: The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

Root hairs are single cells that develop by tip growth and are specialized in the absorption of nutrients. Their cell walls are composed of polysaccharides and hydroxyproline-rich glycoproteins (HRGPs) that include extensins (EXTs) and arabinogalactan-proteins (AGPs). Proline hydroxylation, an early posttranslational modification of HRGPs that is catalyzed by prolyl 4-hydroxylases (P4Hs), defines the subsequent O-glycosylation sites in EXTs (which are mainly arabinosylated) and AGPs (which are mainly arabinogalactosylated). We explored the biological function of P4Hs, arabinosyltransferases, and EXTs in root hair cell growth. Biochemical inhibition or genetic disruption resulted in the blockage of polarized growth in root hairs and reduced arabinosylation of EXTs. Our results demonstrate that correct O-glycosylation on EXTs is essential for cell-wall self-assembly and, hence, root hair elongation in Arabidopsis thaliana.

https://science.sciencemag.org/content/sci/332/6036/1401.full.pdf

O-Glycosylated Cell Wall Proteins Are Essential in Root Hair Growth

1,2-Amino alcohols are high-value, versatile functional groups that are found in scores of biologically active molecules and other interesting synthetic targets such as ligands and auxiliaries. Given their prominent position within organic compounds of import, it is no surprise to note that many routes have been developed to access this motif and there are many different starting points from which a synthetic chemist might embark on a synthesis. However, one particular approach stands out from the others, and this is the direct conversion of an alkene to a vicinal amino alcohol derivative (oxyamination). Research in this field has been particularly active in recent years and many interesting new methodologies have been reported. The purpose of this review is to give the reader a tour of the methods that have emerged in the last few years so one can appreciate the myriad of different metals and reagents that can accomplish the oxyamination of alkenes. There are still many challenges to be overcome and, herein, we also outline the areas that are ripe for further development and which bode well for the future.

Recent developments in methodology for the direct oxyamination of olefins.

Under eons of evolutionary and environmental pressure, biological systems have developed strong and lightweight peptide-based polymeric materials by using the 20 naturally occurring amino acids as principal monomeric units. These materials outperform their man-made counterparts in the following ways: 1) multifunctionality/tunability, 2) adaptability/stimuli-responsiveness, 3) synthesis and processing under ambient and aqueous conditions, and 4) recyclability and biodegradability. The universal design strategy that affords these advanced properties involves "bottom-up" synthesis and modular, hierarchical organization both within and across multiple length-scales. The field of "biomimicry"-elucidating and co-opting nature's basic material design principles and molecular building blocks-is rapidly evolving. This Review describes what has been discovered about the structure and molecular mechanisms of natural polymeric materials, as well as the progress towards synthetic "mimics" of these remarkable systems.

Modular design in natural and biomimetic soft materials.

Post-translationally modified proteins make up the majority of the proteome and establish, to a large part, the impressive level of functional diversity in higher, multi-cellular organisms. Most eukaryotic post-translational protein modifications (PTMs) denote reversible, covalent additions of small chemical entities such as phosphate-, acyl-, alkyl- and glycosyl-groups onto selected subsets of modifiable amino acids. In turn, these modifications induce highly specific changes in the chemical environments of individual protein residues, which are readily detected by high-resolution NMR spectroscopy. In the following, we provide a concise compendium of NMR characteristics of the main types of eukaryotic PTMs: serine, threonine, tyrosine and histidine phosphorylation, lysine acetylation, lysine and arginine methylation, and serine, threonine O-glycosylation. We further delineate the previously uncharacterized NMR properties of lysine propionylation, butyrylation, succinylation, malonylation and crotonylation, which, altogether, define an initial reference frame for comprehensive PTM studies by high-resolution NMR spectroscopy.

/pdf/cell-signaling-post-translational-protein-modifications-and-3bakwn335f.pdf

Cell signaling, post-translational protein modifications and NMR spectroscopy

The hydroxyproline-rich glycoproteins (HRGPs) are the major structural proteins of the extracellular matrix of algae and land plants. They are characterized by a rigid polyproline type II (PPII) conformation and extensive O-glycosylation of 4(R)-hydroxy-l-proline (Hyp) residues, which is a unique post-translational modification of proteins. The functional consequences of HRGP glycosylation remains unclear, but they have been implicated in contributing to their structural rigidity. Here, we have investigated the effects of naturally occurring beta-O-galactosylation of Hyp residues on the conformational stability of the PPII helix. In a series of well-defined model peptides Ac-(l-proline)(9)-NH(2) (1), Ac-(Hyp)(9)-NH(2) (2), and Ac-[Hyp(beta-d-galactose)](9)-NH(2) (3) we demonstrate that contiguous O-glycosylation of Hyp residues causes a dramatic increase in the thermal stability of the PPII helix according to analysis of thermal melting curves. This represents the first quantitative data on the contributions of glycosylation to stabilizing the PPII conformation. Molecular modeling indicates the increase in conformational stability may be due to a regular network of interglycan and glycan-peptide hydrogen bonds, in which the carbohydrate residues form a hydrophilic "overcoat" of the PPII helix. Evidence of this shielding effect of the amide backbone may be provided by analysis of the circular dichroism bands, which indicates an increase in the rho value of 3 relative to 1 and 2. This study gives further insight into the effects of naturally occurring Hyp beta-O-linked glycans on the PPII conformation as found in HRGPs in plant cell walls and also indicates that polyproline sequences may be suitable for the development of molecular scaffolds for the presentation of glycan structures.

Contiguous O-galactosylation of 4(R)-hydroxy-l-proline residues forms very stable polyproline II helices.

conformational implications of Hyp-glycosylation on peptide backbone conformation. Hyp and proline (Pro) are unique among the proteinogenic amino acids since they are characterized by limited rotation of the o dihedral angle (Figure 1) as their side chain is fused to the peptide backbone. As a consequence, there is a reduction in the energy difference between the prolyl amide cis and trans isomers, making them nearly isoenergetic; this leads to higher cis N-terminal amide content relative to the other amino acids. Moreover, the isomerization of the prolyl amide bond has been shown to be the ratedetermining step in the folding pathways of many peptides and proteins. 4 Herein we describe the effects of galactosylation of Hyp on the conformation as well as the thermodynamics and kinetics of prolyl N-terminal amide isomerization. Compounds 4a AcHyp(R-D-Gal)NHMe and 4b AcHyp(‚-D-Gal)NHMe were selected as glycopeptide mimics, while AcProNHMe 1, AcHypNHMe 2, and AcHyp(Otert-butyl)NHMe 3 served as non-glycosylated reference compounds

/pdf/effects-of-glycosylation-of-2s-4r-4-hydroxyproline-on-the-d3inlxkdsf.pdf

Effects of Glycosylation of (2S,4R)-4-Hydroxyproline on the Conformation, Kinetics, and Thermodynamics of Prolyl Amide Isomerization

We describe the synthesis of a fused bicyclic C-glucosylproline hybrid (GlcProH) from commercially available 2,3,4,6-tetra-O-benzyl-d-glucopyranose. The GlcProH was incorporated into the model peptides Ac-GlcProH-NHMe and Ac-Gly-GlcProH-NHMe. Postsynthetic modifications can be introduced via derivatization of the carbohydrate scaffold. Conformational analysis of the GlcProH-modified model peptides shows that while the conformation of GlcProH remains fixed, the prolyl N-terminal amide equilibrium (Kt/c) can be varied with different modifications of the carbohydrate scaffold. Simple N-acyl derivatives studied by NMR spectroscopy showed that in CD3OD there was an increase in the cis-amide content as the sugar substituents changed from benzyl (10%) to hydroxyl (22%) to acetate (36%). Similar effects were observed in DMSO-d6. The exact nature of the influence is unclear, but it most likely arises through intramolecular interactions between sugar groups and the peptidic amide backbone. Overall, our GlcProH demo...

Tuning of the prolyl trans/cis-amide rotamer population by use of C-glucosylproline hybrids.

The conformations of peptides and proteins are often influenced by glycans O-linked to serine (Ser) or threonine (Thr). (2S,4R)-4-Hydroxyproline (Hyp), together with L-proline (Pro), are interesting targets for O-glycosylation because they have a unique influence on peptide and protein conformation. In previous work we found that glycosylation of Hyp does not affect the N-terminal amide trans/cis ratios (K(trans/cis)) or the rates of amide isomerization in model amides. The stereoisomer of Hyp--(2S,4S)-4-hydroxyproline (hyp)--is rarely found in nature, and has a different influence both on the conformation of the pyrrolidine ring and on K(trans/cis). Glycans attached to hyp would be expected to be projected from the opposite face of the prolyl side chain relative to Hyp; the impact this would have on K(trans/cis) was unknown. Measurements of (3)J coupling constants indicate that the glycan has little impact on the C(gamma)-endo conformation produced by hyp. As a result, it was found that the D-galactose residue extending from a C(gamma)-endo pucker affects both K(trans/cis) and the rate of isomerization, which is not found to occur when it is projected from a C(gamma)-exo pucker; this reflects the different environments delineated by the proline side chain. The enthalpic contributions to the stabilization of the trans amide isomer may be due to disruption of intramolecular interactions present in hyp; the change in enthalpy is balanced by a decrease in entropy incurred upon glycosylation. Because the different stereoisomers--Hyp and hyp--project the O-linked carbohydrates in opposite spatial orientations, these glycosylated amino acids may be useful for understanding of how the projection of a glycan from the peptide or protein backbone exerts its influence.

The implications of (2S,4S)-hydroxyproline 4-O-glycosylation for prolyl amide isomerization.

The structure of fused C-glucosylproline hybrid (GlcProH) has been studied in detail computationally. A systematic molecular mechanics/Monte Carlo search has been performed in order to cover the entire conformational space of GlcProH. This has been followed by density-functional (DFT B3LYP) calculations in the gas phase and in aqueous solution, using the polarizable continuum model (PCM). In the gas phase, a large excess of the cis conformation with respect to the prolyl amide bond is found. This is reversed in aqueous solution where the calculations show 80% trans conformers, which is in accordance with experimental data. Thus, the PCM model is capable of accurately predicting cis–trans ratios. The free energy of solvation is not correlated with the dipole moment. Hence, a model (such as PCM) is required that takes into account the complete charge distribution. The reversal of the cis–trans ratio between gas phase and solution also emphasizes the effects of different free energies of solvation for the di...

Neil W. Owens

Papers

Contiguous O-galactosylation of 4(R)-hydroxy-l-proline residues forms very stable polyproline II helices.

Effects of Glycosylation of (2S,4R)-4-Hydroxyproline on the Conformation, Kinetics, and Thermodynamics of Prolyl Amide Isomerization

Tuning of the prolyl trans/cis-amide rotamer population by use of C-glucosylproline hybrids.

The implications of (2S,4S)-hydroxyproline 4-O-glycosylation for prolyl amide isomerization.

Conformational preference of fused carbohydrate-templated proline analogues--a computational study.