scholarly journals 13C-n.m.r. of the cyanylated apoflavodoxin and flavodoxin from Clostridium pasteurianum

1993 ◽  
Vol 294 (1) ◽  
pp. 215-218 ◽  
Author(s):  
G M Doherty ◽  
S G Mayhew ◽  
J P G Malthouse
Keyword(s):  
Hydrogen Bonding ◽  
Chemical Shift ◽  
Chemical Modification ◽  
Dissociation Constant ◽  
Chemical Shifts ◽  
Thiol Group ◽  
Cysteine Residue ◽  
Single Step ◽  
Clostridium Pasteurianum ◽  
Megasphaera Elsdenii

The thiol group of the flavodoxin from Clostridium pasteurianum has been cyanylated in a single step using [cyanato-13C]2-nitro-5-thiocyanatobenzoic acid. This chemical modification increases the dissociation constant of the apoflavodoxin-FMN complex 10-fold from 0.33 +/- 0.15 nM to 2.9 +/- 1.3 nM. The thiocyanate carbons of the cyanylated cysteine residue of apoflavodoxin and flavodoxin had chemical shift values of 114.7 and 112.3 p.p.m. respectively. From these chemical shifts we conclude that the binding of FMN by the cyanylated apoflavodoxin causes a decrease in the polarity and/or hydrogen bonding capacity of the environment of the thiocyanate group. We compare these results with those obtained from similar studies on the cyanylated apoflavodoxin and flavodoxin from Megasphaera elsdenii and we discuss how FMN binding and cyanylation perturb the structures of apoflavodoxins from Megasphaera elsdenii and Clostridium pasteurianum.

scholarly journals ProCS15: A DFT-based chemical shift predictor for backbone and Cβ atoms in proteins

2015 ◽  
Author(s):  
Anders S Larsen ◽  
Lars A Bratholm ◽  
Anders S Christensen ◽  
Maher Jan Channir ◽  
Jan H. Jensen
Keyword(s):  
Hydrogen Bonding ◽  
Chemical Shift ◽  
Chemical Shifts ◽  
Structural Models ◽  
Protein G ◽  
Chemical Shielding ◽  
The Third ◽  
Entire Structure ◽  
Igg Binding ◽  
Structural Ensembles

We present ProCS15: A program that computes the isotropic chemical shielding values of backbone and C β atoms given a protein structure in less than a second. ProCS15 is based on around 2.35 million OPBE/6-31G(d,p)//PM6 calculations on tripeptides and small structural models of hydrogen-bonding. The ProCS15-predicted chemical shielding values are compared to experimentally measured chemical shifts for Ubiquitin and the third IgG-binding domain of Protein G through linear regression and yield RMSD values of up to 2.2, 0.7, and 4.8 ppm for carbon, hydrogen, and nitrogen atoms. These RMSD values are very similar to corresponding RMSD values computed using OPBE/6-31G(d,p) for the entire structure for each proteins. These maximum RMSD values can be reduced by using NMR-derived structural ensembles of Ubiquitin. For example, for the largest ensemble the largest RMSD values are 1.7, 0.5, and 3.5 ppm for carbon, hydrogen, and nitrogen. The corresponding RMSD values predicted by several empirical chemical shift predictors range between 0.7 - 1.1, 0.2 - 0.4, and 1.8 - 2.8 ppm for carbon, hydrogen, and nitrogen atoms, respectively.

scholarly journals ProCS15: A DFT-based chemical shift predictor for backbone and Cβ atoms in proteins

2015 ◽  
Author(s):  
Anders S Larsen ◽  
Lars A Bratholm ◽  
Anders S Christensen ◽  
Maher Jan Channir ◽  
Jan H. Jensen
Keyword(s):  
Hydrogen Bonding ◽  
Chemical Shift ◽  
Chemical Shifts ◽  
Structural Models ◽  
Protein G ◽  
Chemical Shielding ◽  
The Third ◽  
Entire Structure ◽  
Igg Binding ◽  
Structural Ensembles

We present ProCS15: A program that computes the isotropic chemical shielding values of backbone and C β atoms given a protein structure in less than a second. ProCS15 is based on around 2.35 million OPBE/6-31G(d,p)//PM6 calculations on tripeptides and small structural models of hydrogen-bonding. The ProCS15-predicted chemical shielding values are compared to experimentally measured chemical shifts for Ubiquitin and the third IgG-binding domain of Protein G through linear regression and yield RMSD values of up to 2.2, 0.7, and 4.8 ppm for carbon, hydrogen, and nitrogen atoms. These RMSD values are very similar to corresponding RMSD values computed using OPBE/6-31G(d,p) for the entire structure for each proteins. These maximum RMSD values can be reduced by using NMR-derived structural ensembles of Ubiquitin. For example, for the largest ensemble the largest RMSD values are 1.7, 0.5, and 3.5 ppm for carbon, hydrogen, and nitrogen. The corresponding RMSD values predicted by several empirical chemical shift predictors range between 0.7 - 1.1, 0.2 - 0.4, and 1.8 - 2.8 ppm for carbon, hydrogen, and nitrogen atoms, respectively.

scholarly journals Rat α-foetoprotein. Purification, physicochemical characterization, oestrogen-binding properties and chemical modification of the thiol group

1978 ◽  
Vol 175 (1) ◽  
pp. 73-81 ◽  
Author(s):  
Vera Versée ◽  
André O. Barel
Keyword(s):  
Chemical Modification ◽  
Binding Site ◽  
Physicochemical Characterization ◽  
Thiol Group ◽  
Iodoacetic Acid ◽  
Cysteine Residue ◽  
Sulphonic Acid ◽  
Electrophoretic Variants ◽  
Thiol Reagent ◽  
Displacement Experiments

1. Rat α-foetoprotein, an oestrogen-binding foetal globulin, was isolated in large quantities from amniotic fluid and serum by preparative electrophoresis on polyacrylamide slab gels or by chromatography on an immunoadsorbent column. Subsequently the two electrophoretic forms of this protein were separated by electrophoresis on the same medium. 2. Both forms were found to show identical binding with oestradiol. From the extrinsic fluorescence of the bound dye 8-anilinonaphthalene-1-sulphonic acid it was shown that the polarity of the binding site is practically identical for both forms. One residue of tryptophan was determined for both forms. The two electrophoretic variants display the same amount of secondary structure as demonstrated by circular dichroism. 3. The affinity of total α-foetoprotein for oestradiol as a function of pH was studied by using a Sephadex G-25 gel-equilibration method. Maximal binding occurred at pH8.5. Only a fractional number of binding sites per molecule could be measured at pH7.4, whereas at higher pH the number of sites was very close to unity. There was no significant effect of pH on the value of the association constant (Ka=4.3×107±1.2×107m−1). 4. Displacement experiments of bound labelled oestradiol with various steroids have permitted investigation of the specificity of α-foetoprotein. This foetal globulin binds rather strongly compounds that display the rigid structure of the oestratriene skeleton (oestradiol, oestrone). Diminished binding for diethylstilboestrol and a diethylstilboestrol affinity label was observed. No binding was measured with a more flexible structure such as hexoestrol [4,4′-(1,2-diethylethane-1,2-diyl)bisphenol]. 5. Chemical modification of cysteine residues of α-foetoprotein with two alkylating reagents [iodoacetic acid and 8-[N-(iodoacetylaminoethyl)amino]naphthalene-1-sulphonic acid] has very little effect on the oestrogen binding. It is suggested that the oestrogen-binding site does not contain a cysteine residue. From the kinetics of alkylation and from the fluorescence properties of the chemically bound thiol reagent 8-[N-(iodoacetylaminoethyl)amino]naphthalene-1-sulphonic acid], it was demonstrated that the very-slow-reacting thiol group is probably located in a non-polar region of the molecule.

scholarly journals ProCS15: A DFT-based chemical shift predictor for backbone and C β atoms in proteins

2015 ◽  
Author(s):  
Anders S Larsen ◽  
Lars A Bratholm ◽  
Anders S Christensen ◽  
Maher Jan Channir ◽  
Jan H. Jensen
Keyword(s):  
Hydrogen Bonding ◽  
Chemical Shift ◽  
Chemical Shifts ◽  
Structural Models ◽  
Protein G ◽  
Chemical Shielding ◽  
The Third ◽  
Entire Structure ◽  
Igg Binding ◽  
Structural Ensembles

We present ProCS15: A program that computes the isotropic chemical shielding values of backbone and C β atoms given a protein structure in less than a second. ProCS15 is based on around 2.35 million OPBE/6-31G(d,p)//PM6 calculations on tripeptides and small structural models of hydrogen-bonding. The ProCS15-predicted chemical shielding values are compared to experimentally measured chemical shifts for Ubiquitin and the third IgG-binding domain of Protein G through linear regression and yield RMSD values of up to 2.2, 0.7, and 4.8 ppm for carbon, hydrogen, and nitrogen atoms. These RMSD values are very similar to corresponding RMSD values computed using OPBE/6-31G(d,p) for the entire structure for each proteins. These maximum RMSD values can be reduced by using NMR-derived structural ensembles of Ubiquitin. For example, for the largest ensemble the largest RMSD values are 1.7, 0.5, and 3.5 ppm for carbon, hydrogen, and nitrogen. The corresponding RMSD values predicted by several empirical chemical shift predictors range between 0.7 - 1.1, 0.2 - 0.4, and 1.8 - 2.8 ppm for carbon, hydrogen, and nitrogen atoms, respectively.

Proton N.M.R. of the muramyl dipeptide adjuvant in dimethyl sulfoxide

1982 ◽  
Vol 35 (3) ◽  
pp. 489 ◽  
Author(s):  
BE Chapman ◽  
M Batley ◽  
JW Redmond
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Chemical Shift ◽  
Dimethyl Sulfoxide ◽  
Chemical Shifts ◽  
Muramyl Dipeptide ◽  
Side Chain ◽  
Active Principle ◽  
Temperature Dependences ◽  
Amide Protons

The active principle of complete Freund's adjuvant, N-acetylmuramyl-L-alanyl-D-isoglutamine, was studied in the α-anomeric form in dimethyl sulfoxide solutions by 1H n.m.r, at 200 MHz. All resonances except those of the nonanomeric sugar protons were assigned. Temperature dependences of the chemical shifts of the amide protons indicated that the alanyl NH is involved in hydrogen bonding. The isoglutamine β-CH2 protons showed large chemical-shift nonequivalence, an effect consistent with a hydrogen bond to the side chain carboxyl of this residue.

scholarly journals ProCS15: a DFT-based chemical shift predictor for backbone and Cβatoms in proteins

PeerJ ◽  
2015 ◽  
Vol 3 ◽  
pp. e1344 ◽  
Author(s):  
Anders S. Larsen ◽  
Lars A. Bratholm ◽  
Anders S. Christensen ◽  
Maher Channir ◽  
Jan H. Jensen
Keyword(s):  
Hydrogen Bonding ◽  
Chemical Shift ◽  
Chemical Shifts ◽  
Structural Models ◽  
Protein G ◽  
Chemical Shielding ◽  
The Third ◽  
Entire Structure ◽  
Igg Binding ◽  
Structural Ensembles

We present ProCS15: a program that computes the isotropic chemical shielding values of backbone and Cβatoms given a protein structure in less than a second. ProCS15 is based on around 2.35 million OPBE/6-31G(d,p)//PM6 calculations on tripeptides and small structural models of hydrogen-bonding. The ProCS15-predicted chemical shielding values are compared to experimentally measured chemical shifts for Ubiquitin and the third IgG-binding domain of Protein G through linear regression and yield RMSD values of up to 2.2, 0.7, and 4.8 ppm for carbon, hydrogen, and nitrogen atoms. These RMSD values are very similar to corresponding RMSD values computed using OPBE/6-31G(d,p) for the entire structure for each proteins. These maximum RMSD values can be reduced by using NMR-derived structural ensembles of Ubiquitin. For example, for the largest ensemble the largest RMSD values are 1.7, 0.5, and 3.5 ppm for carbon, hydrogen, and nitrogen. The corresponding RMSD values predicted by several empirical chemical shift predictors range between 0.7–1.1, 0.2–0.4, and 1.8–2.8 ppm for carbon, hydrogen, and nitrogen atoms, respectively.

scholarly journals 13C-n.m.r. of the cyanylated β-lactoglobulins: evidence that Cys-121 provides the thiol group of β-lactoglobulins A and B

1994 ◽  
Vol 302 (2) ◽  
pp. 511-516 ◽  
Author(s):  
P Phelan ◽  
J P Malthouse
Keyword(s):  
Chemical Shift ◽  
Chemical Shifts ◽  
Thiol Group ◽  
Equimolar Mixture ◽  
Thiol Groups ◽  
Exchange Reactions ◽  
Polar Environment ◽  
Alkaline Denaturation ◽  
The One

The thiol groups of beta-lactoglobulins A and B have been cyanylated using [13C]KCN. The samples of [cyanato-13C]-cyanylated-beta-lactoglobulins A and B which we prepared had signals at 109.7 p.p.m. and 114.4 p.p.m. We conclude that the thiocyanate carbon having a chemical shift of 109.7 p.p.m. is in an apolar environment similar to a cyclohexane solvent, whereas the thiocyanate carbon having a chemical shift of 114.4 p.p.m. is in a polar environment similar to water. The signals with chemical shifts of 109.7 p.p.m. are assigned to the thiocyanate carbons of the native [cyanato-13C]cyanylated-beta-lactoglobulins A and B. We deduce that the signal at 114.4 p.p.m. is due to an irreversibly denatured/unfolded species produced by alkaline denaturation, which is caused by intramolecular thiol/disulphide exchange occurring during our cyanylation procedure. We propose that Cys-119 is cyanylated in the irreversibly denatured species and Cys-121 is cyanylated in the native [cyanato-13C]cyanylated-beta-lactoglobulins A and B. We suggest that the same intramolecular thiol-disulphide exchange reactions occurred when McKenzie and co-workers [McKenzie, Ralston and Shaw (1972) Biochemistry 11, 4539-4547] alkylated beta-lactoglobulins with iodoacetamide. Therefore the one mol of thiol/mol of monomer in the native beta-lactoglobulins is due to the thiol of Cys-121 and is not due to an equimolar mixture of Cys-119 and Cys-121 as they suggested.

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.

scholarly journals NMR of Natural Products as Potential Drugs

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3763
Author(s):  
Poul Erik Hansen
Keyword(s):  
Natural Products ◽  
Hydrogen Bonding ◽  
Density Functional ◽  
Chemical Shifts ◽  
Isotope Effects ◽  
Density Functional Theory Calculations ◽  
Intramolecular Hydrogen Bonding ◽  
Chemical Equilibria ◽  
Nmr Techniques ◽  
Intramolecular Hydrogen

This review outlines methods to investigate the structure of natural products with emphasis on intramolecular hydrogen bonding, tautomerism and ionic structures using NMR techniques. The focus is on 1H chemical shifts, isotope effects on chemical shifts and diffusion ordered spectroscopy. In addition, density functional theory calculations are performed to support NMR results. The review demonstrates how hydrogen bonding may lead to specific structures and how chemical equilibria, as well as tautomeric equilibria and ionic structures, can be detected. All these features are important for biological activity and a prerequisite for correct docking experiments and future use as drugs.

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.

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