Random coil carbon chemical shifts of deoxyribonucleic acids

AbstractTransmissible spongiform encephalopathies (TSEs) are fatal neurodegenerative disorders associated with the misfolding and aggregation of the human prion protein (huPrP). Despite efforts into investigating the process of huPrP aggregation, the mechanisms triggering its misfolding remain elusive. A number of TSE-associated mutations of huPrP have been identified, but their role at the onset and progression of prion diseases is unclear. Here we report the NMR assignments of the C-terminal globular domain of the wild type huPrP and the pathological mutant T183A. The differences in chemical shifts between the two variants reveal conformational alterations in some structural elements of the mutant, whereas the analyses of secondary shifts and random coil index provide indications on the putative mechanisms of misfolding of T183A huPrP.

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Presence of β-Turn Structure in Recombinant Spider Silk Dissolved in Formic Acid Revealed with NMR

Molecules ◽

10.3390/molecules27020511 ◽

2022 ◽

Vol 27 (2) ◽

pp. 511

Author(s):

Yu Suzuki ◽

Takanori Higashi ◽

Takahiro Yamamoto ◽

Hideyasu Okamura ◽

Takehiro K. Sato ◽

...

Keyword(s):

Mechanical Properties ◽

Formic Acid ◽

Spider Silk ◽

Chemical Shifts ◽

Repetitive Sequences ◽

Silk Protein ◽

Random Coil ◽

Oh Groups ◽

Spider Silk Protein ◽

Turn Structure

Spider dragline silk is a biopolymer with excellent mechanical properties. The development of recombinant spider silk protein (RSP)-based materials with these properties is desirable. Formic acid (FA) is a spinning solvent for regenerated Bombyx mori silk fiber with excellent mechanical properties. To use FA as a spinning solvent for RSP with the sequence of major ampullate spider silk protein from Araneus diadematus, we determined the conformation of RSP in FA using solution NMR to determine the role of FA as a spinning solvent. We assigned 1H, 13C, and 15N chemical shifts to 32-residue repetitive sequences, including polyAla and Gly-rich regions of RSP. Chemical shift evaluation revealed that RSP is in mainly random coil conformation with partially type II β-turn structure in the Gly-Pro-Gly-X motifs of the Gly-rich region in FA, which was confirmed by the 15N NOE data. In addition, formylation at the Ser OH groups occurred in FA. Furthermore, we evaluated the conformation of the as-cast film of RSP dissolved in FA using solid-state NMR and found that β-sheet structure was predominantly formed.

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Random coil chemical shifts for serine, threonine and tyrosine phosphorylation over a broad pH range

Journal of Biomolecular NMR ◽

10.1007/s10858-019-00283-z ◽

2019 ◽

Vol 73 (12) ◽

pp. 713-725 ◽

Cited By ~ 4

Author(s):

Ruth Hendus-Altenburger ◽

Catarina B. Fernandes ◽

Katrine Bugge ◽

Micha B. A. Kunze ◽

Wouter Boomsma ◽

...

Keyword(s):

Chemical Shift ◽

Secondary Structure ◽

Intrinsically Disordered Proteins ◽

Chemical Shifts ◽

Random Coil ◽

Disordered Proteins ◽

Phosphoryl Group ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Secondary Chemical

Abstract Phosphorylation is one of the main regulators of cellular signaling typically occurring in flexible parts of folded proteins and in intrinsically disordered regions. It can have distinct effects on the chemical environment as well as on the structural properties near the modification site. Secondary chemical shift analysis is the main NMR method for detection of transiently formed secondary structure in intrinsically disordered proteins (IDPs) and the reliability of the analysis depends on an appropriate choice of random coil model. Random coil chemical shifts and sequence correction factors were previously determined for an Ac-QQXQQ-NH2-peptide series with X being any of the 20 common amino acids. However, a matching dataset on the phosphorylated states has so far only been incompletely determined or determined only at a single pH value. Here we extend the database by the addition of the random coil chemical shifts of the phosphorylated states of serine, threonine and tyrosine measured over a range of pH values covering the pKas of the phosphates and at several temperatures (www.bio.ku.dk/sbinlab/randomcoil). The combined results allow for accurate random coil chemical shift determination of phosphorylated regions at any pH and temperature, minimizing systematic biases of the secondary chemical shifts. Comparison of chemical shifts using random coil sets with and without inclusion of the phosphoryl group, revealed under/over estimations of helicity of up to 33%. The expanded set of random coil values will improve the reliability in detection and quantification of transient secondary structure in phosphorylation-modified IDPs.

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Pressure dependence of side chain 1H and 15N-chemical shifts in the model peptides Ac-Gly-Gly-Xxx-Ala-NH2

Journal of Biomolecular NMR ◽

10.1007/s10858-020-00326-w ◽

2020 ◽

Vol 74 (8-9) ◽

pp. 381-399

Author(s):

Markus Beck Erlach ◽

Joerg Koehler ◽

Claudia E. Munte ◽

Werner Kremer ◽

Edson Crusca ◽

...

Keyword(s):

Amino Acids ◽

Pressure Dependence ◽

Chemical Shifts ◽

Model Systems ◽

Random Coil ◽

Nonlinear Dependence ◽

Side Chain ◽

Unfolded Proteins ◽

Pressure Coefficients ◽

Compression Effects

Abstract For interpreting the pressure induced shifts of resonance lines of folded as well as unfolded proteins the availability of data from well-defined model systems is indispensable. Here, we report the pressure dependence of 1H and 15N chemical shifts of the side chain atoms in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (Xxx is one of the 20 canonical amino acids) measured at 800 MHz proton frequency. As observed earlier for other nuclei the chemical shifts of the side chain nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The pressure response is described by a second degree polynomial with the pressure coefficients B1 and B2 that are dependent on the atom type and type of amino acid studied. A number of resonances could be assigned stereospecifically including the 1H and 15N resonances of the guanidine group of arginine. In addition, stereoselectively isotope labeled SAIL amino acids were used to support the stereochemical assignments. The random-coil pressure coefficients are also dependent on the neighbor in the sequence as an analysis of the data shows. For Hα and HN correction factors for different amino acids were derived. In addition, a simple correction of compression effects in thermodynamic analysis of structural transitions in proteins was derived on the basis of random-coil pressure coefficients.

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1H NMR studies on the solution conformation of contulakin-G and analogues

Canadian Journal of Chemistry ◽

10.1139/v02-115 ◽

2002 ◽

Vol 80 (8) ◽

pp. 1022-1031 ◽

Cited By ~ 9

Author(s):

Lill Kindahl ◽

Corine Sandström ◽

A Grey Craig ◽

Thomas Norberg ◽

Lennart Kenne

Keyword(s):

Hydrogen Bond ◽

Chemical Shifts ◽

Torsional Rigidity ◽

Peptide Chain ◽

Random Coil ◽

Amide Proton ◽

Solution Conformation ◽

Nmr Studies ◽

H Nmr ◽

Intramolecular Hydrogen

The conformation of contulakin-G, a bioactive 16 amino acid O-linked glycopeptide (ZSEEGGSNAT*KKPYIL) with the disaccharide β-D-Gal(1[Formula: see text]3)α-D-GalNAc attached to the threonine residue in position 10, has been investigated by 1H NMR spectroscopy. The 1H NMR data for the non-glycosylated peptide and for two glycopeptide analogues, one with the monosaccharide α-D-GalNAc at Thr10 and one with the disaccharide β-D-Gal(1–>3)α-D-GalNAc at Ser7, all of lower bioactivity than contulakin-G, have also been collected. The chemical shifts, NOEs, temperature coefficients of amide protons, and 3JNH,αH-values suggest that all four compounds exist mainly in random coil conformations. Some transient populations of folded conformations are also present in the glycopeptides and turns, probably induced by the sugars, are present in the peptide chain around the site of glycosylation. In the two peptides O-glycosylated at Thr10, the rotation of α-D-GalNAc around the linkage between the sugar and the peptide is restricted. There is evidence for a hydrogen bond between the amide proton of α-D-GalNAc and the peptide chain that could contribute to this torsional rigidity. An intramolecular hydrogen bond between the carbohydrate and the peptide chain does not exist in the peptide O-glycosylated at the Ser7 residue. Key words: conformation, contulakin-G, NMR, O-linked glycopeptide.

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CheSPI: Chemical shift Secondary structure Population Inference

10.1101/2021.02.20.432095 ◽

2021 ◽

Author(s):

Jakob Toudahl Nielsen ◽

Frans A.A. Mulder

Keyword(s):

Intrinsically Disordered Proteins ◽

Chemical Shifts ◽

Protein Structures ◽

Random Coil ◽

Disordered Proteins ◽

Residual Structure ◽

Intrinsically Disordered ◽

Population Inference ◽

Local Protein Structure ◽

Structural Classes

AbstractNMR chemical shifts (CSs) are delicate reporters of local protein structure, and recent advances in random coil CS (RCCS) prediction and interpretation now offer the compelling prospect of inferring small populations of structure from small deviations from RCCSs. Here, we present CheSPI, a simple and efficient method that provides unbiased and sensitive aggregate measures of local structure and disorder. It is demonstrated that CheSPI can predict even very small amounts of residual structure and robustly delineate subtle differences into four structural classes for intrinsically disordered proteins. For structured regions and proteins, CheSPI can assign up to eight structural classes, which coincide with the well-known DSSP classification. The program is freely available, and can either be invoked from URL www.protein-nmr.org as a web implementation, or run locally from command line as a python program. CheSPI generates comprehensive numeric and graphical output for intuitive annotation and visualization of protein structures. A number of examples are provided.

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An evaluation of chemical shift index-based secondary structure determination in proteins: Influence of random coil chemical shifts*

Journal of Biomolecular NMR ◽

10.1023/b:jnmr.0000048940.51331.49 ◽

2004 ◽

Vol 30 (2) ◽

pp. 143-153 ◽

Cited By ~ 28

Author(s):

S.P. Mielke ◽

V.V. Krishnan

Keyword(s):

Chemical Shift ◽

Secondary Structure ◽

Structure Determination ◽

Chemical Shifts ◽

Random Coil ◽

Chemical Shift Index

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The solution conformations of amino acids from molecular dynamics simulations of Gly-X-Gly peptides: comparison with NMR parameters

Biochemistry and Cell Biology ◽

10.1139/o98-025 ◽

1998 ◽

Vol 76 (2-3) ◽

pp. 164-170 ◽

Cited By ~ 10

Author(s):

David van der Spoel

Keyword(s):

Molecular Dynamics ◽

Amino Acids ◽

Nuclear Magnetic Resonance ◽

Magnetic Resonance ◽

Chemical Shifts ◽

Coupling Constants ◽

Random Coil ◽

J Coupling ◽

Dynamics Simulations ◽

Nuclear Magnetic

The conformations that amino acids can adopt in the random coil state are of fundamental interest in the context of protein folding research and studies of proteinpeptide interactions. To date, no detailed quantitative data from experimental studies have been reported; only nuclear magnetic resonance parameters such as chemical shifts and J coupling constants have been reported. These experimental nuclear magnetic resonance data represent averages over multiple conformations, and hence they do not provide unique structural information. I have performed relatively long (2.5 ns) molecular dynamics simulations of Gly-X-Gly tripeptides, surrounded by explicit water molecules, where X represents eight different amino acids with long side chains. From the trajectories one can calculate time averaged backbone chemical shifts and 3JNHα coupling constants and compare these with experimental data. These calculated quantities are quite close to the experimental values for most amino acids, suggesting that these simulations are a good model for the random coil state of the tripeptides. On the basis of my simulations I predict 3Jαβ coupling constants and present dihedral distributions for the Φ, Ψ, as well as χ1 and χ2 angles. Finally, I present correlation plots for these dihedral angles.Key words: molecular dynamics (MD), nuclear magnetic resonance (NMR) spectroscopy, J-coupling, chemical shift, dihedral probability distribution.

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