Ab initio models for receptor-ligand interactions in proteins. 3. Model assembly study of the proton transfer in the hydroxylation step of the catalytic mechanism of p-hydroxybenzoate hydroxylase

1993 ◽  
Vol 115 (23) ◽  
pp. 10958-10963 ◽  
Author(s):  
Mikael Perakyla ◽  
Tapani A. Pakkanen
Keyword(s):  
Proton Transfer ◽  
Ab Initio ◽  
Catalytic Mechanism ◽  
Receptor Ligand ◽  
Ligand Interactions ◽  
Hydroxybenzoate Hydroxylase ◽  
Ab Initio Models

Identifying Receptor−Ligand Interactions through an ab Initio Approach

2008 ◽  
Vol 112 (4) ◽  
pp. 1290-1292 ◽  
Author(s):  
Pablo F. Salazar ◽  
Jorge M. Seminario
Keyword(s):  
Ab Initio ◽  
Receptor Ligand ◽  
Ligand Interactions ◽  
Ab Initio Approach

Modulation of Platelet Activation by Native DNA – Initial Description of Platelet Receptor Type, Number and Discrimination for Native DNA

1981 ◽  
Vol 45 (03) ◽  
pp. 263-266 ◽  
Author(s):  
B A Fiedel ◽  
M E Frenzke
Keyword(s):  
Platelet Aggregation ◽  
Human Platelets ◽  
Scatchard Analysis ◽  
Type Number ◽  
Single Class ◽  
Receptor Ligand ◽  
Platelet Receptor ◽  
Platelet Binding ◽  
Ligand Interactions ◽  
Initial Description

SummaryNative DNA (dsDNA) induces the aggregation of isolated human platelets. Using isotopically labeled dsDNA (125I-dsDNA) and Scatchard analysis, a single class of platelet receptor was detected with a KD = 190 pM and numbering ~275/platelet. This receptor was discriminatory in that heat denatured dsDNA, poly A, poly C, poly C · I and poly C · poly I failed to substantially inhibit either the platelet binding of, or platelet aggregation induced by, dsDNA; by themselves, these polynucleotides were ineffective as platelet agonists. However, poly G, poly I and poly G · I effectively and competitively inhibited platelet binding of the radioligand, independently activated the platelet and when used at a sub-activating concentration decreased the extent of dsDNA stimulated platelet aggregation. These data depict a receptor on human platelets for dsDNA and perhaps certain additional polynucleotides and relate receptor-ligand interactions to a physiologic platelet function.

scholarly journals A Peptides Prediction Methodology for Tertiary Structure Based on Simulated Annealing

2021 ◽  
Vol 26 (2) ◽  
pp. 39
Author(s):  
Juan P. Sánchez-Hernández ◽  
Juan Frausto-Solís ◽  
Juan J. González-Barbosa ◽  
Diego A. Soto-Monterrubio ◽  
Fanny G. Maldonado-Nava ◽  
...  
Keyword(s):  
Simulated Annealing ◽  
Ab Initio ◽  
Primary Structure ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Secondary Structure Prediction ◽  
Golden Ratio ◽  
Small Peptides ◽  
Hybrid Simulated Annealing ◽  
Ab Initio Models

The Protein Folding Problem (PFP) is a big challenge that has remained unsolved for more than fifty years. This problem consists of obtaining the tertiary structure or Native Structure (NS) of a protein knowing its amino acid sequence. The computational methodologies applied to this problem are classified into two groups, known as Template-Based Modeling (TBM) and ab initio models. In the latter methodology, only information from the primary structure of the target protein is used. In the literature, Hybrid Simulated Annealing (HSA) algorithms are among the best ab initio algorithms for PFP; Golden Ratio Simulated Annealing (GRSA) is a PFP family of these algorithms designed for peptides. Moreover, for the algorithms designed with TBM, they use information from a target protein’s primary structure and information from similar or analog proteins. This paper presents GRSA-SSP methodology that implements a secondary structure prediction to build an initial model and refine it with HSA algorithms. Additionally, we compare the performance of the GRSAX-SSP algorithms versus its corresponding GRSAX. Finally, our best algorithm GRSAX-SSP is compared with PEP-FOLD3, I-TASSER, QUARK, and Rosetta, showing that it competes in small peptides except when predicting the largest peptides.

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