Rod structures of bound water: a possible role in self-organization of biological systems and nondissipative energy transmission

Cluster–rod structure were designed, which are comprised of tetrahedral atoms with a typical torsion angle of ~38° at interatomic bonds. These structures correspond to a muscle tissue and clathrin lattice by their metrics and topology and can be formed by bound water in these systems. It is shown that the considered rod structures, which are fragments of bound water structures, can also be involved in nondissipative energy transmission as elastic energy storing structures. The estimated length of the bound water rod structure required to absorb the energy of decomposition of an ATP molecule into ADP and a phosphate group is comparable with myosin head sizes and its step along an actin filament. A mechanism of cooperative transition of the rod structure to a fragment of the ice Ih structure was demonstrated. This transition is accompanied by nondissipative release of stored energy.     

Effects of annealing on the polymorphic structure of starches from sweet potatoes (Ayamurasaki and Sunnyred cultivars) grown at various soil temperatures

Starches extracted from the sweet potato cultivars Sunnyred and Ayamurasaki grown at 15 or 33 degrees C (soil temperature) were annealed in excess water (3 mg starch/mL water) for different times (1, 4, 8 or 10h) at the temperatures 2-3 degrees K below the onset melting temperature. The structures of annealed starches, as well as their gelatinisation (melting) properties, were studied using high-sensitivity differential scanning calorimetry (HSDSC). In excess water, the single endothermic peak shifted to higher temperatures, while the melting (gelatinisation) enthalpy changed only very slightly, if any. The elevation of gelatinisation temperature was associated with increasing order/thickness of the crystalline lamellae. The only DSC endotherm identified in 0.6 M KCl for Sunnyred starch grown at 33 degrees C was attributed to A-type polymorphic structure. The multiple endothermic forms observed by DSC performed in 0.6M KCl for annealed starches from both cultivars grown at 15 degrees C provided evidence of a complex C-type (A- plus B-type) polymorphic structure of crystalline lamellae. The A:B-ratio of two polymorphic forms increased upon annealing due to partial transformation of B- to A-polymorph, which was time dependent. Long heating periods facilitated the maximal transformation of B- to A-polymorph associated with limited A:B ratio.     

Intercalation of water molecules between nucleic acid bases in the crystal structures of 6-azathymine hemihydrate and 5-amino-2-thiocytosine dihydrochloride dihydrate

The crystal structure of 6-azathymine hemihydrate (6AzTH) exhibits a novel intercalation of water molecules interposed half-way between the modified bases 6.3 to 6.7 A apart. The crystal contains four molecules of 6-azathymine (6AzT) and two water molecules as the independent repeating unit. These two water molecules together with the four bases form two separate water sandwiches. In the crystal structure these sandwiches form two sets of local clusters. The anhydrous crystalline form of 6AzT, on the other hand, is stabilized by base stacking interactions. Both the water molecules in 6AzTH that are involved in sandwich formation have trigonal coordination around them. A reexamination of the crystal structure of 5-amino-2-thiocytosine (5A2TC) revealed that one of the water molecules in this structure also forms a water sandwich and has trigonal coordination whereas the other water molecule with tetrahedral coordination does not form a sandwich. The environment and the characteristics of the intercalated water molecule in these structures suggest a possible role for such water intercalations in the dynamics of DNA. Crystals of 6AzTH are monoclinic, space group P21/n, with unit cell parameters a = 8.861 (1), b = 13.177 (3), c = 20.662 (2) A, beta = 93.35 (1) degrees, and Z = 16. From diffractometer data (2503 reflections, greater than or equal to 3 sigma), the crystal structure was solved and refined to an R of 0.056.     

Multibilayer structure of dimyristoylphosphatidylcholine dihydrate as determined by energy minimization

Complete energy minimization was carried out on the multibilayer crystal structure of 1,2-dimyristoyl-sn-glycero-3-phosphocholine dihydrate (DMPC.2H2O), starting from the X-ray structure determination reported by Pearson and Pascher (1979) Nature 281, 499-501. The asymmetric unit contains two nonidentical DMPC molecules and four water molecules. Minimization removed the acyl chain disorder present in the X-ray structure and caused the carbon planes of the acyl chains to become mutually parallel. Two energy-minimized structures (structures I and II) were found which mainly differed in the hydrogen-bonding arrangement of the waters of hydration. In structure I as in the X-ray structure, one of the water molecules forms a hydrogen-bonded bridge between successive bilayers; but in structure II, all hydrogen bonds are satisfied on the same bilayer. Structure II corresponds to the global energy minimum and is also a suitable structure for single bilayers. The lattice constants and cell volume of the minimized structures are close to the experimental values. The electrostatic force between DMPC bilayers is attractive. The mean hydration energy of the water is -14.2 kcal/mol, which is 2.5 kcal/mol lower than the binding energy of ice.     

Two crystal structures of the leupeptin-trypsin complex.

Three-dimensional structures of trypsin with the reversible inhibitor leupeptin have been determined in two different crystal forms. The first structure was determined at 1.7 A resolution with R-factor = 17.7% in the trigonal crystal space group P3(1)21, with unit cell dimensions of a = b = 55.62 A, c = 110.51 A. The second structure was determined at a resolution of 1.8 A with R-factor = 17.5% in the orthorhombic space group P2(1)2(1)2(1), with unit cell dimensions of a = 63.69 A, b = 69.37 A, c = 63.01 A. The overall protein structure is very similar in both crystal forms, with RMS difference for main-chain atoms of 0.27 A. The leupeptin backbone forms four hydrogen bonds with trypsin and a fifth hydrogen bond interaction is mediated by a water molecule. The aldehyde carbonyl of leupeptin forms a covalent bond of 1.42 A length with side-chain oxygen of Ser-195 in the active site. The reaction of trypsin with leupeptin proceeds through the formation of stable tetrahedral complex in which the hemiacetal oxygen atom is pointing out of the oxyanion hole and forming a hydrogen bond with His-57.     

Scale invariance of biosystems: From embryo to community

Phenomena having the property of a scale invariance (that is, maintaining invariable structure in certain range of scales) are typical for biosystems of different levels. In this review, main manifestations of the scale-invariant phenomena at different levels of biological organization (including ontogenetic aspects) are stated, and the reasons of such wide distribution of fractal structures in biology are discussed. Almost all biological systems can be described in terms of synergetics as open nonequilibrium systems that exist due to substance and energy flow passing through them. The phenomenon of self-organization is typical for such dissipative systems; maintenance of energy flow requires the existence of complex structures that emerge spontaneously in the presence of the appropriate gradient. Critical systems, which form as a results of their activity scale-invariant structures (that are a kind of distribution channels), are optimal relative to the efficiency of substance and energy distribution. Thus, scale invariance of biological phenomena is a natural consequence of their dissipative nature.     

Three-dimensional structure of a light chain dimer crystallized in water. Conformational flexibility of a molecule in two crystal forms

The three-dimensional structure of an immunoglobulin light chain dimer (Mcg) crystallized in deionized water (orthorhombic form) was determined at 2.0 A resolution by phase extension and crystallographic refinement. This structure was refined side-by-side with that of the same molecule crystallized in ammonium sulfate (trigonal form). The dimer adopted markedly different structures in the two solvents. "Elbow bend" angles between pseudo 2-fold axes of rotation relating pairs of "variable" (V) and "constant" (C) domains were found to be 132 degrees in the orthorhombic form and 115 degrees in the trigonal form. Modes of association of the V domains and, to a lesser extent, the pairing interactions of the C domains were different in the two structures. Alterations in the V domain pairing were reflected in the shapes of the binding regions and in the orientations of the side-chains lining the walls of the binding sites. In the trigonal form, for instance, the V domain interface was compartmentalized into a main binding cavity and a deep pocket, whereas these spaces were continuous in the orthorhombic structure. Patterns of ordered water molecules were quite distinct in the two crystal types. In some cases, the solvent structures could be correlated with conformational changes in the proteins. For example, close contacts between V and C domains of monomer 1 of the trigonal form were not retained in orthorhombic crystals. Ordered water molecules filled the space created when the two domains moved apart.     

Peptide--water association in peptide crystals.

The structures of 37 peptide crystals, containing 78 water-peptide hydrogen bonds and 77 other hydrogen bonds involving water, were surveyed to identify the geometry of peptide backbone hydration. In the sample, hydration of peptide carbonyl occurred more frequently than hydration of peptide N--H. The most probable value of the C'=O ... O water angle was near 138 degrees, considerably greater than the 120 degrees to the axis of a lone electron pair on the carbonyl oxygen. Associated water oxygens tended to be in the plane of the peptide bond, bui--H and Ci+1=O atoms, was common in glycine-containing cyclic hexapeptides. The distribution of angles between two hydrogen bonds at a single water molecule, as defined by the three nonhydrogen atoms involved, was centered near the tetrahedral angle.     

X-ray structural evidence for a local helix-loop transition in alpha-lactalbumin.

The three-dimensional structure of human alpha-lactalbumin for two crystal forms has been determined by x-ray analysis. One crystal (the form LT) was obtained at pH 4.2 and room temperature, while the other crystal (the form HT) was grown at pH 6.5 and 37 degrees C. The backbone structure for Lys1-Ile95 residues is almost conserved between the two structures as indicated by the root mean square difference of 0.30 A for the superposition of equivalent C alpha atoms. The calcium ion is surrounded by seven oxygen atoms of three carboxyl groups, two carbonyl groups, and two water molecules, which form a distorted pentagonal bipyramid in both structures. A large difference in polypeptide folding is found in the region of Leu96-Leu123 residues. Especially in the region of Trp104-Cys111 residues, a distorted alpha-helix is observed in the form HT while a loop structure is formed in the other crystal. The fact that the crystals of both forms appeared in the same batch at pH 6.5 and room temperature indicates that the human alpha-lactalbumin structure is highly fluctuated in solution and the folding and unfolding of the alpha-helix of Trp104-Cys111 residues are in equilibrium. Since the crystal of the form HT exclusively appeared around the physiological temperature, the structure of this form can be considered as the native structure. The partially unfolded structure in the form LT indicates that the local denaturation occurs even at room temperature.     

Linkage and pyranosyl ring twisting in cyclodextrins

Acylated beta-cyclodextrins (beta-CDs) were studied to gain perspective on maltose octapropanoate, the crystal structure of which was reported in the preceding paper in this issue. Acylated beta-CDs are distorted so we looked at other CDs and gained increased understanding of distortion in CDs and possibly, shapes in starch. Classic CDs have six to eight glucose residues in a doughnut shape that is stabilized by a ring of inter-residue O3,,,O2' hydrogen bonds. On a phi,psi energy map for a maltose analog that does not form hydrogen bonds, classic CD linkages have higher energies than structures that are stabilized by the exo-anomeric effect. In distorted beta-CDs, which lack hydrogen bonding, some linkages attain low-energies from the exo-anomeric effect and acyl stacking. Those linkages result in left-handed helical geometry so other linkages are forced by the CD macrocycle to have counter-balancing right-handed character. Permethylated gamma-CDs have two 'flipping' linkages as do some larger native CDs. Flipping linkages allow two left-handed segments to join into a macrocycle, thus avoiding the higher-energy, right-handed forms. Some glucose rings in derivatized beta-CDs have substantial positive twists of the pseudo torsion angle O1-C1...C4-O4, adding right-handed character to balance the left-handed linkages. In substituted gamma-CD, all residues have negative twists, giving extra left-handed character to the short, pseudo-helical segments. In non-macrocyclic molecules the twists ranged from -14 degrees to +2 degrees , averaging -6.1 degrees. In these beta- and gamma-CDs, the twists ranged from -22 degrees to +16 degrees for (4)C(1) rings, and the (O)S(2) ring in acetylated beta-CD has a twist of +34 degrees . Glucose residues in other CDs were less twisted.     

The relationship between the glucose oxidase subunit structure and its thermostability

The thermostability of glucose oxidase (beta-D-glucose: oxygen 1-oxidoreductase, EC 1.1.3.4) at 60 degrees C has been studied as a function of its concentration in various media (pure water and pure deuterium oxide). In deuterium oxide, glucose oxidase is more stable than in water, and two kinds of stabilizing effect have been observed: the medium-organization effect and the enzyme-concentration effect. This effect has been related to the glucose oxidase subunit structure. This enzyme contains four forms of subunit: monomer, dimer, trimer, and tetramer, which are all composed of the identical monomer. The monomers of glucose oxidase subunits are linked by the non-covalent bond. Only dimer and trimer possess the enzymatic activity. During glucose oxidase denaturing, monomers assemble into dimer, trimer, or tetramer. This redistribution behavior depends on the enzyme concentration and the nature of the medium.     

20世纪下半叶上海城市景观镶嵌结构演变的数量特征与分形结构模型研究

以上海中心城区为空间范围,以RS和GIS为技术手段,运用多样指数、优势度、破碎度、分离度等指标,研究20世纪下半叶以来上海城市景观镶嵌结构及其演变的数量特征;运用分形理论建立各种景观形态的分形结构模型,以分维数为依据分析各种景观形态的复杂性;基于GIS的空间分析功能,探讨影响景观格局及其演变的主要因素。研究结果表明:(1)上海城市景观的空间扩展,在空间上和时间都是不均匀;(2)随着时间的推移,景观多样性和破碎度变大。优势度变小;(3)住宅、工矿和其它城市景观的分离度明显地呈减小趋势,农田和村镇的分离度呈增大趋势,道路和河流水域的分离度变化幅度不大;(4)各种景观斑块形态的复杂性程度(分维数的平均值)排序为:道路>河流水域>农田>住宅>村镇>工矿>在建景观>其它城市景观;(5)从各种景观形态的演变过程来看,住宅斑块形态逐渐趋于复杂化,斑其块形态的分维数呈缓慢地增大趋势;工矿、道路、其它城市景观、农田、村镇等五种景观斑块形态的变化,经历了由简单到复杂,再到简单的变化过程,其分维数在1947-1988年期间呈增大趋势,1988年时增至最大,随后开始逐渐减小;(6)影响上海城市景观格局及其演变的因素主要包括河流廊道、原有基础、交通廊道、经济发展、规划控制等几个方面。     

Molecular dynamics simulations of the acyl-enzyme and the tetrahedral intermediate in the deacylation step of serine proteases

Despite the availability of many experimental data and some modeling studies, questions remain as to the precise mechanism of the serine proteases. Here we report molecular dynamics simulations on the acyl-enzyme complex and the tetrahedral intermediate during the deacylation step in elastase catalyzed hydrolysis of a simple peptide. The models are based on recent crystallographic data for an acyl-enzyme intermediate at pH 5 and a time-resolved study on the deacylation step. Simulations were carried out on the acyl enzyme complex with His-57 in protonated (as for the pH 5 crystallographic work) and deprotonated forms. In both cases, a water molecule that could provide the nucleophilic hydroxide ion to attack the ester carbonyl was located between the imidazole ring of His-57 and the carbonyl carbon, close to the hydrolytic position assigned in the crystal structure. In the "neutral pH" simulations of the acyl-enzyme complex, the hydrolytic water oxygen was hydrogen bonded to the imidazole ring and the side chain of Arg-61. Alternative stable locations for water in the active site were also observed. Movement of the His-57 side-chain from that observed in the crystal structure allowed more solvent waters to enter the active site, suggesting that an alternative hydrolytic process directly involving two water molecules may be possible. At the acyl-enzyme stage, the ester carbonyl was found to flip easily in and out of the oxyanion hole. In contrast, simulations on the tetrahedral intermediate showed no significant movement of His-57 and the ester carbonyl was constantly located in the oxyanion hole. A comparison between the simulated tetrahedral intermediate and a time-resolved crystallographic structure assigned as predominantly reflecting the tetrahedral intermediate suggests that the experimental structure may not precisely represent an optimal arrangement for catalysis in solution. Movement of loop residues 216-223 and P3 residue, seen both in the tetrahedral simulation and the experimental analysis, could be related to product release. Furthermore, an analysis of the geometric data obtained from the simulations and the pH 5 crystal structure of the acyl-enzyme suggests that since His-57 is protonated, in some aspects, this crystal structure resembles the tetrahedral intermediate.     

Exploring the effect of oxygen-containing functional groups on the water-holding capacity of lignite

Graphene oxide with different degrees of oxidation was prepared and selected as a model compound of lignite to study quantitatively, using both experiment and theoretical calculation methods, the effect on water-holding capacity of oxygen-containing functional groups. The experimental results showed that graphite can be oxidized, and forms epoxy groups most easily, followed by hydroxyl and carboxyl groups. The prepared graphene oxide forms a membrane-state as a single layer structure, with an irregular surface. The water-holding capacity of lignite increased with the content of oxygen-containing functional groups. The influence on the configuration of water molecule clusters and binding energy of water molecules of different oxygen-containing functional groups was calculated by density functional theory. The calculation results indicated that the configuration of water molecule clusters was totally changed by oxygen-containing functional groups. The order of binding energy produced by oxygen-containing functional groups and water molecules was as follows: carboxyl > edge phenol hydroxyl >epoxy group. Finally, it can be concluded that the potential to form more hydrogen bonds is the key factor influencing the interaction energy between model compounds and water molecules.     

Crystal structures of arginine deiminase with covalent reaction intermediates; implications for catalytic mechanism

Arginine deiminase (ADI), an enzyme that hydrolyzes arginine to generate energy in many parasitic microorganisms, has potent anticancer activities and can halt growth of solid tumors. We determined the crystal structure of ADI from Mycoplasma arginini in two different forms (1.6 and 2.0 A resolution) using multiple isomorphous replacement. ADI shares common structural features with the arginine-catabolizing enzymes Arg:Gly amidinotransferase and dimethylarginine dimethyl-aminohydrolase; ADI contains an additional domain of five helices. The scissile C-N bonds of the substrates and the catalytic triads (Cys398-His269-Glu213 of ADI) for the three enzymes superimpose on each other. The ADI structure from form I crystals corresponds to a tetrahedral intermediate with four heteroatoms (1S, 2N, 1O) covalently bonded to the reaction-center carbon. The structure from form II crystals represents an amidino-enzyme complex; the reaction-center carbon is covalently bonded to Cys398 sulfur and two nitrogens, and the reacting water molecule is only 2.54 A away.     

A small-angle X-ray solution scattering study of bovine alpha-crystallin.

The native high molecular mass form of alpha-crystallin, the most important soluble protein in the eye lens, and its low molecular mass form obtained at 37 degrees C in dilute solutions were investigated by synchrotron radiation small-angle X-ray scattering. The alpha-crystallin solutions are polydisperse and good fits to the experimental data can be obtained using distributions of spheres with radii varying between about 5 and 10 nm. In spite of the polydispersity, two different ab initio methods were used to retrieve low resolution shapes from the scattering data. These shapes correspond to the z-average structure of the oligomers. In the absence of any symmetry constraints, the scattering curves of the two forms of alpha-crystallin yield bean-like shapes. The shape corresponding to the low molecular mass form has about 20% less mass at the periphery. Imposing tetrahedral symmetry on the average structures worsens the fit to the experimental data. We emphasized the apparent contradiction between hydrodynamic and molecular properties of alpha-crystallin. An explanation was put forward based on the presence of solvent-exposed flexible C-terminal extensions. We present two bead models ('hollow globule with tentacles' and 'bean with tentacles') based on NMR and cryo-electron microscopy studies and discuss how well they correspond with our data from X-ray scattering, light scattering and analytical ultracentrifugation.     

On fractal properties of arterial trees

The question of fractal properties of arterial trees is considered in light of data from the extensive tree structure of the right coronary artery of a human heart. Because of the highly non-uniform structure of this tree, the study focuses on the purely geometrical rather than statistical aspects of fractal properties. The large number of arterial bifurcations comprising the tree were found to have a mixed degree of asymmetry at all levels of the tree, including the depth of the tree where it has been generally supposed that they would be symmetrical. Cross-sectional area ratios of daughter to parent vessels were also found to be highly mixed at all levels, having values both above and below 1.0, rather than consistently above as has been generally supposed in the past. Calculated values of the power law index which describes the theoretical relation between the diameters of the three vessel segments at an arterial bifurcation were found to range far beyond the two values associated with the cube and square laws, and not clearly favoring one or the other. On the whole the tree structure was found to have what we have termed "pseudo-fractal" properties, in the sense that vessels of different calibers displayed the same branching pattern but with a range of values of the branching parameters. The results suggest that a higher degree of fractal character, one in which the branching parameters are constant throughout the tree structure, is unlikely to be attained in non-uniform vascular structures.     

Crystal structures of an ATP-dependent hexokinase with broad substrate specificity from the hyperthermophilic archaeon Sulfolobus tokodaii

Hexokinase catalyzes the phosphorylation of glucose to glucose 6-phosphate by using ATP as a phosphoryl donor. Recently, we identified and characterized an ATP-dependent hexokinase (StHK) from the hyperthermophilic archaeon Sulfolobus tokodaii, which can phosphorylate a broad range of sugar substrates, including glucose, mannose, glucosamine, and N-acetylglucosamine. Here we present the crystal structures of StHK in four different forms: (i) apo-form, (ii) binary complex with glucose, (iii) binary complex with ADP, and (iv) quaternary complex with xylose, Mg(2+), and ADP. Forms i and iii are in the open state, and forms ii and iv are in the closed state, indicating that sugar binding induces a large conformational change, whereas ADP binding does not. The four different crystal structures of the same enzyme provide "snapshots" of the conformational changes during the catalytic cycle. StHK exhibits a core fold characteristic of the hexokinase family, but the structures of several loop regions responsible for substrate binding are significantly different from those of other known hexokinase family members. Structural comparison of StHK with human N-acetylglucosamine kinase and other hexokinases provides an explanation for the ability of StHK to phosphorylate both glucose and N-acetylglucosamine. A Mg(2+) ion and coordinating water molecules are well defined in the electron density of the quaternary complex structure. This structure represents the first direct visualization of the binding mode for magnesium to hexokinase and thus allows for a better understanding of the catalytic mechanism proposed for the entire hexokinase family.     

Dimerisation and an increase in active site aromatic groups as adaptations to high temperatures: X-ray solution scattering and substrate-bound crystal structures of Rhodothermus marinus endoglucanase Cel12A

Cellulose, a polysaccharide consisting of beta-1,4-linked glucose, is the major component of plant cell walls and consequently one of the most abundant biopolymers on earth. Carbohydrate polymers such as cellulose are molecules with vast diversity in structure and function, and a multiplicity of hydrolases operating in concert are required for depolymerisation. The bacterium Rhodothermus marinus, isolated from shallow water marine hot springs, produces a number of carbohydrate-degrading enzymes including a family 12 cellulase Cel12A. The structure of R.marinus Cel12A in the ligand-free form (at 1.54 angstroms) and structures of RmCel12A after crystals were soaked in cellopentaose for two different lengths of time, have been determined. The shorter soaked complex revealed the conformation of unhydrolysed cellotetraose, while cellopentaose had been degraded more completely during the longer soak. Comparison of these structures with those of mesophilic family 12 cellulases in complex with inhibitors and substrate revealed that RmCel12A has a more extensive aromatic network in the active site cleft which ejects products after hydrolysis. The substrate structure confirms that during hydrolysis by family 12 cellulases glucose does not pass through a (2,5)B conformation. Small-angle X-ray scattering analysis of RmCel12A showed that the enzyme forms a loosely associated antiparallel dimer in solution, which may target the enzyme to the antiparallel polymer strands in cellulose.     

毛竹杉木混交林土壤团粒结构的分形特征研究

运用分形理论对杉木纯林（19年生）、毛竹纯林（19年生）、6种杉木毛竹混交林（杉木19年生）的土壤团粒结构进行研究,建立了土壤团粒结构的分形维数与土壤团聚体含量、土壤结构体破坏率之间的回归模型,在此基础上,运用弹性分析与边际分析法进一步探讨了土壤团粒结构的分形维数对土壤性质变化所产生的影响效应。结果表明:土壤>0.25mm水稳定性团聚体含量越大,团粒结构的分形维数越小,土壤的结构与稳定性就越好;土壤团粒结构分形维数与水稳定性团聚体（>0.25 mm及>5.0mm）含量及结构体破坏率之间均存在极显著的回归关系;土壤团粒结构分形维数对土壤性质的变化产生较大的影响效应。本研究为毛竹杉木混交林的栽培管理,土壤肥力的科学评价提供依据。