The inhibitory effect of KN-93 and KN-62 as a result of CaM-directed blocking animal CaMK2 and plant CDPK activation

Aim. The goal of the study was determine whether, from a molecular point of view, inhibitors KN-93 and KN-62 are capable to disrupt the functioning of plant homologs of CaMK2 and being used as tools for the experimental study of Ca2+-dependent phosphorylation in higher plants. Methods. Selected calmodulin 1 H.sapiens reference structure and reconstructed spatial structure of calcium-binding domain of CPK1 A.thaliana. We have conducted the molecular docking of calmodulin-mediated inhibitors to CaMK2: KN-93 and KN-62 for CALM1 H. sapiens and calcium-binding domain of CPK1 A. thaliana with full ligand mobility and static amino acid residues with the use of CCDC GOLD Suite. Results. We have established the presence of spatially homologous structures within CALM1 and CPK1 that might be the binding sites for KN-93 and KN-62. Performing the molecular docking we have shown the utility of those pockets from the point of binding energy for KN-93 and KN-62. We have conducted comparative analysis basing on the results of the CCDC GOLD Suite score functions (GoldScore and ASPScore). Conclusions. It has been shown that the inhibitors of animal CaMK2 - KN93 and KN62 are capable of interacting with the site of the CaM-like domain of the plant protein kinase CPK1 homologous to the similar site of animal calmodulin, which may impair its functionality. Keywords: CaMK2, CDPK, CPK1, protein kinases, molecular docking, KN-93, KN-62.

Download Full-text

FRCaMP, a Red Fluorescent Genetically Encoded Calcium Indicator Based on Calmodulin from Schizosaccharomyces Pombe Fungus

International Journal of Molecular Sciences ◽

10.3390/ijms22010111 ◽

2020 ◽

Vol 22 (1) ◽

pp. 111

Author(s):

Oksana M. Subach ◽

Natalia V. Barykina ◽

Elizaveta S. Chefanova ◽

Anna V. Vlaskina ◽

Vladimir P. Sotskov ◽

...

Keyword(s):

Schizosaccharomyces Pombe ◽

Hela Cells ◽

Calcium Binding ◽

Dynamic Range ◽

Spectral Characteristics ◽

Binding Domain ◽

Calcium Transients ◽

Neuronal Cultures ◽

Decay Kinetics ◽

Calcium Binding Domain

Red fluorescent genetically encoded calcium indicators (GECIs) have expanded the available pallet of colors used for the visualization of neuronal calcium activity in vivo. However, their calcium-binding domain is restricted by calmodulin from metazoans. In this study, we developed red GECI, called FRCaMP, using calmodulin (CaM) from Schizosaccharomyces pombe fungus as a calcium binding domain. Compared to the R-GECO1 indicator in vitro, the purified protein FRCaMP had similar spectral characteristics, brightness, and pH stability but a 1.3-fold lower ΔF/F calcium response and 2.6-fold tighter calcium affinity with Kd of 441 nM and 2.4–6.6-fold lower photostability. In the cytosol of cultured HeLa cells, FRCaMP visualized calcium transients with a ΔF/F dynamic range of 5.6, which was similar to that of R-GECO1. FRCaMP robustly visualized the spontaneous activity of neuronal cultures and had a similar ΔF/F dynamic range of 1.7 but 2.1-fold faster decay kinetics vs. NCaMP7. On electrically stimulated cultured neurons, FRCaMP demonstrated 1.8-fold faster decay kinetics and 1.7-fold lower ΔF/F values per one action potential of 0.23 compared to the NCaMP7 indicator. The fungus-originating CaM of the FRCaMP indicator version with a deleted M13-like peptide did not interact with the cytosolic environment of the HeLa cells in contrast to the metazoa-originating CaM of the similarly truncated version of the GCaMP6s indicator with a deleted M13-like peptide. Finally, we generated a split version of the FRCaMP indicator, which allowed the simultaneous detection of calcium transients and the heterodimerization of bJun/bFos interacting proteins in the nuclei of HeLa cells with a ΔF/F dynamic range of 9.4 and a contrast of 2.3–3.5, respectively.

Download Full-text

Mutagenesis of the fourth calcium-binding domain of yeast calmodulin

Journal of Biological Chemistry ◽

10.1016/s0021-9258(19)38647-8 ◽

1993 ◽

Vol 268 (18) ◽

pp. 13267-13273

Author(s):

I. Matsuura ◽

E. Kimura ◽

K. Tai ◽

M. Yazawa

Keyword(s):

Calcium Binding ◽

Binding Domain ◽

Calcium Binding Domain

Download Full-text

A single amino acid substitution flanking the fourth calcium binding domain of alpha IIb prevents maturation of the alpha IIb beta 3 integrin complex.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(17)41800-x ◽

1994 ◽

Vol 269 (6) ◽

pp. 4450-4457

Author(s):

D.A. Wilcox ◽

J.L. Wautier ◽

D. Pidard ◽

P.J. Newman

Keyword(s):

Amino Acid ◽

Amino Acid Substitution ◽

Calcium Binding ◽

Binding Domain ◽

Single Amino Acid Substitution ◽

Single Amino Acid ◽

Calcium Binding Domain

Download Full-text

A novel GSN variant outside the G2 calcium‐binding domain associated with Amyloidosis of the Finnish type

Human Mutation ◽

10.1002/humu.24214 ◽

2021 ◽

Author(s):

Sean Mullany ◽

Emmanuelle Souzeau ◽

Sonja Klebe ◽

Tiger Zhou ◽

Lachlan S. W. Knight ◽

...

Keyword(s):

Calcium Binding ◽

Binding Domain ◽

Finnish Type ◽

Calcium Binding Domain

Download Full-text

The ligand binding site of the platelet integrin receptor GPIIb-IIIa is proximal to the second calcium binding domain of its alpha subunit.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(19)39787-x ◽

1990 ◽

Vol 265 (6) ◽

pp. 3440-3446 ◽

Cited By ~ 6

Author(s):

S E D'Souza ◽

M H Ginsberg ◽

T A Burke ◽

E F Plow

Keyword(s):

Ligand Binding ◽

Binding Site ◽

Calcium Binding ◽

Binding Domain ◽

Alpha Subunit ◽

Ligand Binding Site ◽

Integrin Receptor ◽

Calcium Binding Domain

Download Full-text

The effect of plant metabolites on coronaviruses: A comprehensive review focusing on their IC50 values and molecular docking scores

Mini-Reviews in Medicinal Chemistry ◽

10.2174/1389557521666210831152511 ◽

2021 ◽

Vol 21 ◽

Author(s):

Parastou Farshi ◽

Eda Ceren Kaya ◽

Fataneh Hashempour-Baltork ◽

Kianoush Khosravi-Darani

Keyword(s):

Molecular Docking ◽

Inhibitory Effect ◽

Organosulfur Compounds ◽

Amino Acid Residues ◽

Plant Metabolites ◽

Primary Metabolites ◽

Secondary Plant Metabolites ◽

Protein Receptors ◽

Ic50 Values ◽

Natural Drugs

: Coronaviruses have caused worldwide outbreaks in different periods. SARS (severe acute respiratory syndrome), was the first emerged virus from this family, followed by MERS (Middle East respiratory syndrome) and SARS-CoV-2 (2019-nCoV or COVID 19), which is newly emerged. Many studies have been conducted on the application of chemical and natural drugs for treating these coronaviruses and they are mostly focused on inhibiting the proteases of viruses or blocking their protein receptors through binding to amino acid residues. Among many substances which are introduced to have an inhibitory effect against coronaviruses through the mentioned pathways, natural components are of specific interest. Secondary and primary metabolites from plants, are considered as potential drugs to have an inhibitory effect on coronaviruses. IC50 value (the concentration in which there is 50% loss in enzyme activity), molecular docking score and binding energy are parameters to understand the ability of metabolites to inhibit the specific virus. In this study we did a review of 154 papers on the effect of plant metabolites on different coronaviruses and data of their IC50 values, molecular docking scores and inhibition percentages are collected in tables. Secondary plant metabolites such as polyphenol, alkaloids, terpenoids, organosulfur compounds, saponins and saikosaponins, lectins, essential oil, and nicotianamine, and primary metabolites such as vitamins are included in this study.

Download Full-text