Solvent–amino acid interaction energies in 3-D-lattice MC simulations of model proteins. Aggregation thermodynamics and kinetics

2003 ◽  
Vol 5 (23) ◽  
pp. 5291-5299 ◽  
Author(s):  
K. Leonhard ◽  
J. M. Prausnitz ◽  
C. J. Radke
Keyword(s):  
Amino Acid ◽  
Interaction Energies ◽  
Acid Interaction ◽  
Thermodynamics And Kinetics ◽  
Amino Acid Interaction

Theoretical prediction of protein antigenic determinants from amino acid sequences

1982 ◽  
Vol 60 (20) ◽  
pp. 2606-2610 ◽  
Author(s):  
Serafin Fraga
Keyword(s):  
Amino Acid ◽  
Semiempirical Method ◽  
Amino Acid Sequences ◽  
Antigenic Determinants ◽  
Interaction Energies ◽  
Acid Interaction ◽  
Present Procedure ◽  
Amino Acid Interaction ◽  
Satisfactory Prediction ◽  
Scf Calculations

The locations of the antigenic determinants in a protein are predicted from its amino acid sequence by a modified Hopp–Woods method, proposed in this work, using both hydrophihcity and recognition factors. The amino acid – amino acid interaction energies, from which the recognition factors have been defined, have been evaluated by a semiempirical method, developed at this laboratory, using 1/R expansions parameterized on the basis of the results from accurate SCF calculations. The present procedure, which eliminates most of the uncertainties in the original Hopp–Woods method, leads to a very satisfactory prediction of the antigenic determinants.

Chromopeptides from Phytochrome and Phycocyanin. NM R Studies o f the Pfr and Pr Chromophore of Phytochrome and E,Z Isomeric Chromophores of Phycocyanin

1983 ◽  
Vol 38 (5-6) ◽  
pp. 359-368 ◽  
Author(s):  
Fritz Thümmler ◽  
Wolfhart Rüdiger ◽  
Edmund Cmiel ◽  
Siegfried Schneider
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Avena Sativa ◽  
Maximum Amount ◽  
Acid Interaction ◽  
Spirulina Maxima ◽  
Nmr Spectrum ◽  
Pepsin Digestion ◽  
H Nmr ◽  
Amino Acid Interaction

Chromopeptides were prepared by pepsin digestion of C-phycocyanin isolated from the cyano­bacterium Spirulina maxima and of phytochrome isolated from seedlings of Avena sativa L. The chromopeptides were characterized by amino acid analysis. The ZZZ configurated chromophore of the phycocyanin peptide was transformed into its ZZE configurated isomer by the method of Falk et al. (Mh. Chemie 111, 159- 175, 1980) which had previously been applied to biliverdins. The 500 MHz 1HNMR spectrum of the ZZE configurated chromopeptides confirmed that its chromophore has the 15 E configuration. Irradiation yielded the ZZZ configurated isomer for which the 1H NMR spectrum was also recorded. Native phytochrome was irradiated at 660 nm to yield the maximum amount of the Pfr from (about 75% of total phytochrome). By digestion in the dark the previously described Pfr chromopeptide was obtained. The 500 MHz 1H NMR spectrum was compared with that of the ZZE phycocyanin peptide. It confirmed the 15 E con­figuration of the Pfr chromopeptide. Irradiation yielded the 15 Z configurated Pr chromopeptide. Comparison of the high resolution 1HNMR spectra of Pfr and Pr chromopeptides revealed that not only the chromophore resonances but also those of some amino acids are changed by the Pfr → Pr chromopeptide phototransformation. The results are discussed in terms of chromophore amino acid interaction.

scholarly journals A Topological Description of Hubs in Amino Acid Interaction Networks

2010 ◽  
Vol 2010 ◽  
pp. 1-9 ◽  
Author(s):  
Omar Gaci
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Interaction Networks ◽  
Acid Interaction ◽  
Scale Free ◽  
Topological Description ◽  
General Rules ◽  
Scale Free Networks ◽  
Amino Acid Interaction ◽  
Folded Proteins

We represent proteins by amino acid interaction networks. This is a graph whose vertices are the proteins amino acids and whose edges are the interactions between them. Once we have compared this type of graphs to the general model of scale-free networks, we analyze the existence of nodes which highly interact, the hubs. We describe these nodes taking into account their position in the primary structure to study their apparition frequency in the folded proteins. Finally, we observe that their interaction level is a consequence of the general rules which govern the folding process.

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