A Modified Version of the Cornell et al. Force Field with Improved Sugar Pucker Phases and Helical Repeat

Abstract

We have examined some subtle parameter modifications to the Cornell et al. force field, which has proven quite successful in reproducing nucleic acid properties, but whose C2′-endo sugar pucker phase and helical repeat for B DNA appear to be somewhat underestimated. Encouragingly, the addition of a single V₂ term involving the atoms C(sp³)-O-(sp³)-C(sp³)- N(sp²), which can be nicely rationalized because of the anomeric effect (lone pairs on oxygen are preferentially oriented relative to the electron withdrawing N), brings the sugar pucker phase of C2′-endo sugars to near perfect agreement with ab initio calculations (W near 162°). Secondly, the use of high level ab initio calculations on entire nucleosides (in contrast to smaller model systems necessitated in 1994–95 by computer limitations) lets one improve the % torsional potential for nucleic acids. Finally, the O(sp³)-C(sp³)- C(sp³)-O(sp³) V₂ torsional potential has been empirically adjusted to reproduce the ab initio calculated relative energy of C2′- endo and C3′-endo nucleosides. These modifications are tested in molecular dynamics simulations of mononucleosides (to assess sugar pucker percentages) and double helices of DNA and RNA (to assess helical and sequence specific structural properties). In both areas, the modified force field leads to improved agreement with experimental data.     

Release of O-linked sugar chains from glycoproteins with anhydrous hydrazine and pyridylamination of the sugar chains with improved reaction conditions.

A method for preparation of pyridylamino (PA-) derivatives of O-linked sugar chains from glycoproteins was developed. A glycopeptide containing O-linked Gal beta 1-3GalNAc was prepared from fetuin and treated with anhydrous hydrazine followed by N-acetylation of free amino groups. Sugar chains released were pyridylaminated with improved reaction conditions and excess reagents were removed by gel filtration. Gal beta 1-3GalNAc-PA obtained together with PA-Gal as a by-product was quantified by HPLC. Conditions for the hydrazine treatment were investigated and the treatment at 40 degrees C for 350 h gave the best results for releasing O-linked sugar chains. The total yield of Gal beta 1-3GalNAc-PA from the glycopeptide was 53% under the established conditions and that of PA-Gal was 18%. The present method was applied to a glycoprotein, and the expected PA-O-linked sugar chains were obtained. Under these conditions, N-linked sugar chains were also released.     

Prediction of the enantioselectivity of lipases and esterases by molecular docking method with modified force field parameters

In the work, molecular docking method was applied to extensively predict the enantioselectivity of lipases and esterases. A ligand library consisted of 69 chiral substrates was docked to four lipases and two esterases to set up the prediction model. During the docking process, necessary modification was carried out on van de Waals and hydrogen bond parameters of enzyme/substrate pair so that the ligands were able to adopt productive geometry in the enzymes. The docking results correctly indicated the enantiopreference for 91% (63/69) of docking pairs and the docking energy difference between substrate enantiomers (ΔΔG_docking) was significantly (correlation coefficient = 0.72, P < 0.05) correlated with the activation free energy difference (ΔΔG^≠) that was quantitatively correlated with enantioselectivity of the enzymes. The prediction method was further validated by docking with another 12 enzyme/substrate pairs. Moreover, the prediction error was susceptible to the size of groups bonded to substrate's chiral center and expected ΔΔG^≠ values but was not related to the substrate type and reaction medium. The possible reasons of observed error were discussed. It is demonstrated that the docking method has great application potential in high performance prediction of enzyme enantioselectivity. Biotechnol. Bioeng. 2010. 105: 687–696. © 2009 Wiley Periodicals, Inc.     

High dose refuge strategies and genetically modified crops – reply to Tabashnik et al.

Cultivating non‐toxic conventional crops (refuges) in the proximity to transgenic crops that produce Bacillus thuringienesis (Bt) toxins is widely recommended to delay pest adaptation to these toxins. Using a spatially structured model of resistance evolution, Vacher and co‐workers (Vacher, C., Bourguet, D., Rousset, F., Chevillon, C. & Hochberg, M.E. 2003. J. Evol. Biol. 16 : 378–387.) show that the percentage of refuge fields required for the sustainable control of pests can be reduced through intermediate levels of refuge field aggregation and by lowering the toxin dose produced by Bt plants. Tabashnik, B.E., Gould, F. & Carrière, Y. (2004 J. Evol. Biol doi: 10.1111/j1420–9101.2004.00695.x) call into question the results of Vacher et al. (2003) concerning the effect of toxin dose. They argue that these results arise from invalid assumptions about larval concentration–mortality responses for the insect considered, the cotton pest Heliothis virescens. We show here that the models presented by Vacher et al. (2003) and Tabashnik et al. (2004) both show inaccuracies in their definitions of genotypic fitness. The level of dominance estimated by Tabashnik et al. (2004) from larval mortality rates data is irrelevant to resistance evolution, and the fitness cost of resistance evolution, and the fitness cost of resistance is inaccurately integrated into their framework. Neverthless, the comments of Tabashnik et al. (2004) are very helpful in elucidating the definitions of genotypic fitness used in Vacher et al. (2003) and in pointing out the essential factors in predicting the evolution of insect resistance to Bt transgenic crops, namely, accurate estimations of the fitness cost of resistance, of the dominance level of this cost, and of the variations in the dominance level of the advantage conferred by the resistance with Bt toxin dose.     

Reply to the comments of Ryman et al.

If we want to address 'genetic concerns' we should not forget the issue of 'mental concerns' in the process. Nyman & Ring (1989) set out to display how a couple of polymorphic loci in Arctic charr ( Salvelinus alpinus L.) may and will be used as standard genetic tags for studies on hatchery and wild populations. However, Ryman et al . (1993) address 'conceptual misunderstandings' of a general nature. Instead of discussing all the detailed points raised by Ryman et al ., I have tried below to address the major issues in Nyman and Ring's original paper.     

A test of improved force field parameters for urea: molecular-dynamics simulations of urea crystals

Molecular-dynamics (MD) simulations of urea crystals of different shapes (cubic, rectangular prismatic, and sheet) have been performed using our previously published force field for urea. This force field has been validated by calculating values for the cohesive energy, sublimation temperature, and melting point from the MD data. The cohesive energies computed from simulations of cubic and rectangular prismatic urea crystals in vacuo at 300 K agreed very well with the experimental sublimation enthalpies reported at 298 K. We also found very good agreement between the melting points as observed experimentally and from simulations. Annealing the crystals just below the melting point leads to reconstruction to form crystal faces that are consistent with experimental observations. The simulations reveal a melting mechanism that involves surface (corner/edge) melting well below the melting point, and rotational disordering of the urea molecules in the corner/edge regions of the crystal, which then facilitates the translational motion of these molecules.     

A charge-modified general amber force field for phospholipids: improved structural properties in the tensionless ensemble

Accurately predicting the structural properties of phospholipid with a fully atomistic molecular model is critical for the study of pure phospholipid bilayers, mixed bilayer systems and bilayers containing proteins. The general amber force field (GAFF) has traditionally required the presence of a surface tension parameter to correctly model phospholipid bilayer properties such as area per lipid and order parameters. In this work, the GAFF partial charges for 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphate (POPA), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphochiline (POPC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) were re-parameterised utilising high-level ab initio calculations and the restrained electrostatic potential method. Simulations of pure POPA, POPC and POPG bilayers using the charge-modified GAFF and no applied surface tension are compared with available experimental data, the original GAFF model and the recent Lipid14 variant. The results indicate a significant improvement in the accuracy of the lipid model for reproducing experimental observables without the need for a surface tension parameter. The successful application of modifying the lipid charge distributions represents an alternative to the use of a surface tension parameter within GAFF, and highlights the importance of the partial charge calculations when modelling lipid bilayers.     

Decisions in force field development: an alternative to those described by Roterman et al. (J. Biomol. Struct. Dyn. 7, 421 (1989))

We attempt to give an alternate point of view of the analysis by Roterman et al. (J. Biolmol. Struct. Dyn. 7,415 (1989]. In particular, we argue for the use of flexible geometry and explicit inclusion of solvent effects in analyzing phi, psi maps of peptides.     

Further support for the alignment of cattle along magnetic field lines: reply to Hert et al.

Hert et al. (J Comp Physiol A, 2011) challenged one part of the study by Begall et al. (PNAS 105:13451–13455, 2008) claiming that they could not replicate the finding of preferential magnetic alignment of cattle recorded in aerial images of Google Earth. However, Hert and co-authors used a different statistical approach and applied the statistics on a sample partly unsuitable to examine magnetic alignment. About 50% of their data represent noise (resolution of the images is too poor to enable unambiguous measurement of the direction of body axes, pastures are on slopes, near settlements or high voltage power-lines, etc.). Moreover, the authors have selected for their analysis only ~ 40% of cattle that were present on the pastures analyzed. Here, we reanalyze all usable data and show that cattle significantly align their body axes in North–South direction on pastures analyzed by Hert and co-authors. This finding thus supports our previous study. In addition, we show by using aerial Google Earth images with good resolution, that the magnetic alignment is more pronounced in resting than in standing cattle.