Effect of a hydrophobic amino acid at position (i −1) on the stability of β-turns in hydrophilic pentapeptides as studied by NMR and molecular mechanics

1995 ◽  
Vol 73 (7) ◽  
pp. 972-980
Author(s):  
Xiaohong Liu ◽  
Serafin Fraga ◽  
Albin Otter ◽  
George Kotovych ◽  
Paul G. Scott
Keyword(s):  
Amino Acid ◽  
Molecular Mechanics ◽  
Ideal Type ◽  
Type I ◽  
Hydrophobic Amino Acid ◽  
Molecular Mechanics Calculations ◽  
Nmr Data ◽  
Nmr Study ◽  
Protected Tetrapeptide ◽  
The Stability

A detailed NMR study of the peptide NAc-FDEKA-NH2 in aqueous and in CD3OH/H2O solutions as well as the N-acetylpentapeptide amides YDEKA, VDEKA, GDEKA, and the protected tetrapeptide NAc-DEKA-NH2 in methanolic solutions indicates the importance of the first amino acid (at i −1) on stabilizing the type I β-turn. The data illustrate the hydrophobic stabilization of this turn, which is present in FDEKA, YDEKA, and VDEKA. For GDEKA and DEKA, the NMR data indicate that this turn is not present. Molecular mechanics calculations support this conclusion and indicate that for FDEKA and GDEKA the type I β-turn is distorted in both the vacuum and the solvated structures. For the solvated structures, the Cα(i) − Cα(i + 3) distance is 4.87 Å for FDEKA and 6.00 Å for GDEKA, which are to be compared with the value of 4.64 Å for an ideal type I β-turn, i.e., the distortion is far greater in GDEKA than in FDEKA. The calculations can be interpreted to indicate the presence of two major conformations in solution. Keywords: β-turns, FDEKA, pentapeptide.

Olefin−Amino Acid Complexes of Platinum(II). 2. NMR Study of the Effect of Olefin Structure on the Stability and on the Stereoselectivity of Binding for η2-Coordinated Prochiral Olefins

1997 ◽  
Vol 36 (3) ◽  
pp. 284-290 ◽  
Author(s):  
Luther E. Erickson ◽  
Peter Hayes ◽  
Joanna J. Hooper ◽  
Kevin F. Morris ◽  
Sally A. Newbrough ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Complexes ◽  
Nmr Study ◽  
The Stability

Enhanced stability of Cu2+–ATCUN complexes under physiologically relevant conditions by insertion of structurally bulky and hydrophobic amino acid residues into the ATCUN motif

2016 ◽  
Vol 45 (23) ◽  
pp. 9436-9445 ◽  
Author(s):  
Takaaki Miyamoto ◽  
Yuta Fukino ◽  
Shinichiro Kamino ◽  
Masashi Ueda ◽  
Shuichi Enomoto
Keyword(s):  
Amino Acid ◽  
Amino Acid Residues ◽  
Hydrophobic Amino Acid ◽  
Hydrophobic Residues ◽  
The Stability ◽  
Enhanced Stability

The stability of Cu2+–ATCUN complexes under physiologically relevant conditions is enhanced by inserting bulky and hydrophobic residues at positions 1 and 2 of the ATCUN peptide.

Synthesis, Conformational Analysis and Transannular Reactions of 5,9-Propanobenzo[7]annulene Derivatives

1997 ◽  
Vol 62 (10) ◽  
pp. 1585-1598 ◽  
Author(s):  
Pelayo Camps ◽  
Diana Görbig ◽  
Victoria Muñoz-Torrero ◽  
Francesc Pérez
Keyword(s):  
Conformational Analysis ◽  
Molecular Mechanics ◽  
Related Compound ◽  
Methyl Derivative ◽  
Reaction Conditions ◽  
Molecular Mechanics Calculations ◽  
H Nmr ◽  
Nmr Data ◽  
Acid Catalyzed

(5α,9α,11β)-11-Hydroxy-6,7,8,9-tetrahydro-5H-5,9-propanobenzo[7]annulen-7-one ethylene ketal (6a) and its 11α-methyl derivative (6b) were prepared from monoketal 3. These compounds underwent acid-catalyzed transannular reactions leading to 6,7,8,9-tetrahydro-5H-5,9-propanobenzo[7]annulene derivatives 5a, 8a and 5b, 8b, respectively, depending on the reaction conditions. The compounds 6a and 6b were dehydrated to 6,7,8,9-tetrahydro-5H-5,9-prop[1]enobenzo[7]annulen-7-one (9a) and its 11-methyl derivative (9b), respectively. The conformational analysis of the 5,9-propanobenzo[7]annulene derivatives by molecular mechanics calculations (MM3 program) and the 1H NMR data show that hydroxyketal 6a and the related compound (5α,7β,9α)-6,7,8,9-tetrahydro-5H-5,9-propanobenzo[7]annulen-7-ol (4) exist mainly in the boat-chair conformation with the boat cycloheptenol ring, while for hydroxyketal 6b the chair-boat conformation (chair cycloheptenol ring) seems to be the preferred one.

The conformational properties of calix[4]arenes 1h NMR and molecular mechanics calculations

1989 ◽  
Vol 86 ◽  
pp. 945-954 ◽  
Author(s):  
F. Bayard ◽  
D. Decoret ◽  
D. Pattou ◽  
J. Royer ◽  
A. Satrallah ◽  
...  
Keyword(s):  
Molecular Mechanics ◽  
1H Nmr ◽  
Molecular Mechanics Calculations ◽  
Conformational Properties

scholarly journals Charged Residues Flanking the Transmembrane Domain of Two Related Toxin–Antitoxin System Toxins Affect Host Response

Toxins ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 329
Author(s):  
Andrew Holmes ◽  
Jessie Sadlon ◽  
Keith Weaver
Keyword(s):  
Amino Acid ◽  
Enterococcus Faecalis ◽  
Host Response ◽  
Cytoplasmic Membrane ◽  
Transmembrane Domain ◽  
The Other ◽  
Type I ◽  
Transcriptomic Response ◽  
Specific Amino Acid ◽  
Transporter Protein

A majority of toxins produced by type I toxin–antitoxin (TA-1) systems are small membrane-localized proteins that were initially proposed to kill cells by forming non-specific pores in the cytoplasmic membrane. The examination of the effects of numerous TA-1 systems indicates that this is not the mechanism of action of many of these proteins. Enterococcus faecalis produces two toxins of the Fst/Ldr family, one encoded on pheromone-responsive conjugative plasmids (FstpAD1) and the other on the chromosome, FstEF0409. Previous results demonstrated that overexpression of the toxins produced a differential transcriptomic response in E. faecalis cells. In this report, we identify the specific amino acid differences between the two toxins responsible for the differential response of a gene highly induced by FstpAD1 but not FstEF0409. In addition, we demonstrate that a transporter protein that is genetically linked to the chromosomal version of the TA-1 system functions to limit the toxicity of the protein.

scholarly journals Mitigating the Adverse Effects of Polychlorinated Biphenyl Derivatives on Estrogenic Activity via Molecular Modification Techniques

2021 ◽  
Vol 18 (9) ◽  
pp. 4999
Author(s):  
Wei He ◽  
Wenhui Zhang ◽  
Zhenhua Chu ◽  
Yu Li
Keyword(s):  
Amino Acid ◽  
Binding Site ◽  
Hydrophobic Interaction ◽  
Oestrogen Receptor ◽  
Polychlorinated Biphenyl ◽  
Hydrophobic Interactions ◽  
Estrogenic Activity ◽  
Average Distance ◽  
Amino Acid Residues ◽  
Hydrophobic Amino Acid

The aim of this paper is to explore the mechanism of the change in oestrogenic activity of PCBs molecules before and after modification by designing new PCBs derivatives in combination with molecular docking techniques through the constructed model of oestrogenic activity of PCBs molecules. We found that the weakened hydrophobic interaction between the hydrophobic amino acid residues and hydrophobic substituents at the binding site of PCB derivatives and human oestrogen receptor alpha (hERα) was the main reason for the weakened binding force and reduced anti-oestrogenic activity. It was consistent with the information that the hydrophobic field displayed by the 3D contour maps in the constructed oestrogen activity CoMSIA model was one of the main influencing force fields. The hydrophobic interaction between PCB derivatives and oestrogen-active receptors was negatively correlated with the average distance between hydrophobic substituents and hydrophobic amino acid residues at the hERα-binding site, and positively correlated with the number of hydrophobic amino acid residues. In other words, the smaller the average distance between the hydrophobic amino acid residues at the binding sites between the two and the more the number of them, and the stronger the oestrogen activity expression degree of PCBS derivative molecules. Therefore, hydrophobic interactions between PCB derivatives and the oestrogen receptor can be reduced by altering the microenvironmental conditions in humans. This reduces the ability of PCB derivatives to bind to the oestrogen receptor and can effectively modulate the risk of residual PCB derivatives to produce oestrogenic activity in humans.

Photonic topological Weyl degeneracies and ideal type-I Weyl points in the gyromagnetic metamaterials

2021 ◽  
Vol 103 (4) ◽  
Author(s):  
Mingzhu Li ◽  
Jie Song ◽  
Yongyuan Jiang
Keyword(s):  
Ideal Type ◽  
Type I
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