scholarly journals acACS: Improving the Prediction Accuracy of Protein Subcellular Locations and Protein Classification by Incorporating the Average Chemical Shifts Composition

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Guo-Liang Fan ◽  
Yan-Ling Liu ◽  
Yong-Chun Zuo ◽  
Han-Xue Mei ◽  
Yi Rang ◽  
...  
Keyword(s):  
Chemical Shift ◽  
Prediction Accuracy ◽  
Structural Changes ◽  
Chemical Shifts ◽  
Protein Classification ◽  
Structure Information ◽  
Local Environments ◽  
Protein Subcellular Locations ◽  
Auto Covariance ◽  
Online Web

The chemical shift is sensitive to changes in the local environments and can report the structural changes. The structure information of a protein can be represented by the average chemical shifts (ACS) composition, which has been broadly applied for enhancing the prediction accuracy in protein subcellular locations and protein classification. However, different kinds of ACS composition can solve different problems. We established an online web server named acACS, which can convert secondary structure into average chemical shift and then compose the vector for representing a protein by using the algorithm of auto covariance. Our solution is easy to use and can meet the needs of users.

scholarly journals Inverse PI by NMR: Analysis of Ligand 1H-Chemical Shifts in the Protein-Bound State

2021 ◽  
Author(s):  
Gerald Platzer ◽  
Moriz Mayer ◽  
Jark Boettcher ◽  
Leonhard Geist ◽  
Julian E. Fuchs ◽  
...  
Keyword(s):  
Chemical Shift ◽  
Chemical Shifts ◽  
Bound State ◽  
Structure Information ◽  
Π Interactions ◽  
Protein Ligand Interactions ◽  
Protein Deuteration ◽  
Ligand Interactions ◽  
A Site ◽  
Ligand Conformation

The study of protein-ligand interactions via protein-based NMR generally relies on the detection of chemical-shift changes induced by ligand binding. However, the chemical shift of the ligand when bound to the protein is rarely discussed, since it is not readily detectable. In this work we use protein deuteration in combination with [1H-1H]-NOESY NMR to extract 1H chemical shift values of the ligand in the bound state. The chemical shift perturbations (CSPs) experienced by the proton ligand resonances (free vs bound) are an extremely rich source of information on protein-ligand complexes. Besides allowing for the detection of intermolecular CH-π interactions and elucidation of the protein-bound ligand conformation, the CSP information can be used to analyse (de)solvation effects in a site-specific manner. In conjunction with crystal structure information, it is possible to distinguish protons whose desolvation penalty is compensated for upon protein-binding, from those that are not. Combined with the previously reported PI by NMR technique for the protein-based detection of intermolecular CH-π interactions, this method represents another important step towards the ultimate goal of Interaction-Based Drug Discovery.

scholarly journals The 125Te Chemical Shift of Diphenyl Ditelluride: Chasing Conformers over a Flat Energy Surface

Molecules ◽  
2019 ◽  
Vol 24 (7) ◽  
pp. 1250 ◽  
Author(s):  
Marco Bortoli ◽  
Marco Dalla Tiezza ◽  
Cecilia Muraro ◽  
Giacomo Saielli ◽  
Laura Orian
Keyword(s):  
Chemical Shift ◽  
Density Functional ◽  
Structural Changes ◽  
Chemical Shifts ◽  
Promising Candidate ◽  
Functional Theory ◽  
Detailed Structural Analysis ◽  
Diphenyl Ditelluride ◽  
Conformational Freedom ◽  
Structure In Solution

The interest in diphenyl ditelluride (Ph2Te2) is related to its strict analogy to diphenyl diselenide (Ph2Se2), whose capacity to reduce organic peroxides is largely exploited in catalysis and green chemistry. Since the latter is also a promising candidate as an antioxidant drug and mimic of the ubiquitous enzyme glutathione peroxidase (GPx), the use of organotellurides in medicinal chemistry is gaining importance, despite the fact that tellurium has no recognized biological role and its toxicity must be cautiously pondered. Both Ph2Se2 and Ph2Te2 exhibit significant conformational freedom due to the softness of the inter-chalcogen and carbon–chalcogen bonds, preventing the existence of a unique structure in solution. Therefore, the accurate calculation of the NMR chemical shifts of these flexible molecules is not trivial. In this study, a detailed structural analysis of Ph2Te2 is carried out using a computational approach combining classical molecular dynamics and relativistic density functional theory methods. The goal is to establish how structural changes affect the electronic structure of diphenyl ditelluride, particularly the 125Te chemical shift.

scholarly journals Structure of Nanobody Nb23

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3567
Author(s):  
Mathias Percipalle ◽  
Yamanappa Hunashal ◽  
Jan Steyaert ◽  
Federico Fogolari ◽  
Gennaro Esposito
Keyword(s):  
Nmr Spectroscopy ◽  
Chemical Shift ◽  
Solution Structure ◽  
Chemical Shifts ◽  
Molecular Size ◽  
Side Chain ◽  
3D Nmr ◽  
Target Antigen ◽  
Internuclear Distances ◽  
2D And 3D

Background: Nanobodies, or VHHs, are derived from heavy chain-only antibodies (hcAbs) found in camelids. They overcome some of the inherent limitations of monoclonal antibodies (mAbs) and derivatives thereof, due to their smaller molecular size and higher stability, and thus present an alternative to mAbs for therapeutic use. Two nanobodies, Nb23 and Nb24, have been shown to similarly inhibit the self-aggregation of very amyloidogenic variants of β2-microglobulin. Here, the structure of Nb23 was modeled with the Chemical-Shift (CS)-Rosetta server using chemical shift assignments from nuclear magnetic resonance (NMR) spectroscopy experiments, and used as prior knowledge in PONDEROSA restrained modeling based on experimentally assessed internuclear distances. Further validation was comparatively obtained with the results of molecular dynamics trajectories calculated from the resulting best energy-minimized Nb23 conformers. Methods: 2D and 3D NMR spectroscopy experiments were carried out to determine the assignment of the backbone and side chain hydrogen, nitrogen and carbon resonances to extract chemical shifts and interproton separations for restrained modeling. Results: The solution structure of isolated Nb23 nanobody was determined. Conclusions: The structural analysis indicated that isolated Nb23 has a dynamic CDR3 loop distributed over different orientations with respect to Nb24, which could determine differences in target antigen affinity or complex lability.

Circular dichroism spectra of tetraamminecobalt(III) complexes of amino alcohols

1978 ◽  
Vol 31 (11) ◽  
pp. 2399 ◽  
Author(s):  
CJ Hawkins ◽  
GA Lawrance ◽  
JA Palmer
Keyword(s):  
Circular Dichroism ◽  
Chemical Shift ◽  
Chemical Shifts ◽  
Amino Alcohols ◽  
Circular Dichroism Spectra ◽  
Chemical Shift Difference ◽  
Solvent Dependence ◽  
Cotton Effects ◽  
Circular Dichroïsm ◽  
Chiral Amino Alcohols

The circular dichroism spectra are reported for tetraamminecobalt(III) complexes with the chiral amino alcohols 2-aminopropan-1-ol, 2- aminobutan-1-ol, 1-aminopropan-2-ol, 2-amino-1-phenyl-ethanol, ψ- ephedrine and ephedrine with the alcohol groups protonated (OH) and deprotonated (O-). The solvent dependence of the chemical shifts of the NH protons was investigated to determine the effects of stereoselective solvation on the circular dichroism, but, in contrast to some other related systems, the chemical shift difference between the two NH2 protons was relatively insensitive to solvent. Consistent with this, the circular dichroism spectra of the tetraphenylborate salts of the deprotonated complexes were found not to be markedly dependent on solvent. Tetraammine-{(-)-ψ-ephedrine)cobalt(III) and tetraammine{(-)- ephedrine}cobalt(III) were found to have the same signs of Cotton effects for the various d-d transitions, whereas bis{(-)-ψ- ephedrine}copper(II) and bis{(-)-ephedrine}copper(II) had opposite signs. This has been explained in terms of different conformer populations in the cobalt(III) and copper(II) systems.

NMR studies of tandem WW domains of Nedd4 in complex with a PY motif-containing region of the epithelial sodium channel

1998 ◽  
Vol 76 (2-3) ◽  
pp. 341-350 ◽  
Author(s):  
Voula Kanelis ◽  
Neil A Farrow ◽  
Lewis E Kay ◽  
Daniela Rotin ◽  
Julie D Forman-Kay
Keyword(s):  
Chemical Shift ◽  
Sodium Channel ◽  
Chemical Shifts ◽  
Epithelial Sodium Channel ◽  
Chemical Shift Assignment ◽  
Nmr Studies ◽  
Ww Domains ◽  
Ww Ii ◽  
Py Motif ◽  
Shift Assignment

Nedd4 (neuronal precursor cell-expressed developmentally down-regulated 4) is a ubiquitin-protein ligase containing multiple WW domains. We have previously demonstrated the association between the WW domains of Nedd4 and PPxY (PY) motifs of the epithelial sodium channel (ENaC). In this paper, we report the assignment of backbone 1Hα, 1HN, 15N, 13C', 13Cα, and aliphatic 13C resonances of a fragment of rat Nedd4 (rNedd4) containing the two C-terminal WW domains, WW(II+III), complexed to a PY motif-containing peptide derived from the β subunit of rat ENaC, the βP2 peptide. The secondary structures of these two WW domains, determined from chemical shifts of 13Cα and 13Cβ resonances, are virtually identical to those of the WW domains of the Yes-associated protein YAP65 and the peptidyl-prolyl isomerase Pin1. Triple resonance experiments that detect the 1Hα chemical shift were necessary to complete the chemical shift assignment, owing to the large number of proline residues in this fragment of rNedd4. A new experiment, which correlates sequential residues via their 15N nuclei and also detects 1Hα chemical shifts, is introduced and its utility for the chemical shift assignment of sequential proline residues is discussed. Data collected on the WW(II+III)-βP2 complex indicate that these WW domains have different affinities for the βP2 peptide.Key words: WW domain, PY motif, Nedd4, ENaC, NMR.

Determination of chemical shifts in 6-condensed syringylic lignin model compounds

Holzforschung ◽  
2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Lucas Lagerquist ◽  
Jani Rahkila ◽  
Patrik Eklund
Keyword(s):  
Chemical Shift ◽  
Methoxy Group ◽  
Chemical Shifts ◽  
Model Compounds ◽  
Correlation Peak ◽  
Lignin Model Compounds ◽  
Benzylic Alcohols ◽  
Lignin Model ◽  
C Nmr

Abstract A small library of 6-substituted syringyl model compounds with aliphatic, carboxylic, phenylic, benzylic alcohols and brominated substituents were prepared. The influence of the substituents on the chemical shifts of the compounds was analyzed. All of model compounds showed a characteristic increase in the 13C NMR chemical shift of the methoxy group vicinal to the substitution. This 13C NMR peak and its corresponding correlation peak in HSQC could potentially be used to identify 6-condensation in syringylic lignin samples.

scholarly journals XPS Investigations on Solid and Vacuum Deposited, Oxidized and Non-oxidized Palladium

1995 ◽  
Vol 50 (4-5) ◽  
pp. 381-387 ◽  
Author(s):  
Jürgen Kintrup ◽  
Harald Züchner
Keyword(s):  
Chemical Shift ◽  
Curve Fitting ◽  
Photoelectron Spectroscopy ◽  
Chemical Shifts ◽  
Atmospheric Oxygen ◽  
Hydrogen Permeability ◽  
Photoelectric Effect ◽  
High Accuracy ◽  
X Ray ◽  
Charging Effect

Abstract X-ray photoelectron spectroscopy (XPS) has been carried out to study the reaction of differently prepared palladium samples (solid and film Pd) with atmospheric oxygen. A careful curve fitting of the measured Pd-3d5/2 peak allows to separate the Pd-3d5/2 peak for Pd in surface PdO from the dominant Pd-3d5/2 peak of the non-oxidized bulk palladium and to determine the chemical shift of the "oxidized" Pa line with high accuracy. Differences in the chemical shifts for the surface PdO on solid and film palladium are explained by a different charging caused by the photoelectric effect in XPS measurements. The smaller charging effect observed for film palladium as compared to solid palladium indicates a stronger oxygen bonding to the (rougher) film palladium. The strong Pd-O bonding seems to be an essential reason for the reduced hydrogen-permeability of film palladium compared to solid palladium

Are the amide bonds in N-acyl imidazoles twisted? A combined solid-state 17O NMR, crystallographic, and computational study

2015 ◽  
Vol 93 (4) ◽  
pp. 451-458 ◽  
Author(s):  
Xianqi Kong ◽  
Aaron Tang ◽  
Ruiyao Wang ◽  
Eric Ye ◽  
Victor Terskikh ◽  
...  
Keyword(s):  
Solid State ◽  
Chemical Shift ◽  
Crystal Structures ◽  
Computational Study ◽  
Chemical Shifts ◽  
Amide Bond ◽  
Chemical Shift Tensors ◽  
Amide Bonds ◽  
Bond Rotation ◽  
Quadrupole Coupling

We report synthesis of 17O-labeling and solid-state 17O NMR measurements of three N-acyl imidazoles of the type R-C(17O)-Im: R = p-methoxycinnamoyl (MCA-Im), R = 4-(dimethylamino)benzoyl (DAB-Im), and R = 2,4,6-trimethylbenzoyl (TMB-Im). Solid-state 17O NMR experiments allowed us to determine for the first time the 17O quadrupole coupling and chemical shift tensors in this class of organic compounds. We also determined the crystal structures of these compounds using single-crystal X-ray diffraction. The crystal structures show that, while the C(O)–N amide bond in DAB-Im exhibits a small twist, those in MCA-Im and TMB-Im are essentially planar. We found that, in these N-acyl imidazoles, the 17O quadrupole coupling and chemical shift tensors depend critically on the torsion angle between the conjugated acyl group and the C(O)–N amide plane. The computational results from a plane-wave DFT approach, which takes into consideration the entire crystal lattice, are in excellent agreement with the experimental solid-state 17O NMR results. Quantum chemical computations also show that the dependence of 17O NMR parameters on the Ar–C(O) bond rotation is very similar to that previously observed for the C(O)–N bond rotation in twisted amides. We conclude that one should be cautious in linking the observed NMR chemical shifts only to the twist of the C(O)–N amide bond.

scholarly journals Исследование строения, ионной, молекулярной подвижности и термических свойств гидратов пентафторидоцирконата аммония

2019 ◽  
Vol 126 (2) ◽  
pp. 147
Author(s):  
Е.И. Войт ◽  
А.Б. Слободюк ◽  
Н.А. Диденко
Keyword(s):  
Structural Changes ◽  
Chemical Shifts ◽  
Molecular State ◽  
Structural Motif ◽  
Nmr Data ◽  
State Of Water ◽  
Hydrate Number ◽  
Bond Strengths ◽  
Isotropic Chemical Shifts ◽  
Ir And Raman

AbstractThe effect of hydrate number on the structural changes, thermal properties, and ionic (molecular) mobility character in NH_4ZrF_5 ⋅ H_2O, NH_4ZrF_5 ⋅ 0.75H_2O crystal hydrates have been investigated by the methods of IR, Raman, nuclear magnetic resonance (NMR) (^1H, ^19F, including ^19F MAS), and TG-DTA spectroscopy. Differences in crystal hydrate structures—anion structure, molecular state of water, and O–H⋅⋅⋅F, N–H⋅⋅⋅F hydrogen bond strengths—have been corroborated by IR and Raman spectroscopy data. Isotropic chemical shifts of magnetic inequivalent positions have been determined and attributed to crystal structures of the studied compounds by the method of ^19F MAS NMR. It has been established that the removal of water molecules from NH_4ZrF_5 ⋅ H_2O and NH_4ZrF_5 ⋅ 0.75H_2O results in the transformation of chain or layered structures accompanied by the increase of the number of bridge bonds while retaining or increasing the dimensionality of the anion structural motif. According to the ^1H NMR data, the NH $$_{4}^{ + }$$ cation diffusion in NH_4ZrF_5 occurs only in the temperature range of 370–520 K.

scholarly journals Following excited-state chemical shifts in molecular ultrafast x-ray photoelectron spectroscopy

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
D. Mayer ◽  
F. Lever ◽  
D. Picconi ◽  
J. Metje ◽  
S. Alisauskas ◽  
...  
Keyword(s):  
Excited State ◽  
Chemical Shift ◽  
Photoelectron Spectroscopy ◽  
Chemical Shifts ◽  
Excited Molecule ◽  
Charge Motion ◽  
Core Electron ◽  
Xps Spectra ◽  
X Ray ◽  
State Chemical

AbstractThe conversion of photon energy into other energetic forms in molecules is accompanied by charge moving on ultrafast timescales. We directly observe the charge motion at a specific site in an electronically excited molecule using time-resolved x-ray photoelectron spectroscopy (TR-XPS). We extend the concept of static chemical shift from conventional XPS by the excited-state chemical shift (ESCS), which is connected to the charge in the framework of a potential model. This allows us to invert TR-XPS spectra to the dynamic charge at a specific atom. We demonstrate the power of TR-XPS by using sulphur 2p-core-electron-emission probing to study the UV-excited dynamics of 2-thiouracil. The method allows us to discover that a major part of the population relaxes to the molecular ground state within 220–250 fs. In addition, a 250-fs oscillation, visible in the kinetic energy of the TR-XPS, reveals a coherent exchange of population among electronic states.

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