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

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 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.

scholarly journals Molecular Basis of Valine-Citrulline-PABC Linker Instability in Site-Specific ADCs and Its Mitigation by Linker Design

2016 ◽  
Vol 15 (5) ◽  
pp. 958-970 ◽  
Author(s):  
Magdalena Dorywalska ◽  
Russell Dushin ◽  
Ludivine Moine ◽  
Santiago E. Farias ◽  
Dahui Zhou ◽  
...  
Keyword(s):  
Molecular Basis ◽  
Site Specific

Molecular basis of sweet taste in dipeptide taste ligands

2002 ◽  
Vol 74 (7) ◽  
pp. 1109-1116 ◽  
Author(s):  
M. Goodman ◽  
J. R. Del Valle ◽  
Y. Amino ◽  
E. Benedetti
Keyword(s):  
Molecular Modeling ◽  
Molecular Basis ◽  
Integrated Approach ◽  
Sweet Taste ◽  
Nmr Analysis ◽  
X Ray Diffraction ◽  
High Potency ◽  
Enhancing Effect ◽  
X Ray

In this presentation, we describe an integrated approach for the molecular basis for sweet taste among dipeptide-based ligands. By comparing the results obtained from X-ray diffraction studies with the conformations from NMR analysis and molecular modeling, we have observed recurring topochemical motifs that agree with previous models for sweet taste. In our examination of the unexplored D zone of the Tinti­Nofre model, we have uncovered a sweet potency enhancing effect of a new set of aralkyl-substitutions on dipeptide ligands, which reveals the importance of aromatic­aromatic interactions in maintaining high potency.

The molecular basis of interaction domains of full-length PrP with lipid membranes

Nanoscale ◽  
2019 ◽  
Vol 11 (25) ◽  
pp. 12087-12091 ◽  
Author(s):  
Yangang Pan ◽  
Bin Wang ◽  
R. Alexander Reese ◽  
Bingqian Xu
Keyword(s):  
Molecular Modeling ◽  
Lipid Membranes ◽  
Molecular Basis ◽  
Full Length ◽  
New Method ◽  
Interaction Domains

A new method combining AFM measurements and molecular modeling was used to unravel the molecular basis of the interaction domains of full-length PrP with lipid membranes.

scholarly journals The binding site for an inhibitor of squalene:hopene cyclase determined using photoaffinity labeling and molecular modeling

1999 ◽  
Vol 6 (6) ◽  
pp. 333-341 ◽  
Author(s):  
Tongyun Dang ◽  
Ikuro Abe ◽  
Yi Feng Zheng ◽  
Glenn D Prestwich
Keyword(s):  
Molecular Modeling ◽  
Binding Site ◽  
Photoaffinity Labeling
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