Benjamin E. Turk

AMPK phosphorylation of raptor mediates a metabolic checkpoint

AMPK is a highly conserved sensor of cellular energy status that is activated under conditions of low intracellular ATP. AMPK responds to energy stress by suppressing cell growth and biosynthetic processes, in part through its inhibition of the rapamycin-sensitive mTOR (mTORC1) pathway. AMPK phosphorylation of the TSC2 tumor suppressor contributes to suppression of mTORC1; however, TSC2-deficient cells remain responsive to energy stress. Using a proteomic and bioinformatics approach, we sought to identify additional substrates of AMPK that mediate its effects on growth control. We report here that AMPK directly phosphorylates the mTOR binding partner raptor on two well-conserved serine residues, and this phosphorylation induces 14-3-3 binding to raptor. The phosphorylation of raptor by AMPK is required for the inhibition of mTORC1 and cell-cycle arrest induced by energy stress. These findings uncover a conserved effector of AMPK that mediates its role as a metabolic checkpoint coordinating cell growth with energy status.

Determination of protease cleavage site motifs using mixture-based oriented peptide libraries

The number of known proteases is increasing at a tremendous rate as a consequence of genome sequencing projects. Although one can guess at the functions of these novel enzymes by considering sequence homology to known proteases, there is a need for new tools to rapidly provide functional information on large numbers of proteins. We describe a method for determining the cleavage site specificity of proteolytic enzymes that involves pooled sequencing of peptide library mixtures. The method was used to determine cleavage site motifs for six enzymes in the matrix metalloprotease (MMP) family. The results were validated by comparison with previous literature and by analyzing the cleavage of individually synthesized peptide substrates. The library data led us to identify the proteoglycan neurocan as a novel MMP-2 substrate. Our results indicate that a small set of libraries can be used to quickly profile an expanding protease family, providing information applicable to the design of inhibitors and to the identification of protein substrates.

Methionine aminopeptidase (type 2) is the common target for angiogenesis inhibitors AGM-1470 and ovalicin

BACKGROUND Angiogenesis, the formation of new blood vessels, is essential for tumor growth. The inhibition of angiogenesis is therefore emerging as a promising therapy for cancer. Two natural products, fumagillin and ovalicin, were discovered to be potent inhibitors of angiogenesis due to their inhibition of endothelial cell proliferation. An analog of fumagillin, AGM-1470, is currently undergoing clinical trials for the treatment of a variety of cancers. The underlying molecular mechanism of the inhibition of angiogenesis by these natural drugs has remained unknown. RESULTS Both AGM-1470 and ovalicin bind to a common bifunctional protein, identified by mass spectrometry as the type 2 methionine aminopeptidase (MetAP2). This protein also acts as an inhibitor of eukaryotic initiation factor 2alpha (elF-2alpha) phosphorylation. Both drugs potently inhibit the methionine aminopeptidase activity of MetAP2 without affecting its ability to block elF-2alpha phosphorylation. There are two types of methionine aminopeptidase found in eukaryotes, but only the type 2 enzyme is inhibited by the drugs. A series of analogs of fumagillin and ovalicin were synthesized and their potency for inhibition of endothelial cell proliferation and inhibition of methionine aminopeptidase activity was determined. A significant correlation was found between the two activities. CONCLUSIONS The protein MetAP2 is a common molecular target for both AGM-1470 and ovalicin. This finding suggests that MetAP2 may play a critical role in the proliferation of endothelial cells and may serve as a promising target for the development of new anti-angiogenic drugs.

Linear Motif Atlas for Phosphorylation-Dependent Signaling

Created with both in vitro and in vivo data, NetPhorest is an atlas of consensus sequence motifs for 179 kinases and 104 phosphorylation-dependent binding domains and reveals new insight into phosphorylation-dependent signaling. An Atlas of Phosphorylation NetPhorest is a community resource that uses phylogenetic trees to organize data from both in vivo and in vitro experiments to derive sequence specificities for 179 kinases and 104 domains (SH2, PTB, BRCT, WW, and 14–3–3) that bind to phosphorylated sites. The resulting atlas of linear motifs revealed that oncogenic kinases tend to be less specific in the target sequences they phosphorylate than their non-oncogenic counterparts, that autophosphorylation sites tend to be more variable than other substrates of a given kinase, and that coupling interaction domains with kinase domains may allow phosphorylation site specificity to be low while still maintaining substrate specificity. Systematic and quantitative analysis of protein phosphorylation is revealing dynamic regulatory networks underlying cellular responses to environmental cues. However, matching these sites to the kinases that phosphorylate them and the phosphorylation-dependent binding domains that may subsequently bind to them remains a challenge. NetPhorest is an atlas of consensus sequence motifs that covers 179 kinases and 104 phosphorylation-dependent binding domains [Src homology 2 (SH2), phosphotyrosine binding (PTB), BRCA1 C-terminal (BRCT), WW, and 14–3–3]. The atlas reveals new aspects of signaling systems, including the observation that tyrosine kinases mutated in cancer have lower specificity than their non-oncogenic relatives. The resource is maintained by an automated pipeline, which uses phylogenetic trees to structure the currently available in vivo and in vitro data to derive probabilistic sequence models of linear motifs. The atlas is available as a community resource (http://netphorest.info).

A rapid method for determining protein kinase phosphorylation specificity

Selection of target substrates by protein kinases is strongly influenced by the amino acid sequence surrounding the phosphoacceptor site. Identification of the preferred peptide phosphorylation motif for a given kinase permits the production of efficient peptide substrates and greatly simplifies the mapping of phosphorylation sites in protein substrates. Here we describe a combinatorial peptide library method that allows rapid generation of phosphorylation motifs for serine/threonine kinases.

Deciphering Protein Kinase Specificity Through Large-Scale Analysis of Yeast Phosphorylation Site Motifs

A high-throughput peptide array approach reveals insight into kinase substrates and specificity. Exploring Kinase Selectivity Kinases are master regulators of cellular behavior. Because of the large number of kinases and the even larger number of substrates, approaches that permit global analysis are valuable tools for investigating kinase biology. Mok et al. identified the phosphorylation site selectivity for 61 of the 122 kinases in Saccharomyces cerevisiae by screening a miniaturized peptide library. By integrating these data with other data sets and structural information, they revealed information about the relationship between kinase catalytic residues and substrate selectivity. They also identified and experimentally verified substrates for kinases, including one for which limited functional information was previously available, showing the potential for this type of analysis as a launching point for the exploration of the biological functions of kinases. Phosphorylation is a universal mechanism for regulating cell behavior in eukaryotes. Although protein kinases target short linear sequence motifs on their substrates, the rules for kinase substrate recognition are not completely understood. We used a rapid peptide screening approach to determine consensus phosphorylation site motifs targeted by 61 of the 122 kinases in Saccharomyces cerevisiae. By correlating these motifs with kinase primary sequence, we uncovered previously unappreciated rules for determining specificity within the kinase family, including a residue determining P−3 arginine specificity among members of the CMGC [CDK (cyclin-dependent kinase), MAPK (mitogen-activated protein kinase), GSK (glycogen synthase kinase), and CDK-like] group of kinases. Furthermore, computational scanning of the yeast proteome enabled the prediction of thousands of new kinase-substrate relationships. We experimentally verified several candidate substrates of the Prk1 family of kinases in vitro and in vivo and identified a protein substrate of the kinase Vhs1. Together, these results elucidate how kinase catalytic domains recognize their phosphorylation targets and suggest general avenues for the identification of previously unknown kinase substrates across eukaryotes.

mTORC1 Phosphorylation Sites Encode Their Sensitivity to Starvation and Rapamycin

Introduction The mechanistic target of rapamycin (mTOR) complex 1 (mTORC1) protein kinase promotes cell growth by controlling major anabolic and catabolic processes in response to a variety of environmental and intracellular stimuli, and is deregulated in aging and human diseases such as cancer and diabetes. Rapamycin, an allosteric inhibitor of mTORC1, is used clinically in organ transplantation and the treatment of certain cancers. Exactly how rapamycin perturbs mTORC1 signaling is poorly understood and it remains unknown why certain mTORC1 phosphorylation sites are sensitive to the drug whereas others are not. Here, we test the hypothesis that the inherent capacity of a phosphorylation site to serve as an mTORC1 substrate (a property we call substrate quality) is a key determinant of its sensitivity to rapamycin as well as nutrient and growth factor starvation. mTORC1 Phosphorylation sites encode their sensitivity to physiological and pharmacological modulators of mTORC1. Substrate quality is an important determinant of how effectively mTORC1 phosphorylates its substrates in the response to both pharmacological and natural regulators ofthe kinase. Methods We measured the in vitro kinase activity of mTORC1 towards short synthetic peptides encompassing single mTORC1 phosphorylation sites and refined the established mTORC1 phosphorylation motif. We introduced subtle mutations into bona fide mTORC1 phosphorylation sites that we found to enhance or reduce their phosphorylation by mTORC1 in vitro and monitored the corresponding changes in the sensitivity of these sites to rapamycin treatment within cells. Finally, we assessed whether the modifications of the mTORC1 phosphorylation sites also altered their sensitivities to nutrient and growth factor starvation. Results The response of an mTORC1 phosphorylation site to rapamycin treatment should depend on the balance between the activity of mTORC1 and of the protein phosphatase(s) that dephosphorylates it. We found that the in vitro kinase activity of mTORC1 toward peptides containing established phosphorylation sites strongly correlates with the resistance of the sites to rapamycin within cells. Moreover, the relative affinities of the mTOR kinase domain for the peptides also correlated with its capacity to phosphorylate them. In addition to a preference for either proline or a nonproline hydrophobic residue in the +1 position, our refinement of the mTORC1 phosphorylation motif revealed preferences for noncharged residues surrounding the phosphoacceptor site and for serine over threonine as the phosphoacceptor. Utilizing this improved understanding of the sequence motif specificity of mTORC1, we were able to manipulate mTORC1 activity toward its phosphorylation sites in vitro and alter their sensitivities to rapamycin treatment within cells. Interestingly, mTORC1 phosphorylation sites also varied in their sensitivities to nutrient and growth factor levels and manipulations in substrate quality were sufficient to alter their responses to nutrient and growth factor starvation. Discussion Our findings suggest that the sequence composition of an mTORC1 phosphorylation site, including the presence of serine or threonine as the phosphoacceptor, is one of the key determinants of whether the site is a good or poor mTORC1 substrate within cells. Even though the phosphorylation of mTORC1 sites is subject to varied regulatory mechanisms, we propose that differences in substrate quality are one mechanism for allowing downstream effectors of mTORC1 to respond differentially to temporal and intensity changes in the levels of nutrients and growth factors as well as pharmacological inhibitors such as rapamycin. Such differential responses are likely important for mTORC1 to coordinate and appropriately time the myriad processes that make up the vast starvation program it controls. Lastly, it is likely that the form of hierarchical regulation we describe for mTORC1 substrates also exists in other kinase-driven signaling pathways. Not mTORCing Inhibition of the protein kinase complex mTORC1 has potentially beneficial therapeutic affects that include inhibition of cancer and extension of life span. However, effects of its inhibition in vivo have sometimes been disappointing. One reason may be that the well-studied inhibitor of mTORC1, rapamycin, inhibits some effects of mTORC1 but not others. In line with this idea, Kang et al. (1236566) show that the effect of rapamycin depends on the substrate. Characteristics of the phosphorylation sites on various substrates caused them to be phosphorylated with different efficiency by mTORC1. The substrates that were most efficiently phosphorylated were resistant to inhibition of mTORC1. The results explain how various sites, sometimes within the same protein, can differ in their sensitivity to rapamycin. Inhibition of a protein kinase differentially affects its targets, depending on phosphorylation site characteristics. The mechanistic target of rapamycin (mTOR) complex 1 (mTORC1) protein kinase promotes growth and is the target of rapamycin, a clinically useful drug that also prolongs life span in model organisms. A persistent mystery is why the phosphorylation of many bona fide mTORC1 substrates is resistant to rapamycin. We find that the in vitro kinase activity of mTORC1 toward peptides encompassing established phosphorylation sites varies widely and correlates strongly with the resistance of the sites to rapamycin, as well as to nutrient and growth factor starvation within cells. Slight modifications of the sites were sufficient to alter mTORC1 activity toward them in vitro and to cause concomitant changes within cells in their sensitivity to rapamycin and starvation. Thus, the intrinsic capacity of a phosphorylation site to serve as an mTORC1 substrate, a property we call substrate quality, is a major determinant of its sensitivity to modulators of the pathway. Our results reveal a mechanism through which mTORC1 effectors can respond differentially to the same signals.

Inhibition of papain-like cysteine proteases and legumain by caspase-specific inhibitors: when reaction mechanism is more important than specificity

AbstractWe report here that a number of commonly used small peptide caspase inhibitors consisting of a caspase recognition sequence linked to chloromethylketone, fluoromethylketone or aldehyde reactive group efficiently inhibit other cysteine proteases than caspases. The in vitro studies included cathepsins B, H, L, S, K, F, V, X and C, papain and legumain. Z-DEVD-cmk was shown to be the preferred irreversible inhibitor of most of the cathepsins in vitro, followed by Z-DEVD-fmk, Ac-YVAD-cmk, Z-YVAD-fmk and Z-VAD-fmk. Inactivation of legumain by all the inhibitors investigated was moderate, whereas cathepsins H and C were poorly inhibited or not inhibited at all. Inhibition by aldehydes was not very potent. All the three fluoromethylketones efficiently inhibited cathepsins in Jurkat and human embryonic kidney 293 cells at concentrations of 100 μM. Furthermore, they completely inhibited cathepsins B and X activity in tissue extracts at concentrations as low as 1 μM. These results suggest that data based on the use of these inhibitors should be taken with caution and that other proteases may be implicated in the processes previously ascribed solely to caspases.

The structural basis for substrate and inhibitor selectivity of the anthrax lethal factor

Recent events have created an urgent need for new therapeutic strategies to treat anthrax. We have applied a mixture-based peptide library approach to rapidly determine the optimal peptide substrate for the anthrax lethal factor (LF), a metalloproteinase with an important role in the pathogenesis of the disease. Using this approach we have identified peptide analogs that inhibit the enzyme in vitro and that protect cultured macrophages from LF-mediated cytolysis. The crystal structures of LF bound to an optimized peptide substrate and to peptide-based inhibitors provide a rationale for the observed selectivity and may be exploited in the design of future generations of LF inhibitors.

Structural Coupling of SH2-Kinase Domains Links Fes and Abl Substrate Recognition and Kinase Activation

Summary The SH2 domain of cytoplasmic tyrosine kinases can enhance catalytic activity and substrate recognition, but the molecular mechanisms by which this is achieved are poorly understood. We have solved the structure of the prototypic SH2-kinase unit of the human Fes tyrosine kinase, which appears specialized for positive signaling. In its active conformation, the SH2 domain tightly interacts with the kinase N-terminal lobe and positions the kinase αC helix in an active configuration through essential packing and electrostatic interactions. This interaction is stabilized by ligand binding to the SH2 domain. Our data indicate that Fes kinase activation is closely coupled to substrate recognition through cooperative SH2-kinase-substrate interactions. Similarly, we find that the SH2 domain of the active Abl kinase stimulates catalytic activity and substrate phosphorylation through a distinct SH2-kinase interface. Thus, the SH2 and catalytic domains of active Fes and Abl pro-oncogenic kinases form integrated structures essential for effective tyrosine kinase signaling.