Robust Classification of “Relevant” Water Molecules in Putative Protein Binding Sites

2008 ◽  
Vol 51 (4) ◽  
pp. 1063-1067 ◽  
Author(s):  
Alessio Amadasi ◽  
J. Andrew Surface ◽  
Francesca Spyrakis ◽  
Pietro Cozzini ◽  
Andrea Mozzarelli ◽  
...  
Keyword(s):  
Protein Binding ◽  
Binding Sites ◽  
Water Molecules ◽  
Protein Binding Sites ◽  
Robust Classification ◽  
Putative Protein

Classification of Water Molecules in Protein Binding Sites

2007 ◽  
Vol 129 (9) ◽  
pp. 2577-2587 ◽  
Author(s):  
Caterina Barillari ◽  
Justine Taylor ◽  
Russell Viner ◽  
Jonathan W. Essex
Keyword(s):  
Protein Binding ◽  
Binding Sites ◽  
Water Molecules ◽  
Protein Binding Sites

scholarly journals Energetics of Displacing Water Molecules from Protein Binding Sites: Consequences for Ligand Optimization

2009 ◽  
Vol 131 (42) ◽  
pp. 15403-15411 ◽  
Author(s):  
Julien Michel ◽  
Julian Tirado-Rives ◽  
William L. Jorgensen
Keyword(s):  
Protein Binding ◽  
Binding Sites ◽  
Water Molecules ◽  
Protein Binding Sites

scholarly journals Analysis of Highly Conserved Regions of the 3’UTR ofMECP2Gene in Patients with Clinical Diagnosis of Rett Syndrome and Other Disorders Associated with Mental Retardation

2008 ◽  
Vol 24 (6) ◽  
pp. 319-324 ◽  
Author(s):  
Mónica Santos ◽  
Jin Yan ◽  
Teresa Temudo ◽  
Guiomar Oliveira ◽  
José Pedro Vieira ◽  
...  
Keyword(s):  
Mental Retardation ◽  
Protein Binding ◽  
Clinical Diagnosis ◽  
Binding Sites ◽  
Pathogenic Role ◽  
Nucleotide Level ◽  
Protein Binding Sites ◽  
Mutation Scanning ◽  
Putative Protein

In this work we explored the role of the 3’UTR of theMECP2gene in patients with clinical diagnosis of RTT and mental retardation; focusing on regions of the 3’UTR with almost 100% conservation at the nucleotide level among mouse and human. By mutation scanning (DOVAM-S technique) theMECP23’UTR of a total of 66 affected females were studied. Five 3’UTR variants in theMECP2were found (c.1461+9G>A, c.1461+98insA, c.2595G>A, c.9961C>G and c.9964delC) in our group of patients. None of the variants found is located in putative protein-binding sites nor predicted to have a pathogenic role. Our data suggest that mutations in this region do not account for a large proportion of the RTT cases without a genetic explanation.

scholarly journals Rapid and Accurate Prediction and Scoring of Water Molecules in Protein Binding Sites

PLoS ONE ◽  
2012 ◽  
Vol 7 (3) ◽  
pp. e32036 ◽  
Author(s):  
Gregory A. Ross ◽  
Garrett M. Morris ◽  
Philip C. Biggin
Keyword(s):  
Protein Binding ◽  
Binding Sites ◽  
Accurate Prediction ◽  
Water Molecules ◽  
Protein Binding Sites

EVALUATION OF TISSUE STEROID BINDING IN VITRO

1971 ◽  
Vol 68 (1_Suppl) ◽  
pp. S223-S246 ◽  
Author(s):  
C. R. Wira ◽  
H. Rochefort ◽  
E. E. Baulieu
Keyword(s):  
Protein Binding ◽  
Binding Sites ◽  
Experimental System ◽  
Specific Protein ◽  
Coupling Mechanism ◽  
Target Tissue ◽  
Protein Binding Sites ◽  
Definition Of ◽  
Hormone Specificity

ABSTRACT The definition of a RECEPTOR* in terms of a receptive site, an executive site and a coupling mechanism, is followed by a general consideration of four binding criteria, which include hormone specificity, tissue specificity, high affinity and saturation, essential for distinguishing between specific and nonspecific binding. Experimental approaches are proposed for choosing an experimental system (either organized or soluble) and detecting the presence of protein binding sites. Techniques are then presented for evaluating the specific protein binding sites (receptors) in terms of the four criteria. This is followed by a brief consideration of how receptors may be located in cells and characterized when extracted. Finally various examples of oestrogen, androgen, progestagen, glucocorticoid and mineralocorticoid binding to their respective target tissues are presented, to illustrate how researchers have identified specific corticoid and mineralocorticoid binding in their respective target tissue receptors.

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