Molecular dynamics simulation of a decasaccharide fragment of heparin in aqueous solution

Molecular dynamics (MD) simulations on heparin-water-sodium systems were carried out in order to establish a simulation protocol able to represent heparin solution conformation under physiological conditions. Atomic charges suitable for heparin oligosaccharides were obtained from ab initio quantum-mechanical computations, at the 6-31G(**) level. The GROMACS forcefield, the SPC, and SPC/E water models were employed. Also heparin was simulated with IdoA residues in 1C(4) or 2S(0) conformational states. The results of the performed MD simulations are in agreement with the available experimental data, suggesting that this approach can be applied for the study of heparin interactions with its target proteins and thus play a role in the development of new antithrombotic agents.     

Conformational transitions induced in heparin octasaccharides by binding with antithrombin III

The present study deals with the conformation in solution of two heparin octasaccharides containing the pentasaccharide sequence GlcN(NAc,6S)-GlcA-GlcN(NS,3,6S)-IdoA(2S)-GlcN(NS,6S) [AGA*IA; where GlcN(NAc,6S) is N-acetylated, 6-O-sulfated alpha-D-glucosamine, GlcN(NS,3,6S) is N,3,6-O-trisulfated alpha-D-glucosamine and IdoA(2S) is 2-O-sulfated IdoA (alpha-L-iduronic acid)] located at different positions in the heparin chain and focuses on establishing geometries of IdoA residues (IdoA(2S) and IdoA) both inside and outside the AGA*IA sequence. AGA*IA constitutes the active site for AT (antithrombin) and is essential for the expression of high anticoagulant and antithrombotic activities. Analysis of NMR parameters [NOEs (nuclear Overhauser effects), transferred NOEs and coupling constants] for the two octasaccharides indicated that between the 1C4 and 2S0 conformations present in dynamic equilibrium in the free state for the IdoA(2S) residue within AGA*IA, AT selects the 2S0 form, as previously shown [Hricovini, Guerrini, Bisio, Torri, Petitou and Casu (2001) Biochem. J. 359, 265-272]. Notably, the 2S0 conformation is also adopted by the non-sulfated IdoA residue preceding AGA*IA that, in the absence of AT, adopts predominantly the 1C4 form. These results further support the concept that heparin-binding proteins influence the conformational equilibrium of iduronic acid residues that are directly or indirectly involved in binding and select one of their equi-energetic conformations for best fitting in the complex. The complete reversal of an iduronic acid conformation preferred in the free state is also demonstrated for the first time. Preliminary docking studies provided information on the octasaccharide binding location agreeing most closely with the experimental data. These results suggest a possible biological role for the non-sulfated IdoA residue preceding AGA*IA, previously thought not to influence the AT-binding properties of the pentasaccharide. Thus, for each AT binding sequence longer than AGA*IA, the interactions with the protein could differ and give to each heparin fragment a specific biological response.     

Depiction of the forces participating in the 2-O-sulfo-alpha-L-iduronic acid conformational preference in heparin sequences in aqueous solutions

2-O-Sulfo-alpha-l-iduronic acid (IdoA2S) is one of the main components of heparin, an anticoagulant and antithrombotic polysaccharide able to potentiate the inhibitory effect of antithrombin over plasma serine proteases. This monosaccharide unit adopts an equilibrium between chair (1C4) and skew-boat (2SO) forms as a function of heparin sequence size and composition. Although the prevalence of the 1C4 chair conformation in monosaccharides is understood, the reasons for the increase in 2SO contribution in the whole polysaccharide chain are still uncertain. In this context, 0.2 mus molecular dynamics simulations of IdoA2S-containing oligosaccharides indicated that stabilization due to intramolecular hydrogen bonds around IdoA2S is highly correlated (p0.001) with the expected conformational equilibrium for this residue in solution. This behavior explains the known effect of different heparin compositions, at the monosaccharide level, on IdoA2S conformation in biological solutions.     

Theoretical investigation of the triphosphate forms of azidothymidine and thymidine

In this paper we investigate (using AM1 semi-empirical as well as HF methods at the STO-3G, 3-21G, 6-31G, 6-31G* and 6-31+G** level) the conformations, geometrical parameters, Mulliken charges, and solvation effects of the triphosphate form of AZT (AZTTP), as well as the thymidine nucleotide (dTTP) structure. Our calculated geometrical parameters and Mulliken charges, with and without solvation effects, are correlated with recent experimental results.     

B3LYP/6-311++G* * study of structure and spin-spin coupling constant in heparin disaccharide

Structures of heparin disaccharide have been analyzed by DFT using the B3LYP/6-311++G( * *) method. The optimized geometries of two forms of this disaccharide, differing in the conformation ((1)C(4) and (2)S(0)) of the IdoA2S residue, confirmed considerable influences of the sulfate and the carboxylate groups upon the pyranose ring geometries. The computed energies showed that disaccharide having the (1)C(4) form of the IdoA2S residue is more stable than that with the (2)S(0) form. Interatomic distances, bond and torsion angles showed that interconversion of the IdoA2S residue results in geometry changes in the GlcN,6S residue as well. Three-bond proton-proton and proton-carbon spin-spin coupling constants computed for both forms agree with the experimental data and indicate that only two chair forms contribute to the conformational equilibrium in disaccharide. Influences of the charged groups upon the magnitudes of spin-spin coupling constants are also discussed.     

Hybridization-displaced charges for amino-acids: a new model using two point charges per atom along with bond-center charges

A new charge distribution is proposed for the amino acids where each atom is associated with two point charges while each bond center is associated with one point charge. Centroids of charges arising due to atomic orbital hybridization called hybridization-displaced charges (HDC) and those located at the atomic sites and bond centers obtained by a modified form of the Mulliken scheme were combined. The density matrix calculations required for this analysis were performed at the B3LYP/6-31G** level of density functional theory. The combination of HDC centroids with the modified Mulliken charges was found to yield dipole moments and surface molecular electrostatic potentials (MEP) of the amino acids in good agreement with those obtained by rigorous DFT calculations or those obtained using the MEP-fitted CHelpG charges. This study shows that the combination of HDC centroids with the modified Mulliken charges is significantly superior to the conventional Mulliken charges.     

N.m.r. studies of the disulphated disaccharide obtained by degradation of bovine lung heparin with nitrous acid

The disulphated disaccharide IdoA(2SO3)-anManOH(6SO3) was prepared from bovine lung heparin by treatment with nitrous acid followed by borohydride reduction. The 1H- (400 MHz) and 13C-n.m.r. (100 MHz) spectra of this disaccharide derivative have been assigned completely using homonuclear spin-decoupling experiments, 13C-1H correlations, and a COSY-45 two-dimensional homonuclear correlation experiment. The 3JH,H values show that the IdoA(2SO3) residue exists in a single conformation throughout the temperature range 20-90 degrees.     

Effects of cation charges on the binding of stabilizers with human telomere and TERRA G-quadruplexes

Both telomere and telomeric repeat-containing RNAs (TERRA) can fold into G-quadruplexes (G4) in eukaryotic cells. Given their key roles in the regulation of telomere length and translation, telomere and TERRA G4 are interesting targets of novel drug development strategies. It is known that the cation charge of a stabilizer is crucial to the binding of G4 and stabilizer. However, the quantitative relationship between the cation charge of a stabilizer and the binding strengths with telomere and TERRA G4 remain unclear. In the current study, by substituting positive charged TMPyP4 with neutral and negative charged groups, the effects of cation charges on the binding conformation and binding strength of porphyrin stabilizers are investigated via molecular docking and molecular dynamic (MD) simulations. The results show that all TMPyP4 analogs form stable binding complexes with telomere and TERRA G4 and that, stabilizer charges have limited effects on binding conformation and can hardly lead to any special conformational alternations of G4. Our hydrogen bond analysis shows that all stabilizers can hardly form stable intermolecular hydrogen bonds with G4. Regarding binding strength levels, a linear correlation is found between the binding free energies and cation charges of stabilizers in all G4?stabilizer complexes, revealing the pivotal role of electrostatic interactions. The present work is the first to reveal a quantitative correlation between the charges and binding strengths of stabilizers in their binding with human telomere and TERRA G4, which will prove pivotal for G4 targeted drug design and development.     

Structure and activity of a unique heparin-derived hexasaccharide

A hexasaccharide representing a major sequence in porcine mucosal heparin has been enzymatically prepared from heparin. Its structure was determined by an integrated approach using chemical, enzymatic, and spectroscopic methods. Two-dimensional 1H homonuclear COSY, C-H correlation NMR, and selective irradiation were used to assign many of the NMR resonances. In addition, new techniques including sulfate determination by ion chromatography and Fourier transform IR and californium plasma desorption mass spectroscopy have been applied, resulting in an unambiguous structural assignment of delta IdoAp2S(1----4)-alpha-D-GlcNp2S6S(1----4)-alpha-L-IdoAp++ +(1----4)-alpha-D-GlcNA cp6S-(1----4)-beta-D-GlcAp(1----4)-alpha-D-GlcNp2S3S6S (where delta IdoA represents 4-deoxy-alpha-L-threo-hex-4-enopyranosyluronic acid, p represents pyranose, and GlcA and IdoA represent glucuronic and iduronic acid). This hexasaccharide contains a portion of the antithrombin III-binding site and has a Kd of 4 X 10(-5) M. Unlike other small heparin oligosaccharides, which are specific for coagulation factor Xa, it inhibits both factors IIa and Xa equally through antithrombin III. This hexasaccharide may have the unique capacity to act primarily through heparin cofactor II to inhibit thrombin (factor IIa) and shows over half of heparin's heparin cofactor II-mediated anti-factor IIa activity. These studies suggest the occurrence of contiguous binding sites on heparin for Xa, antithrombin III, and heparin cofactor II.     

DFT study of a substrate and inhibitors of 1-deoxy-2-xylulose-5-phosphate reductoisomerase – the potential novel target molecule for anti-malaria drug development

1-Deoxy-2-xylulose-5-phosphate (DOXP) reductoisomerase is a novel target for developing anti-malaria drugs. The determination of structural and electronic properties of the inhibitor molecules is of crucial importance for analyzing the interactions between DOXP-reductoisomerase and its inhibitors. Geometry-optimizations and single point calculations at the B3LYP/3-21G*//B3LYP/3-21G** and B3LYP/3-21G*//MP2/3-21G** levels were performed to determine the structures and charge distributions of an enzyme substrate (1-deoxy-D-xylulose 5-phosphate) and the two inhibitors (fosmidomycin and FR-900098). The theoretically derived bond lengths are in excellent agreement with the corresponding experimental values reported for similar structures. Partial charges and dipole moments are assigned using the Mulliken and natural population analyses. The calculated structures and partial charge distributions can readily be used for the further development of biologically active inhibitors of DOXP-reductoisomerase as well as parameters for docking experiments.Electronic Supplementary Material available.     

Purification and characterization of dermatan sulfate from the skin of the eel,Anguilla japonica

Glycosaminoglycans were isolated from the eel skin (Anguilla japonica) by actinase and endonuclease digestions, followed by a beta-elimination reaction and DEAE-Sephacel chromatography. Dermatan sulfate was the major glycosaminoglycan in the eel skin with 88% of the total uronic acid. The content of the IdoA2Salpha1-->4GalNAc4S sequence in eel skin, which shows anticoagulant activity through binding to heparin cofactor II, was two times higher than that of dermatan sulfate from porcine skin. The anti-IIa activity of eel skin dermatan sulfate was determined to be 2.4 units/mg, whereas dermatan sulfate from porcine skin shows 23.2 units/mg. The average molecular weight of dermatan sulfate was determined by gel chromatography on a TSKgel G3000SWXL column as 14 kDa. Based on 1H NMR spectroscopy, the presence of 3-sulfated and/or 2,3-sulfated IdoA residues was suggested. The reason why highly sulfated dermatan sulfate does not show anticoagulant activity is discussed. In addition to dermatan sulfate, the eel skin contained a small amount of keratan sulfate, which was identified by keratanase treatment.     

Generation of affinity for antithrombin III by supplemental sulfation of heparin species with low affinity for the protein

The tributylammonium salt of a porcine heparin subfraction with low affinity for antithrombin III (Mr 7,500-18,000; anti-clotting activity, 7 USP units/mg), having degrees of sulfate substitution at D-glucosamine and L-iduronic acid residues of GlcNS 0.786, GlcN6s 0.628, and IdoA2s 0.682 mol, was reacted with 10 or 20 mol of pyridine-sulfur trioxide per mol equiv. of available hydroxyl groups in N,N-dimethylformamide at -10 degrees C for 1 h. Both chemical and NMR spectroscopic analyses revealed that sulfation proceeded exclusively at HO-6 in D-glucosamine and HO-2 in L-iduronic acid residues, according to the amount of the sulfating reagent used (GlcNS: 0.825, 0.830; GlcN6s: 0.872, 0.928; IdoA2s: 0.687, 0.749 mol, respectively). Affinity chromatography of the sulfated products on antithrombin III-Sepharose gel indicated that the polysaccharide acquired some affinity for the protein following the sulfation, as shown by the increase in the proportion of the high-affinity heparin fraction (%) from 1.1 to 6.7. Biological examination of these products indicated that sulfation at natural positions along with the polysaccharide chain resulted in significant increases in all the activities (blood anti-clotting, anti-Factor IIa, and anti-Factor Xa), and in the strength of intrinsic fluorescence of antithrombin III.     

Changes in the structure and biological property of N----O sulfate-transferred, N-resulfated heparin

The N----O sulfate transfer of heparin has been investigated as an approach to chemical 3-O-sulfation of the D-glucosamine residues in heparin. The pyridinium salt of porcine heparin was heated at 90 degrees C in solid state for 90 min (in vacuo over P2O5) to effect the transfer of the N-sulfate groups to the HO groups in the polysaccharide, followed by N-resulfation. The product (N----O sulfate-transferred, N-resulfated heparin (ST heparin] was depolymerized with HONO to generate a mixture of di- and higher oligosaccharides. The borohydride-reduced oligosaccharides were separated on Bio-Gel P-4 and DEAE-Sephacel. The disaccharide trisulfate fraction (10.4% yield) was found to be a mixture of nearly equal amounts of IdoA(2-SO4)-AManR(3,6-diSO4) and IdoA(2,3-diSO4)-AManR(6-SO4), where IdoA represents L-iduronic acid and AManR represents the alditol formed by reduction of 2,5-anhydro-D-mannose with NaBH4. Chemical and NMR spectroscopic analyses revealed that the N----O sulfate transfer proceeded preferentially at HO-3 positions in both 6-O-sulfo-D-glucosamine and 2-O-sulfo-L-iduronic acid residues. Chromatography on antithrombin III-Sepharose gel indicated that the structural change involved in ST heparin resulted in an obvious increase in the ability to bind antithrombin III. Biological examination also indicated that this structural change resulted in moderate increases in all the activities (blood anti-clotting, anti-Factor IIa, and anti-Factor Xa) and in the strength of intrinsic fluorescence of antithrombin III.     

Improved electrostatic properties using combined Mulliken and hybridization-displaced charges for radicals

Effects of explicit consideration of charges displaced from atomic sites due to atomic orbital hybridization called hybridization-displaced charges (HDC) on dipole moments and surface molecular electrostatic potentials of certain radicals and their complexes with closed-shell molecules have been studied. HDC were computed for several radicals and their complexes at the B3LYP/6–31G** level of theory. At this level, HDC consist of three point charges associated with hydrogen atoms and seven point charges associated with heavy atoms belonging to the second row of the periodic table. HDC are so calculated that the contribution of each atom to the component of molecular dipole moment arising due to atomic orbital hybridization is preserved. It is found that dipole moments and electrostatic potentials of the systems studied here can be obtained with a significantly improved accuracy using a combination of Mulliken charges and HDC over that obtained by Mulliken charges only. Figure Surface MEP map of H₂O-HO· radical complex obtained using Mulliken charges combined with HDC     

Calculation of atom-centered partial charges for heme

Atom-centered partial charges are calculated for the Fe-heme in cytochrome P450cam for use in molecular dynamics simulations of polar substrates bound in the active site of the enzyme. Charges are fit to the electrostatic potential produced by ab initio UHF wavefunctions for an Fe-porphine model. Basis set dependence of these charges is observed using the LANL1DZ, LANL2DZ and augmented 6–31G levels of theory. Upon geometry optimization of the enzyme, these charge sets cause varying degrees of distortion of the porphyrin from its crystallographically observed conformation. Scaling the charges calculated from the augmented 6–31G basis by 75% reduces the heme distortion while preserving reasonable interactions with a polar substrate. A comparison of the calculated charges with other published values is presented.     

Theoretical and experimental studies of vibrational spectra and thermal analysis of 2-nitroaniline and its cation

The FTIR spectrum of 2-nitroaniline was recorded in the regions 4000–400 cm⁻¹. The optimized molecular geometry, bond orders, atomic charges, harmonic vibrational wave numbers and intensities of vibrational bands of 2-nitroaniline and its cation were calculated at DFT levels invoking two different basis sets 6-31G** and 6-31+G** using Gaussian 03W program. The X-ray geometry and FTIR vibrational frequencies were compared with the results of DFT calculations. The thermal stability of 2NA is studied by the thermo gravimetric analysis (TGA). Experimental degradation process of 2-nitroaniline was interpreted with the bond order analysis. The Mulliken atomic charge analysis was also made in the present study. Based on the molecular geometry and Mulliken charge analysis, intra molecular hydrogen bonding was identified.     

A sulfatase specific for glucuronic acid 2-sulfate residues in glycosaminoglycans

Although 2-O-sulfated L-iduronic acid (IdoA) residues have been known to occur in heparin, 2-O-sulfated D-glucuronic acid (GlcA) residues have been reported only recently (Bienkowski, M. J., and Conrad, H. E. (1985) J. Biol. Chem. 250, 356-365). Disaccharides prepared by cleavage of heparin and N-deacetylated chondroitin 6-sulfate with nitrous acid were used to demonstrate a new sulfatase that catalyzed the removal of the 2-O-sulfate substituents from GlcA but not IdoA residues. The deamination products were labeled by NaB3H4 reduction to give disaccharides from heparin and chondroitin sulfate which had reducing terminal 2,5-anhydro-D-mannitol ([3H]AManR) and 2,5-anhydro-D-talitol ([3H]ATalR) residues, respectively. IdoA(2-SO4)-[3H]AManR(6-SO4) from heparin and GlcA(2-SO4)-[3H]ATalR(6-SO4) from chondroitin sulfate were purified for use as substrates. GlcA(2-SO4)-[3H]AManR(6-SO4) was prepared by epimerization of IdoA(2-SO4)-[3H]AManR(6-SO4) with hydrazine at 100 degrees C. Lysosomal enzyme preparations from chick embryo chondrocytes and from two normal human fibroblast cell lines catalyzed the removal of the 2-O-SO4 substituent from the uronic acid residues of IdoA(2-SO4)-[3H]AManR(6-SO4), GlcA(2-SO4)-[3H] AManR(6-SO4), and GlcA(2-SO4)-[3H]ATalR(6-SO4). In contrast, a lysosomal enzyme preparation from a human fibroblast cell line deficient in idurono-2-sulfatase (Hunter's-syndrome), which had no activity on the IdoA(2-SO4)-[3H]AManR(6-SO4), converted GlcA(2-SO4)-[3H]AManR(6-SO4) to a mixture of GlcA-[3H] AManR(6-SO4) and [3H]AManR(6-SO4). This enzyme also converted GlcA(2-SO4)-[3H]ATalR(6-SO4) to a mixture of GlcA-[3H]ATalR(6-SO4) and [3H]ATalR(6-SO4). Digestion of both GlcA(2-SO4)-[3H]AManR(6-SO4) and GlcA(2-SO4)-[3H]ATalR(6-SO4) was inhibited by 35SO2-4 and was arrested at the monosulfated disaccharide stage by 1,4-saccharolactone. The glucurono-2-sulfatase exhibited a pH optimum of 4. The results indicate that there exists a separate sulfatase for the removal of sulfate substituents from C-2 of GlcA residues in glycosaminoglycans.     

Heparan sulfate C5-epimerase is essential for heparin biosynthesis in mast cells

Biosynthesis of heparin, a mast cell-derived glycosaminoglycan with widespread importance in medicine, has not been fully elucidated. In biosynthesis of heparan sulfate (HS), a structurally related polysaccharide, HS glucuronyl C5-epimerase (Hsepi) converts D-glucuronic acid (GlcA) to L-iduronic acid (IdoA) residues. We have generated Hsepi-null mouse mutant mast cells, and we show that the same enzyme catalyzes the generation of IdoA in heparin and that 'heparin' lacking IdoA shows a distorted O-sulfation pattern.     

Can current force fields reproduce ring puckering in 2-O-sulfo-α-l-iduronic acid? A molecular dynamics simulation study

The monosaccharide 2-O-sulfo-α-l-iduronic acid (IdoA2S) is one of the major components of glycosaminoglycans. The ability of molecular mechanics force fields to reproduce ring-puckering conformational equilibrium is important for the successful prediction of the free energies of interaction of these carbohydrates with proteins. Here we report unconstrained molecular dynamics simulations of IdoA2S monosaccharide that were carried out to investigate the ability of commonly used force fields to reproduce its ring conformational flexibility in aqueous solution. In particular, the distribution of ring conformer populations of IdoA2S was determined. The GROMOS96 force field with the SPC/E water potential can predict successfully the dominant skew-boat to chair conformational transition of the IdoA2S monosaccharide in aqueous solution. On the other hand, the GLYCAM06 force field with the TIP3P water potential sampled transitional conformations between the boat and chair forms. Simulations using the GROMOS96 force field showed no pseudorotational equilibrium fluctuations and hence no inter-conversion between the boat and twist boat ring conformers. Calculations of theoretical proton NMR coupling constants showed that the GROMOS96 force field can predict the skew-boat to chair conformational ratio in good agreement with the experiment, whereas GLYCAM06 shows worse agreement. The omega rotamer distribution about the C5-C6 bond was predicted by both force fields to have torsions around 10°, 190°, and 360°.