A study of the reactivity of S(VI)–F containing warheads with nucleophilic amino-acid side chains under physiological conditions

2017 ◽  
Vol 15 (45) ◽  
pp. 9685-9695 ◽  
Author(s):  
H. Mukherjee ◽  
J. Debreczeni ◽  
J. Breed ◽  
S. Tentarelli ◽  
B. Aquila ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Side Chains ◽  
Physiological Conditions ◽  
Amino Acid Side Chains

Profiling the reactivity and stability of SVI–F warheads towards nucleophilic amino acids for the development of biochemical probe compounds.

ChemInform Abstract: Highly Diastereoselective Preparation of anti-α,β-Dialkyl β-Amino Acids Containing Natural α-Amino Acid Side Chains.

ChemInform ◽  
2008 ◽  
Vol 39 (11) ◽  
Author(s):  
Stefania Capone ◽  
Silvana Pedatella ◽  
Annalisa Guaragna ◽  
Mauro De Nisco ◽  
Giovanni Palumbo
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Side Chains ◽  
Amino Acid Side Chains

scholarly journals Proposal of the Annotation of Phosphorylated Amino Acids and Peptides Using Biological and Chemical Codes

Molecules ◽  
2021 ◽  
Vol 26 (3) ◽  
pp. 712
Author(s):  
Piotr Minkiewicz ◽  
Małgorzata Darewicz ◽  
Anna Iwaniak ◽  
Marta Turło
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Functional Properties ◽  
Side Chains ◽  
Amino Acid Side Chains ◽  
The Future ◽  
Chemical Code ◽  
Internet Databases

Phosphorylation represents one of the most important modifications of amino acids, peptides, and proteins. By modifying the latter, it is useful in improving the functional properties of foods. Although all these substances are broadly annotated in internet databases, there is no unified code for their annotation. The present publication aims to describe a simple code for the annotation of phosphopeptide sequences. The proposed code describes the location of phosphate residues in amino acid side chains (including new rules of atom numbering in amino acids) and the diversity of phosphate residues (e.g., di- and triphosphate residues and phosphate amidation). This article also includes translating the proposed biological code into SMILES, being the most commonly used chemical code. Finally, it discusses possible errors associated with applying the proposed code and in the resulting SMILES representations of phosphopeptides. The proposed code can be extended to describe other modifications in the future.

scholarly journals Characterizing hydrophobicity of amino acid side chains in a protein environment via measuring contact angle of a water nanodroplet on planar peptide network

2016 ◽  
Vol 113 (46) ◽  
pp. 12946-12951 ◽  
Author(s):  
Chongqin Zhu ◽  
Yurui Gao ◽  
Hui Li ◽  
Sheng Meng ◽  
Lei Li ◽  
...  
Keyword(s):  
Amino Acids ◽  
Contact Angle ◽  
Amino Acid ◽  
Contact Angles ◽  
Side Chains ◽  
Complete Wetting ◽  
Charged Amino Acids ◽  
Engineering Measurement ◽  
Amino Acid Side Chains ◽  
Protein Environment

Hydrophobicity of macroscopic planar surface is conventionally characterized by the contact angle of water droplets. However, this engineering measurement cannot be directly extended to surfaces of proteins, due to the nanometer scale of amino acids and inherent nonplanar structures. To measure the hydrophobicity of side chains of proteins quantitatively, numerous parameters were developed to characterize behavior of hydrophobic solvation. However, consistency among these parameters is not always apparent. Herein, we demonstrate an alternative way of characterizing hydrophobicity of amino acid side chains in a protein environment by constructing a monolayer of amino acids (i.e., artificial planar peptide network) according to the primary and the β-sheet secondary structures of protein so that the conventional engineering measurement of the contact angle of a water droplet can be brought to bear. Using molecular dynamics simulations, contact angles θ of a water nanodroplet on the planar peptide network, together with excess chemical potentials of purely repulsive methane-sized Weeks−Chandler−Andersen solute, are computed. All of the 20 types of amino acids and the corresponding planar peptide networks are studied. Expectedly, all of the planar peptide networks with nonpolar amino acids are hydrophobic due to θ> 90°, whereas all of the planar peptide networks of the polar and charged amino acids are hydrophilic due to θ< 90°. Planar peptide networks of the charged amino acids exhibit complete-wetting behavior due to θ= 0°. This computational approach for characterization of hydrophobicity can be extended to artificial planar networks of other soft matter.

Highly diastereoselective preparation of anti-α,β-dialkyl β-amino acids containing natural α-amino acid side chains

Tetrahedron ◽  
2007 ◽  
Vol 63 (49) ◽  
pp. 12202-12206 ◽  
Author(s):  
Stefania Capone ◽  
Silvana Pedatella ◽  
Annalisa Guaragna ◽  
Mauro De Nisco ◽  
Giovanni Palumbo
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Side Chains ◽  
Amino Acid Side Chains
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