Unique Water Molecule Research Articles

Long-range charge transfer mechanism of the III2IV2 mycobacterial supercomplex

Aerobic life is powered by membrane-bound redox enzymes that shuttle electrons to oxygen and transfer protons across a biological membrane. Structural studies suggest that these energy-transducing enzymes operate as higher-order supercomplexes, but their functional role remains poorly understood and highly debated. Here we resolve the functional dynamics of the 0.7 MDa III2IV2 obligate supercomplex from Mycobacterium smegmatis, a close relative of M. tuberculosis, the causative agent of tuberculosis. By combining computational, biochemical, and high-resolution (2.3 Å) cryo-electron microscopy experiments, we show how the mycobacterial supercomplex catalyses long-range charge transport from its menaquinol oxidation site to the binuclear active site for oxygen reduction. Our data reveal proton and electron pathways responsible for the charge transfer reactions, mechanistic principles of the quinone catalysis, and how unique molecular adaptations, water molecules, and lipid interactions enable the proton-coupled electron transfer (PCET) reactions. Our combined findings provide a mechanistic blueprint of mycobacterial supercomplexes and a basis for developing drugs against pathogenic bacteria.

Identification of Unique Water Molecules in Human GRK2 Protein with Bound and Unbound GβGγ Subunit: A Study by Structural Bioinformatics Method

The human G-protein coupled receptor kinase 2 (hGRK2) regulates the desensitization of beta-adrenergic receptors (β-AR), and its overexpression has been implicated in heart failure. The hGRK2 is a serine/ threonine kinase and is one of the members of the AGC family, and it contains the four domains (i) RGS or RH domain (regulator of G-protein signaling res. id. 54-175), (ii) protein kinase or CAT domain (res. id. 191-453), (iii) AGC Kinase domain (res. Id 454-521), and (iv) PH domain (Pleckstrin homology, res. Id. 558-652). Present computational investigations on multiple analyses of X-ray structures (bound and unbound conformation of GβGγ) highlight the presence of seventeen unique water molecules (W1 to W17) that are only available either in hGRK2 with GβGγ or without GβGγ. These water molecules are subdivided into category-I (W1 to W8), which is observed with unbound GβGγ conformation, and category-II (W9 to W17) in hGRK2 with bound GβGγ conformation. The MD simulation results suggest the non-crystal and crystal water molecules are inaccessible to reaching W3, W10, and W12 water sites because they are deeply buried and shielded by neighboring residues, whereas W9, W11, and W13 are accessible by crystal water in MD simulation but not allow entering non-crystal or MD water molecules. During the structural transition of hGRK2 from unbound to bound hGβGγ state, water molecules of category-I (W1 to W8) departed from their respective domains, and water molecules of Category-II (W9 to W17) were reached simultaneously during unbound to bound GβGγ conformation. In this context, the present work identifies new biochemical insights to highlight some rationale clues for heart disease.

Quantum chemical modeling of the thermodynamics of the formation of Au(III), Pd(II), and Pt(II) chloride complexes.

Quantitative prediction of physical properties of liquids and equilibrium constants is important for many applications. Computational methods based on either explicit or implicit solvent models can be used to approximate thermodynamics of complexation. A practical method for calculating the stability constant of d8 chlorocomplexes (PdCl42-, PtCl42-, AuCl4-) in aqueous solution has been developed by using DFT and DLPNO-CCSD with the SMD solvation model and 100 unique explicit water molecules. Stability constants have been calculated by using methods, such as DFT/PBE0-D3, DLPNO-CCSD, DLPNO-CCSD-DK, and DLPNO-CCSD(T), and basis sets, such as def2-TZVPD, def2-TZVPP, ma-def2-TZVP, ma-DKH-def2-TZVP, SARC-TZVP, and SARC-TZVPP. Calculations using DFT/PBE0-D3/def2-TZVPD and DLPNO-CCSD-DK/ma-DKH-Def2-TZVP/SARC-DKH-TZVP with SMD solvation with explicit waters are found to have errors of 2-3 logunits relative to experimental data. The best results are obtained by using 8 explicit waters for d8 aqua complexes, 14 explicit waters for d8 chlorocomplexes, and 4 explicit waters for chloride ion.

Synthesis and crystal structure of bis-[trans-di-aqua-(1,4,8,11-tetra-aza-cyclo-tetra-decane-κ4 N 1,N 4,N 8,N 11)nickel(II)] trans-(1,4,8,11-tetra-aza-cyclo-tetra-decane-κ4 N 1,N 4,N 8,N 11)bis-[4,4',4''-(1,3,5-tri-methyl-benzene-2,4,6-tri-yl)tris-(hydrogen phenyl-phospho-nato-κO)]nickel(II) deca-hydrate.

The components of the title compound, [Ni(C10H24N4)(H2O)2]2[Ni(C10H24N4)(C27H24O9P3)2]·10H2O are two centrosymmetric [Ni(C10H24N4)(H2O)2]2+ dications, a centrosymmetric [Ni(C10H24N4)(C27H24O9P3)2]4- tetra-anion and five crystallographically unique water mol-ecules of crystallization. All of the nickel ions are coordinated by the four secondary N atoms of the macrocyclic cyclam ligands, which adopt the most energetically stable trans-III conformation, and the mutually trans O atoms of either water mol-ecules in the cations or the phospho-nate groups in the anion in a tetra-gonally distorted NiN4O2 octa-hedral coordination geometry. Strong O-H⋯O hydrogen bonds between the protonated and the non-protonated phospho-nate O atoms of neighboring anions result in the formation of layers oriented parallel to the bc plane, which are linked into a three-dimensional network by virtue of numerous N-H⋯O and O-H⋯O hydrogen bonds arising from the sec-NH groups of the macrocycles, phospho-nate O atoms and coordinated and non-coordinated water mol-ecules.

Synthesis, crystal structure and properties of hepta(ammonium) penta(1H-imidazol-3-ium) paratungstate B tetrahydrate

An attempted isolation of the elusive diammonium tetraoxidotungstate (NH4)2[WO4] as its imidazole (Im) adduct resulted in the serendipitous formation of hepta(ammonium) penta(1H-imidazol-3-ium) paratungstate B tetrahydrate having formula [NH4]7[ImH]5[W12O42]·4H2O (1). The synthesis, vibrational spectra, crystal structure and thermal study of the mixed cationic paratungstate tetrahydrate 1 are reported. The structure of 1 consists of a centrosymmetric paratungstate [W12O42]12– anion devoid of internal hydrogen atoms, which is charge balanced by ammonium and 1H-imidazol-3-ium cations. One of the four unique NH4 + cations and one of the three crystallographically independent 1H-imidazol-3-ium cations are disordered around a center of inversion. The cations, [W12O42]12– anion and the unique lattice water molecules are joined with the aid of five varieties of hydrogen bonding interactions. A comparative study of twenty-three partaungstates is described. Thermal decomposition of 1 results in the formation of monoclinic tungsten trioxide WO3.

Diffusion Monte Carlo Studies on the Detection of Structural Changes in the Water Hexamer upon Isotopic Substitution.

The ground-state structures of water hexamer and several deuterated variants are studied by using the diffusion Monte Carlo (DMC) method. We demonstrate that a recently developed guided DMC approach allows us to study these systems using substantially smaller ensembles than are required for standard DMC approaches. DMC calculations of the ground states of (H2O)6 and (D2O)6 using the MB-pol potential with 50 000 walkers and a 1 au time step show that for (H2O)6 the cage structure is 51 ± 7 cm-1 lower in energy than the prism structure. In the case of (D2O)6, the two structures have nearly equal energies (ΔE = 9 ± 11 cm-1). The structures of the singly substituted, (H2O)(D2O)5 and (H2O)5(D2O), variants of water hexamer are also explored to identify the impact of the location of the unique water molecule on the relative stability of the possible structure. The effect on the stability of the hydrogen bond on whether a hydrogen bond has an OD or OH bond as the donor is also explored.

A variable temperature infrared spectroscopy study of NaY zeolite dehydration.

Variable temperature diffuse reflection infrared spectroscopy is used to monitor molecular vibration changes associated with water molecules and zeolite framework during thermal dehydration of NaY zeolite. Absorbance bands are assigned to three unique water molecule environments. These three water types exhibit different temperature-dependent band intensity profiles. A band at 3700 cm-1 is assigned to framework acid sites. The intensity of this band was found to vary with temperature in a manner consistent with the occupancy of sodium cations in II' unit cell locations. Specific framework vibrations exhibit temperature-dependent intensity change profiles. Band intensities at 1190, 1060, and 960 cm-1, associated with Si-O-Si and Si-O-Al asymmetric stretching vibrations, are sensitive to water content. Band intensity at 800 cm-1, assigned to Si-O-Si symmetric stretching, is inversely correlated with temperature-dependent unit cell volume changes. All framework band intensity changes detected during heating are reversible after re-hydration during sample cooling.

Structure-based reconstruction of a Mycobacterium hypothetical protein into an active Δ5–3-ketosteroid isomerase

Protein engineering based on structure homology holds the potential to engineer steroid-transforming enzymes on demand. Based on the genome sequencing analysis of industrial Mycobacterium strain HGMS2 to produce 4-androstene-3,17-dione (4-AD), three hypothetical proteins were predicted as putative Δ5–3-ketosteroid isomerases (KSIs) to catalyze an intramolecular proton transfer involving the transformation of 5-androstene-3,17-dione (5-AD) into 4-AD, which were defined as mKSI228, mKSI291 and mKSI753. Activity assays indicated that mKSI228 and mKSI291 exhibited weak activity, as low as 0.7% and 1.5%, respectively, of a well-studied and highly active KSI from Pseudomonas putida KSI (pKSI), while mKSI753 had no activity similar to Mycobacterium tuberculosis KSI (mtKSI). Although the 3D structures of the putative mKSIs were homologous to pKSI, their amino acid sequences were significantly different from those of pKSI and tKSI. Thus, by use of these two KSIs as homology models, we were able to convert the low-active mKSI291 into a high-active active KSI by site-directed mutagenesis. On the other hand, an X-ray crystallographic structure of mKSI291 identified a water molecule in its active site. This unique water molecule might function as a bridge to connect Ser-OH, Tyr57-OH and C3O of the intermediate form a hydrogen-bonding network that was responsible for its weak activity, compared with that of mtKSI. Our results not only demonstrated the use of a protein engineering approach to understanding KSI catalytic mechanism, but also provided an example for engineering the catalytic active sites and gaining a functional enzyme based on homologous structures.

Mechanism of MgAl-LDH-induced enhancement in the plasmonic photocatalytic performance over bismuth nanospheres

The rapid development of industry, automobiles and manufacturing has emitted an ever-growth amount of the atmospheric gas pollutants to the atmosphere, such as nitric oxide (NO x ), sulfur oxide (SO x ), volatile organic compounds (VOC) and particle matters (PM). NO is deemed as one critical air pollutant as it is the leading origins of several environmental issues, such as the acidic rain, haze, and photochemical smog. To eliminate its environmental risk, it is highly desired to develop one effective, cost-effective and environmental-friendly technology to detect, regulate and remove them. Till now, various technologies have been developed, including the selective physical/chemical adsorption, heterogeneous catalytic reduction/oxidation and photocatalysis, to show high efficiency in separation, conversion and detoxification of NO. Among them, photocatalysis is receiving an ever-increased attention by its high efficiency, low cost and green feature (this technology enables the direct utilization of solar light to trigger the generation of highly active oxidative free radicals for pollutant degradation and mineralization). In the development of photocatalytic technology, the core part is the design and synthesis of highly effective and durable photocatalyst. Plasmonic metal with a unique localized surface plasmon resonance (LSPR) feature have now emerged as one appealing class of photocatalysts with wide applications in environmental remediation and energy conversion. In the plasmonic metal-directed photocatalysis, the surface electrons of plasmonic metal oscillate resonated with the incident photon, giving rise to the generation of hot carriers for catalytic redox reactions. However, most of the current LSPR-directed photocatalysis is limited to the noble metal (Au and Ag). Very recently, the earth-abundant bismuth metal (Bi) was confirmed to show a unique LSPR feature in visible light region, and more importantly, can serve as a direct plasmonic photocatalyst in ppb-level NO removal from a gas flow under UV illumination. However, bare Bi particles do not show enough redox capability as the hot carriers produced via LSPR in Bi metal cannot travel over distances longer than tens of nanometers. In this study, we attempt to introduce the MgAl-layered double hydroxide (MgAl-LDH) to intensify photocatalytic efficiency of the Bi metal. A facile liquid-phase ultrasound-assisted assembly approach was firstly used to synthesize the Bi@MgAl-LDH nanocomposite, in which Bi-NPs are uniformly supported on MgAl-LDH nanosheets. This composite can efficiently and steadily photocatalyze the removal of ppb-level NO from a continuous air flow under ultraviolet light irradiation via the plasmonic effect Bi metal. The removal efficiency reaches 43% for Bi@MgAl-LDH, much higher than the bare Bi-NPs (43%). The combined study of the composite phase/morphology/structure, its optical property, band structure and ESR oxidation radical capture experiments reveal that MgAl-LDH cannot form a heterojunction with Bi-NPs, and the enhanced photocatalysis on Bi@MgAl-LDH originates from the abundant hydroxide ions (OH−) on the surface of MgAl-LDH. These OH− can quickly capture the photoexcited holes to generate ·OH radicals, and simultaneously promote the electron-hole separation by consuming the holes, both of which can raise the utilization efficiency of the photoexcited hot carriers and provide sufficient oxidative radicals for NO oxidation. Additionally, MgAl-LDH has a unique water molecule memory effect, and the OH− that is consumed in photocatalysis can be replenished by adsorbing water from the air, leading to a stable photocatalytic performance. The reaction pathway study of the photocatalytic NO oxidation over Bi@MgAl-LDH by in-situ DRIFTS reveals that NO is completely mineralized into nitrate. The present work should contribute to a deeper understanding of the photocatalytic mechanism and then the design of robust catalysts for air purification.

Syntheses, structure and properties of Alkaline-earth metal salts of 4-Nitrophenylacetic acid

The synthesis, crystal structure, spectral characteristics and thermal properties of alkaline-earth metal salts of 4-nitrophenylacetic acid (4-npaH) namely, [Mg(H2O)6](4-npa)2⋅4H 2O (4-npa = 4-nitrophenyl-acetate) (1), [Ca(H 2O) 2(4-npa) 2] (2) and [Sr(H 2O) 3(4-npa) 2] ⋅4.5H 2O(3) are reported. In 1, the 4-npa ion functions as a charge balancing counter anion for the octahedral [Mg(H 2O) 6] 2+ unit with the Mg(II) ion situated on a centre of inversion. The two unique lattice water molecules link the [Mg(H 2O) 6] 2+ cations and 4-npa anions with the aid of O-H ⋯O interactions. Compounds 2 and 3 are one-dimensional (1-D) coordination polymers containing an eight coordinated Ca(II) situated in a general position and a nine coordinated Sr(II) located on a twofold axis. The μ 2-bridging tridentate binding modes of the crystallographically independent 4-npa ligands in 2 and the unique 4-npa ligand in 3 link the bivalent metal ions into an infinite chain with alternating Ca ⋯Ca separations of 3.989 and 4.009 Å, respectively, and a single Sr ⋯Sr separation of 4.194 Å in the 1-D chain. Synthesis, structure and properties of [Mg(H2O)6](4-npa)2·4H2O (4-npa =4-nitrophenylacetate) (1), [Ca(4-npa)2(H2O)2] (2), and [Sr(4-npa)2(H2O)3]·4.5H2O (3) are reported.

Synthesis, crystal structure and photochemistry of Hexakis(butan-1-aminium) heptamolybdate(VI) tetrahydrate

The synthesis, crystal structure, spectral characterization, photochemistry, electrochemical and thermal studies of the hexakis(butan-1-aminium) heptamolybdate(VI) tetrahydrate (1) are reported. Dissolution of a mixed mono-hepta compound (BuNH3)8[(Mo7O24)(MoO4)] ⋅3H2O in water results in its transformation to the title compound viz., (BuNH3)6[Mo7O24] ⋅4H2O 1 (BuNH3= butan-1-aminium). The structure of the title compound consists of two crystallographically unique [Mo7O24]6− anions, twelve independent (BuNH3)+ cations and eight unique lattice water molecules, all of which are interlinked with the aid of three varieties of H-bonding interactions. Solar irradiation of 1 results in the formation of a bis(μ 2-oxo) bridged diheptamolybdate product. Electrochemical studies reveal the role of 1 in the photodimerization process. Thermal decomposition of 1 results in the formation of crystalline α-MoO3. Synthesis, structure, photochemistry and redox characteristics of hexakis(butan-1-aminium) heptamolybdate(VI) tetrahydrate are reported.

Synthesis, crystal structure and properties of magnesium and calcium salts of p-anisic acid

The synthesis, crystal structure and properties of the magnesium and calcium salts of p-anisic acid viz. [Mg(H 2O) 6](C 8H7O3) 2⋅2H 2O (C 8H7O3 = p-anisate or 4-methoxybenzoate) (1) and [Ca(H 2O)(C 8H7O3) 2] (2) are reported. The p-anisate ion is not coordinated to Mg(II) and functions as a charge balancing counter anion for the centrosymmetric octahedral [Mg(H 2O) 6] 2+ unit in 1. The unique lattice water molecule links pairs of [Mg(H 2O) 6] 2+cations and p-anisate anions with the aid of O-H ⋯O interactions. The μ2-bridging bidentate and the μ3-bridging tetradentate binding modes of the crystallographically unique p-anisate ligands in (2) result in a two-dimensional (2-D) coordination polymer.

H‐bond and electric field correlations for water in highly hydrated crystals

We present periodic plane‐wave density functional theory (DFT) Perdew–Burke–Ernzerhof (PBE‐D2) calculations for four highly hydrated crystals, Na2CO3·10H2O, MgSO4·7H2O, MgSO4·11H2O, and Al(NO3)3·9H2O, containing 37 structurally unique water molecules and 74 unique hydrogen bonds. The calculated R(H···O) distances lie in the range 1.60–2.05 Å, the anharmonic OH frequencies in the range 2570–3425 cm−1, and the water dipole moments lie in the range 2.9–4.3 Debye, as calculated from the Wannier function centers and the nuclei. We present the following findings. (i) Our optimized intramolecular r(OH) distances are always larger than the gas‐phase value and thus more accurate than those derived from neutron diffraction experiments; (ii) The local in situ electric field over the molecule, calculated from the positions of the nuclei and the Wannier centers in the surrounding crystal, appears to be a good descriptor of the pertturbation from the water molecule's surroundings as the internal molecular properties (re, ν, μ) are found to correlate well with the crystal‐generated electric field; (iii) We have added DFT‐calculated data points to the well‐known experimental ‘OH frequency versus R(H···O)' correlation curve in a region where the experimental data points are scarce; (iv) For all 37 water molecules, the Wannier centers located in the lone‐pair region, and those located in the OH bonds, displace about equally much due to the polarizing environment. Finally, we propose that our resulting 'OH frequency versus Wannier‐type electric field' correlation curve may constitute a useful tool for predicting OH vibrational frequencies from snapshots from PBE‐D2‐based ab initio molecular dynamics simulations of water‐containing systems. © 2015 Wiley Periodicals, Inc.

Stacked ring-like coordination complex molecules threaded by infinite water tapes

Crystals of {[Cu2(mal)2(bpfp)2(H2O)2]·10H2O}n (1, mal=malonate, bpfp=bis(4-pyridylformyl)piperazine) were prepared by slow diffusion of an ethanolic solution of bpfp into an aqueous solution of copper malonate. Single-crystal X-ray diffraction showed the presence of supramolecular stacks of ring-like [Cu2(mal)2(bpfp)2(H2O)2] neutral coordination complex molecules threaded by unique infinite water molecule tapes with a T6(6)4(4)4(3)4(3)A(2) classification. These feature six-membered chair conformation rings, four-membered rings, and are decorated by single water molecules. Hydrogen bonding acceptance by the formyl groups of the bpfp ligands proved critical in stabilizing the water molecule tapes within the nanotubular incipient channels.

Control of water molecule aggregations in copper 1,4-cyclohexanedicarboxylate coordination polymers containing pyridyl–piperazine type ligands

A series of layered divalent copper coordination polymers containing 1,4-cyclohexanedicarboxylate and long-spanning pyridyl–piperazine type ligands exhibits greatly different co-crystallized water molecule aggregations depending on the specific ligands used. Both [Cu(t-14cdc)(4-bpmp)]n (1, t-14cdc=trans-1,4-cyclohexanedicarboxylate, 4-bpmp=bis(4-pyridylmethyl)piperazine) and {[Cu(t-14cdc)(4-bpfp)(H2O)2]·6H2O}n (2, 4-bpfp=bis(4-pyridylformyl)piperazine) possess 2D (4,4) coordination polymer grids. However 1 lacks any co-crystallized water and has pinched grid apertures, while 2 manifests infinite water tapes with T6(2)4(2) classification and rectangular grid apertures. {[Cu2(c-14cdc)2(4-bpmp)]·2H2O}n (3, c-14cdc=cis-1,4-cyclohexanedicarboxylate) has [Cu2(c-14cdc)]2 ribbons with paddlewheel dimeric units linked into 2D slabs by 4-bpmp tethers, along with isolated water molecule pairs. In contrast, {[Cu2(c-14cdc)2(4-bpfp)]·10H2O}n (4) shows a very similar underlying coordination polymer topology but entrains unique decameric water molecule clusters. The minor product {[Cu2(c-14cdcH)2(t-1,4-cdc)(4-bpfp)2(H2O)2]·2H2O}n (5) was isolated along with 4; this compound underwent some in situ cis to trans cyclohexane-dicarboxylate ligand isomerization and exhibits a ladder polymer motif.

Bis(2,2′-bipyridyl-κ2N,N′)(sulfato-κ2O,O′)nickel(II) 2.5-hydrate

The title compound, [Ni(SO4)(C10H8N2)2]·2.5H2O, is a nickel(II) complex with a distorted octa­hedral coordination geometry. The NiII atom is bonded by two O atoms of the bidentate chelating sulfate ligand and the four N atoms of two chelating 2,2′-bi­pyridine ligands. The Ni—N bond lengths range from 2.059 (3) to 2.075 (3) Å and the Ni—O bond lengths are 2.098 (3) and 2.123 (3) Å. The bipyridyl ligands are both close to planar (r.m.s. deviations of 0.254 and 0.0572 Å) and are almost orthogonal, making a dihedral angle of 82.77 (1)°. In the crystal, the complex and water mol­ecules are connected by O—H⋯O hydrogen bonds. Inter­estingly, six water mol­ecules form a chain linking two complex mol­ecules via sulfate O atoms. There are also stacking inter­actions between the aromatic rings of neighbouring 2,2′-bi­pyridine ligands with shortest non-covalent contacts of 3.268 (6), 3.393 (6) and 3.435 (5) Å. One of the three unique water molecules shows half-occupation.

Water-capsule strategy in crystal engineering for water-solubility conversion from insoluble to soluble

(H(2)O)(32)-shell structure constructed by two unique water molecules in high symmetry crystal leads to good water-solubility of the obtained compound 1.

Determination of nucleic acid hydration using osmotic stress.

Water plays an important role in structure and molecular recognition of biopolymers. Understanding hydration of biopolymers is a significant problem in structural chemistry and biology. However, hydration is a dynamic process that is difficult to study. While X-ray crystallography, NMR, and molecular modeling have provided structural detail on nucleic acid hydration and valuable insights into water dynamics, the thermodynamic contribution of water molecules to conformational equilibria and recognition of nucleic acids remains poorly understood. This unit describes a thermodynamic analysis of nucleic acid hydration using osmotic stress. Osmotic stress monitors the depression of melting temperature upon decreasing water activity, and calculates the number of thermodynamically unique water molecules associated with the double helix and released from single strands upon melting. Comparison of the number of water molecules released upon melting of nucleic acids with different sequences and chemical modifications provides insights that complement and enhance information obtained by other methods.

Metasideronatrite: Crystal structure and its relation with sideronatrite

Metasideronatrite was obtained as the first dehydration product of sideronatrite, Na 2 Fe(SO 4 ) 2 (OH)∙3H 2 O, from Sierra Gorda, Chile. The crystal structure of metasideronatrite was solved by direct methods and refined by full-matrix least-squares to R = 0.039, using 574 independent reflections with I > 3.0σ(I). It is orthorhombic, space group Pbnm, with a = 7.3959(8), b = 16.0979(15), c = 7.1607(8) Å, V = 852.5(2) Å 3 , Z = 4. The crystal-chemical formula derived from this structural study is Na2Fe(SO 4 ) 2 (OH)∙H 2 O. The backbone of the structure is the same as that in sideronatrite: infinite [Fe 3+ (SO 4 ) 2 (OH)] 2- chains of interconnected octahedra and tetrahedra parallel to the c axis. These chains are linked primarily by Na atoms to build a 3-dimensional network of strong (Fe-O-S) and weak (Na-O) bonds. Another prominent feature of the structure is the arrangement of distorted (NaO 5 H 2 O) octahedra, which alternately share one edge and one face to form columns parallel to the [Fe 3+ (SO 4 ) 2 (OH)] chains. Subsidiary intra-chain bonds are provided by H atoms belonging to OH- groups shared by adjacent Fe octahedra, and to the unique water molecule shared between two adjacent (NaO 5 H 2 O) octahedra. At normal conditions of relative humidity (RH) and temperature (i.e., RH > 60% and T < 40 °C), metasideronatrite rehydrates rapidly to sideronatrite. The structure solution has allowed us to: (1) investigate the strong relation between sideronatrite and metasideronitrite; (2) elucidate the mechanism involved in the transformation of metasideronatrite into the order/disorder (OD) structure of sideronatrite; and (3) get insight into the stability of this mineral from the valence-matching principle applied to the main structural unit [Fe 3+ (SO 4 ) 2 (OH)] 2 and Na + interstitial species. The weak hydrogen bonds and the particular arrangement of the face-sharing adjacent [NaO 5 (H 2 O)] octahedra are the main factors affecting the stability of metasideronatrite.

Binding Regularities in Complexes of Transcription Factors with Operator DNA: Homeodomain Family

In order to disclose general regularities of binding in homeodomain-DNA complexes we considered five of them and extended the observed regularities over the entire homeodomain family. The five complexes have been selected by similarity of protein structures and patterns of contacting residues. Their long range interactions and interfaces were compared. The long-range stage of the recognition process was characterized by electrostatic potentials about 5 A away from molecular surfaces of protein or DNA. For proteins, clear positive potential is displayed only at the side contacting the DNA. The double-chained DNA molecule displays a rather strong negative potential, especially in their grooves. Thus, a functional role of electrostatics is a guiding of the protein into the DNA major groove, so the protein and DNA could form a loose non-specific complex. At the close-range stage, neutralization of the phosphate charges by positively charged residues is necessary for decreasing the strong electrostatic potential of DNA, allowing nucleotide bases to participate in the formation of protein-DNA atomic contacts in the interface. The recognizing ?-helix of protein was shown to form both invariant and variable groups of contacts with DNA by means of certain specific side groups. The invariant contacts included highly specific protein-DNA hydrogen bonds between asparagine and adenine, nonpolar contacts of hydrophobic amino acids serving as a stereochemical barrier for fixing the protein factor on DNA, and an interface cluster of water molecules providing local conformational mobility necessary for the dissociation process. There is a unique water molecule within the interface that is conservative and located at the interface center. Invariant contacts of the proteins are mostly formed with the TAAT motif of the promoter DNA forward strand. While the invariant contacts specify the family of homeodomains, the variable contacts that are formed with the reverse strand of DNA provide specificity of individual complexes within the homeodomain family.