Site-Specific Interaction between 2-Dibenzofuran Carboxylate and β- and γ-Cyclodextrins Determined by Intermolecular NOE and Molecular Modeling

2004 ◽  
Vol 108 (37) ◽  
pp. 14154-14162 ◽  
Author(s):  
Gustavo González-Gaitano ◽  
Pablo R. Sainz-Rozas ◽  
José Ramón Isasi ◽  
Andrés Guerrero-Martínez ◽  
Gloria Tardajos
Keyword(s):  
Molecular Modeling ◽  
Specific Interaction ◽  
Site Specific ◽  
Intermolecular Noe

Molecular modulation of calcium oxalate crystallization

2006 ◽  
Vol 291 (6) ◽  
pp. F1123-F1132 ◽  
Author(s):  
James J. De Yoreo ◽  
S. Roger Qiu ◽  
John R. Hoyer
Keyword(s):  
Molecular Modeling ◽  
Calcium Oxalate ◽  
Stone Formation ◽  
Energy Levels ◽  
Critical Role ◽  
Specific Interactions ◽  
Crystal Surfaces ◽  
Site Specific

Calcium oxalate monohydrate (COM) is the primary constituent of the majority of renal stones. Osteopontin (OPN), an aspartic acid-rich urinary protein, and citrate, a much smaller molecule, are potent inhibitors of COM crystallization at levels present in normal urine. Current concepts of the role of site-specific interactions in crystallization derived from studies of biomineralization are reviewed to provide a context for understanding modulation of COM growth at a molecular level. Results from in situ atomic force microscopy (AFM) analyses of the effects of citrate and OPN on growth verified the critical role of site-specific interactions between these growth modulators and individual steps on COM crystal surfaces. Molecular modeling investigations of interactions of citrate with steps and faces on COM crystal surfaces provided links between the stereochemistry of interaction and the binding energy levels that underlie mechanisms of growth modification and changes in overall crystal morphology. The combination of in situ AFM and molecular modeling provides new knowledge that will aid rationale design of therapeutic agents for inhibition of stone formation.

scholarly journals Elucidation of the Molecular Basis of Cholecystokinin Peptide Docking to Its Receptor Using Site-Specific Intrinsic Photoaffinity Labeling and Molecular Modeling

Biochemistry ◽  
2009 ◽  
Vol 48 (23) ◽  
pp. 5303-5312 ◽  
Author(s):  
Maoqing Dong ◽  
Polo C.-H. Lam ◽  
Delia I. Pinon ◽  
Ruben Abagyan ◽  
Laurence J. Miller
Keyword(s):  
Molecular Modeling ◽  
Molecular Basis ◽  
Photoaffinity Labeling ◽  
Site Specific ◽  
Peptide Docking

scholarly journals Molecular Modeling of Differentially Phosphorylated Serine 10 and Acetylated lysine 9/14 of Histone H3 Regulates their Interactions with 14-3-3ζ, MSK1, and MKP1

2013 ◽  
Vol 7 ◽  
pp. BBI.S12449 ◽  
Author(s):  
Ajit K. Sharma ◽  
Abhilasha Mansukh ◽  
Ashok Varma ◽  
Nikhil Gadewal ◽  
Sanjay Gupta
Keyword(s):  
Molecular Modeling ◽  
Protein Kinase ◽  
Chromatin Structure ◽  
In Silico ◽  
Association Studies ◽  
Regulatory Proteins ◽  
Mitogen Activated Protein Kinase ◽  
Site Specific ◽  
Mitogen Activated Protein ◽  
Neighboring Site

Histone modifications occur in precise patterns, with several modifications known to affect the binding of proteins. These interactions affect the chromatin structure, gene regulation, and cell cycle events. The dual modifications on the H3 tail, serine10 phosphorylation, and lysine14 acetylation (H3Ser10PLys14Ac) are reported to be crucial for interaction with 14-3-3ζ. However, the mechanism by which H3Ser10P along with neighboring site-specific acetylation(s) is targeted by its regulatory proteins, including kinase and phosphatase, is not fully understood. We carried out molecular modeling studies to understand the interaction of 14-3-3ζ, and its regulatory proteins, mitogen-activated protein kinase phosphatase-1 (MKP1), and mitogen- and stress-activated protein kinase-1 (MSK1) with phosphorylated H3Ser10 alone or in combination with acetylated H3Lys9 and Lys14. In silico molecular association studies suggested that acetylated Lys14 and phosphorylated Ser10 of H3 shows the highest binding affinity towards 14-3-3ζ. In addition, acetylation of H3Lys9 along with Ser10PLys14Ac favors the interaction of the phosphatase, MKP1, for dephosphorylation of H3Ser10P. Further, MAP kinase, MSK1 phosphorylates the unmodified H3Ser10 containing N-terminal tail with maximum affinity compared to the N-terminal tail with H3Lys9AcLys14Ac. The data clearly suggest that opposing enzymatic activity of MSK1 and MKP1 corroborates with non-acetylated and acetylated, H3Lys9Lys14, respectively. Our in silico data highlights that site-specific phosphorylation (H3Ser10P) and acetylation (H3Lys9 and H3Lys14) of H3 are essential for the interaction with their regulatory proteins (MKP1, MSK1, and 14-3-3ζ) and plays a major role in the regulation of chromatin structure.

RETRACTED ARTICLE: Site Specific Interaction Between TiO2 Nanoparticles and Phenanthrimidazole—A First Principles Quantum Mechanical Study

2015 ◽  
Vol 25 (4) ◽  
pp. 1063-1083 ◽  
Author(s):  
Jayaraman Jayabharathi ◽  
Periyasamy Ramanathan ◽  
Chockalingam Karunakaran ◽  
Venugopal Thanikachalam
Keyword(s):  
Tio2 Nanoparticles ◽  
First Principles ◽  
Specific Interaction ◽  
Quantum Mechanical ◽  
Site Specific ◽  
Mechanical Study ◽  
Retracted Article ◽  
Quantum Mechanical Study

scholarly journals Site-Specific Interaction between α-Synuclein and Membranes Probed by NMR-Observed Methionine Oxidation Rates

2013 ◽  
Vol 135 (8) ◽  
pp. 2943-2946 ◽  
Author(s):  
Alexander S. Maltsev ◽  
Jue Chen ◽  
Rodney L. Levine ◽  
Ad Bax
Keyword(s):  
Specific Interaction ◽  
Methionine Oxidation ◽  
Site Specific ◽  
Oxidation Rates
Sign in / Sign up

Export Citation Format

Share Document