Manuel Martín-Pastor

The use of CVFF and CFF91 force fields in conformational analysis of carbohydrate molecules. Comparison with AMBER molecular mechanics and dynamics calculations for methyl α-lactoside

The solution conformation of methyl alpha-lactoside has been studied through molecular mechanics calculations using the AMBER/Homans, CVFF and CFF91 force fields, and compared to NMR nuclear Overhauser data. Steady-state and transient nuclear Overhauser effects (NOEs) have been interpreted in terms of the ensemble average distribution of conformers. The NOEs have been analysed using the complete relaxation matrix approach for a rigid and isotropic motion model. The molecular mechanics calculations have been performed at two dielectric constants (i.e. epsilon = 1 and 80 debyes, or epsilon = r and 80 debyes) in an exhaustive way, and, in some cases, have been complemented by specific calculations at intermediate epsilon values. Relaxed energy maps and adiabatic surfaces have been generated for the different dielectric constants. The probability distribution of conformers has been estimated from these steric energy maps. Molecular dynamics simulations in vacuo have also been performed. Our results indicate that the beta-(1-->4) glycosidic linkage shows some fluctuations between three low-energy regions, although it spends about 90% of its time in the region close to the global minimum. The observed conformation of methyl alpha-lactoside seems to be closer to that predicted by CVFF, although the AMBER/Homans results are also in qualitative agreement with the experimental data.

A comparison of the geometry and of the energy results obtained by application of different molecular mechanics force fields to methyl α-lactoside and the C-analogue of lactose

Abstract The applicability of a number of standard molecular mechanics force fields, namely AMBER/Homans, CVFF, CFF91, ESFF, and MM3 ∗ , and of the AMI semiempirical Hamiltonian, to the molecular modelling of methyl α-lactoside is described. A protocol based on the calculation of relaxed energy maps for a significant number of initial structures has been employed. Different dielectric constants, as well as a continuum model solvent have been used. The geometric characteristics (distances and torsion and valence angles) of the low energy minima have been gathered and compared to experimental solution NMR and solid state X-ray data. Concerning the energies, the relative steric energy values provided by the different programs have been translated into ensemble average distributions of conformers which, in turn, have been employed to generate NMR parameters, i.e. NOE, NOESY, and ROESY intensities and homo- and hetero-nuclear coupling constants. The results indicate that MM3 ∗ and CVFF provide conformer distributions which account for the solution NMR observables in a satisfactory way. AMBER/Homans provide a reasonable agreement, while conformational analysis of oligosaccharides by AM1, ESFF, and CFF91 is not advised. The best fit between the experimental X-ray distances and angles and the modeling studies is found when CVFF is used. Results from the different force fields (and AM1) for C-lactose were compared.

Experimental and theoretical evidences of conformational flexibility of C-glycosides. NMR analysis and molecular mechanics calculations of C-lactose and its O-analogue

NMR data (NOEs and coupling constants) and MM3∗ molecular mechanics calculations have allowed to demonstrate that the conformational behaviour of C-lactose is different of its O-analogue. The glycosidic linkages, particularly the C-aglyconic bond, present a high degree of flexibility and, therefore, the conformational entropy of C-lactose is higher than that of its O-counterpart.

Solution conformation and dynamics of a tetrasaccharide related to the LewisX antigen deduced by NMR relaxation measurements

Abstract1H-NMR cross-relaxation rates and nonselectivelongitudinal relaxation times have been obtained at two magnetic fields (7.0and 11.8 T) and at a variety of temperatures for the branchedtetrasaccharide methyl3-O-α-N-acetyl-galactosaminyl-β-galactopyranosyl-(1→4)[3-O-α-fucosyl]-glucopyranoside (1), an inhibitor of astrocyte growth. Inaddition, 13C-NMR relaxation data have also been recorded atboth fields. The 1H-NMR relaxation data have been interpretedusing different motional models to obtain proton–proton correlationtimes. The results indicate that the GalNAc and Fuc rings display moreextensive local motion than the two inner Glc and Gal moieties, since thosepresent significantly shorter local correlation times. The13C-NMR relaxation parameters have been interpreted in termsof the Lipari–Szabo model-free approach. Thus, order parameters andinternal motion correlation times have been deduced. As obtained for the1H-NMR relaxation data, the two outer residues possess smallerorder parameters than the two inner rings. Internal correlation times are inthe order of 100 ps. The hydroxymethyl groups have also different behaviour,with the exocyclic carbon on the glucopyranoside unit showing the highestS2. Molecular dynamics simulations using a solvated systemhave also been performed and internal motion correlation functions have beendeduced from these calculations. Order parameters and interproton distanceshave been compared to those inferred from the NMR measurements. The obtainedresults are in fair agreement with the experimental data.

The Dynamics of Dendrimers by NMR Relaxation: Interpretation Pitfalls

NMR is a powerful tool to study the dynamics of dendrimers. By analogy to linear polymers, shorter T(1) relaxation times have been traditionally associated to less mobile nuclei and hence, dendrimers described with reduced local motions at either the core or the periphery. Herein we report a NMR relaxation study [(1)H and (13)C T(1), T(2); (13)C{(1)H}NOE; various fields and temperatures] which reveals profound differences between the relaxation behavior of dendrimers and linear polymers. Dendrimers show slower dynamics at internal layers and on increasing generation and may display internal nuclei in the slow motional regime with larger T(1) values than the periphery. In contrast to the relaxation properties of linear polymers, these T(1) increments should not be interpreted as resulting from faster dynamics. Only the recording of T(1) data at various temperatures (alternatively, T(2) or NOE at one temperature) ensures the correct interpretation of dendrimer dynamics.

Applications of nuclear magnetic resonance spectroscopy and molecular modeling to the study of protein-carbohydrate interactions☆

This work provides an overview of the applications of NMR to the study of protein-carbohydrate interactions. The use of TR-NOE experiments in this context is given. In particular, the study of Ricin/lactose and Hevein/chitobiose complexes is detailed.

SYNTHESIS AND CONFORMATIONAL ANALYSIS OF A LIPOTETRASACCHARIDE RELATED TO THE NODULATION FACTOR OF RHIZOBIUM BACTERIA

Abstract The synthesis of the lipotetrasaccharide glycoside, p -methoxyphenylO-{2-deoxy-2-[(11Z)-11-octadecenoylamido]-β-D-glucopyranosyl}-(1→4)- O -(β-D-glucopyranosyl)-(1→4)- O -β-D-glucopyranosyl)- (1→4)-2-acetamido-2-deoxy-β-D-glucopyranoside 16 , starting from acetobromocellobiose is reported. Compound 16 is an analogue of the nodulation factors of Rhizobium bacteria having the central chitobiose unit substituted by a cellobiose unit. A conformational study indicates that 16 have restricted fluctuations around the glycosidic torsion angles, but can adopt a variety of shapes.

The use of the MM3∗ and ESFF force fields in conformational analysis of carbohydrate molecules in solution: The methyl α-lactoside case

Abstract The solution conformation of methyl α-lactoside has been studied through NMR spectroscopy and molecular mechanics calculations using the MM3 ∗ and ESFF force fields. The steady-state and transient NOEs have been interpreted in terms of an ensemble average distribution of conformers, making use of the complete relaxation matrix approach. The molecular mechanics calculations have been performed at two dielectric constants ( e = 1 and 80 Debyes) for both force fields in an exhaustive way, and in the case of MM3 ∗ have been complemented with calculations using the continuum solvent model GB/ SA. Relaxed energy maps and adiabatic surfaces have been generated for the different dielectric constants. The probability distribution of conformers has been estimated from these steric energy maps. MM3 ∗ molecular dynamics simulations in vacuo and with GB/SA have also been performed. The comparison between predicted and experimental results indicate that the β -(1 > 4) glycosidic linkage shows some fluctuations among three low-energy regions, although it spends ca. 90% of its time in the region close to the global minimum. The results indicate that MM3 ∗ , when used with high dielectric constants or with the GB/ SA solvent model, satisfactorily reproduces the conformational properties of methyl α-lactoside in water solution. The use of ESFF only provides a qualitative agreement between experimental and theoretical results.

Solution conformation and dynamics of a fungal cell wall polysaccharide isolated from Microsporum gypseum.

The conformational and dynamical features of a branched mannan isolated from a fungal cell wall have been analysed by homo and heteronuclear NMR methods, employing different magnetic fields. 1HNMR cross relaxation times have been obtained for this polysaccharide and have been interpreted qualitatively using different motional models. 13C NMR relaxation parameters (T1, T2, NOE) have also been measured and interpreted using different approximations based on the Lipari and Szabo model free approach. The analysis of the data indicate the existence of important flexibility for the different linkages of the polysaccharide. Motions in the range of 4–6 ns contribute to the relaxation of the macromolecule, although faster internal motions in the 500 ps and 100 ps timescales are also present. These time scales indicate that segmental motions as well as internal motions around the glycosidic linkages are the major sources of relaxation for this molecule at 318 K. Molecular dynamics simulations have also been performed. The obtained results also indicate that the polysaccharide possess a substantial amount of conformational freedom.

Solution conformation dynamics of a tetrasaccharide related to the Lewisx antigen deduced by 1H NMR NOESY, ROESY, and T-ROESY measurements

The conformational and dynamical features of a Le(X) tetrasaccharide analogue GalNAc (alpha 1-3)Gal(beta 1-4)[Fuc(alpha 1-3)]Glc(beta OMe) 1 have been studied through 1H NMR relaxation measurements. The results indicate that the different glycosidic linkages of 1 present distinct conformational flexibility in solution. In addition, the use of T-ROESY experiments in conformational analysis of oligosaccharides is explored emphasizing its scope and limitations.