Water Molecules In Cavities Research Articles

What Gives an Insulin Hexamer Its Unique Shape and Stability? Role of Ten Confined Water Molecules.

Self-assembly of proteins often gives rise to interesting quasi-stable structures that serve important biological purposes. Insulin hexamer is such an assembly. While monomer is the biologically active form of insulin, hexamer serves as the storehouse of the hormone. The hexamer also prevents the formation of higher order aggregates. While several studies explored the role of bivalent metal ions like Zn2+, Ca2+, etc., in the stabilization of the hexameric form, the role of water molecules has been ignored. We combine molecular dynamics simulations, quantum calculations, and X-ray analyses to discover that a team of approximately 10 water molecules confined inside a barrel-shaped nanocavity at the center of insulin hexamer is one of the major causes that account for the unusual stability of the biomolecular assembly. These cavity water molecules exhibit interesting dynamical features like intermittent escape and reentrance. We find that these water molecules are dynamically slower than the bulk and weave an intricate hydrogen bond network among themselves and with neighboring protein residues to generate a robust backbone at the center of the hexamer that holds the association strongly from inside and maintains the barrel shape.

Cucurbit[8]uril and Blue-Box: High-Energy Water Release Overwhelms Electrostatic Interactions

The design of high-affinity and analyte-selective receptors operating in aqueous solutions is an outstanding problem in supramolecular chemistry. Directing the focus toward the unique properties of water, we present here a new strategy toward this goal and support it by molecular dynamics simulations and calorimetric measurements. We illustrate the procedure in the case of self-assembled 1:1 complexes of the rigid macrocycle cucurbit[8]uril (CB8) and dicationic auxiliary guests (AG). These CB8•AG complexes contain residual water molecules whose conformational space and hydrogen-bond formation ability is restricted by the geometrically confined and hydrophobic cavity of the receptor. We show that upon inclusion of an analyte to form a 1:1:1 CB8•AG•analyte complex, these "high-energy" cavity water molecules are released to the aqueous bulk, providing a strong enthalpic driving force to the association, and resulting in binding constants of up to 10(6) M(-1) for aromatic analytes. This binding model is supported by the measurements of large solvent and solvent isotope effects. The selectivity of the CB8•AG receptor can be modified or even switched toward small aliphatic analytes by a rational choice of the auxiliary guest, demonstrating the tunable recognition features of such self-assembled receptors. Furthermore, by comparison of the results to those for the extensively studied macrocyclic host cyclobis(paraquat-p-phenylene)--the so-called "blue-box"--it is shown that in aqueous solution the release of "high-energy" water molecules from the CB8•AG cavity can be more favorable than the use of direct host-guest interactions.

Hydration Properties of α-, β-, and γ-Cyclodextrins from Molecular Dynamics Simulations

Atomistic molecular dynamics (MD) simulations of α-, β-, and γ-cyclodextrins (ACD, BCD, and GCD) in aqueous solutions have been performed. Detailed analyses were carried out to compare the microscopic properties of water confined within the cavities of these macromolecules and in the hydration layers around them. It is noticed that reduced tetrahedral ordering of water in and around the CD molecules are associated with their restricted motions. Interestingly, unlike the translational motions, the rotational motions of cavity water molecules are found to be highly dependent on cavity dimensions. Additionally, it is found that severely hindered rotational motion of cavity water molecules is the origin of drastically restricted structural relaxation of hydrogen bonds involving those water molecules. It is demonstrated that the geometrical constraints within the cavities of the CD molecules enhance the rate of reformation of broken hydrogen bonds, thereby resulting in rapid establishment of the breaking and reformation equilibria for hydrogen bonds involving cavity water molecules.

Erratum to: Distribution of Extraframework Cations and Water Molecules in the Structure of Synthetic Paulingite

The distribution of extraframework cations and water molecules in cavities of synthetic paulingite (Si/Al = 3.85) has been determined from X-ray powder diffraction data. An analysis performed has demonstrated that K and Na cations are located in four out of the seven types of cavities contained in paulingite: oto, phi, plg, and pau. It has been established that the synthetic paulingite has the composition H26.8Na42.4K69.2Al138.4Si533.6O1344 · 283H2O.

Low-Frequency Vibrational Spectrum of Water around Cyclodextrin and Its Methyl-Substituted Derivatives

Atomistic molecular dynamics (MD) simulations have been carried out to study the low-frequency intermolecular vibrational spectrum of water present in the surrounding hydration layers and inside the cavities of beta-cyclodextrin (BCD) and its di- and trimethyl substituted derivatives, namely, heptakis(2,6-di-O-methyl)-beta-cyclodextrin (DIMEB) and heptakis(2,3,6-tri-O-methyl)-beta-cyclodextrin (TRIMEB) in aqueous solutions. Attempts have been made to explore the effects of confinement in and around these cyclic macromolecules and the formation of hydrogen bonds between water and the glucopyranose rings on the distribution of the intermolecular vibrational density of states of water. The calculations revealed that compared to bulk water these bands are blue-shifted for water in proximity to these molecules, the extents of the shifts being more pronounced for the cavity water molecules. It is further noticed that the relatively more restricted local motions of water bound to the cyclodextrins by hydrogen bonds result in larger blue shifts of these bands. These results can be verified by suitable experiments.

Three NEW butane-1,2,3,4-tetracarboxylato-bridged coordination polymers: Syntheses, crystal structures and charaterization

Three new butane-1,2,3,4-tetracarboxylato bridged coordination polymers [Zn2(H2O)4(BTC)]·3H2O 1, [Cd2(H2O)4(BTC)]·2H2O 2 and [Y2(H2O)6(H2BTC)(BTC)]·5H2O 3 (H4BTC = butane-1,2,3,4-tetracarboxylic acid) were synthesized and characterized by IR spectroscopy, TG–DTA analyses, elemental analyses and single-crystal X-ray diffraction, and their fluorescence properties were also investigated. In 1, the trigonal pyramidally coordinated Zn atoms are brigded by both μ6η6 and μ6η8 centrosymmetric BTC4− anions into 2D layers, which are connected by the octahedrally coordinated Zn atoms to build up 3D (44·610·8)(44·62)2(44·68·82·10) topological framework with the lattice water molecules in cavities. In 2, the CdO7 pentagonal bipyramids and the CdO8 4,4′-bicapped triagonal antiprisms are edge-shared to generate the Cd2O13 bipolyhedra, which are further corner-shared into 1D metal-oxide chains. The resulting chains are interconnected by the μ6η8 BTC4− anion to form 2D (43)2(46·66·83) networks, which are assembled via interlayer hydrogen bonds into a 3D (411·611·86)(43)(49·6) topological supramolecular architecture with the lattice H2O molecules located in holes. The distorted 4,4′-bicapped triagonal antiprismatically coordinated Y atoms in 3 are interconnected μ4η4 H2BTC2− and μ4η6 BTC4− anions to from 2D (44·62) topological networks, which are held together via strong interlayer hydrogen bonds into a 3D fsc topological supramolecular architecture with the lattice water molecules residing in cavities.

Crystallographic and computational studies on 4‐phenyl‐N‐(β‐D‐glucopyranosyl)‐1H‐1,2,3‐triazole‐1‐acetamide, an inhibitor of glycogen phosphorylase: Comparison with α‐D‐glucose, N‐acetyl‐β‐D‐glucopyranosylamine and N‐benzoyl‐N′‐β‐D‐glucopyranosyl urea binding

4-Phenyl-N-(beta-D-glucopyranosyl)-1H-1,2,3-triazole-1-acetamide (glucosyltriazolylacetamide) has been studied in kinetic and crystallographic experiments with glycogen phosphorylase b (GPb), in an effort to utilize its potential as a lead for the design of potent antihyperglycaemic agents. Docking and molecular dynamics (MD) calculations have been used to monitor more closely the binding modes in operation and compare the results with experiment. Kinetic experiments in the direction of glycogen synthesis showed that glucosyltriazolylacetamide is a better inhibitor (K(i) = 0.18 mM) than the parent compound alpha-D-glucose (K(i) = 1.7 mM) or beta-D-glucose (K(i) = 7.4 mM) but less potent inhibitor than the lead compound N-acetyl-beta-D-glucopyranosylamine (K(i) = 32 microM). To elucidate the molecular basis underlying the inhibition of the newly identified compound, we determined the structure of GPb in complex with glucosyltriazolylacetamide at 100 K to 1.88 A resolution, and the structure of the compound in the free form. Glucosyltriazolylacetamide is accommodated in the catalytic site of the enzyme and the glucopyranose interacts in a manner similar to that observed in the GPb-alpha-D-glucose complex, while the substituent group in the beta-position of the C1 atom makes additional hydrogen bonding and van der Waals interactions to the protein. A bifurcated donor type hydrogen bonding involving O3H, N3, and N4 is seen as an important structural motif strengthening the binding of glucosyltriazolylacetamide with GP which necessitated change in the torsion about C8-N2 bond by about 62 degrees going from its free to the complex form with GPb. On binding to GP, glucosyltriazolylacetamide induces significant conformational changes in the vicinity of this site. Specifically, the 280s loop (residues 282-288) shifts 0.7 to 3.1 A (CA atoms) to accommodate glucosyltriazolylacetamide. These conformational changes do not lead to increased contacts between the inhibitor and the protein that would improve ligand binding compared with the lead compound. In the molecular modeling calculations, the GOLD docking runs with and without the crystallographic ordered cavity waters using the GoldScore scoring function, and without cavity waters using the ChemScore scoring function successfully reproduced the crystallographic binding conformation. However, the GLIDE docking calculations both with (GLIDE XP) and without (GLIDE SP and XP) the cavity water molecules were, impressively, further able to accurately reproduce the finer details of the GPb-glucosyltriazolylacetamide complex structure. The importance of cavity waters in flexible receptor MD calculations compared to "rigid" (docking) is analyzed and highlighted, while in the MD itself very little conformational flexibility of the glucosyltriazolylacetamide ligand was observed over the time scale of the simulations.

Locating missing water molecules in protein cavities by the three‐dimensional reference interaction site model theory of molecular solvation

Water molecules confined in protein cavities are of great importance in understanding the protein structure and functions. However, it is a nontrivial task to locate such water molecules in protein by the ordinary molecular simulation and modeling techniques as well as experimental methods. The present study proves that the three-dimensional reference interaction site model (3D-RISM) theory, a recently developed statistical-mechanical theory of molecular solvation, has an outstanding advantage in locating such water molecules. In this paper, we demonstrate that the 3D-RISM theory is able to reproduce the structure and the number of water molecules in cavities of hen egg-white lysozyme observed commonly in the X-ray structures of different resolutions and conditions. Furthermore, we show that the theory successfully identified a water molecule in a cavity, the existence of which has been ambiguous even from the X-ray results. In contrast, we confirmed that molecular dynamics simulation is helpless at present to find such water molecules because the results substantially depend on the initial coordinates of water molecules. Possible applications of the theory to problems in the fields of biochemistry and biophysics are also discussed.

Mapping the Energetics of Water–Protein and Water–Ligand Interactions with the “Natural” HINT Forcefield: Predictive Tools for Characterizing the Roles of Water in Biomolecules

The energetics and hydrogen bonding pattern of water molecules bound to proteins were mapped by analyzing structural data (resolution better than 2.3A) for sets of uncomplexed and ligand-complexed proteins. Water-protein and water-ligand interactions were evaluated using hydropatic interactions (HINT), a non-Newtonian forcefield based on experimentally determined logP(octanol/water) values. Potential water hydrogen bonding ability was assessed by a new Rank algorithm. The HINT-derived binding energies and Ranks for second shell water molecules were -0.04 kcal mol(-1) and 0.0, respectively, for first shell water molecules -0.38 kcal mol(-1) and 1.6, for active site water molecules -0.45 kcal mol(-1) and 2.3, for cavity water molecules -0.55 kcal mol(-1) and 3.3, and for buried water molecules -0.56 kcal mol(-1) and 4.4. For the last four classes, similar energies indicate that internal and external water molecules interact with protein almost equally, despite different degrees of hydrogen bonding. The binding energies and Ranks for water molecules bridging ligand-protein were -1.13 kcal mol(-1) and 4.5, respectively. This energetic contribution is shared equally between protein and ligand, whereas Rank favors the protein. Lastly, by comparing the uncomplexed and complexed forms of proteins, guidelines were developed for prediction of the roles played by active site water molecules in ligand binding. A water molecule with high Rank and HINT score is unlikely to make further interactions with the ligand and is largely irrelevant to the binding process, while a water molecule with moderate Rank and high HINT score is available for ligand interaction. Water molecule displaced for steric reasons were characterized by lower Rank and HINT score. These guidelines, tested by calculating HINT score and Rank for 50 water molecules bound in the active site of four uncomplexed proteins (for which the structures of the liganded forms were also available), correctly predicted the ultimate roles (in the complex) for 76% of water molecules. Some failures were likely due to ambiguities in the structural data.

Water molecules in the binding cavity of intestinal fatty acid binding protein: dynamic characterization by Water 17O and 2H magnetic relaxation dispersion

The hydration of intestinal fatty acid binding protein (IFABP) in apo-form and complexed with palmitate, oleate, and 1-anilino-8-naphthalene sulfonate (ANS) has been studied by water 17O and 2H magnetic relaxation dispersion (MRD) measurements. These ligands bind in a large internal cavity, displacing most of the crystallographically identified cavity water molecules. Unlike most other proteins, IFABP gives rise to MRD profiles with two dispersion steps. The low-frequency dispersion yields a correlation time of 7 ns at 300 K, matching the known tumbling time of IFABP. The dispersion amplitude requires only three (apo) or four (holo) long-lived and ordered water molecules (residence time 0.01-4 μs at 300 K). Comparison of MRD profiles from the different complexes indicates that the displaced cavity water molecules are short-lived. The few long-lived (>10 ns) water molecules required by the MRD data are tentatively assigned to crystallographic hydration sites on the basis of accessibility, positional order, and H-bonding. The amplitude of the high-frequency dispersion corresponds to 10-20 moderately ordered water molecules, with a correlation time of ca. 1 ns that may reflect a transient opening of the cavity required for exchange with external water.

Neutron powder diffraction study of α-Ti(HPO4)2.H2O and α-Hf(HPO4)2.H2O; H-atom positions

The complete crystal structures, including H-atom positions, of α-Ti(HPO4)2.H2O (α-TiP) and α-Hf(HPO4)2.H2O (αHfP) were determined by Rietveld refinement and Fourier synthesis, using constant-wavelength neutron diffraction data. This work is one of few recent examples of the determination of H atoms using neutron powder diffraction with an intense source. The orientation of water molecules in the cavities of α-TiP is similar to that previously found for α-ZrP. For α-HfP, although the hydrogen-bonding scheme is identical, the orientation of water molecules in similar cavities was found to be different.

Arrangement of water molecules in cavities and channels of the lattice of [Phe4Val6]antamanide dodecahydrate.

The synthetic, biologically active, [Phe4Val6] analog of natural antamanide has been crystallized from a solution containing calcium nitrate, acetone, and acetonitrile. The crystal does not contain any Ca2+ ions but does contain 12 water molecules per peptide molecule. The conformation of this dodecahydrate is identical to the trihydrate crystallized from n-hexane/methyl acetate. The packing in both crystals is very similar, governed by parallel bands of phenyl and pyrrolidine ring stacking and by continuous channels for the solvement molecules, water in this case and n-hexane/methyl acetate in the previous study. The two structures are not ideally isomorphous, since the c cell parameter differs by more than 1.0 A in the two cells. There are three functions for H2O molecules: the three intrinsic H2O molecules in the interior of the peptide ring, the H2O bound to the exposed C=O groups, and the H2O molecules that fill space in the solvent channels. There are no direct hydrogen bonds between neighboring peptide molecules and there are only two intramolecular NH-O=C bonds (of the 5 leads to 1 type).

Calculation of the thermodynamic properties of cavity water molecules based on an expansion of the density function

Calculation of the thermodynamic properties of cavity water molecules based on an expansion of the density function

Position of water molecules in cavities of the ice-like structure of liquid water, and the degree of filling the cavities

Position of water molecules in cavities of the ice-like structure of liquid water, and the degree of filling the cavities