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

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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The effect of the length and flexibility of the side chain of basic amino acids on the binding of antimicrobial peptides to zwitterionic and anionic membrane model systems

Bioorganic & Medicinal Chemistry ◽

10.1016/j.bmc.2012.01.015 ◽

2012 ◽

Vol 20 (5) ◽

pp. 1723-1739 ◽

Cited By ~ 15

Author(s):

Amanda L. Russell ◽

Brittany C. Williams ◽

Anne Spuches ◽

David Klapper ◽

Antoine H. Srouji ◽

...

Keyword(s):

Amino Acids ◽

Antimicrobial Peptides ◽

Model Systems ◽

Membrane Model ◽

Side Chain ◽

Basic Amino Acids

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On the atomic or “local” contributions to chemical shifts due to the anisotropy of the diamagnetic susceptibility of the aromatic side chain of amino acids and of the porphyrin ring

Biochemical and Biophysical Research Communications ◽

10.1016/0006-291x(81)91837-4 ◽

1981 ◽

Vol 101 (3) ◽

pp. 921-926 ◽

Cited By ~ 10

Author(s):

C. Giessner-Prettre ◽

B. Pullman

Keyword(s):

Amino Acids ◽

Diamagnetic Susceptibility ◽

Chemical Shifts ◽

Side Chain ◽

Porphyrin Ring ◽

Aromatic Side Chain

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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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1H, 13C and 15N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects

Journal of Biomolecular NMR ◽

10.1007/bf00211764 ◽

1995 ◽

Vol 5 (3) ◽

Cited By ~ 26

Author(s):

D.S. Wishart ◽

C.G. Bigam ◽

A. Holm ◽

R.S. Hodges ◽

B.D. Sykes

Keyword(s):

Amino Acids ◽

Nearest Neighbor ◽

Chemical Shifts ◽

Random Coil ◽

Nmr Chemical Shifts ◽

Neighbor Effects ◽

The Common

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Pressure dependence of side chain 13C chemical shifts in model peptides Ac-Gly-Gly-Xxx-Ala-NH2

Journal of Biomolecular NMR ◽

10.1007/s10858-017-0134-5 ◽

2017 ◽

Vol 69 (2) ◽

pp. 53-67 ◽

Cited By ~ 6

Author(s):

Markus Beck Erlach ◽

Joerg Koehler ◽

Edson Crusca ◽

Claudia E. Munte ◽

Masatsune Kainosho ◽

...

Keyword(s):

Pressure Dependence ◽

Chemical Shifts ◽

Side Chain ◽

13C Chemical Shifts ◽

Model Peptides

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The interaction of dimethyl sulfoxide with N-benzoyl amino acids

Australian Journal of Chemistry ◽

10.1071/ch9811869 ◽

1981 ◽

Vol 34 (9) ◽

pp. 1869 ◽

Cited By ~ 1

Author(s):

CW Fong ◽

HG Grant

Keyword(s):

Amino Acids ◽

Hydrogen Bonding ◽

Dimethyl Sulfoxide ◽

Benzene Ring ◽

Chemical Shifts ◽

Side Chain ◽

Torsional Angle ◽

Intermolecular Hydrogen Bonding ◽

Atom Increase ◽

Self Association

The interaction of dimethyl sulfoxide with N-benzoyl amino acids in deuterochloroform has been investigated by 13C n.m.r. spectroscopy. Examination of the chemical shifts of the benzene ring reveals that intermolecular hydrogen bonding between dimethyl sulfoxide and the amido-hydrogen atom increase the effective steric size of the amino hydrogen, resulting in an increase in the torsional angle between the benzene ring and the C(O)NHCH(R)COOH side chain. Self-association of N- benzoyl amino acids in deuterochloroform occurs largely through two COOH...O=C hydrogen bonds and does not involve intermolecular hydrogen bonding to the N-H proton.

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13C Nuclear Magnetic Resonance Investigation of Ethylene Homopolymers, Copolymers and Model Systems. Chemical Shifts and Relaxation Times

Applied Spectroscopy ◽

10.1366/0003702794925985 ◽

1979 ◽

Vol 33 (2) ◽

pp. 138-145 ◽

Cited By ~ 3

Author(s):

Leon Petrakis ◽

K. S. Seshadri

Keyword(s):

Chemical Shifts ◽

Relaxation Times ◽

Lattice Relaxation ◽

Model Systems ◽

Spin Lattice Relaxation ◽

Side Chain ◽

Side Chains ◽

Spin Lattice ◽

13C Nuclear Magnetic Resonance ◽

Magnetic Resonance Investigation

This is a report on the use of 13C NMR spectroscopy to study the structure of polyethylenes, polyethylene-olefin copolymers, and polyethylene model systems, through the observation of chemical shifts and spin-lattice relaxation times of individual carbons. Information is obtained on the type and numbers of side chains of polyethylenes from solution spectra at higher temperatures. The level of detectability of side chains is established at 2 side chain carbons per 1000 skeletal carbons. The observed chemical shifts are accounted for well by standard additivity schemes. The low-density polyethylenes show spectra which are distinctly different from high-density polyethylenes. The 13C-determined branch frequencies show the same general trend as the IR results, but it is also argued that the former are more accurate. Relaxation times of the various carbons of the model system C44 paraffin vary from 2.94 s for the backbone methylenes to 8.33 s for the terminal methyls to 11.11 s for α-methyls. Indicative of the behavior of olefin/polyethylene copolymers is the finding that all carbons of the copolymer have spin-lattice relaxation times of about 1.5 s, except for branch methyls which are 6 s. A series of polyethylenes at this high temperature shows relaxation times for the backbone methylene varying from 1.4 to 1.7 s, indicating that at this temperature, branching does not substantially affect the dynamic behavior of polyethylene.

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