scholarly journals Knowledge-based Homology Modeling and Experimental Determination of Amino Acid Side Chain Accessibility by the Laser Photo CIDNP (Chemically Induced Dynamic Nuclear Polarization) Approach in Solution: Lessons from the Small Sialidase of Clostridium perfringens

1996 ◽  
Vol 2 (11) ◽  
pp. 446-455 ◽  
Author(s):  
Claus-Wilhelm von der Lieth ◽  
Hans-Christian Siebert ◽  
Emadeddin Tajkhorshid ◽  
Susanne Kruse ◽  
Roland Schauer ◽  
...  
Keyword(s):  
Amino Acid ◽  
Homology Modeling ◽  
Clostridium Perfringens ◽  
Dynamic Nuclear Polarization ◽  
Nuclear Polarization ◽  
Side Chain ◽  
Amino Acid Side Chain ◽  
Knowledge Based ◽  
Chemically Induced

scholarly journals Synthesis of nucleotide–amino acid conjugates designed for photo-CIDNP experiments by a phosphotriester approach

2013 ◽  
Vol 9 ◽  
pp. 2898-2909 ◽  
Author(s):  
Tatyana V Abramova ◽  
Olga B Morozova ◽  
Vladimir N Silnikov ◽  
Alexandra V Yurkovskaya
Keyword(s):  
Amino Acid ◽  
Liquid Phase ◽  
Dynamic Nuclear Polarization ◽  
Nuclear Polarization ◽  
Radical Reactions ◽  
Oligonucleotide Synthesis ◽  
High Quality ◽  
Phase Synthesis ◽  
Amino Acid Conjugates ◽  
Chemically Induced

Conjugates of 2’-deoxyguanosine, L-tryptophan and benzophenone designed to study pathways of fast radical reactions by the photo Chemically Induced Dynamic Nuclear Polarization (photo-CIDNP) method were obtained by the phosphotriester block liquid phase synthesis. The phosphotriester approach to the oligonucleotide synthesis was shown to be a versatile and economic strategy for preparing the required amount of high quality samples of nucleotide–amino acid conjugates.

scholarly journals Studies on the biotin-binding sites of avidin and streptavidin. A chemically induced dynamic nuclear polarization investigation of the status of tyrosine residues

1989 ◽  
Vol 259 (2) ◽  
pp. 493-498 ◽  
Author(s):  
G Gitlin ◽  
I Khait ◽  
E A Bayer ◽  
M Wilchek ◽  
K A Muszkat
Keyword(s):  
Dynamic Nuclear Polarization ◽  
Nuclear Polarization ◽  
Side Chain ◽  
Side Chains ◽  
Tyrosine Residues ◽  
Chemically Induced ◽  
The Status ◽  
Biotin Binding ◽  
Polarization Investigation ◽  
Binding Cleft

We applied the protein photochemically induced dynamic nuclear polarization (photo-c.i.d.n.p.) method to explore the conformation of the side chains of tyrosine, tryptophan and histidine residues in three biotin-binding proteins. The c.i.d.n.p. spectra of avidin, streptavidin and ‘core’ streptavidin were compared with those of their complexes with biotin and its derivatives. The data indicate that the single tyrosine residue (Tyr-33) of avidin is clearly inaccessible to the triplet flavin photo-c.i.d.n.p. probe. The same holds for all tryptophan and histidine side chains. Although the analogous Tyr-43 residue of streptavidin is also buried, at least three of the other tyrosine residues of this protein are exposed. The same conclusions apply to the truncated form of the protein, core streptavidin. As judged by the photo-c.i.d.n.p. results, complexing of avidin and streptavidin with biotin, N-epsilon-biotinyl-L-lysine (biocytin) or biotinyltyrosine has little or no effect on tyrosine accessibility in these proteins. Biotinyltyrosine can be used to probe the depth of the corresponding binding site. The accessibility of the tyrosine side chain of biotinyltyrosine in the complex demonstrates the exquisite fit of the biotin-binding cleft of avidin: only the biotin moiety appears to be accommodated, leaving the tyrosine side chain exposed.

Polypeptides Folding: Rules for the Calculation of the Backbone Dihedral Angles φ starting from the Amino Acid Sequence

2020 ◽  
Author(s):  
Michele Larocca
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Theoretical Approach ◽  
Polypeptide Chain ◽  
Hydrophobic Effect ◽  
Side Chain ◽  
Dihedral Angles ◽  
Mechanical Forces ◽  
Specific Chemical

<p>Protein folding is strictly related to the determination of the backbone dihedral angles and depends on the information contained in the amino acid sequence as well as on the hydrophobic effect. To date, the type of information embedded in the amino acid sequence has not yet been revealed. The present study deals with these problematics and aims to furnish a possible explanation of the information contained in the amino acid sequence, showing and reporting rules to calculate the backbone dihedral angles φ. The study is based on the development of mechanical forces once specific chemical interactions are established among the side chain of the residues in a polypeptide chain. It aims to furnish a theoretical approach to predict backbone dihedral angles which, in the future, may be applied to computational developments focused on the prediction of polypeptide structures.</p>

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