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Large differences in phosphorylation stoichiometry for sites within the same protein were also observed, raising the possibility of more important functional roles for such highly phosphorylated pTyr sites.

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By mapping to major signaling networks, such as the EGF receptor and insulin growth factor-1 receptor signaling pathways, many known proteins involved in these pathways were revealed to be tyrosine phosphorylated , which provides interesting targets for future hypothesis-driven and targeted quantitative studies involving tyrosine phosphorylation in HMEC or other human systems. Site -specific quantitative analysis of cardiac mitochondrial protein phosphorylation.

We report the development of a multiple-reaction monitoring MRM strategy specifically tailored to the detection and quantification of mitochondrial protein phosphorylation. We recently derived 68 MRM transitions specific to protein modifications in the respiratory chain, voltage-dependent anion channel, and adenine nucleotide translocase.

Here, we have now expanded the total number of MRM transitions to to cover proteins from the tricarboxylic acid cycle, pyruvate dehydrogenase complex, and branched-chain alpha-keto acid dehydrogenase complex. We utilized the transition set to analyze endogenous protein phosphorylation in human heart, mouse heart, and mouse liver.

The data demonstrate the potential utility of the MRM workflow for studying the functional details of mitochondrial phosphorylation signaling.

This article is part of a Special Issue entitled: From protein structures to clinical applications. Miro phosphorylation sites regulate Parkin recruitment and mitochondrial motility. Before the onset of mitophagy, the pathway blocks mitochondrial motility by causing Miro degradation.

PINK1, however, has other mitochondrial substrates, including Miro also called RhoT1 and -2 , although the significance of those substrates is less clear.

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We show that mimicking PINK1 phosphorylation of Miro on S promoted the interaction of Parkin with Miro, stimulated Miro ubiquitination and degradation, recruited Parkin to the mitochondria, and via Parkin arrested axonal transport of mitochondria. We propose that the status of Miro phosphorylation influences the decision to undergo Parkin-dependent mitochondrial arrest, which, in the context of PINK1 action on other substrates, can restrict mitochondrial dynamics before mitophagy.

Protein phosphorylation is a major mechanism in the regulation of protein function. In chloroplast thylakoids several photosystem II subunits, including the major antenna light-harvesting complex II and several core complex components, are reversibly phosphorylated depending on the redox state of the electron carriers.

A previously unknown reversible phosphorylation event has recently been described on the CP29 subunit which leads to conformational changes and protection from cold stress Bergantino, E. Sechi, S. Biol Chem. In this study, we have identified the phosphorylation site on the N-terminal, stroma-exposed domain, showing that it is located in a sequence not homologous to the other members of the Lhc family. The phosphorylated sequence is unique in chloroplast membranes since it meets the requirements for CK2 casein kinase II kinases.

The possibility that this phosphorylation is involved in a signal transduction pathway is discussed. Identification of Ser as the major regulatory phosphorylation site in spinach leaf nitrate reductase. Bachmann, M. Principal Investigator. Spinach leaf NADH: We have identified the major regulatory phosphorylation site as Ser, which is located in the hinge 1 region connecting the cytochrome b domain with the molybdenum-pterin cofactor binding domain of NR, using recombinant NR fragments containing or lacking the phosphorylation site sequence.

Studies with NR partial reactions indicated that the block in electron flow caused by phosphorylation also could be localized to the hinge 1 region.

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A synthetic peptide NR6 based on the phosphorylation site sequence was phosphorylated readily by NR kinase NRk in vitro. Two forms of NRk were resolved by using anion exchange chromatography. Studies with synthetic peptide analogs indicated that both forms of NRk had similar specificity determinants, requiring a basic residue at P-3 i. Both forms are strictly calcium dependent but belong to distinct families of protein kinases because they are distinct immunochemically. The identification of Cdk1-specific phosphorylation sites is important, as they provide mechanistic insights into how Cdk1 controls the cell cycle.

Cell cycle regulation is critical for faithful chromosome segregation, and defects in this complicated process lead to chromosomal aberrations and cancer. Here, we describe an in vitro kinase assay that is used to identify Cdk1-specific phosphorylation sites. To aid with experimental design, we review approaches for the prediction of Cdk1-specific phosphorylation sites from protein sequences.

Together these protocols present a very powerful approach that yields Cdk1-specific phosphorylation sites and enables mechanistic studies into how Cdk1 controls the cell cycle. Since this method relies on purified proteins, it can be applied to any model organism and yields reliable results, especially when combined with cell functional studies. Characterization and validation of new tools for measuring site -specific cardiac troponin I phosphorylation.

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Phosphorylation of cardiac troponin I is a well established mechanism by which cardiac contractility is modulated. However, there are a number of phosphorylation sites on TnI which contribute singly or in combination to influence cardiac function. Accordingly, methods for accurately measuring site -specific TnI phosphorylation are needed. Currently, two strategies are employed: In this report, we describe a cohort of new site -specific TnI phosphoantibodies, generated against physiologically relevant phosphorylation sites , that are superior to the current commercially available antibodies: These new antibodies demonstrated greater sensitivity and specificity for the phosphorylated TnI than the most widely used commercially available reagents.

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These new tools should allow a more accurate assessment and a better understanding of the role of TnI phosphorylation in the response of the heart to pathologic stress. CD34 Antigen: Deterding, Leesa J. CD34, a type I transmembrane glycoprotein, is a surface antigen which is expressed on several cell types, including hematopoietic progenitors, endothelial cells, as well as mast cells.

Recently, CD34 has been described as a marker for epidermal stem cells in mouse hair follicles, and is expressed in outer root sheath cells of the human hair follicle. Although the biological function and regulation of CD34 is not well understood, it is thought to be involved in cell adhesion as well as possibly having a role in signal transduction.

In addition, CD34 was shown to be critical for skin tumor development in mice, although the exact mechanism remains unknown. Many proteins' functions and biological activities are regulated through post-translational modifications. The extracellular domain of CD34 is heavily glycosylated but the role of these glycans in CD34 function is unknown. Additionally, two sites of tyrosine phosphorylation have been reported on human CD34 and it is known that CD34 is phosphorylated , at least in part, by protein kinase C; however, the precise location of the sites of phosphorylation has not been reported.

In an effort to identify specific phosphorylation sites in CD34 and delineate the possible role of protein kinase C, we undertook the identification of the in vitro sites of phosphorylation on the intracellular domain of mouse CD34 aa — following PKC treatment. For this work, we are using a combination of enzymatic proteolysis and peptide sequencing by mass spectrometry. After which the in vivo sites of phosphorylation of full-length mouse CD34 expressed from HEKF cells were determined. The observed in vivo sites of phosphorylation , however, are not consensus PKC sites , but our data indicate that one of these sites may possibly be phosphorylated by AKT2.

These results suggest that other kinases, as well as PKC, may have important signaling functions in CD Identifying protein phosphorylation sites with kinase substrate specificity on human viruses. Viruses infect humans and progress inside the body leading to various diseases and complications. The phosphorylation of viral proteins catalyzed by host kinases plays crucial regulatory roles in enhancing replication and inhibition of normal host-cell functions.

Due to its biological importance, there is a desire to identify the protein phosphorylation sites on human viruses. However, the use of mass spectrometry-based experiments is proven to be expensive and labor-intensive. Furthermore, previous studies which have identified phosphorylation sites in human viruses do not include the investigation of the responsible kinases. Thus, we are motivated to propose a new method to identify protein phosphorylation sites with its kinase substrate specificity on human viruses.

The experimentally verified phosphorylation data were extracted from virPTM--a database containing experimentally verified phosphorylation data on human kinase- phosphorylated virus proteins. In an attempt to investigate kinase substrate specificities in viral protein phosphorylation sites , maximal dependence decomposition MDD is employed to cluster a large set of phosphorylation data into subgroups containing significantly conserved motifs. The experimental human phosphorylation sites are collected from Phospho. Profile hidden Markov model is then applied to learn a predictive model for each subgroup.

ELM is used to make a comparison of predictive performance on three popular kinase-specific phosphorylation site. Protein phosphorylation is one of the most widespread regulatory mechanisms in eukaryotes. Over the past decade, phosphorylation site prediction has emerged as an important problem in the field of bioinformatics.

Here, we report a new method, termed Random Forest-based Phosphosite predictor 2. RF-Phos 2. In side-by-side comparisons based on fold cross validation and an independent dataset, RF-Phos 2. Fast and accurate phosphorylation site assignment algorithm for mass spectrometry data.

Correctly assigning phosphorylated residues helps us understand their biological significance. The design of common search algorithms such as Sequest, Mascot etc. The main contribution of this study is the design and implementation of a linear time and space dynamic programming strategy for phosphorylation site assignment referred to as PhosSA. The proposed algorithm uses summation of peak intensities associated with theoretical spectra as an objective function.

Quality control of the assigned sites is achieved using a post-processing redundancy criteria that indicates the signal-to-noise ratio properties of the fragmented spectra. The quality assessment of the algorithm was determined using experimentally generated data sets using synthetic peptides for which phosphorylation sites were known.


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We report that PhosSA was able to achieve a high degree of accuracy and sensitivity with all the experimentally generated mass spectrometry data sets. The implemented algorithm is shown to be extremely fast and scalable with increasing number of spectra we report up to 0. The algorithm is designed to accept results from both Sequest and Mascot search engines. An executable is freely available at http: Mps1 phosphorylation sites regulate the function of centrin 2 in centriole assembly. Here we identify three Mps1 phosphorylation sites within the centriolar protein Centrin 2 Cetn2.

Although centrioles can be assembled in the absence of Cetn2, centriole assembly is attenuated in the absence of Cetn2.