Transferability of different classical force fields for right and left handed α-helices constructed from enantiomeric amino acids

2016 ◽  
Vol 18 (7) ◽  
pp. 5550-5563 ◽  
Author(s):  
Santu Biswas ◽  
Sujit Sarkar ◽  
Prithvi Raj Pandey ◽  
Sudip Roy
Keyword(s):  
Amino Acids ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Force Fields ◽  
Left Handed ◽  
Helical Peptide ◽  
Left And Right ◽  
Alpha Helical Peptide

The energetic differences between left and right handed alpha helical peptide chains constructed from enantiomeric amino acids are investigated using quantum chemical calculations.

Quantum-Chemical Investigations of 5-Bromo-2'-Deoxyuridine Derivatives with Antiviral Activity

2006 ◽  
Vol 71 (5) ◽  
pp. 691-697
Author(s):  
Zhivko A. Velkov ◽  
Yasen Zh. Velkov ◽  
Alia V. Tadjer ◽  
Ivanka G. Stankova
Keyword(s):  
Amino Acids ◽  
Antiviral Activity ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Molecular Descriptors ◽  
Structure Investigation ◽  
Determining Factor ◽  
Semiempirical Quantum Chemical Calculations

The article describes the results of semiempirical quantum-chemical calculations for a series of 3',5'-esters of 5-bromo-2'-deoxyuridine with amino acids or peptides. These compounds were synthesized and tested for antiviral activity as potential prodrugs of the parent 5-bromonucleoside. It was not clear why only some of the compounds were active. On the basis of structure investigation and the calculated molecular descriptors, it was found that the determining factor for obtaining appropriate prodrugs of 5-bromo-2'-deoxyuridine is the lipophilicity of the esters.

scholarly journals The design and NMR structure determination of yttrium-oligopeptide tags for recombinant proteins and antibodies

2018 ◽  
Vol 11 (2) ◽  
pp. 120-133
Author(s):  
Marcela Múdra ◽  
Martin Breza ◽  
Lucia Lintnerová ◽  
Juraj Filo ◽  
Jacob Bauer
Keyword(s):  
Amino Acids ◽  
Quantum Chemical Calculations ◽  
Recombinant Proteins ◽  
Quantum Chemical ◽  
Dissociation Constants ◽  
Heavy Atom ◽  
Titration Calorimetry ◽  
Nmr Structure Determination ◽  
Stability Of Complexes ◽  
Natural Amino Acids

Abstract A strategy for the design of new yttrium(III) tags consisting of sequences of naturally occurring amino acids is described. These tags are 4–6 amino acids in length and consist of aspartic and glutamic acids. The use of natural amino acids would allow these oligopeptides to be incorporated into recombinant proteins at the DNA level, enabling the protein to be Y(III)-labelled after protein isolation. This allows a radionuclide or heavy atom to be associated with the protein without the necessity of further synthetic modification. Suitable peptides able to chelate Y(III) in stable complexes were designed based on quantum-chemical calculations. The stability of complexes formed by these peptides was tested by isothermal titration calorimetry, giving dissociation constants in the micromolar range. The likely structure of the most tightly bound complex was inferred from a combination of NMR experiments and quantum-chemical calculations. This structure will serve as the basis for future optimizations.

The electronic structure properties of 20 L-amino acids in neutral and zwitterion forms: Quantum-chemical calculations

BIOPHYSICS ◽  
2016 ◽  
Vol 61 (3) ◽  
pp. 361-372 ◽  
Author(s):  
K. A. Scherbakov ◽  
M. S. Kondratiev ◽  
A. A. Samchenko ◽  
A. V. Kabanov ◽  
V. M. Komarov
Keyword(s):  
Amino Acids ◽  
Electronic Structure ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Structure Properties
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