Carlo Andrea Mattia

Bovine seminal ribonuclease: structure at 1.9 A resolution.

The crystal structure of bovine seminal ribonuclease, a homodimeric enzyme closely related to pancreatic ribonuclease, has been refined at a nominal resolution of 1.9 A employing data collected on an electronic area detector. The final model consists of two chains containing 1990 non-H atoms, seven sulfate anions and 113 water molecules per asymmetric unit. The unit-cell parameters are a = 36.5 (1), b = 66.7 (1) and c = 107.5 (2) A, space group P22(1)2(1). The R factor is 0.177 for 16 492 reflections in the resolution range 6.0-1.9 A and the deviations from ideal values of bond lengths and bond angles are 0.020 A and 3.7 degrees, respectively. The molecule is formed by two pancreatic like chains, which have their N-terminal segments interchanged so that each active site is formed by residues from both subunits. The two chains are related by a non-crystallographic twofold symmetry and are covalently linked by two consecutive disulfide bridges, which form an unusual sixteen-membered ring across the dimer interface. The deviations from the molecular symmetry, the hydration shell and the sulfate-binding sites are also discussed in relation to the known structure of the pancreatic enzyme.

Applications of Isothermal Titration Calorimetry in Biophysical Studies of G-quadruplexes

G-quadruplexes are higher-order nucleic acids structures formed by G-rich sequences that are stabilized by tetrads of hydrogen-bonded guanine bases. Recently, there has been growing interest in the study of G-quadruplexes because of their possible involvement in many biological processes. Isothermal titration calorimetry (ITC) has been proven to be a useful tool to study the energetic aspects of G-quadruplex interactions. Particularly, ITC has been applied many times to determine the thermodynamic properties of drug-quadruplex interactions to screening among various drugs and to address drug design. In the present review, we will focus on the ITC studies of G-quadruplex structures and their interaction with proteins and drugs and the most significant results will be discussed.

Targeting DNA quadruplexes with distamycin A and its derivatives: An ITC and NMR study

The use of small molecules that bind and stabilize G-quadruplex structures is emerging as a promising way to inhibit telomerase activity in tumor cells. In this paper, isothermal titration calorimetry (ITC) and 1H NMR studies have been conducted to examine the binding of distamycin A and its two carbamoyl derivatives (compounds 1 and 2) to the target [d(TGGGGT)]4 and d[AG3(T2AG3)3] quadruplexes from the Tetrahymena and human telomeres, respectively. The interactions were examined using two different buffered solutions containing either K+ or Na+ at a fixed ionic strength, to evaluate any influence of the ions present in solution on the binding behaviour. Experiments reveal that distamycin A and compound 1 bind the investigated quadruplexes in both solution conditions; conversely, compound 2 appears to have a poor affinity in any case. Moreover, these studies indicate that the presence of different cations in solution affects the stoichiometry and thermodynamics of the interactions.

Selective Binding of Distamycin A Derivative to G-Quadruplex Structure [d(TGGGGT)](4).

Guanine-rich nucleic acid sequences can adopt G-quadruplex structures stabilized by layers of four Hoogsteen-paired guanine residues. Quadruplex-prone sequences are found in many regions of human genome and in the telomeres of all eukaryotic organisms. Since small molecules that target G-quadruplexes have been found to be effective telomerase inhibitors, the identification of new specific ligands for G-quadruplexes is emerging as a promising approach to develop new anticancer drugs. Distamycin A is known to bind to AT-rich sequences of duplex DNA, but it has recently been shown to interact also with G-quadruplexes. Here, isothermal titration calorimetry (ITC) and NMR techniques have been employed to characterize the interaction between a dicationic derivative of distamycin A (compound 1) and the [d(TGGGGT)]4 quadruplex. Additionally, to compare the binding behaviour of netropsin and compound 1 to the same target, a calometric study of the interaction between netropsin and [d(TGGGGT)]4 has been performed. Experiments show that netropsin and compound 1 are able to bind to [d(TGGGGT)]4 with good affinity and comparable thermodynamic profiles. In both cases the interactions are entropically driven processes with a small favourable enthalpic contribution. Interestingly, the structural modifications of compound 1 decrease the affinity of the ligand toward the duplex, enhancing the selectivity.

Increasing the X-ray Diffraction Power of Protein Crystals by Dehydration: The Case of Bovine Serum Albumin and a Survey of Literature Data

Serum albumin is one of the most widely studied proteins. It is the most abundant protein in plasma with a typical concentration of 5 g/100 mL and the principal transporter of fatty acids in plasma. While the crystal structures of human serum albumin (HSA) free and in complex with fatty acids, hemin, and local anesthetics have been characterized, no crystallographic models are available on bovine serum albumin (BSA), presumably because of the poor diffraction power of existing hexagonal BSA crystals. Here, the crystallization and diffraction data of a new BSA crystal form, obtained by the hanging drop method using MPEG 5K as precipitating agent, are presented. The crystals belong to space group C2, with unit-cell parameters a = 216.45 Å, b = 44.72 Å, c = 140.18 Å, β = 114.5°. Dehydration was found to increase the diffraction limit of BSA crystals from ~8 Å to 3.2 Å, probably by improving the packing of protein molecules in the crystal lattice. These results, together with a survey of more than 60 successful cases of protein crystal dehydration, confirm that it can be a useful procedure to be used in initial screening as a method of improving the diffraction limits of existing crystals.

Dolabriferol: A new polypropionate from the skin of the anaspidean mollusc Dolabrifera dolabrifera

Abstract A novel polypropionate, dolabriferol ( 1 ), has been isolated from the anaspidean mollusc Dolabrifera dolabrifera . The structure has been suggested mainly by spectral methods whereas the relative stereochemistry has been determined by X-ray analysis.

STRUCTURE OF ACRIDINE ORANGE HEXAFLUOROSILICATE TETRAHYDRATE

Abstract The crystal structure of acridine orange hexafluorosilicate tetrahydrate is reported. (C 17 H 20 N 3 ) 2 SiF 6 ·4H 2 O, M r = 746.88, triclinic, space group P1, a = 7.262(2), b = 3.110(2), c = 18.846(2) A , α = 94.10(1), β = 92.28(2), γ = 95.49(2)°, V = 1779(1) A 3 , Z = 2, D calc = 1.394 g cm −3 , F (000) = 788, CuKα monochromated radiation ( λ = 1.54056 A ), μ = 1.251 mm −1 . Final R = 0.068 for 1946 reflections ( I ⩾ 2.5 σ ( I )) and 460 refined parameters. The two orange acridinium moieties, which are present in the asymmetric unit, are related by a non-crystallographic translation coupled with rotation of less than 3°. The packing is characterized by stacks of isooriented dye cations which pile up along a . Hexafluorosilicate anion and water molecules assemble in channels surrounded in b and c directions by stacks of dye. The acridine protonated nitrogen atoms, hexafluorosilicate anion and water molecules are involved in an extensive network of hydrogen bonds. The stacking interactions of the dye have been tested also by visible absorption spectra both in solution and in the solid state.

Thermodynamic Analysis Of Quadruplex Dna-Drug Interaction

This work studies the binding properties of distamycin and its carbamoyl analog, containing four pyrrole units, with the [d(TGGGGT)] 4 quadruplex by means of isothermal titration calorimetry (ITC). Analysis of the ITC data reveals that drug/quadruplex binding stoichiometry is 1:1 for both interactions and that distamycin analog gives approximately a 10-fold increase in the quadruplex affinity.

25-deoxycacospongionolide B and cacospongionolide C, two new terpenoids from the sponge Fasciospongia cavernosa

Abstract 25-Deoxycacospongionolide B (3), a new bioactive sesterterpene, and a diterpene, cacospongionolide C (4), have been isolated as minor components from the Adriatic sponge Fasciospongia cavernosa. The structures were proposed on the basis of spectroscopic data and defined for the former on the basis of X-ray analysis. Brine shrimp and fish lethalities of 25-deoxycacospongionolide B are reported.

Amazing new alkaloid skeletons from the marine sponge Reniera sarai

Reniera sarai possesses two homologous series of alkaloids, sarains 1-3 and sarains A-C, along with some rela- ted minor metabolites which include isosarain-I (1). We now report the complete structural elucidation of 1, which suppor- ts and further clarifies the previously only partially charac- terized structures of sarains 1-3. X-ray structure of an ace- tate derivative of sarain-A has discovered an amazing new ma- crocyclic alkaloid skeleton. All the sarains have been charac- terized by an extensive use of 2D NMR methods.