Pseudoknot preorganization of the preQ1 class I riboswitch

To explore folding and ligand recognition of metabolite-responsive RNAs is of major importance to comprehend gene regulation by riboswitches. Here, we demonstrate, using NMR spectroscopy, that the free aptamer of a preQ(1) class I riboswitch preorganizes into a pseudoknot fold in a temperature- and Mg(2+)-dependent manner. The preformed pseudoknot represents a structure that is close to the ligand-bound state and that likely represents the conformation selected by the ligand. Importantly, a defined base pair mutation within the pseudoknot interaction stipulates whether, in the absence of ligand, dimer formation of the aptamer competes with intramolecular pseudoknot formation. This study pinpoints how RNA preorganization is a crucial determinant for the adaptive recognition process of RNA and ligand.     

Comparison of solution and crystal structures of preQ1 riboswitch reveals calcium-induced changes in conformation and dynamics

Riboswitches regulate gene expression via specific recognition of cognate metabolites by their aptamer domains, which fold into stable conformations upon ligand binding. However, the recently reported solution and crystal structures of the Bacillus subtilis preQ(1) riboswitch aptamer show small but significant differences, suggesting that there may be conformational heterogeneity in the ligand-bound state. We present a structural and dynamic characterization of this aptamer by solution NMR spectroscopy. The aptamer-preQ(1) complex is intrinsically flexible in solution, with two regions that undergo motions on different time scales. Three residues move in concert on the micro-to-millisecond time scale and may serve as the lid of the preQ(1)-binding pocket. Several Ca(2+) ions are present in the crystal structure, one of which binds with an affinity of 47 ± 2 μM in solution to a site that is formed only upon ligand binding. Addition of Ca(2+) to the aptamer-preQ(1) complex in solution results in conformational changes that account for the differences between the solution and crystal structures. Remarkably, the Ca(2+) ions present in the crystal structure, which were proposed to be important for folding and ligand recognition, are not required for either in solution.     

Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch

The tetracycline aptamer is an in vitro selected RNA that binds to the antibiotic with the highest known affinity of an artificial RNA for a small molecule (Kd approximately 0.8 nM). It is one of few aptamers known to be capable of modulating gene expression in vivo. The 2.2 A resolution cocrystal structure of the aptamer reveals a pseudoknot-like fold formed by tertiary interactions between an 11 nucleotide loop and the minor groove of an irregular helix. Tetracycline binds within this interface as a magnesium ion chelate. The structure, together with previous biochemical and biophysical data, indicates that the aptamer undergoes localized folding concomitant with tetracycline binding. The three-helix junction, h-shaped architecture of this artificial RNA is more complex than those of most aptamers and is reminiscent of the structures of some natural riboswitches.     

Development and characterization of an aptamer binding ligand of fractalkine using domain targeted SELEX

Fractalkine (FKN) is a unique cell surface protein with potential as a therapeutic target because of its role in inflammatory diseases and cancer. We developed an aptamer, named FKN-S2, with a dissociation constant of 3.4 ± 0.7 nM that is specific to the chemokine domain of fractalkine.     

Synthesis of azide congeners of preQ1 as potential substrates for tRNA guanine transglycosylase

PreQ₁ ( 2 ) is a precursor of queuine ( 1 ) that in eubacteria is incorporated into transfer RNA (tRNA) by tRNA guanine transglycosylase (TGT) before being further elaborated into queuine. The queuine modification is unusual and occurs across all eukaryotes and eubacteria with few exceptions, but its function remains unclear. As the modified nucleotide occurs through incorporation of a specially synthesized nucleotide instead of via modification of a genetically encoded base, a study of the sites of modification by prepared probes is possible. We report the synthesis of two novel azide congeners ( 3 , 4 ) of preQ₁ for this purpose. The evaluation of their interaction with TGT shows that both probes act as weak competitive inhibitors of guanine exchange of guanine(34) tRNA^Tyr with a K_i of ~70 μM. However, we could not show that these are substrates for TGT-catalyzed incorporation into tRNA. We believe the reason for this is a marked loss of binding due to the azide functionality of 3 and 4 abrogating the possibility of two hydrogen bonds to the carbonyl group of Leu231 and Met260 of TGT, previously observed for the terminal methylene amine of preQ₁ by x-ray crystallography.     

Rerouting the folding pathway of the Notch ankyrin domain by reshaping the energy landscape

The modular nature of repeat proteins has made them a successful target for protein design. Ankyrin repeat, TPR, and leucine rich repeat domains that have been designed solely on consensus information have been shown to have higher thermostability than their biological counterparts. We have previously shown that we can reshape the energy landscape of a repeat protein by adding multiple C-terminal consensus ankyrin repeats to the five N-terminal repeats of the Notch ankyrin domain. Here we explore how the folding mechanism responds to reshaping of the energy landscape. We have used analogous substitutions of a conserved alanine with glycine in each repeat to determine the distribution of structure in the transition state ensembles of constructs containing one (Nank1-5C1) and two consensus (Nank1-5C2) ankyrin repeats. Whereas folding of the wild-type Notch ankyrin domain is slowed by substitutions in its central repeats, (1) folding of Nank1-5C1 and Nank1-5C2 is slowed by substitutions in the C-terminal repeats. Thus, the addition of C-terminal stabilizing repeats shifts the transition state ensemble toward the C-terminal repeats, rerouting the folding pathway of the ankyrin repeat domain. These findings indicate that, for the Notch ankyrin domain, folding pathways are selected based on local energetics.     

Thermodynamical properties of reaction intermediates during apoplastocyanin folding in time domain

Two intermediates observed for the folding process of apoplastocyanin (apoPC) were investigated by using a photoinduced triggering system combined with the transient grating and transient lens methods. The thermodynamic quantities, enthalpy, heat capacity, partial volume, and thermal expansion volume changes during the protein folding reaction were measured in time domain for the first time. An interesting observation is the positive enthalpy changes during the folding process. This positive enthalpy change must be compensated by positive entropy changes, which could be originated from the dehydration effect of hydrophobic residues and/or the translational entropy gain of bulk water molecules. Observed negative heat capacity change was explained by the dehydration effect of hydrophilic residues and/or motional confinement of amino acid side chains and water molecules in apoPC. The signs of the volume change and thermal expansion volume were different for two processes and these changes were interpreted in terms of the different relative contributions of the hydration and the dehydration of the hydrophilic residues. These results indicated two-step hydrophobic collapses in the early stage of the apoPC folding, but the nature of the dynamics was different.     

Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation

Ab initio folding with all-atom model remains to be a difficult task even for small proteins. In this report, we conducted an accumulated 24 mus simulations on the wild type and two mutants of albumin binding domain (ABD) using the AMBER FF03 all-atom force field and a generalized-Born solvation model. Folding events have been observed in multiple trajectories, and the best folded structures achieved root-mean-square deviation (RMSD) of 2.0 A. The folding of this three-helix bundle protein followed a diffusion-collision process, where substantial formation of the individual helices was critical and preceded the global packing. Owing to the difference in the intrinsic helicity, helix I formed faster than the other two helices. The order of the formation of helices II and III varied in different trajectories, indicating heterogeneity of the folding process. The slightly shifted boundaries of the helical segments had direct impact on the global packing, suggesting room for improvement on the simulation force field and solvation model.     

Understanding the folding rates and folding nuclei of globular proteins

The first part of this paper contains an overview of protein structures, their spontaneous formation ("folding"), and the thermodynamic and kinetic aspects of this phenomenon, as revealed by in vitro experiments. It is stressed that universal features of folding are observed near the point of thermodynamic equilibrium between the native and denatured states of the protein. Here the "two-state" ("denatured state" <--> "native state") transition proceeds without accumulation of metastable intermediates, but includes only the unstable "transition state". This state, which is the most unstable in the folding pathway, and its structured core (a "nucleus") are distinguished by their essential influence on the folding/unfolding kinetics. In the second part of the paper, a theory of protein folding rates and related phenomena is presented. First, it is shown that the protein size determines the range of a protein's folding rates in the vicinity of the point of thermodynamic equilibrium between the native and denatured states of the protein. Then, we present methods for calculating folding and unfolding rates of globular proteins from their sizes, stabilities and either 3D structures or amino acid sequences. Finally, we show that the same theory outlines the location of the protein folding nucleus (i.e., the structured part of the transition state) in reasonable agreement with experimental data.     

The ensemble folding dynamics of EF-hand domain in parvalbumin from a Monte Carlo simulation

The helix-loop-helix (i.e., EF-hand) is the most common motif in the superfamily of Ca\(^{2+}\)-binding proteins. Parvalbumins, as the classical EF-hand proteins, are associated with the muscle relaxation/contration, the calcium buffering etc. The previous researches focus more of interest on the ion coupled/decoupled mechanism using molecular dynamics (MD) computations. We developed the novel approach instead of MD, in which the Landau free energy was introduced to describe the protein in term of the skeletal C\(_\alpha \) chain. The unfolding and folding processes were simulated by the Glauber algorithm under the repeated heating and cooling cycles. The high-quality crystal structure (2PVB) was as the trigger of non-equilibrium dynamics simulation for parvalbumin-\(\beta \) (Parv). The evolution of three dimensional structure during the folding was displayed for the residues 8–64 fragment in Parv. The phenomenon of helix nucleation was observed, that was, the 3\(_{10}\) helix at residues 35–37 and the front of \(\alpha \)-helix at residues 40–50 were firstly formed in the folding process. We also found two potential misfoldings which were caused by the distortion of the local structures at residues 35–37, 45–50.     

Transform and relax sampling for highly anisotropic systems: application to protein domain motion and folding

Transform and relax sampling (TRS) is proposed as a conformational sampling method to enhance "soft" fluctuation in highly anisotropic systems using molecular dynamics simulation. This method consists of three stages; transform, relax, and sampling. In the transform stage, molecular dynamics simulation is performed with randomly assigned force bias to enhance the fluctuations along relatively soft collective movements, as expected from the linear response theory. After relaxing the heated system to equilibrium without force bias in the relax stage, Monte Carlo-type determination is made as to whether the generated state is accepted or not. The sampling stage is then conducted for conformational sampling by conventional molecular dynamics simulation. TRS is first applied for the idealized multidimensional double-well C(α) model to mimic protein open-close transition. Subsequently, it is applied to three different all-atom protein systems in an explicit solvent model; T4 lysozyme, glutamine binding protein, and a mini-protein chignolin. Investigation of structural variations in the hinge angle of T4 lysozyme in crystals is demonstrated by TRS. The liganded close structure of the glutamine binding protein is sampled starting from the unliganded open form. Chignolin is shown to fold into a native structure multiple times starting from highly extended structures within 100 ns. It is concluded that TRS sampled a reasonable conformational space within a relatively short simulation time in these cases. Possible future extensions of TRS are also discussed.     

Structural basis of cooperative ligand binding by the glycine riboswitch

The glycine riboswitch regulates gene expression through the cooperative recognition of its amino acid ligand by a tandem pair of aptamers. A 3.6 ? crystal structure of the tandem riboswitch from the glycine permease operon of Fusobacterium nucleatum reveals the glycine binding sites and an extensive network of interactions, largely mediated by asymmetric A-minor contacts, that serve to communicate ligand binding status between the aptamers. These interactions provide a structural basis for how the glycine riboswitch cooperatively regulates gene expression.     

Structural basis of thiamine pyrophosphate analogues binding to the eukaryotic riboswitch

The thiamine pyrophosphate (TPP)-sensing riboswitch is the only riboswitch found in eukaryotes. In plants, TPP regulates its own production by binding to the 3' untranslated region of the mRNA encoding ThiC, a critical enzyme in thiamine biosynthesis, which promotes the formation of an unstable splicing variant. In order to better understand the molecular basis of TPP-analogue binding to the eukaryotic TPP-responsive riboswitch, we have determined the crystal structures of the Arabidopsis thaliana TPP-riboswitch in complex with oxythiamine pyrophosphate (OTPP) and with the antimicrobial compound pyrithiamine pyrophosphate (PTPP). The OTPP-riboswitch complex reveals that the pyrimidine ring of OTPP is stabilized in its enol form in order to retain key interactions with guanosine 28 of the riboswitch previously observed in the TPP complex. The structure of PTPP in complex with the riboswitch shows that the base moiety of guanosine 60 undergoes a conformational change to cradle the pyridine ring of the PTPP. Structural information from these complexes has implications for the design of novel antimicrobials targeting TPP-sensing riboswitches.     

A simple aptamer molecular beacon assay for rapid detection of aflatoxin B1

A simple aptamer molecular beacon assay for rapid detection of aflatoxin B1 (AFB1) was achieved. AFB1-binding induced formation of a hairpin structure and closeness of fluorophore label and quencher probe, causing fluorescence decrease.     

Synthesis of a liposome incorporated 1-carboxyalkylxanthine-phospholipid conjugate and its recognition by an RNA aptamer

RNA or DNA aptamers have received much attention in recent literature as therapeutic agents and chromatographic matrices, however, their use in analytical methodologies is relatively unexplored. We describe here investigations aiming to combine this promising technology with versatile liposomes in a competitive assay format. Thus, a phospholipid derivative of an unsymmetrical 1,3-disubstituted xanthine (1-carboxyethyl-3-methylxanthine-DPPE) was prepared for incorporation into the lipid bilayers of dye-encapsulating liposomes. Its synthesis and characterization using GC-MS, ¹H NMR, and HPLC are described. Equilibrium filtration experiments using enzyme linked immunosorbent assays (ELISAs) were completed to assess the affinity for theophylline of an unmodified RNA aptamer and one that had been modified on the 3′ end with biotin. A dissociation constant (K_d) for theophylline with the unmodified RNA aptamer of 0.9 μM and biotinylated aptamer of 1.0 μM was determined which showed that this modification did not affect the aptamer's affinity using this technique. The observed K_d values correlated well to the previously reported value of 0.6 μM. Experiments were also carried out in a competitive manner with the prepared 1-carboxypropyl-3-methylxanthine intermediate, and the final 1-carboxypropyl-3-methylxanthine-DPPE conjugate once it had been incorporated into the bilayers of liposomes. The K_d value for 1-carboxypropyl-3-methylxanthine was approximately 2.7 μM. Finally, successful binding to theophylline-analog-tagged liposomes in a competitive assay format was shown versus liposomes prepared without the tag.