Structural study of modified fibrinogen microcrystals by electron microscopy

The same molecular shape of proteolytically modified fibrinogen has been identified in two different crystalline forms: orthorhombic P2₁2₁2 with a = 44.7(± 1.7) nm, b = 11.8(± 1.0) nm, c = 3.8 nm and monoclinic P2₁ with a = 17.7(± 0.6) nm, b = 16.2(± 1.0) nm, c = 4.8 nm and β = 95 °. The shape of the molecule is more detailed than has been reported. It has the commonly accepted elongated form 44.5(± 1.5) nm long with a 2-fold axis perpendicular to the major axis of the molecule. Each end domain shows a distinctive substructure and has an asymmetry similar to that reported by Williams (1981) and Mosesson et al. (1981) from single molecule observations. The ends are flattened, having overall dimensions of approximately 12 nm × 9 nm × 4 nm. The major difference between this model and previous models is the absence of a central nodule. There are, however, two small additional protein-dense regions at 5.0 nm from the centre of the rod connecting the two ends. A rough estimate of the relative heights of the different parts of the molecule was obtained using the two different projections of the molecule obtained from the two different crystalline forms. The molecule appears to be slightly bent at the centre, as predicted by Doolittle (1977).     

Crystal Structure Prediction based on Statistical Potentials

Organic molecule crystals are becoming more and more important in applications like piezoelectricity, ferroelectricity and pigments. These properties depend on the molecule and on the crystal structure. For this reason much effort is being made to predict the crystal structure of organic molecules. We have developed a new algorithm differing mainly in three features from other approaches (simulated annealing, Monte Carlo etc.). First, we analyze just one molecule for proper symmetry operations building up the crystal; second, the program works in a discrete space; and finally the scoring function (energy function) is derived statistically from known crystal structures and tabulated. Our program computes a list of crystal structures weighted according to our scoring function. The new algorithm FlexCryst is currently implemented for the four space groups P1, Pbar1, P2₁, and P2₁2₁2₁. The three latter space groups are widespread in nature. The algorithm computes structural models of acceptable quality and shows excellent time performance. During our validation we found the experimental structure among the structures proposed by the algorithm in 123 of 129 cases for P1, in 66 of 95 cases for Pbar1, in 73 of 100 cases for P2₁, and in 94 of 98 cases for P2₁2₁2₁. The performance depends on the space group. In the case of P1 the run time per molecule is about two minutes and increases up to roughly one hour for the space group P2₁.     

Spectral and photochemical properties of borohydride-treated D1-D2-cytochrome b-559 complex of photosystem II

The D1-D2-cytochrome b-559 reaction center complex of photosystem II with an altered pigment composition was prepared from the original complex by treatment with sodium borohydride (BH⁻₄). The absorption spectra of the modified and original complexes were compared to each other and to the spectra of purified chlorophyll a and pheophytin a (Pheo a) treated with BH⁻₄ in methanolic solution. The results of these comparisons are consistent with the presence in the modified complex of an irreversibly reduced Pheo a molecule, most likely 13¹-deoxo-13¹-hydroxy-Pheo a, replacing one of the two native Pheo a molecules present in the original complex. Similar to the original preparation, the modified complex was capable of a steady-state photoaccumulation of Pheo⁻ and P680⁺. It is concluded that the pheophytin a molecule which undergoes borohydride reduction is not involved in the primary charge separation and seems to represent a previously postulated photochemically inactive Pheo a molecule. The Q_y and Q_x transitions of this molecule were determined to be located at 5°C at 679.5–680 nm and 542 nm, respectively.     

Ab initio structure solution of a dimeric cytochrome c 3 from Desulfovibrio gigas containing disulfide bridges

The 1.2?Å resolution crystal structure of the 29?kDa di-tetrahaem cytochrome c ₃ from the sulfate reducing bacterium Desulfovibrio gigas was solved by ab initio methods, making this the largest molecule to be solved by this procedure. The actual refined model of the cysteine-linked dimeric molecule reveals that this molecule is very similar to the non-covalently linked symmetrical dimer of the di-tetrahaem cytochrome c ₃ from Desulfomicrobium norvegicum. Each monomer has the typical polypeptide fold, haem arrangement and iron coordination found for the tetrahaem cytochrome c ₃ molecules. The interface between the covalently linked monomers in the asymmetric unit of the crystal shows a pseudo two-fold arrangement, disturbed from symmetry by crystal packing forces. The fact that D. gigas contains a dimeric tetrahaem cytochrome with solvent accessible disulfide bridges and that this cytochrome specifically couples hydrogen oxidation to thiosulfate reduction in bacterial extracts provides an interesting aspect related to disulfide exchange reactions in this microorganism.     

Biochemical and biophysical studies on cytochrome aa3. VI. Reaction of cyanide with oxidized and reduced enzyme

1.

1. The reaction of cyanide with cytochrome aa₃ in the fully oxidized and reduced states has been studied. In both cases a single molecule of cyanide is bound reversibly per molecule of aa₃ (that is, 1 mole cyanide per 2 equivalents of haem a).     

Determination of 1-aryl-4-propylpiperazine pKa values: The substituent on aryl modulates basicity

In order to design a potential drug, it is important to know its pK_a because the protonation state of the molecule will be critical for ligand–receptor interaction and for the pharmacokinetic of the molecule. pK_a values of a series of 1-(substitutedphenyl)-4-propylpiperazines were measured to study how the presence of a substituent on the phenyl ring modulates the basicity of N-4 nitrogen. pK_a values indicated that the position of the substituent was crucial. In general, the introduction of the substituent in ortho-position of the phenyl ring increased the basicity of the molecule. This effect appeared to be related to steric and conformational effects and not to the electronic properties of the substituent. On the other hand, meta- and para-substituted derivatives showed a slight decrease of pK_a that was qualitatively consistent with the electronic properties of the substituent.     

Cytochrome c4 from Pseudomonas aeruginosa

The dihaem cytochrome c₄ from Pseudomonas aeruginosa has been crystallized in space group P6₅22 with cell dimensions $\text{a = b = 62.4}\text{A}\text{?}\text{, c = 174.2}\text{A}\text{?}$, and one molecule per asymmetric unit. Two heavy-atom derivatives, UO₂(NO₃)₂ and K₂Pt(NO₂)₄, which substitute at one and three sites, respectively, have allowed a low-resolution electron density map to be obtained. This shows clearly the two domains of the molecule.     

The effects of external electric field: creating non-zero first hyperpolarizability for centrosymmetric benzene and strongly enhancing first hyperpolarizability for non-centrosymmetric edge-modified graphene ribbon H2N-(3,3)ZGNR-NO2

How to generate a non-zero first hyperpolarizability for a centrosymmetric molecule is a challenging question. In this paper, an external (pump) electric field is used to make a centrosymmetric benzene molecule generate a non-zero value of the electric field induced first hyperpolarizability (β ^F ). This comes from the centrosymmetry breaking of electron cloud. Two interesting rules are exhibited. (1) β ^F is anisotropic for different directional fields (F _i, i?=?X, Y, Z). (2) The field dependence of β ^F is a non-monotonic function, and an optimum external electric field causes the maximum value of β ^F . The largest first hyperpolarizability β ^F reaches the considerable level of 3.9?×?10⁵ a.u. under F _Y?=?330?×?10^?4 a.u. for benzene. The external electric field effects on non-centrosymmetric edge-modified graphene ribbon H₂N-(3,3)ZGNR-NO₂ was also studied in this work. The first hyperpolarizability reaches as much as 2.1?×?10⁷ a.u. under F _X?=?600?×?10^?4 a.u. for H₂N-(3,3)ZGNR-NO₂. We show that the external electric field can not only create a non-zero first hyperpolarizability for centrosymmetric molecule, but also remarkably enhance the first hyperpolarizability for a non-centrosymmetric molecule.     

Minimal models of multi-site ligand-binding kinetics

Mathematical models based on the current understanding of co-operativity in ligand binding to the (macro) molecule and relating the dose-response (saturation) curve of the (macro) molecule ligation to intrinsic dissociation constants characterizing the affinities of ligand for binding sites of both unliganded and partly liganded (macro) molecule have been developed. The simplified models disregarding the structural properties and considerations concerning conformational changes of the (macro) molecule retain the ability to yield sigmoid curves of ligand binding and reflect the co-operativity. Model 1 contains only three parameters, parameter κ (a multiplier characterising the change in the affinity) reflects also the existence and type of co-operativity of ligand binding: κ<1 corresponds to positive co-operativity, κ>1 to the negative and κ=1 to the absence of any co-operativity. Model 2 contains an extra parameter, ω, equilibrium constant for the T₀↔R₀ transition but fails to produce dose-response, which would suggest negative co-operativity. For any fixed n>1, the deviation of the dose-response (saturation) curve from the Henri hyperbola depends either solely on parameter κ (Model 1) or also on parameter ω (Model 2). The (macro) molecule being a receptor, both models yield a diversity of dose-response curves due to possible variety of efficacies of the (macro) molecule. The models may be considered as extensions of the Henri model: in case the dissociation constants remain unchanged, the proposed models are reduced to the latter.     

Kinetic Theory Model for Ion Movement through Biological Membranes: II. Interionic Selectivity

The equation presented in the previous paper for steady-state membrane ionic current as a function of externally applied electric field strength is numerically analyzed to determine the influence of ionic and membrane molecule parameters on current densities. The model displays selectivity between different ions. A selectivity coefficient S_i, defined as the ratio of current carried by an ionic species i at a given field strength to the current carried by a reference species at the same field strength, has the following properties: (a) S_i is a function of electric field strength except for ion-membrane molecule interactions yielding velocity independent collision frequencies; (b) for ion-membrane molecule interactions characterized by a collision frequency that is a decreasing (increasing) function of increasing ionic velocity, ions whose S_i > 1 (<1) at zero field strength will show maxima (minima) (minima[maxima]) in their S_i vs. electric field strength curves.     

Molecular orientation and position of the pig M4 and H4 isoenzymes of lactate dehydrogenase in their crystal cells

Ternary complexes of M₄ and H₄ isoenzymes of porcine lactate dehydrogenase have been crystallized, the M₄ isoenzyme in space group P22₁2₁ with one half molecule per asymmetric unit, and the H₄ isoenzyme in space group C₂ with one whole molecule per asymmetric unit. The orientation and position of the tetramers in their unit cells have been determined by X-ray analysis. Rotation function results comparing the ternary complexes of the pig M₄ isoenzyme with the known structure of the dogfish M₄ enzyme not only defined the direction but also permitted recognition of the individual P, Q and R molecular 2-fold axes. The position of the molecular center was determined by placing a properly oriented dogfish M₄ lactate dehydrogenase electron density into the pig muscle cell. Structure factors were calculated as the molecular center was varied along the common crystallographic and molecular 2-fold axis and compared with observed amplitudes. Precession photographs of the three major zones of the monoclinic pig H₄ isoenzyme exhibited striking similarities to the corresponding zones of the orthorhombio pig M₄ isoenzyme, in spite of the differences in space groups. These similarities permit the determination of approximate phases from the implied orientation and position of the pig H₄ lactate dehydrogenase molecule in its monoclinic cell.     

Theoretical studies of clonal selection: minimal antibody repertoire size and reliability of self-non-self discrimination.

Viewing the immune system as a molecular recognition device designed to identify “foreign shapes”, we estimate the probability that an immune system with N_Ab monospecific antibodies in its repertoire can recognize a random foreign antigen. Furthermore, we estimate the improvement in recognition if antibodies are multispecific rather than monospecific. From our probabilistic model we conclude: (1) clonal selection is feasible, i.e. with a finite number of antibodies an animal can recognize an effectively infinite number of antigens; (2) there should not be great differences in the specificities of antibody molecules among different species; (3) the region of a foreign molecule recognized by an antibody must be severely limited in extent; (4) the probability of recognizing a foreign molecule, P, increases with the antibody repertoire size N_Ab; however, below a certain value of N_Ab the immune system would be very ineffectual, while beyond some high value of N_Ab further increases in N_Ab yield diminishing small increases in P; (5) multispecificity is equivalent to a modest increase (probably less than 10) in the antibody repertoire size N_Ab, but this increase can substantially improve the probability of an immune system recognizing a foreign molecule.Besides recognizing foreign molecules, the immune system must distinguish them from self molecules. Using the mathematical theory of reliability we argue that multisite recognition is a more reliable method of distinguishing between molecules than single site recognition. This may have been an important evolutionary consideration in the selection of weak non-covalent interactions as the basis of antigen-antibody bonds.     

Structure of cytochrome c551 from Pseudomonas aeruginosa refined at 1.6 Å resolution and comparison of the two redox forms

The molecular structures of ferri- and ferrocytochrome c₅₅₁ from Pseudomonas aeruginosa have been refined at a resolution of 1.6 Å, to an R factor of 19.5% for the oxidized molecule and 18.7% for the reduced. Reduction of oxidized crystals with ascorbate produced little change in cell dimensions, a 10% mean change in F_obs, and no damage to the crystals. The heme iron is not significantly displaced from the porphyrin plane. Bond lengths from axial ligands to the heme iron are as expected in a low-spin iron compound. A total of 67 solvent molecules were incorporated in the oxidized structure, and 73 in the reduced, of which four are found inside the protein molecule. The oxidized and reduced forms have virtually identical tertiary structures with 2 ° root-mean-square differences in main-chain torsion angles φ and ψ, but with larger differences along the two edges of the heme crevice. The difference map and pyrrole ring tilt suggest that a partially buried water molecule (no. 23) in the heme crevice moves upon change of oxidation state.Pseudomonas cytochrome c₅₅₁ differs from tuna cytochrome c in having: (1) a water molecule (no. 23) at the upper left of the heme crevice; that is, between Pro62 and the heme pyrrol 3 ring on the sixth ligand Met61 side, where tuna cytochrome c has an evolutionary invariant Phe82 ring; (2) a string of hydrophobic side-chains along the left side of the heme crevice, and fewer positively charged lysines in the vicinity; and (3) a more exposed and presumably more easily ionizable heme propionate group at the bottom of the molecule. A network of hydrogen bonds in the heme crevice is reminiscent of that inside the heme crevice of tuna cytochrome c. As in tuna, a slight motion of the water molecule toward the heme is observed in the oxidized state, helping to give the heme a more polar microenvironment. The continuity of solvent environment between the heme crevice and the outer medium could explain the greater dependence of redox potential on pH in cytochrome c₅₅₁ than in cytochrome c.     

Reversible dehydration process in a novel three-dimensional covalent network based on pyrimidine-4,6-dionato bridging ligand

The novel metal-organic polymer [Zn(μ-pmdt)(H₂O)]_n (1) (pmdt = pyrimidine-4,6-dionate) exhibits an extended three-dimensional network with two crystallographically independent pmdt bridging ligands, one zinc(II) atom and a coordinated water molecule. The Zn(II) atoms are located at the centre of a distorted ZnN₂OOw tetrahedral chromophore. One of the pmdt ligands acts as tetradentate bridge linking four metal centers, while the other pmdt ligand shows a bidentate coordination mode bridging two metal centers. The compound shows a reversible dehydration process, involving a coordinated water molecule, to lead an amorphous anhydrous phase. This transition has been characterized by thermogravimetric and variable-temperature X-ray powder diffraction techniques.     

A structural study of the synergic envelopment of acetonitrile by a Cd(II) activated molecular receptor formed from cyclen with appended 2-hydroxy-3-phenylpropyl moieties

The newly synthesised metal ion activated molecular receptor [Cd{1,4,7,10-tetrakis((R)-(−)-2-hydroxy-3-phenylpropyl)-1,4,7,10-tetraazacyclododecane}](ClO₄)₂ (hereafter [CdL](ClO₄)₂) acts as a molecular receptor for acetonitrile. The receptor was characterised by X-ray crystallography in its metal free form, as its Cd(II) complex with no included molecule, as its Cd(II) complex with an included acetonitrile molecule and, for comparative purposes, as its Zn(II) complex with a partially included acetonitrile molecule. These structural studies demonstrated that the Cd(II) complex is eight-coordinate, with the potential to form a well defined hydrophobic cavity that can contain one acetonitrile molecule through four hydrogen-bonds, whereas the Zn(II) complex is six-coordinate, with a less rigidly constituted binding cavity, such that when solvated by acetonitrile the solvating molecule is retained by only a single hydrogen-bond.     

Topography of cyclodextrin inclusion complexes : Part II. The iodine-cyclohexa-amylose tetrahydrate complex; its molecular geometry and cage-type crystal structure

Iodine-cyclohexa-amylose tetrahydrate [(C₆H₁₀O₅)₆ ·I₂·d4H₂O] crystallizes in the orthorhombic space-group P2₁2₁2₁, a  14.240 Å, b  36.014 Å, c  9.558 Å. The structure was solved by heavy-atom techniques and refined by least-squares methods to a conventional discrepancy index R  0.148 for the 2872 observed data. The six d-glucose residues are in the C1 chair conformation; the conformational angles vary in magnitude from 45 to 66°, the angles O(5)-C(5)-C(6)-O(6) are close to · 70°, and the six O(4) atoms are almost coplanar (r.m. s. displacement 0.13 Å). Only four of the six O(2) ?O(3) intramolecular hydrogen bonds have formed, which renders the molecule less symmetrical and more conical-shaped than in the previously determined α-cyclodextrin-potassium acetate complex. The iodine molecule is coaxial with the cyclohexa-amylose molecule. The I-I distance is a conventional 2.677 Å. Close interactions between the iodine atoms and the host molecule comprise carbon atoms C(5) and C(6) and oxygen atoms O(4), with interatomic distances all equal to or greater than van der Waals contacts. Intermolecular, almost-linear, short contacts O ? I-I?O with I?O distances of 3.22 and 3.07 Å indicate attractive interaction.The molecules are arranged in herring-bone “cage-type” fashion, with the four water molecules as space-filling mediators; the structure is held together by an intricate network of hydrogen bonds.     

Interaction between lanthanum ion and horseradish peroxidase in vitro

The interaction between lanthanum ion (La³⁺) and horseradish peroxidase (HRP) in vitro was investigated using a combination of biophysical and biochemical methods. When the molar ratio of La³⁺ and HRP is low, it was found that the interaction between La³⁺ and HRP mainly depends on the electrostatic attraction, van der waals force and hydrogen bond etc. Thus, the interaction is weak and the La–HRP complex cannot be formed in vitro. As expected, the interaction can change the conformation of HRP molecule, leading to the increase in the non-planarity of the porphyrin ring in the heme group of HRP molecule, and then in the exposure degree of the active center, Fe(III) of the porphyrin ring of HRP molecule. Therefore, the catalytic activity of HRP for the H₂O₂ reduction is improved. When the molar ratio of La³⁺ and HRP is high, La³⁺ can strongly coordinate with O and/or N in the amide group of the polypeptide chain of HRP molecule, forming the La–HRP complex. The formation of the La–HRP complex causes the change in the conformation of HRP molecule, leading to the decrease in the non-planarity of the porphyrin ring in the heme group of HRP molecule, and then in the exposure degree of the active center, Fe(III) of the porphyrin ring of HRP molecule. Thus, the catalytic activity of HRP for the H₂O₂ reduction is decreased comparing with that of HRP in the absence of La³⁺. The results can provide some references for understanding the interaction mechanism between trace elements ions and peroxidase in living organisms.     

Specific cleavage of the native type III collagen molecule with trypsin. Similarity of the cleavage products to collagenase-produced fragments and primary structure at the cleavage site.

Solutions of native Type III collagen (chain composition, [α1(III)]₃) exhibit a rapid and dramatic decrease in relative viscosity when incubated with trypsin. Cleavage products of the reaction were precipitated with ammonium sulfate and isolated in denatured form by molecular sieve chromatography. They were found to be comprised of: α1(III)-T1 (molecular weight, 71,000) derived from the NH₂-terminal portion of the Type III molecule; and α1(III)-T2 (molecular weight, 24,000) from the COOH-terminal portion of the molecule. Determination of the amino acid sequence at the NH₂-terminal portion of α1(III)-T2 as well as at the COOH-terminus of α(III)-T1 demonstrated that the products arose from specific cleavage of the type III molecule at an arginine-glycine bond corresponding to residues 780–781 in the repetitive triplet sequence of the α1(III) chain. The results suggest that the trypsin-susceptible bond in the native Type III collagen molecule resides in a region characterized by a relative lack of the normal collagen helicity.     

Inactivation of Hydrogenase in Cell-free Extracts and Whole Cells of Chlamydomonas reinhardi by Oxygen

O₂ irreversibly inactivates hydrogenase from Chlamydomonas reinhardi. The mechanism for the inactivation involves the reaction of one molecule of hydrogenase with one molecule of O₂ (or two oxygen atoms) in the transition complex of the rate-limiting step. The second order rate constant for this reaction is 190 atmospheres⁻¹ minute⁻¹ (1.4 × 10⁵ molar⁻¹ minute⁻¹). At levels above 0.01 atmosphere O₂, the increased numbers of O₂ molecules may compete for the site of inactivation hindering the proper orientation for inactivation of any one O₂ molecule and resulting in lowered rates of inactivation.     

Structures and excitation energies of ozone-water clusters O3(H2O)n (n = 1-4)

Hybrid density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations have been carried out for ozone-water clusters O₃(H₂O)_n (n = 1-4) in order to obtain hydration effects on the absorption spectrum of ozone. The first water molecule in n = 1 is bound to the ozone molecule by an oxygen orientation form in which the oxygen atom of H₂O orients the central oxygen atom of O₃. In n = 2, the water dimer is bound to O₃ and then the cyclic structure is formed as the most stable structure. For n = 3 (or n = 4), the cyclic water trimer (or tetramer) is bound by a hydrogen bond to the ozone molecule. The TD-DFT calculations of O₃(H₂O)_n (n = 0-4) show that the first and second excitation energies of O₃ are blue-shifted by the interaction with the water clusters. The magnitude of the spectral shift is largest in n = 2, and the shifts of the excitation energies are +0.07 eV for S₁ and +0.13 eV for S₂ states. In addition to the spectral shifts (S₁ and S₂ states), it is suggested that a charge-transfer band is appeared as a low-lying excited state above the S₁ and S₂ states. The origin of the spectrum shifts was discussed on the basis of theoretical results.