scholarly journals Methods for Identification of Substrates/Inhibitors of FCP/SCP Type Protein Ser/Thr Phosphatases

Processes ◽  
2020 ◽  
Vol 8 (12) ◽  
pp. 1598
Author(s):  
Masataka Mizunuma ◽  
Atsushi Kaneko ◽  
Shunta Imai ◽  
Kazuhiro Furukawa ◽  
Yoshiro Chuman
Keyword(s):  
Protein Phosphorylation ◽  
Protein Kinases ◽  
Substrate Recognition ◽  
Phage Library ◽  
Biological Functions ◽  
Post Translational Modification ◽  
Rigid Substrate ◽  
Individual Protein ◽  
Terminal Domain ◽  
The Individual

Protein phosphorylation is the most widespread type of post-translational modification and is properly controlled by protein kinases and phosphatases. Regarding the phosphorylation of serine (Ser) and threonine (Thr) residues, relatively few protein Ser/Thr phosphatases control the specific dephosphorylation of numerous substrates, in contrast with Ser/Thr kinases. Recently, protein Ser/Thr phosphatases were reported to have rigid substrate recognition and exert various biological functions. Therefore, identification of targeted proteins by individual protein Ser/Thr phosphatases is crucial to clarify their own biological functions. However, to date, information on the development of methods for identification of the substrates of protein Ser/Thr phosphatases remains scarce. In turn, substrate-trapping mutants are powerful tools to search the individual substrates of protein tyrosine (Tyr) phosphatases. This review focuses on the development of novel methods for the identification of Ser/Thr phosphatases, especially small C-terminal domain phosphatase 1 (Scp1), using peptide-displayed phage library with AlF4−/BeF3−, and discusses the identification of putative inhibitors.

scholarly journals Structural Insights into Protein Regulation by Phosphorylation and Substrate Recognition of Protein Kinases/Phosphatases

Life ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 957
Author(s):  
Seung-Hyeon Seok
Keyword(s):  
Protein Phosphorylation ◽  
Protein Kinases ◽  
Protein Phosphatases ◽  
Substrate Recognition ◽  
Protein Structures ◽  
Phosphate Group ◽  
Amino Acid Side Chain ◽  
Post Translational Modification ◽  
Cellular Processes ◽  
Structural Insights

Protein phosphorylation is one of the most widely observed and important post-translational modification (PTM) processes. Protein phosphorylation is regulated by protein kinases, each of which covalently attaches a phosphate group to an amino acid side chain on a serine (Ser), threonine (Thr), or tyrosine (Tyr) residue of a protein, and by protein phosphatases, each of which, conversely, removes a phosphate group from a phosphoprotein. These reversible enzyme activities provide a regulatory mechanism by activating or deactivating many diverse functions of proteins in various cellular processes. In this review, their structures and substrate recognition are described and summarized, focusing on Ser/Thr protein kinases and protein Ser/Thr phosphatases, and the regulation of protein structures by phosphorylation. The studies reviewed here and the resulting information could contribute to further structural, biochemical, and combined studies on the mechanisms of protein phosphorylation and to drug discovery approaches targeting protein kinases or protein phosphatases.

Variable contribution of protein kinases to the generation of the human phosphoproteome: a global weblogo analysis

2010 ◽  
Vol 1 (2) ◽  
pp. 185-195 ◽  
Author(s):  
Mauro Salvi ◽  
Luca Cesaro ◽  
Lorenzo A. Pinna
Keyword(s):  
Special Reference ◽  
Protein Kinases ◽  
Substrate Recognition ◽  
Great Majority ◽  
Consensus Sequences ◽  
Individual Protein ◽  
Data Support ◽  
Variable Contribution ◽  
Bona Fide ◽  
The Individual

AbstractIn an attempt to evaluate the contribution of individual protein kinases to the generation of the human phosphoproteome, we performed a global weblogo analysis exploiting a database of 45641 phosphosites (80% pSer, 11% pTyr, 9% pThr). The outcome of this analysis was then interpreted by comparison with similar logos constructed from bona fide phospoacceptor sites of individual pleiotropic kinases. The main conclusions that were drawn are as follows: (i) the hallmarks surrounding phosphorylated Ser/Thr residues are more pronounced than and sharply different from those found around phosphorylated Tyr, which is consistent with the view that local consensus sequences are particularly important for substrate recognition by Ser/Thr protein kinases. (ii) Only six residues are positively selected around phosphorylated Ser/Thr residues, notably Pro (particularly at n+1), Glu, and to a lesser extent Asp, at various positions with special reference to n+3, Arg (and to a much lesser extent Lys), particularly at n-3 and n-5, and Ser, at various positions, particularly n+4 and n-4. (iii) This composite signature reflects the contribution of kinases whose bona fide substrates exhibit logos partially overlapping that of the whole phosphoproteome. These are Pro-directed kinases belonging to the CMGC group, some basophilic kinases belonging to the ACG and CAMK groups, phosphate-directed kinases such as GSK3 and members of the CK1 group and the individual highly acidophilic CK2. Collectively taken our data support the concept that a relatively small number of highly pleiotropic kinases contribute to the generation of the great majority of the human Ser/Thr phosphoproteome.

scholarly journals The C-terminal domain of feline and bovine SAMHD1 proteins has a crucial role in lentiviral restriction

2020 ◽  
Vol 295 (13) ◽  
pp. 4252-4264 ◽  
Author(s):  
Chu Wang ◽  
Kaikai Zhang ◽  
Lina Meng ◽  
Xin Zhang ◽  
Yanan Song ◽  
...  
Keyword(s):  
Proteasomal Degradation ◽  
Acid Sites ◽  
Accessory Protein ◽  
Restriction Profile ◽  
Biological Functions ◽  
Terminal Domain ◽  
Functional Regions ◽  
Viral Restriction ◽  
Primate Lentiviruses

SAM and HD domain-containing protein 1 (SAMHD1) is a host factor that restricts reverse transcription of lentiviruses such as HIV in myeloid cells and resting T cells through its dNTP triphosphohydrolase (dNTPase) activity. Lentiviruses counteract this restriction by expressing the accessory protein Vpx or Vpr, which targets SAMHD1 for proteasomal degradation. SAMHD1 is conserved among mammals, and the feline and bovine SAMHD1 proteins (fSAM and bSAM) restrict lentiviruses by reducing cellular dNTP concentrations. However, the functional regions of fSAM and bSAM that are required for their biological functions are not well-characterized. Here, to establish alternative models to investigate SAMHD1 in vivo, we studied the restriction profile of fSAM and bSAM against different primate lentiviruses. We found that both fSAM and bSAM strongly restrict primate lentiviruses and that Vpx induces the proteasomal degradation of both fSAM and bSAM. Further investigation identified one and five amino acid sites in the C-terminal domain (CTD) of fSAM and bSAM, respectively, that are required for Vpx-mediated degradation. We also found that the CTD of bSAM is directly involved in mediating bSAM's antiviral activity by regulating dNTPase activity, whereas the CTD of fSAM is not. Our results suggest that the CTDs of fSAM and bSAM have important roles in their antiviral functions. These findings advance our understanding of the mechanism of fSAM- and bSAM-mediated viral restriction and might inform strategies for improving HIV animal models.

scholarly journals Fluorescent glycan fingerprinting of SARS2 spike proteins

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zhengliang L. Wu ◽  
James M. Ertelt
Keyword(s):  
Sialic Acid ◽  
Gel Electrophoresis ◽  
Fluorescent Labeling ◽  
Biological Functions ◽  
Post Translational Modification ◽  
Quick Method ◽  
New Techniques ◽  
S Protein ◽  
Sds Page ◽  
Novel Coronavirus

AbstractGlycosylation is the most common post-translational modification and has myriad of biological functions. However, glycan analysis has always been a challenge. Here, we would like to present new techniques for glycan fingerprinting based on enzymatic fluorescent labeling and gel electrophoresis. The method is illustrated on SARS2 spike (S) glycoproteins. SARS2, a novel coronavirus and the causative agent of the COVID-19 pandemic, has had significant social and economic impacts since the end of 2019. To obtain the N-glycan fingerprint of an S protein, glycans released from the protein are first labeled through enzymatic incorporation of fluorophore-conjugated sialic acid or fucose, then separated by SDS-PAGE, and finally visualized with a fluorescent imager. To identify the labeled glycans of a fingerprint, glycan standards and glycan ladders are enzymatically generated and run alongside the samples as references. By comparing the mobility of a labeled glycan to that of a glycan standard, the identity of glycans maybe determined. O-glycans can also be fingerprinted. Due to the lack of an enzyme for broad O-glycan release, O-glycans on the S protein can be labeled with fluorescent sialic acid and digested with trypsin to obtain labeled glycan peptides that are then separated by gel electrophoresis. Glycan fingerprinting could serve as a quick method for globally assessing the glycosylation of a specific glycoprotein.

scholarly journals The Distinct Properties of the Consecutive Disordered Regions Inside or Outside Protein Domains and Their Functional Significance

2021 ◽  
Vol 22 (19) ◽  
pp. 10677
Author(s):  
Huqiang Wang ◽  
Haolin Zhong ◽  
Chao Gao ◽  
Jiayin Zang ◽  
Dong Yang
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Protein Domains ◽  
Comprehensive Analysis ◽  
Disordered Proteins ◽  
Functional Constraints ◽  
Biological Functions ◽  
Post Translational Modification ◽  
Intrinsically Disordered ◽  
And Function ◽  
Disordered Regions

The consecutive disordered regions (CDRs) are the basis for the formation of intrinsically disordered proteins, which contribute to various biological functions and increasing organism complexity. Previous studies have revealed that CDRs may be present inside or outside protein domains, but a comprehensive analysis of the property differences between these two types of CDRs and the proteins containing them is lacking. In this study, we investigated this issue from three viewpoints. Firstly, we found that in-domain CDRs are more hydrophilic and stable but have less stickiness and fewer post-translational modification sites compared with out-domain CDRs. Secondly, at the protein level, we found that proteins with only in-domain CDRs originated late, evolved rapidly, and had weak functional constraints, compared with the other two types of CDR-containing proteins. Proteins with only in-domain CDRs tend to be expressed spatiotemporal specifically, but they tend to have higher abundance and are more stable. Thirdly, we screened the CDR-containing protein domains that have a strong correlation with organism complexity. The CDR-containing domains tend to be evolutionarily young, or they changed from a domain without CDR to a CDR-containing domain during evolution. These results provide valuable new insights about the evolution and function of CDRs and protein domains.

Surface Protein Phosphorylation by Ecto-Protein Kinases

1998 ◽  
pp. 51-71 ◽  
Author(s):  
Yigal H. Ehrlich ◽  
Michael V. Hogan ◽  
Zofia Pawlowska ◽  
Andrzej Wieraszko ◽  
Ethel Katz ◽  
...  
Keyword(s):  
Protein Phosphorylation ◽  
Protein Kinases ◽  
Surface Protein

Heterogeneous protein co-assemblies with tunable functional domain stoichiometry

2021 ◽  
Author(s):  
Shaheen Farhadi ◽  
Antonietta Restuccia ◽  
Anthony M Sorrentino ◽  
Andres Cruz-Sanchez ◽  
Gregory A Hudalla
Keyword(s):  
Protein Domains ◽  
Functional Domain ◽  
Protein Subunits ◽  
Individual Protein ◽  
Complex Functions ◽  
The Individual

In nature, the precise heterogeneous co-assembly of different protein domains gives rise to supramolecular machines that perform complex functions through the co-integrated activity of the individual protein subunits. A synthetic...

Leishmania major biotin protein ligase forms a unique cross-handshake dimer

2021 ◽  
Vol 77 (4) ◽  
pp. 510-521
Author(s):  
Manoj Kumar Rajak ◽  
Sonika Bhatnagar ◽  
Shubhant Pandey ◽  
Sunil Kumar ◽  
Shalini Verma ◽  
...  
Keyword(s):  
Leishmania Major ◽  
Size Exclusion ◽  
Covalent Attachment ◽  
Mitochondrial Enzymes ◽  
Dependent Manner ◽  
Post Translational Modification ◽  
Terminal Domain ◽  
Exclusion Chromatography ◽  
Partial Unfolding ◽  
Biotin Protein Ligase

Biotin protein ligase catalyses the post-translational modification of biotin carboxyl carrier protein (BCCP) domains, a modification that is crucial for the function of several carboxylases. It is a two-step process that results in the covalent attachment of biotin to the ɛ-amino group of a conserved lysine of the BCCP domain of a carboxylase in an ATP-dependent manner. In Leishmania, three mitochondrial enzymes, acetyl-CoA carboxylase, methylcrotonyl-CoA carboxylase and propionyl-CoA carboxylase, depend on biotinylation for activity. In view of the indispensable role of the biotinylating enzyme in the activation of these carboxylases, crystal structures of L. major biotin protein ligase complexed with biotin and with biotinyl-5′-AMP have been solved. L. major biotin protein ligase crystallizes as a unique dimer formed by cross-handshake interactions of the hinge region of the two monomers formed by partial unfolding of the C-terminal domain. Interestingly, the substrate (BCCP domain)-binding site of each monomer is occupied by its own C-terminal domain in the dimer structure. This was observed in all of the crystals that were obtained, suggesting a closed/inactive conformation of the enzyme. Size-exclusion chromatography studies carried out using high protein concentrations (0.5 mM) suggest the formation of a concentration-dependent dimer that exists in equilibrium with the monomer.

The Sucrose Non-Fermenting 1-Related Protein Kinase 2 (SnRK2) Genes Are Multifaceted Players in Plant Growth, Development and Response to Environmental Stimuli

2019 ◽  
Vol 61 (2) ◽  
pp. 225-242 ◽  
Author(s):  
Xinguo Mao ◽  
Yuying Li ◽  
Shoaib Ur Rehman ◽  
Lili Miao ◽  
Yanfei Zhang ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Protein Kinases ◽  
Specific Protein ◽  
Regulatory Mechanisms ◽  
Biological Processes ◽  
Related Protein ◽  
Biological Functions ◽  
Reversible Protein Phosphorylation ◽  
Growth Development ◽  
Regulatory Event

Abstract Reversible protein phosphorylation orchestrated by protein kinases and phosphatases is a major regulatory event in plants and animals. The SnRK2 subfamily consists of plant-specific protein kinases in the Ser/Thr protein kinase superfamily. Early observations indicated that SnRK2s are mainly involved in response to abiotic stress. Recent evidence shows that SnRK2s are multifarious players in a variety of biological processes. Here, we summarize the considerable knowledge of SnRK2s, including evolution, classification, biological functions and regulatory mechanisms at the epigenetic, post-transcriptional and post-translation levels.

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