (AANATs) catalyze the transfer of an acetyl group from the acetyl-group donor, acetyl-CoA, to an arylalkylamine acceptor. Although a single AANAT has been identified in mammals, insects utilize multiple AANATs in a diverse array of biological processes. AANATs belong to the GCN5-related acetyltransferase (GNAT) superfamily of enzymes, which despite their overall very low sequence homology, are characterized by a well conserved catalytic core domain. The structural properties of many GNATs have been extensively studied by X-ray crystallography that revealed common features during the catalytic cycle. Here we report the 1H, 13C and 15N backbone NMR resonance assignment of the 24kDa AANAT3 from Bombyx mori (bmAANAT3) as a first step towards understanding the role of protein dynamics in the catalytic properties of AANATs. Our preliminary solution NMR studies reveal that bmAANAT3 is well-folded in solution. The P-loop, which is responsible for cofactor binding, is flexible in the free-state, while a large region of the enzyme interconverts between two distinct conformations in the slow exchange regime.

Molecular Modeling and Solution NMR Studies of the Structure and Dynamics of K-Ras at a Lipid Membrane Containing PIP2

Due to its vital role in regulating the cellular signal transduction and a high occurrence in human tumors, the small GTPase K-Ras has been the object of intense experimental and computational studies recently. In particular, research has focused on the role of membrane anchor on the structure and function of K-Ras. In this research, we investigate the structure and dynamics of K-Ras (GTP bound state) interacting with lipid membranes containing PIP2 (Phosphatidylinositol 4, 5-bisphosphate) by performing long time scale all atom molecular dynamics simulation with the CHAMM36 force field. The simulations show that that the K-Ras catalytic domain binds to the membrane within 100 ns, mainly due to the electrostatic attraction between membrane and K-Ras catalytic domain. PIP2 lipids, which possess four negative charges, form persistent (up to several hundreds of nanoseconds) contacts with residues (Arginine and Lysine) from the GTPase catalytic domain. Further, the lipid bound K-Ras presents several different membrane orientations with respect to the membrane. We find that the competitive interaction between the attraction of membrane with the positively charged protein residues and repulsion of membrane with the negatively charged residues likely determines the K-Ras4A orientation, but this also influenced by the extent of the K-Ras surfaces (in relation to the proteins shape)The simulation results are validated by an NMR solution study of K-Ras with nanodiscs and liposomes. Both the full length and hypervariable region truncated GTPase interact transiently with PIP2 doped membrane model systems through its catalytic domain. Similarly to another experimental and simulation study of K-Ras4B (reviewed by us in [1]), the results imply that membrane orientations could be correlated with K-Ras function by hindering or exposing the effector binding domain of the GTPase to solvent. Furthermore, the effect of membrane binding on the flexibility and conformation of nucleotide binding region, especially with the switch loops of K-Ras will be discussed. Reference: [1] Li, Z. L.; Cao S.; Buck, M.; New & Notable: K-RAS at Anionic Membrane: Orientation, Orientation⋯Orientation. Recent Simulations and Experiments. Biophys. J. 2016, 5, 1033-1035.

Competitive Interactions of PIRT and PI(4,5)P2 Modulate TRPM8

PIRT or Phosphoinositide regulator of TRP is a small membrane protein that has been shown to modulate the function of TRP channels. PIRT is implicated in fine-tuning the physiological roles that TRP channels play in thermosensing and ligand activation; suggesting roles for PIRT:TRP complexes in pathophysiologies such as pruritus and chronic pain. In an effort to better understand the mechanism of PIRT modulation of TRP channels, human PIRT has been expressed and purified. Solution NMR studies of the resulting protein have given way to backbone resonance assignment allowing for experimental determination of its secondary structure and membrane topology. PIRT contains a relatively unstructured N-terminus with two transmembrane helices followed by a positively charged PI(4,5)P2 interacting site in the juxtamembrane region near the C-terminus. Further residue specific characterization of PIRT interactions detail the residue specific binding of the phospholipid, phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), and the TRPM8 S1-S4 sensing domain. Interestingly, PIRT residues that specifically bind PI(4,5)P2 also specifically interact with the TRPM8 sensing domain. The overlap in PIRT binding sites between TRPM8 and PI(4,5)P2 suggest a lipid shuttling mechanism between TRPM8 and PIRT as part of the regulatory function. These studies provide the first glimpses of a structural and molecular framework to begin to dissect the regulatory mechanism of the tripartite PIRT–TRPM8–PI(4,5)P2 complex.

N,N-Bis(2-hy-droxy-eth-yl)di-thio-carbamato-κ2S,S']bis-(tri-phenyl-phosphane-κP)copper(I) chloro-form monosolvate: crystal structure, Hirshfeld surface analysis and solution NMR measurements.

The title compound, [Cu(C5H5NO2S2)(C18H15P)2]·CHCl3, features a tetra-hedrally coordinated CuI atom within a P2S2 donor set defined by two phosphane P atoms and by two S atoms derived from a symmetrically coordinating di-thio-carbamate ligand. Both intra- and inter-molecular hy-droxy-O-H⋯O(hydroxy) hydrogen bonding is observed: the former closes an eight-membered {⋯HOC2NC2O} ring, whereas the latter connects centrosymmetrically related mol-ecules into dimeric aggregates via eight-membered {⋯H-O⋯H-O}2 synthons. The complex mol-ecules are arranged to form channels along the c axis in which reside the chloro-form mol-ecules, being connected by Cl⋯π(arene) and short S⋯Cl [3.3488 (9) Å] inter-actions. The inter-molecular inter-actions have been investigated further by Hirshfeld surface analysis, which shows the conventional hydrogen bonding to be very localized with the main contributors to the surface, at nearly 60%, being H⋯H contacts. Solution NMR studies indicate that whilst the same basic mol-ecular structure is retained in solution, the tri-phenyl-phosphane ligands are highly labile, exchanging rapidly with free Ph3P at room temperature.

Electrospun Lipid Binding Proteins Composite Nanofibers with Antibacterial Properties.

Electrospinning is here used for the first time to prepare nanofibers including a host/guest complex in a keratin/poly(ethylene oxide) matrix. The host is a lipid binding protein and the guest is an insoluble bactericidal molecule, irgasan, bound within the protein internal cavity. The obtained nanofibers, characterized by scanning electron microscopy, exhibit excellent antibacterial activity toward Gram positive and negative bacteria, even with a moderate protein/irgasan cargo. Solution NMR studies, employed to provide molecular information on the cargo system, points to a micromolar affinity, compatible with both the electrospinning process and slow guest release. The versatility of the carrier protein, capable of interacting with a variety of druggable hydrophobic molecules, is exploitable for the development of innovative biomedical devices, whose properties can be tuned by the selected guest.

Probing the free energy landscapes of ALS disease mutants of SOD1 by NMR spectroscopy

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that, in some cases, has been linked with mutations to the antioxidant metalloenzyme superoxide dismutase (SOD1). Although the mature form of this enzyme is highly stable and resistant to aggregation, the most immature form, lacking metal and a stabilizing intrasubunit disulfide bond, apoSOD12SH, is dynamic and hypothesized to be a major cause of toxicity in vivo. Previous solution NMR studies of wild-type apoSOD12SH have shown that the ground state interconverts with a series of sparsely populated and transiently formed conformers, some of which have aberrant nonnative structures. Here, we study seven disease mutants of apoSOD12SH and characterize their free energy landscapes as a first step in understanding the initial stages of disease progression and, more generally, to evaluate the plasticity of low-lying protein conformational states. The mutations lead to little change in the structures and dynamics of the ground states of the mutant proteins. By contrast, the numbers of low-lying excited states that are accessible to each of the disease mutants can vary significantly, with additional conformers accessed in some cases. Our study suggests that the diversity of these structures can provide alternate interaction motifs for different mutants, establishing additional pathways for new and often aberrant intra- and intermolecular contacts. Further, it emphasizes the potential importance of conformationally excited states in directing both folding and misfolding processes.

Solution and solid-state NMR studies of soluble tissue factor

Solution and solid-state NMR studies of soluble tissue factor

Natural structural diversity within a conserved cyclic peptide scaffold.

We recently isolated and described the evolutionary origin of a diverse class of small single-disulfide bonded peptides derived from Preproalbumin with SFTI-1 (PawS1) proteins in the seeds of flowering plants (Asteraceae). The founding member of the PawS derived peptide (PDP) family is the potent trypsin inhibitor SFTI-1 (sunflower trypsin inhibitor-1) from Helianthus annuus, the common sunflower. Here we provide additional structures and describe the structural diversity of this new class of small peptides, derived from solution NMR studies, in detail. We show that although most have a similar backbone framework with a single disulfide bond and in many cases a head-to-tail cyclized backbone, they all have their own characteristics in terms of projections of side-chains, flexibility and physiochemical properties, attributed to the variety of their sequences. Small cyclic and constrained peptides are popular as drug scaffolds in the pharmaceutical industry and our data highlight how amino acid side-chains can fine-tune conformations in these promising peptides.

Specific Lipid Binding of Membrane Proteins in Detergent Micelles Characterized by NMR and Molecular Dynamics.

Many membrane proteins bind specifically to lipids as an integral component of their structures. The ability of detergents to support lipid binding is thus an important consideration when solubilizing membrane proteins for structural studies. In particular, the zwitterionic phosphocholine (PC)-based detergents, which have been widely used in solution NMR studies of channels and transporters, are controversial because of their strong solubilization power and thus perceived as more denaturing than nonionic detergents such as the maltosides. Here, we investigate the ability of the mitochondrial ADP/ATP carrier (AAC) to specifically bind cardiolipin, a mitochondrial lipid important for the carrier function, in dodecylphosphocholine (DPC) micelles. We found that in DPC, the AAC specifically binds cardiolipin in a manner consistent with the bound cardiolipins found in the crystal structures of the AAC determined in n-decyl β-d-maltoside. Our results suggest that PC detergent is compatible with specific lipid binding and that PC detergent mixed with the relevant lipid represents a viable solubilization system for NMR studies of membrane proteins.

Pyclen Tri-n-butylphosphonate Ester as Potential Chelator for Targeted Radiotherapy: From Yttrium(III) Complexation to (90)Y Radiolabeling.

The Y(3+) complex of PCTMB, the tri-n-butyl phosphonate ester of pyclen (3,6,9,15-tetraazabicyclo[9.3.1]pentadeca-1(15),11,13-triene), was synthesized as well as its Ho(3+) and Lu(3+) analogues. X-ray diffraction analyses revealed isomorphous dimeric M2(PCTMB)2·9H2O (M = Y, Ho, Lu) structures that crystallize in the centrosymmetric P1̅ triclinic space group. (1)H NMR and UV studies in aqueous solutions indicated that Y(3+) complexation is fast, being quantitative in 167 min at pH 3.8 and in 13 min at pH 5.5 (25 °C, acetate buffer, I = 0.150 M, [Y(3+)] = [PCTMB] = 0.2 mM). (1)H NMR DOSY and photon correlation spectroscopy experiments evidenced the formation of aggregates in chloroform with a bimodal distribution that changes slightly with concentration (11-24 and 240-258 nm). The behavior of the acid-assisted dissociation of the complex of Y(3+) with PCTMB was studied under pseudo-first-order conditions, and the half-life of the [Y(PCTMB)] complex in 0.5 M HCl at 25 °C was found to be 37 min, a value that decreases to 2.6 min in 5 M HCl. The Y(3+) complex of PCTMB is thermodynamically very stable, with a stability constant of log KY-PCTMB = 19.49 and pY = 16.7 measured by potentiometry. (90)Y complexation studies revealed fast radiolabeling kinetics; optimal radiolabeling conditions were obtained for (90)Y in acetate medium, PCTMB at 10(-4) to 10(-2) M in acetate buffer pH = 4.75, 15 min at 45-60 °C. In vitro stability studies in human serum showed that [(90)Y(PCTMB)] is quite stable, with about 90% of the activity still in the form of the radiotracer at 24 h and 80% from 48 h to 72 h. A comparison with other ligands such as PCTA, DOTA, and DTPA already used for in vivo application shows that [(90)Y(PCTMB)] is an interesting lipophilic and neutral analogue of these reference chelates for therapeutic applications in aqueous and nonaqueous media.

Unfolding the mechanism of the AAA+ unfoldase VAT by a combined cryo-EM, solution NMR study

The AAA+ (ATPases associated with a variety of cellular activities) enzymes play critical roles in a variety of homeostatic processes in all kingdoms of life. Valosin-containing protein-like ATPase of Thermoplasma acidophilum (VAT), the archaeal homolog of the ubiquitous AAA+ protein Cdc48/p97, functions in concert with the 20S proteasome by unfolding substrates and passing them on for degradation. Here, we present electron cryomicroscopy (cryo-EM) maps showing that VAT undergoes large conformational rearrangements during its ATP hydrolysis cycle that differ dramatically from the conformational states observed for Cdc48/p97. We validate key features of the model with biochemical and solution methyl-transverse relaxation optimized spectroscopY (TROSY) NMR experiments and suggest a mechanism for coupling the energy of nucleotide hydrolysis to substrate unfolding. These findings illustrate the unique complementarity between cryo-EM and solution NMR for studies of molecular machines, showing that the structural properties of VAT, as well as the population distributions of conformers, are similar in the frozen specimens used for cryo-EM and in the solution phase where NMR spectra are recorded.

Total Synthesis, Structure, and Biological Activity of Adenosylrhodibalamin, the Non-Natural Rhodium Homologue of Coenzyme B12.

B12 is unique among the vitamins as it is biosynthesized only by certain prokaryotes. The complexity of its synthesis relates to its distinctive cobalt corrin structure, which is essential for B12 biochemistry and renders coenzyme B12 (AdoCbl) so intriguingly suitable for enzymatic radical reactions. However, why is cobalt so fit for its role in B12‐dependent enzymes? To address this question, we considered the substitution of cobalt in AdoCbl with rhodium to generate the rhodium analogue 5′‐deoxy‐5′‐adenosylrhodibalamin (AdoRbl). AdoRbl was prepared by de novo total synthesis involving both biological and chemical steps. AdoRbl was found to be inactive in vivo in microbial bioassays for methionine synthase and acted as an in vitro inhibitor of an AdoCbl‐dependent diol dehydratase. Solution NMR studies of AdoRbl revealed a structure similar to that of AdoCbl. However, the crystal structure of AdoRbl revealed a conspicuously better fit of the corrin ligand for RhIII than for CoIII, challenging the current views concerning the evolution of corrins.

ChemInform Abstract: Principles of Precursor Design for Vapour Deposition Methods

AbstractReview: 32 refs.

Capping β-hairpin with N-terminal d-amino acid stabilizes peptide scaffold.

Various strategies exist to stabilize de novo designed synthetic peptide β-hairpins or β-sheets structures, especially at the non-hydrogen bonding position. However, strategies to stabilize strand termini, which are affected by fraying, are highly limited. Here, by substituting N-terminal aliphatic amino acid with its mirror image counterpart, we achieve a significant increase in scaffold stabilization, resulting from the formation of a terminal aliphatic-aromatic hydrophobic CH…pi cluster. Our extensive solution NMR studies support the incorporation of an N-terminal d-aliphatic amino acid in the design of short β-hairpins, while successfully retaining the overall structural scaffold. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 260-266, 2016.

Triaryl-Like MONO-, BIS-, and TRISKITPHOS Phosphines: Synthesis, Solution NMR Studies, and a Comparison in Gold-Catalyzed Carbon–Heteroatom Bond Forming 5-exo-dig and 6-endo-dig Cyclizations

A homologous series of triaryl-like KITPHOS-type monophosphines containing one, two, or three bulky 12-phenyl-9,10-dihydro-9,10-ethenoanthracene (KITPHOS) units have been developed, and the influence of increasing steric bulk on their efficacy as ligands in gold(I)-catalyzed carbon–heteroatom bond-forming cyclizations has been investigated. Detailed solution NMR studies on Ph-TRISKITPHOS, its oxide, and the corresponding gold(I) chloride adduct identified a conformational exchange process involving a concerted librational motion of the individual anthracene-derived organic substituents about their P–C bonds. The cessation of this motion at reduced temperatures lowers the molecular symmetry such that the two C6H4 rings in each of the KITPHOS units become inequivalent; a lower energy process involving restricted rotation of the biaryl-like phenyl ring has also been identified. Electrophilic gold(I) complexes of these triaryl-like KITPHOS monophosphines catalyze the 5-exo-dig cycloisomerization of propargyl ...