Interaction of Cyclic Cytosine-, Guanine-, Thymine-, Uracil- and Mixed Guanine-Cytosine Base Tetrads with K+, Na+ and Li+ Ions—A Density Functional Study

Abstract

We have carried out B3LYP hybrid density functional studies of complexes formed by cyclic cytosine-, guanine-, thymine-, uracil- and mixed guanine cytosine-tetrads with Li⁺, Na⁺ and K⁺ ions to determine their structures and interaction energies. The conformations studied have been restricted to a hydrogen bond pattern closely related to the tetrads observed in experimental nucleic acid structures. A comparison of the alkali metal ion/tetrad complexes with the tetrads without cations indicates that alkali metal ions modulate the tetrad structures significantly and that even the hydrogen bond pattern may change. Guanine-tetrad cation complexes show the strongest interaction energy compared to other tetrads that occur less frequently in experimental structures. The most stable G-tetrad/metal ion structure adopts a nearly planar geometry that is especially suitable for tetraplex formation, which requires approximately parallel tetrad planes. In the cytosine-tetrad there is a very large central cavity suitable for cation recognition, but the complexes adopt a non-planar structure unsuitable for stacking, except possibly for ions with very large radii. Uracil and thymine tetrads show a significant different characteristics which may contribute to the differences between DNA and RNA.     

Crystal structure of an RNA purine-rich tetraplex containing adenine tetrads: implications for specific binding in RNA tetraplexes

Purine-rich regions in DNA and RNA may contain both guanines and adenines, which have various biological functions. Here we report the crystal structure of an RNA purine-rich fragment containing both guanine and adenine at 1.4 A resolution. Adenines form an adenine tetrad in the N6-H em leader N7 conformation. Substitution of an adenine tetrad in the guanine tetraplex does not change the global conformation but introduces irregularity in both the hydrogen bonding interaction pattern in the groove and the metal ion binding pattern in the central cavity of the tetraplex. The irregularity in groove binding may be critical for specific binding in tetraplexes. The formation of G-U octads provides a mechanism for interaction in the groove. Ba(2+) ions prefer to bind guanine tetrads, and adenine tetrads can only be bound by Na(+) ions, illustrating the binding selectivity of metal ions for the tetraplex.     

A thymine tetrad in d(TGGGGT) quadruplexes stabilized with Tl+/Na+ ions

We report two new structures of the quadruplex d(TGGGGT)₄ obtained by single crystal X-ray diffraction. In one of them a thymine tetrad is found. Thus the yeast telomere sequences d(TG_1–3) might be able to form continuous quadruplex structures, involving both guanine and thymine tetrads. Our study also shows substantial differences in the arrangement of thymines when compared with previous studies. We find five different types of organization: (i) groove binding with hydrogen bonds to guanines from a neighbour quadruplex; (ii) partially ordered groove binding, without any hydrogen bond; (iii) stacked thymine triads, formed at the 3′ends of the quadruplexes; (iv) a thymine tetrad between two guanine tetrads. Thymines are stabilized in pairs by single hydrogen bonds. A central sodium ion interacts with two thymines and contributes to the tetrad structure. (v) Completely disordered thymines which do not show any clear location in the crystal. The tetrads are stabilized by either Na⁺ or Tl⁺ ions. We show that by using MAD methods, Tl⁺ can be unambiguously located and distinguished from Na⁺. We can thus determine the preference for either ion in each ionic site of the structure under the conditions used by us.     

The interaction of analogues of the antimicrobial lipopeptide, iturin A2, with alkali metal ions

Electrospray mass spectrometry was employed as a tool in this first study on the molecular interaction between the alkali metal ions and antifungal lipopeptide iturin A, and some analogues. Cationisation by sodium and signal intensity of lipopeptide species depended on sodium concentration, but was independent of sample solvent, carrier solvent polarity and sample pH between 4 and 11. 8-Beta, a linear analogue of iturin A2 (8-Beta; beta-aminotetradecanoyl-NYNQPNS), and its shorter linear lipopeptide analogues, associated either one or two alkali metal cations, while the N-->C cyclic peptides associated with only one cation. The chirality of the beta-NC14 residue had a limited influence on the cationisation. It was observed that 8-Beta contained at least four interaction sites for a cation of which two, the C-terminal carboxylate and the side-chain of tyrosine, can take part in ionic interaction with a cation. It is proposed that the remaining two interaction centres of alkali metal ions are within the two type II beta-turns found in conformation of natural iturin A. This was corroborated by the diminished capacity of the shorter peptides, in which one of the beta-turns was eliminated to bind a second larger cation. All the lipopeptides showed the same order of alkali metal ion selectivity: Na+ > K+ > Rb+. These results indicated a size limitation in the interaction cavity or cavities. The absence of, or observation of only low abundance, di-cationised complexes of cyclic peptides the indicated association of the cation in the interior of the peptide ring. It is thus hypothesised that alkali metal ions can bind in one of the two beta-turns in the natural iturin A molecule.     

Crystal structure of an RNA quadruplex containing inosine tetrad: implications for the roles of NH2 group in purine tetrads

Polyinosinic acid has been known to adopt the four-stranded helical structure but its basic unit, inosine tetrad (I tetrad), has not been determined at the atomic level. Here we report the crystal structure of an RNA quadruplex containing an I tetrad at 1.4 A resolution. The I tetrad has one cyclic hydrogen bond N1...O6 with the bond length of 2.7 A. A water bridge is observed in the minor groove side of the base tetrad. Even though it is sandwiched by guanine tetrads (G tetrads), the I tetrad is buckled towards the 3' side of the tetrad plane, which results from the different interaction strength with K ions on two sides of the tetrad plane. Comparison with both G tetrad and adenine tetrad indicates that lack of NH2 in the C2 position makes the I tetrad prone to buckle for interactions with ligands. Two U*(G-G-G-G) base pentads are observed at the junction of the 5' termini of two quadruplexes. The uridine residue in the base pentad is engaged in two hydrogen bonding interactions (N2(G)-H...O2(U) and O2'(G)-H...O4(U)) and a water-mediated interaction (N3(G) and N3(U)) with the G tetrad. We also discuss the roles of amino group in purine tetrads and the inter-quadruplex interactions in RNA molecules. These quadruplexes may interact with each other by stacking, groove binding and intercalation.     

Interaction of adenosine 5'-triphosphate with metal ions X-ray structure of ternary complexes containing Mg(II), Ca(II), Mn(II), Co(II), ATP and 2,2'-dipyridylamine

The X-ray structures of the isomorphous Mg2+, Ca2+, Mn2+ and Co2+ complexes of ATP have been determined. The metal ions are wrapped in hexa-coordination by the alpha, beta and gamma phosphate groups of two ATP molecules thus blocking the interaction of the metal ions with the adenine base. A second metal ion which is fully hydrated, M(H2O)2+(6), is engaged in a strong hydrogen bond with the gamma phosphate group of ATP and suggests a possible step in facilitating the cleavage between the beta and gamma phosphates in phosphoryl transfer reactions.     

Is Asp‐His‐Ser/Thr‐Trp tetrad hydrogen‐bond network important to WD40‐repeat proteins: A statistical and theoretical study

WD40‐repeat proteins are abundant and play important roles in forming protein complexes. The domain usually has seven WD40 repeats, which folds into a seven β‐sheet propeller with each β‐sheet in a four‐strand structure. An analysis of 20 available WD40‐repeat proteins in Protein Data Bank reveals that each protein has at least one Asp‐His‐Ser/Thr‐Trp (D‐H‐S/T‐W) hydrogen‐bonded tetrad, and some proteins have up to six or seven such tetrads. The relative positions of the four residues in the tetrads are also found to be conserved. A sequence alignment analysis of 560 WD40‐repeat protein sequences in human reveals very similar features, indicating that such tetrad may be a general feature of WD40‐repeat proteins. We carried out density functional theory and found that these tetrads can lead to significant stabilization including hydrogen‐bonding cooperativity. The hydrogen bond involving Trp is significant. These results lead us to propose that the tetrads may be critical to the stability and the mechanism of folding of these proteins. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

DFT modeling on the suitable crown ether architecture for complexation with Cs<Superscript>+</Superscript> and Sr<Superscript>2+</Superscript> metal ions

Crown ether architectures were explored for the inclusion of Cs⁺ and Sr²⁺ ions within nano-cavity of macrocyclic crown ethers using density functional theory (DFT) modeling. The modeling was undertaken to gain insight into the mechanism of the complexation of Cs⁺ and Sr²⁺ ion with this ligand experimentally. The selectivity of Cs⁺ and Sr²⁺ ions for a particular size of crown ether has been explained based on the fitting and binding interaction of the guest ions in the narrow cavity of crown ethers. Although, Di-Benzo-18-Crown-6 (DB18C6) and Di-Benzo-21-Crown-7 (DB21C7) provide suitable host architecture for Sr²⁺ and Cs⁺ ions respectively as the ion size match with the cavity of the host, but consideration of binding interaction along with the cavity matching both DB18C6 and DB21C7 prefers Sr²⁺ ion. The calculated values of binding enthalpy of Cs metal ion with the crown ethers were found to be in good agreement with the experimental results. The gas phase binding enthalpy for Sr²⁺ ion with crown ether was higher than Cs metal ion. The ion exchange reaction between Sr and Cs always favors the selection of Sr metal ion both in the gas and in micro-solvated systems. The gas phase selectivity remains unchanged in micro-solvated phase. We have demonstrated the effect of micro-solvation on the binding interaction between the metal ions (Cs⁺ and Sr²⁺) and the macrocyclic crown ethers by considering micro-solvated metal ions up to eight water molecules directly attached to the metal ion and also by considering two water molecules attached to metal-ion-crown ether complexes. A metal ion exchange reaction involving the replacement of strontium ion in metal ion-crown ether complexes with cesium ion contained within a metal ion-water cluster serves as the basis for modeling binding preferences in solution. The calculated O-H stretching frequency of H₂O molecule in micro-solvated metal ion-crown complexes is more red-shifted in comparison to hydrated metal ions. The calculated IR spectra can be compared with an experimental spectrum to determine the presence of micro-solvated metal ion–crown ether complexes in extractant phase.     

The influence of Li+, Na+, Mg2+, Ca2+, and Zn2+ ions on the hydrogen bonds of the Watson-Crick base pairs

The interaction of mono- and divalent metal ions with the nucleic acid base pairs A:T and G:C has been studied using ab initio self-consistent field Hartree-Fock computations with minimal basis sets. Energy-optimized structures of the two base pairs with a final base-base distance of L = 10.35 A have been determined and were further used in calculations on ternary complexes Mn+ - A:B together with previously computed coordination geometries of the cations at adenine (Ade), thymine (Thy), and guanine (Gua). Besides the binding energy of the various metal ions to the base pairs, changes in the stability of the H bonds between Ade and Thy or Gua and Cyt have been determined. Polarization effects of the metal ion on the ligand turned out to increase the binding between complementary bases. Regardless of the metal species, cation binding to Gua N(3) and Thy O(2) leads to a special increase in H-bond stability, whereas binding to Ade N(3) changes the H-bond stability least. Situated in between are the stabilizing effects caused by Gua and Ade N(7) coordination. A remarkable relation between the stability of the H bond and the distance from metal binding site to H bonds was found. This relationship has been rationalized in terms of partial charges of the atoms participating in H bonding, which can reveal the trend in the electrostatic part of total H bond energy. It can be shown that a short distance between coordination site and acceptor hydrogen increases the H-bond strength substantially, while a long distance shows minor effects as supposed. On the other hand, the opposite effect is observed for the influence of the distance between binding site and donor atom. A comparison of our findings with a new model of transition metal ion facilitated rewinding of denatured DNA proposed by S. Miller, D. VanDerveer, and L. Marzilli is given [(1985) J. Am. Chem. Soc. 107, 1048-1055].     

Effect of coordinated ions on structure and flexiblity of parallel G-quandruplexes: a molecular dynamics study

Single tract guanine residues can associate to form stable parallel quadruplex structures in the presence of certain cations. Nanosecond scale molecular dynamics simulations have been performed on fully solvated fibre model of parallel d(G7) quadruplex structures with Na+ or K+ ions coordinated in the cavity formed by the 06 atoms of the guanine bases. The AMBER 4.1 force field and Particle Mesh Ewald technique for electrostatic interactions have been used in all simulations. These quadruplex structures are stable during the simulation, with the middle four base tetrads showing root mean square deviation values between 0.5 to 0.8 A from the initial structure as well the high resolution crystal structure. Even in the absence of any coordinated ion in the initial structure, the G-quadruplex structure remains intact throughout the simulation. During the 1.1 ns MD simulation, one Na+ counter ion from the solvent as well as several water molecules enter the central cavity to occupy the empty coordination sites within the parallel quadruplex and help stabilize the structure. Hydrogen bonding pattern depends on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate cations of different sizes. In the absence of any coordinated ion, due to strong mutual repulsion, 06 atoms within G-tetrad are forced farther apart from each other, which leads to a considerably different hydrogen bonding scheme within the G-tetrads and very favourable interaction energy between the guanine bases constituting a G-tetrad. However, a coordinated ion between G-tetrads provides extra stacking energy for the G-tetrads and makes the quadruplex structure more rigid. Na+ ions, within the quadruplex cavity, are more mobile than coordinated K+ ions. A number of hydrogen bonded water molecules are observed within the grooves of all quadruplex structures.     

海南热带雨林土壤中胡敏酸对Pb2+、Cu2+的吸附解吸特性研究

重金属元素在土壤-溶液界面的吸附反应深刻地影响重金属行为及其生态风险。以热带次生雨林土壤中提取的胡敏酸为材料, 采用傅立叶红外光谱、扫描电镜等技术对胡敏酸进行了表征, 通过批量吸附实验研究了胡敏酸对铅、铜的吸附特性, 通过连续解吸方法研究了在不同浓度下饱和吸附的胡敏酸对重金属吸附的形成过程。结果表明, 胡敏酸的腐殖化系数较高, 阳离子交换量为52.84 mmol·g-1, 表面含有羧基和酚羟基官能团。胡敏酸对铜的吸附符合准二级动力学模型, 对铅的吸附符合准一级动力学方程; Langmuir 模型能够更好地描述单一和复合污染条件下胡敏酸对Pb2+的等温吸附行为, Freundlich 模型能够更好的描述单一和复合污染条件下胡敏酸对Cu2+的等温吸附行为。通过连续解吸实验发现, 胡敏酸对铅的吸附过程中4种结合方式的先后饱和顺序为: 物理吸附、络合、离子交换和氢键结合。胡敏酸对铜的吸附过程中4种结合方式的先后饱和顺序为: 络合、氢键结合、离子交换和物理吸附。     

Interaction of Adenosine 5′-Triphosphate with Metal Ions X-ray Structure of Ternary Complexes Containing Mg(II), Ca(II), Mn(II), Co(II), ATP and 2,2′ -Dipyridylamine

Abstract

The X-ray structures of the isomorphous Mg²⁺, Ca²⁺, Mn²⁺ and Co²⁺ complexes of ATP have been determined. The metal ions are wrapped in hexa-coordination by the α, β and γ phosphate groups of two ATP molecules thus blocking the interaction of the metal ions with the adenine base. A second metal ion which is fully hydrated, M(H₂O)²⁺ ₆, is engaged in a strong hydrogen bond with the γ phosphate group of ATP and suggests a possible step in facilitating the cleavage between the β and γ phosphates in phosphoryl transfer reactions.     

Density functional study of isoguanine tetrad and pentad sandwich complexes with alkali metal ions

Isoguanine tetraplexes and pentaplexes contain two or more stacked polyads with intercalating metal ions. We report here the results of a density functional study of sandwiched isoguanine tetrad and pentad complexes consisting of two polyads with Na⁺, K⁺ and Rb⁺ ions at the B3LYP level. In comparison to single polyad metal ion complexes, there is a trend towards increased non-planarity of the polyads in the sandwich complexes. In general, the pentad sandwiches have relatively planar polyad structures, whereas the tetrad complexes contain highly non-planar polyad building blocks. As in other sandwich complexes and in metal ion complexes with single polyads, the metal ion-base interaction energy plays an essential role. In iG sandwich structures, this interaction energy is slightly larger than in the corresponding guanine sandwich complexes. Because the base–base interaction energy is even more increased in passing from guanine to isoguanine, the isoguanine sandwiches are thus far the only examples where the base–base interaction energy is larger than the base–metal ion interaction energy. Stacking interactions have been studied in smaller models consisting of two bases, retaining the geometry from the complete complex structures. From the data obtained at the B3LYP and BH&;H levels and with Møller-Plesset perturbation theory, one can conclude that the B3LYP method overestimates the repulsion in stacked base dimers. For the complexes studied in this work, this is only of minor importance because the direct inter-tetrad or inter-pentad interaction is supplemented by a strong metal ion-base interaction. Using a microsolvation model, the metal ion preference K⁺≈Rb⁺?>?Na⁺ is found for tetrad complexes. On the other hand, for pentads the ordering is Rb⁺?>?K⁺?>?Na⁺. In the latter case experimental data are available that agree with this prediction.

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Figure Structures of isoguanine pentad complexes with Rb⁺ at different symmetries.

     

Interactions between metal ions and carbohydrates. The coordination behavior of neutral erythritol to lanthanum and erbium ions

Lanthanide ions and erythritol form metal–alditol complexes with various structures. Lanthanum nitrate and erbium chloride coordinate to erythritol to give new coordination structures. The lanthanum nitrate–erythritol complex (LaEN), 2La(NO₃)₃·C₄H₁₀O₄·8H₂O, La³⁺ exhibits the coordination number of 11 (namely 11 polar atoms bound to one lanthanum) and is 11-coordinated to two hydroxyl groups from one erythritol molecule, six oxygen atoms from three nitrate ions and three water molecules. One erythritol molecule is coordinated to two La³⁺ ions and links the two metal ions together. The ratio of M:L is 2:1. The erbium chloride–erythritol complex (ErE), ErCl₂·C₄H₉O₄·2C₂H₅OH was obtained from ErCl₃ and erythritol in aqueous ethanol solution and the structure shows that deprotonation reaction occurs in the reaction process. The Er³⁺ cation is 8-coordinated with three hydroxyl groups of one erythritol molecule, two hydroxyl groups from another erythritol molecule, two ethanol molecules, and one chloride ion. Erythritol provides its three hydroxyl groups to one erbium cation and two hydroxyl groups to another erbium cation, that is, one hydroxyl group is coordinated to two metal ions and therefore loses its hydrogen atom and becomes a oxygen bridge. Another chloride ion is hydrogen bonded in the structure. The results indicate the complexity of metal–sugar coordination.     

Binding of sulfonamide and acetamide to the active-site Zn2+ in carbonic anhydrase: a theoretical study

Self-consistent field molecular orbital (SCF MO) calculations at both 4-31G and STO-3G levels have been used to examine the binding conformations of sulfonamide and acetamide compounds to the active site of carbonic anhydrase. The results are as follows: (1) sulfonamide binds to the Zn2+ ion in its deprotonated form through the sulfonamide nitrogen to the fourth coordination site of the metal ion; (2) acetamide as neutral species binds to the basic form of the enzyme through the carbonyl oxygen to the fifth coordination site of the metal ion; and (3) the acetamidate ion binds to the acid form of the enzyme through the amide nitrogen to form a tetracoordinated metal complex with three histidine ligands. Analysis of the effects of individual active-site residues on the binding conformations of these inhibitors suggests that metal alone favors bidentate coordination of sulfonamidate and acetamidate complexes and that electron donation from three histidine ligands to the metal ion determines the formation of a tetracoordinated metal complex, which is further stabilized by the presence of Thr 199, as it receives one hydrogen bond from the sulfonamide NH- or from the acetamide NH- and donates a backbone NH hydrogen bond to a sulfonamide oxygen. The calculated binding conformation of sulfonamide and the hydrogen-bonding interactions between sulfonamide and the enzyme are consistent with the X-ray diffraction study of the AMSulf-HCA II complex. However, no X-ray structures are available for amide-HCA II complexes.(ABSTRACT TRUNCATED AT 250 WORDS)     

Structural exploration of viral matrix protein 40 interaction with the transition metal ions (Ag+ and Cu2+)

Here, a theoretical and comprehensive study of the structural features and interaction properties of viral protein 40 is being briefed out to understand the mechanism of Ebola virus (EV) with structural and orbital analysis. In general, viral protein 40 is the key protein for the oligomerization, the N-terminal loop region in the viral protein 40 and it is essential for the viral replication in Ebola. The electronic structures of native N-terminal loop (His124-Asn134) and metalized (Mⁿ⁺=Ag⁺ and Cu²⁺) complexes are optimized at the M06-2X/LANL2DZ level of theory. Among Mⁿ⁺-interacted N-loop complexes, Cu²⁺-interacted N-terminal loop complex has the highest interaction energy of –973.519?kcal/mol and also it has the stabilization energy in the range of 9.92?kcal/mol. The cation-π interactions between His124, Pro131 and Arg134 residues are the important factor, which enhances the interaction energy of viral protein 40. Due to the chelation behavior of metal ions, the backbone and the side chains of N-terminal loop regions are deviated from the planarity that results in the formation of classical hydrogen bonds between N-terminal loop regions. Molecular dynamics simulation studies also revealed that the structural transformations of Nloop into a stable α-helix and β-sheet folded conformations due to the interaction of Ag⁺ and Cu²⁺ ions in the N-terminal loop region. The hydrogen bond formation and hydrophobic interactions are responsible for the stability and structural changes in N-terminal loop region. Therefore, it is clear that interaction of metal ion with viral protein-40 reduces the replication of the disease by inducing the secondary structural changes.

Communicated by Ramaswamy H. Sarma     

Characterization of ionomycin as a calcium ionophore.

The ionophorous properties of a new antibiotic, ionomycin, have been studied. It was found that the antibiotic is capable of extracting calcium ion from the bulk of an aqueous phase into an organic phase. The antibiotic also acts as a mobile ion carrier to transport the cation across a solvent barrier. The divalent cation selectivity order for ionomycin as determined by ion competition experiments was found to be: Ca greater than Mg greater than Sr = Ba, where the binding of strontium and barium by the antibiotic is insignificant. The antibiotic also binds La3+ to some extent, but its complexation with monovalent alkali metal ions is negligible. Measurement of the binding of ionomycin with Ca2+ indicates that ionomycin complexes and transports calcium ion in a one to one stoichiometry.     

Ionic selectivity in L-type calcium channels by electrostatics and hard-core repulsion

A physical model of selective “ion binding” in the L-type calcium channel is constructed, and consequences of the model are compared with experimental data. This reduced model treats only ions and the carboxylate oxygens of the EEEE locus explicitly and restricts interactions to hard-core repulsion and ion–ion and ion–dielectric electrostatic forces. The structural atoms provide a flexible environment for passing cations, thus resulting in a self-organized induced-fit model of the selectivity filter. Experimental conditions involving binary mixtures of alkali and/or alkaline earth metal ions are computed using equilibrium Monte Carlo simulations in the grand canonical ensemble. The model pore rejects alkali metal ions in the presence of biological concentrations of Ca²⁺ and predicts the blockade of alkali metal ion currents by micromolar Ca²⁺. Conductance patterns observed in varied mixtures containing Na⁺ and Li⁺, or Ba²⁺ and Ca²⁺, are predicted. Ca²⁺ is substantially more potent in blocking Na⁺ current than Ba²⁺. In apparent contrast to experiments using buffered Ca²⁺ solutions, the predicted potency of Ca²⁺ in blocking alkali metal ion currents depends on the species and concentration of the alkali metal ion, as is expected if these ions compete with Ca²⁺ for the pore. These experiments depend on the problematic estimation of Ca²⁺ activity in solutions buffered for Ca²⁺ and pH in a varying background of bulk salt. Simulations of Ca²⁺ distribution with the model pore bathed in solutions containing a varied amount of Li⁺ reveal a “barrier and well” pattern. The entry/exit barrier for Ca²⁺ is strongly modulated by the Li⁺ concentration of the bath, suggesting a physical explanation for observed kinetic phenomena. Our simulations show that the selectivity of L-type calcium channels can arise from an interplay of electrostatic and hard-core repulsion forces among ions and a few crucial channel atoms. The reduced system selects for the cation that delivers the largest charge in the smallest ion volume.     

The effect of Asp-His-Ser/Thr-Trp tetrad on the thermostability of WD40-repeat proteins

We recently found that Asp-His-Ser/Thr-Trp hydrogen-bonded tetrads are widely and uniquely present in the WD40-repeat proteins. WDR5 protein is a seven WD40-repeat propeller with five such tetrads. To explore the effect of the tetrad on the structure and stability of WD40-repeat proteins, the wild-type WDR5 and its seven mutants involving the substitutions of tetrad residues have been isolated. The crystal structures of the wild-type WDR5 and its three WDR5 mutants have been determined by X-ray diffraction method. The mutations of the tetrad residues are found not to change the basic structural features. The denaturing profiles of the wild type and the seven mutants with the use of denaturant guanidine hydrochloride have been studied by circular dichroism spectroscopy to determine the folding free energies of these proteins. The folding free energies of the wild type and the S62A, S146A, S188A, D192E, W330F, W330Y, and D324E mutants are measured to be about -11.6, -2.7, -3.1, -2.9, -3.6, -7.1, -7.0, and -7.5 kcal/mol, respectively. These suggest that (1) the hydrogen bonds in these hydrogen bond networks are unusually strong; (2) each hydrogen-bonded tetrad provides over 12 kcal/mol stability to the protein; thus, the removal of any single tetrad would cause unfolding of the protein; (3) since there are five tetrads, the protein must be in a highly unstable state without the tetrads, which might be related to its biological functions.     

Differential stabilization of adenine quartets by anions and cations

We have investigated the structures and stabilities of four different adenine quartets with alkali and halide ions in the gas phase and in water, using dispersion-corrected density functional theory at the BLYP-D/TZ2P level. First, we examine the empty quartets and how they interact with alkali cations and halide anions with formation of adenine quartet–ion complexes. Second, we examine the interaction in a stack, in which a planar adenine quartet interacts with a cation or anion in the periphery as well as in the center of the quartet. Interestingly, for the latter situation, we find that both cations and anions can stabilize a planar adenine quartet in a stack.