scholarly journals Position-dependent impact of hexafluoroleucine and trifluoroisoleucine on protease digestion

2017 ◽  
Vol 13 ◽  
pp. 2869-2882 ◽  
Author(s):  
Susanne Huhmann ◽  
Anne-Katrin Stegemann ◽  
Kristin Folmert ◽  
Damian Klemczak ◽  
Johann Moschner ◽  
...  
Keyword(s):  
Amino Acids ◽  
Systematic Investigation ◽  
Proteinase K ◽  
Side Chain ◽  
Enzyme Binding ◽  
Fluorinated Amino Acids ◽  
Rp Hplc ◽  
Protease Digestion ◽  
Proteolytic Stability ◽  
The Stability

Rapid digestion by proteases limits the application of peptides as therapeutics. One strategy to increase the proteolytic stability of peptides is the modification with fluorinated amino acids. This study presents a systematic investigation of the effects of fluorinated leucine and isoleucine derivatives on the proteolytic stability of a peptide that was designed to comprise substrate specificities of different proteases. Therefore, leucine, isoleucine, and their side-chain fluorinated variants were site-specifically incorporated at different positions of this peptide resulting in a library of 13 distinct peptides. The stability of these peptides towards proteolysis by α-chymotrypsin, pepsin, proteinase K, and elastase was studied, and this process was followed by an FL-RP-HPLC assay in combination with mass spectrometry. In a few cases, we observed an exceptional increase in proteolytic stability upon introduction of the fluorine substituents. The opposite phenomenon was observed in other cases, and this may be explained by specific interactions of fluorinated residues with the respective enzyme binding sites. Noteworthy is that 5,5,5-trifluoroisoleucine is able to significantly protect peptides from proteolysis by all enzymes included in this study when positioned N-terminal to the cleavage site. These results provide valuable information for the application of fluorinated amino acids in the design of proteolytically stable peptide-based pharmaceuticals.

scholarly journals Unexpected Trends in the Hydrophobicity of Fluorinated Amino Acids Reflect Competing Changes in Polarity and Conformation

2018 ◽  
Author(s):  
João R. Robalo ◽  
Ana Vila Verde
Keyword(s):  
Amino Acids ◽  
Free Energy ◽  
Side Chain ◽  
Side Chains ◽  
Hydration Free Energy ◽  
Crossover Point ◽  
Fluorinated Amino Acids ◽  
Road Map ◽  
Alkyl Side Chains ◽  
The Impact

<div><div><div><p>Fluorination can dramatically improve the thermal and proteolytic stability of proteins and their enzymatic activity. Key to the impact of fluorination on protein properties is the hydrophobicity of fluorinated amino acids. We use molecular dynamics simulations, together with a new fixed-charge, atomistic force field, to quantify the changes in hydration free energy for amino acids with alkyl side chains and with 1 to 6 –CH to –CF side chain substitutions. Fluorination changes the hydration free energy by 1.5 to +2 kcal mol<sup>-</sup>1, but the number of fluorines is a poor predictor of hydrophobicity. Changes in hydration free energy reflect two main contributions: i) fluorination alters side chain-water interactions; we identify a crossover point from hydrophilic to hydrophobic fluoromethyl groups which may be used to estimate the hydrophobicity of fluorinated alkyl side-chains; ii) fluorination alters the number of backbone-water hydrogen bonds via changes in the relative side chain-backbone conformation. Our results offer a road map to mechanistically understand how fluorination alters hydrophobicity of (bio)polymers.</p></div></div></div>

scholarly journals Unexpected Trends in the Hydrophobicity of Fluorinated Amino Acids Reflect Competing Changes in Polarity and Conformation

2018 ◽  
Author(s):  
João R. Robalo ◽  
Ana Vila Verde
Keyword(s):  
Amino Acids ◽  
Free Energy ◽  
Side Chain ◽  
Side Chains ◽  
Hydration Free Energy ◽  
Crossover Point ◽  
Fluorinated Amino Acids ◽  
Road Map ◽  
Alkyl Side Chains ◽  
The Impact

<div><div><div><p>Fluorination can dramatically improve the thermal and proteolytic stability of proteins and their enzymatic activity. Key to the impact of fluorination on protein properties is the hydrophobicity of fluorinated amino acids. We use molecular dynamics simulations, together with a new fixed-charge, atomistic force field, to quantify the changes in hydration free energy for amino acids with alkyl side chains and with 1 to 6 –CH to –CF side chain substitutions. Fluorination changes the hydration free energy by 1.5 to +2 kcal mol<sup>-</sup>1, but the number of fluorines is a poor predictor of hydrophobicity. Changes in hydration free energy reflect two main contributions: i) fluorination alters side chain-water interactions; we identify a crossover point from hydrophilic to hydrophobic fluoromethyl groups which may be used to estimate the hydrophobicity of fluorinated alkyl side-chains; ii) fluorination alters the number of backbone-water hydrogen bonds via changes in the relative side chain-backbone conformation. Our results offer a road map to mechanistically understand how fluorination alters hydrophobicity of (bio)polymers.</p></div></div></div>

Influence of the side chain on the stability of Schiff-bases formed between pyridoxal 5′-phosphate and amino acids

1990 ◽  
Vol 22 (9) ◽  
pp. 905-914 ◽  
Author(s):  
M. A. Vazquez ◽  
F. Muñoz ◽  
J. Donoso ◽  
F. García Blanco
Keyword(s):  
Amino Acids ◽  
Schiff Bases ◽  
Side Chain ◽  
The Stability

scholarly journals Synthetic, structural and biological studies of the ubiquitin system: synthesis and crystal structure of an analogue containing unnatural amino acids

1997 ◽  
Vol 323 (3) ◽  
pp. 727-734 ◽  
Author(s):  
Steven G. LOVE ◽  
Tom W. MUIR ◽  
Robert RAMAGE ◽  
Kevin T. SHAW ◽  
Dmitriy ALEXEEV ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Amino Acids ◽  
Unnatural Amino Acids ◽  
Side Chain ◽  
Hydrophobic Core ◽  
Biological Behaviour ◽  
Methyl Group ◽  
Ubiquitin System ◽  
Biological Studies ◽  
The Stability

Ubiquitin is a 76-amino acid protein involved in the targeting for destruction of proteins in the cell. The protein can readily be synthesized chemically affording an extra dimension to studies of protein stability. Ubiquitin with various modifications to the hydrophobic core has been synthesized. In particular, two core amino acids have been replaced by aminobutyric acid (Val-26) and norvaline (for Ile-30) and the product crystallized. The refined crystal structure shows an overall contraction of the molecule and the side chain of Nva-30 rotates relative to Ile-30. However, the side chain rotation is not sufficient to compensate for the effect of the loss of the methyl group and hence a small cavity is introduced into the structure, which decreases the stability of the protein. The biological behaviour of the modified protein is unaltered. The observed changes in stability are of the magnitude expected for the removal of methyl groups from the hydrophobic core of a protein. Interestingly, the effect appears to be independent of the position of the removed methyl group. The intact structure, but not its stability, is important for recognition by the biological conjugating system.

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