27 August 2003
Net charge center as the simplest model of a protein identifies up to 100% of active/binding site residues
Ivan Y. Torshin, Irene W. Weber, Robert W. HarrisonMed Sci Monit 2003; 9(8): BR289-301 :: ID: 13089
Abstract
Background:Electrostatic steering of ligands into active/binding sites is important for enzymatic catalysis and enhancing the affinity of metal-binding proteins. The net charge center of a protein, which describes the distribution of the charged residues in the protein subunit, has a specific location. As active sites in biological molecules are also located specifically, the biological implications of the model were examined by analyzing the relative locations of the net charge centers and the active/binding sites.Material/Methods:Spatial structures from a set of 11 proteins with experimentally defined electrostatic steering residues and definitely known active site residues were analyzed.Results:In 9 of 11 proteins, 70–100% of the active site residues belong to the residue cluster around the net charge center. On average, the charge center cluster identifies 78% of the active sites and 80% of the steering residues with few false positives. In several cases, comparison of proteins from different sources has shown that the differences in association rates correlate quantitatively with the relative locations of the net charge centers.Conclusions:In most of the proteins studied the net charge center is located close to the active site. Therefore, the active site in a novel enzyme or the binding site in a protein can be predicted solely from the three-dimensional structure of the protein. The residues forming clusters around the net charge center are often organized into continuous hydrophilic sequences, important for rapid and correct formation of the active site region during protein folding.
Keywords: Amino Acid Sequence, Binding Sites, Electrostatics, Models, Molecular, Protein Conformation, Proteins - chemistry, Proteins - genetics
Editorial
01 March 2024 : Editorial
Editorial: First Regulatory Approvals for CRISPR-Cas9 Therapeutic Gene Editing for Sickle Cell Disease and Transfusion-Dependent β-ThalassemiaDOI: 10.12659/MSM.944204
Med Sci Monit 2024; 30:e944204
In Press
18 Mar 2024 : Clinical Research
Sexual Dysfunction in Women After Tibial Fracture: A Retrospective Comparative StudyMed Sci Monit In Press; DOI: 10.12659/MSM.944136
21 Feb 2024 : Clinical Research
Potential Value of HSP90α in Prognosis of Triple-Negative Breast CancerMed Sci Monit In Press; DOI: 10.12659/MSM.943049
22 Feb 2024 : Review article
Differentiation of Native Vertebral Osteomyelitis: A Comprehensive Review of Imaging Techniques and Future ...Med Sci Monit In Press; DOI: 10.12659/MSM.943168
23 Feb 2024 : Clinical Research
A Study of 60 Patients with Low Back Pain to Compare Outcomes Following Magnetotherapy, Ultrasound, Laser, ...Med Sci Monit In Press; DOI: 10.12659/MSM.943732
Most Viewed Current Articles
16 May 2023 : Clinical Research
Electrophysiological Testing for an Auditory Processing Disorder and Reading Performance in 54 School Stude...DOI :10.12659/MSM.940387
Med Sci Monit 2023; 29:e940387
17 Jan 2024 : Review article
Vaccination Guidelines for Pregnant Women: Addressing COVID-19 and the Omicron VariantDOI :10.12659/MSM.942799
Med Sci Monit 2024; 30:e942799
14 Dec 2022 : Clinical Research
Prevalence and Variability of Allergen-Specific Immunoglobulin E in Patients with Elevated Tryptase LevelsDOI :10.12659/MSM.937990
Med Sci Monit 2022; 28:e937990
01 Jan 2022 : Editorial
Editorial: Current Status of Oral Antiviral Drug Treatments for SARS-CoV-2 Infection in Non-Hospitalized Pa...DOI :10.12659/MSM.935952
Med Sci Monit 2022; 28:e935952