Structures and NMR spectra of short amylose-lipid complexes. Insight using molecular dynamics and DFT quantum chemical calculations

Schahl, Adrien; Réat, Valérie; Jolibois, Franck

doi:10.1016/j.carbpol.2020.115846

Cited by 15 publications

(21 citation statements)

References 45 publications

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“…One of these chains was then rotated by 180° around its principal axis of inertia using the Avogadro software 43 in order to obtain a double helix close to the B-polymorph X-ray crystallographic structure. The procedure for solvation and molecular dynamics was the same as recently described 31 . Amylose was solvated in a box of water such that it was placed at 20 Å from the box boundaries.…”

Section: Classical Molecular Dynamicsmentioning

confidence: 99%

“…In a second stage, because it is known that molecular dynamics have an impact on structures and spectroscopic parameters 31 , calculations of NMR parameters have been performed on 100 structures extracted from the molecular dynamics trajectory. To avoid border effects, 24 residues over 40 have been selected in the middle part of B-amylose in order to obtain two chains of 12 residues folded in a double helix fashion.…”

Section: Quantum Chemical Calculations -Molecular Approachmentioning

confidence: 99%

“…Among all calculations, the HBN_2 structure appears to be the best if correlation coefficient and RMSD are considered (Figure 4 -yellow bars). It has been shown recently that the addition of dynamical effects by means of molecular dynamic simulations can improve the calculation of NMR spectra 31 . Therefore, this approach was applied to a B-polymorph model of 2 x 20 residues (see computational details).…”

Section: Opthbn_1mentioning

confidence: 99%

“…They have helped to study changes in the conformation of amylose in different environments, , as well as the complexation process occurring between fatty acids and amylose polymers of different degrees of polymerization (DP). − Computational studies using quantum chemical methods for the calculations of NMR parameters have mainly been focused on relatively small systems . It is only recently that larger systems have been studied, such as cellulose clusters − or medium size amylose–lipid complexes . In the past decades, ab initio or DFT-based quantum chemical approaches using the gauge including atomic orbital (GIAO) method have been widely used for the calculations of 13 C chemical shielding tensors.…”

Section: Introductionmentioning

confidence: 99%

“…Computational studies using quantum chemical methods for the calculations of NMR parameters have mainly been focused on relatively small systems 27 . It is only recently that larger systems have been studied, such as cellulose clusters [28][29][30] or medium size amylose-lipids complexes 31 . In the past decades, ab initio or DFT-based quantum chemical approaches using the Gauge Including Atomic Orbital (GIAO) 32 method have been widely used for the calculations of 13 C chemical shielding tensors.…”

mentioning

confidence: 99%

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Diversity of the Hydrogen Bond Network and Its Impact on NMR Parameters of Amylose B Polymorph: A Study Using Molecular Dynamics and DFT Calculations Within Periodic Boundary Conditions

et al. 2020

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Classical molecular dynamics simulations have been combined to quantum (DFT) calculations of 13 C NMR parameters in order to relate the experimental spectrum of the double-helix form of the amylose B-polymorph in highly crystalline conditions not only to its 3D structure but also to the arrangement of atoms in the crystal lattice. Structures obtained from these simulations or from geometry optimizations procedure at the DFT level have shown the presence of hydrogen bond networks between sugars of the same helix or between residues of the two chains of the double helix. 13 C NMR parameter calculations have revealed the impact of such network on the chemical shifts of carbon atoms. In addition, DFT calculations using periodic boundary conditions were compulsory to highlight the presence of two types of sugar within the crystal sample. It allows us to confirm theoretically, the experimental hypothesis that the existence of two distinct sugar types in the NMR spectrum is a consequence of crystal packing. Introduction.Amylose, one of the major constituents of starch with amylopectin, is an essentially linear polymer composed of glucose residues linked in [α-1→4] and is often used to model the crystalline parts of starch. Most of the experimental structures are originated from X-ray diffraction studies [1][2][3][4] and it is well known that it can adopt different helical conformations, depending on its environment. The single helical structure called the V-polymorph, has been proven to encapsulate guest molecules of various sizes, such as Iodine 5 , flavor molecules 6,7 or even fatty acids [8][9][10][11] . The double helical structures are called A or B-polymorphs (Figure 1) depending on the crystal packing conditions and are known to be present in highly crystalline material amongst starch. The method of choice used for the study of amylose structure is 13 C solid-state NMR spectroscopy 9,10,12-14 ,

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Section: Classical Molecular Dynamicsmentioning

confidence: 99%

Section: Quantum Chemical Calculations -Molecular Approachmentioning

confidence: 99%

Section: Opthbn_1mentioning

confidence: 99%