Tomonori Kaneko

Publications (16)82.69 Total impact

• Article: Phosphotyrosine recognition domains: The typical, the atypical and the versatile.

  Tomonori Kaneko, Rakesh Joshi, Stephan M Feller, Shawn S C Li
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  ABSTRACT: SH2 domains are long known prominent players in the field of phosphotyrosine recognition within signaling protein networks. However, over the years they have been joined by an increasing number of other protein domain families that can, at least with some of their members, also recognise pTyr residues in a sequence-specific context. This superfamily of pTyr recognition modules, which includes substantial fractions of the PTB domains, as well as much smaller, or even single member fractions like the HYB domain, the PKCdelta and PKCtheta C2 domains and RKIP, represents a fascinating, medically relevant and hence intensely studied part of the cellular signaling architecture of metazoans. Protein tyrosine phosphorylation clearly serves a plethora of functions and pTyr recognition domains are used in a similarly wide range of interaction modes, which encompass, for example, partner protein switching, tandem recognition functionalities and the interaction with catalytically active protein domains. If looked upon closely enough, virtually no pTyr recognition and regulation event is an exact mirror image of another one in the same cell. Thus, the more we learn about the biology and ultrastructural details of pTyr recognition domains, the more does it become apparent that nature cleverly combines and varies a few basic principles to generate a sheer endless number of sophisticated and highly effective recognition/regulation events that are, under normal conditions, elegantly orchestrated in time and space. This knowledge is also valuable when exploring pTyr reader domains as diagnostic tools, drug targets or therapeutic reagents to combat human diseases.
  Cell Communication and Signaling 11/2012; 10(1):32. · 5.50 Impact Factor
• Source

  Available from: pnas.org

  Article: Differential regulation of the activity of deleted in liver cancer 1 (DLC1) by tensins controls cell migration and transformation.

  Xuan Cao, Courtney Voss, Bing Zhao, Tomonori Kaneko, Shawn Shun-Cheng Li
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  ABSTRACT: The epithelial growth factor receptor plays an important role in cell migration and cancer metastasis, but the underlying molecular mechanism is not fully understood. We show here that differential regulation of the Ras-homology-GTPase-activating protein [corrected] (Rho-GAP) activity of deleted in liver cancer 1 (DLC1) by tensin3 and COOH-terminal tensin-like protein (cten) controls EGF-driven cell migration and transformation. Tensin3 binds DLC1 through its actin-binding domain, a region that is missing in cten, and thereby releases an autoinhibitory interaction between the sterile alpha motif and Rho-GAP domains of DLC1. Consequently, tensin3, but not cten, promotes the activation of DLC1, which, in turn, leads to inactivation of RhoA and decreased cell migration. Depletion of endogenous tensin3, but not cten, augmented the formation of actin stress fibers and focal adhesions and enhanced cell motility. These effects were, however, ablated by an inhibitor of the Rho-associated protein kinase. Importantly, activation of DLC1 by tensin3 or its actin-binding domain drastically reduced the anchorage-independent growth of transformed cells. Our study therefore links dynamic regulation of tensin family members by EGF to Rho-GAP through DLC1 and suggests that the tensin-DLC1-RhoA signaling axis plays an important role in tumorigenesis and cancer metastasis, and may be explored for cancer intervention.
  Proceedings of the National Academy of Sciences 01/2012; 109(5):1455-60. · 9.68 Impact Factor
• Article: Superbinder SH2 Domains Act as Antagonists of Cell Signaling.

  Tomonori Kaneko, Haiming Huang, Xuan Cao, Xing Li, Chengjun Li, Courtney Voss, Sachdev S Sidhu, Shawn S C Li
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  ABSTRACT: Protein-ligand interactions mediated by modular domains, which often play important roles in regulating cellular functions, are generally of moderate affinities. We examined the Src homology 2 (SH2) domain, a modular domain that recognizes phosphorylated tyrosine (pTyr) residues, to investigate how the binding affinity of a modular domain for its ligand influences the structure and cellular function of the protein. We used the phage display method to perform directed evolution of the pTyr-binding residues in the SH2 domain of the tyrosine kinase Fyn and identified three amino acid substitutions that critically affected binding. We generated three SH2 domain triple-point mutants that were "superbinders" with much higher affinities for pTyr-containing peptides than the natural domain. Crystallographic analysis of one of these superbinders revealed that the superbinder SH2 domain recognized the pTyr moiety in a bipartite binding mode: A hydrophobic surface encompassed the phenyl ring, and a positively charged site engaged the phosphate. When expressed in mammalian cells, the superbinder SH2 domains blocked epidermal growth factor receptor signaling and inhibited anchorage-independent cell proliferation, suggesting that pTyr superbinders might be explored for therapeutic applications and useful as biological research tools. Although the SH2 domain fold can support much higher affinity for its ligand than is observed in nature, our results suggest that natural SH2 domains are not optimized for ligand binding but for specificity and flexibility, which are likely properties important for their function in signaling and regulatory processes.
  Science Signaling 01/2012; 5(243):ra68. · 7.50 Impact Factor
• Article: Accelerated biosynthesis of neolacto-series glycosphingolipids in differentiated mouse embryonal carcinoma F9 cells detected by using dodecyl N-acetylglucosaminide as a saccharide primer.

  Nao Ogasawara, Yohko U Katagiri, Nobutaka Kiyokawa, Tomonori Kaneko, Ban Sato, Hideki Nakajima, Yoshitaka Miyagawa, Yasunori Kushi, Hideharu Ishida, Makoto Kiso, Hajime Okita, Toshinori Sato, Junichiro Fujimoto
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  ABSTRACT: Using dodecyl N-acetylglucosaminide (GlcNAc-C12) as a saccharide primer, we investigated the biosynthetic changes of neolacto-series glycosphingolipids (GSLs) in mouse embryonal carcinoma F9 cells during differentiation induced by retinoic acid plus dibutyryl cyclic AMP (RA/dbcAMP). In the differentiated cells, the glycosylation of GlcNAc-C12 was greatly enhanced. The sugar compositions of glycosylated primers were assigned as Hex-GlcNAc, [Hex](2)-GlcNAc, [Hex](2)[HexNAc]-GlcNAc, and [NeuAc][Hex]-GlcNAc by liquid chromatography-tandem mass spectrometry. The detection of augmented biosynthesis of endogenous sialylparagloboside indicated that [NeuAc][Hex]-GlcNAc was predicted to be the non-reducing end trisaccharide of sialylparagloboside. The transcription of B3gnt5, B4galt1, Ggta1, Fut4 and St3gal6, encoding glycosyltransferases involved in the neolacto-series glycosphingolipids biosynthesis, was increased, whereas that of Fut9 and St6galI was decreased after RA/dbcAMP treatment. Furthermore, the sialyltransferase activity of ST3GalVI sialylating paragloboside was enhanced with the increase in St3gal6 expression. Since most stage-specific embryonic antigen-1 (SSEA-1) active determinants are carried by glycoproteins in F9 cells, the changes in glycolipid metabolism do not seem to be closely related to loss of cell surface SSEA-1 expression upon F9 differentiation. These results indicate that RA/dbcAMP treatment activates the biosynthesis of neolacto-series GSL and enhances sialylation of paragloboside in F9 cells with down-regulation of Fut9 expression.
  Journal of biochemistry 03/2011; 149(3):321-30. · 1.95 Impact Factor
• Article: Evolving specificity from variability for protein interaction domains.

  Tomonori Kaneko, Sachdev S Sidhu, Shawn S C Li
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  ABSTRACT: An important question in modular domain-peptide interactions, which play crucial roles in many biological processes, is how the diverse specificities exhibited by different members of a domain family are encoded in a common scaffold. Analysis of the Src homology (SH) 2 family has revealed that its specificity is determined, in large part, by the configuration of surface loops that regulate ligand access to binding pockets. In a distinct manner, SH3 domains employ loops for ligand recognition. The PDZ domain, in contrast, achieves specificity by co-evolution of binding-site residues. Thus, the conformational and sequence variability afforded by surface loops and binding sites provides a general mechanism by which to encode the wide spectrum of specificities observed for modular protein interaction domains.
  Trends in Biochemical Sciences 01/2011; 36(4):183-90. · 10.85 Impact Factor
• Article: Neuroblastoma cells can be classified according to glycosphingolipid expression profiles identified by liquid chromatography-tandem mass spectrometry.

  Tomonori Kaneko, Hajime Okita, Hideki Nakajima, Kazutoshi Iijima, Nao Ogasawara, Yoshitaka Miyagawa, Yohko U Katagiri, Atsuko Nakagawa, Nobutaka Kiyokawa, Toshinori Sato, Junichiro Fujimoto
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  ABSTRACT: It is hoped that the gangliosides contained in neuroblastomas (NBs) can be used as outcome predictors. We used liquid chromatography-tandem mass spectrometry (LC-MS) to analyze the gangliosides expressed in 11 NB cell lines. LC-MS analysis detected a number of gangliosides, including acetylated forms, with significantly higher sensitivity than conventional high-performance thin-layer chromatography analysis, and the results revealed that the expression profiles of the gangliosides GD1a, GD2, and acetylated GD2 differed according to the NB cell line. Hierarchical clustering based on the ganglioside expression profiles obtained by LC-MS analysis revealed that the NB cell lines could be classified into three types according to their expression of these three gangliosides: A-type characterized by high expression of GD1a and low or no expression of GD2/acetylated GD2, B-type characterized by low or no expression of GD1a and high expression of GD2/acetylated GD2, and AB-type characterized by expression of both GD1a and GD2/acetylated GD2. Interestingly, all three MYCN non-amplified cell lines were classified into the A-type. The classification was found to be correlated with mRNA expression of ganglioside synthase and neural-differentiation-related genes. The results of this study indicate that LC-MS analysis is useful as a tool for glycosphingolipid research on malignancies.
  International Journal of Oncology 11/2010; 37(5):1279-88. · 2.40 Impact Factor
• Article: Loops govern SH2 domain specificity by controlling access to binding pockets.

  Tomonori Kaneko, Haiming Huang, Bing Zhao, Lei Li, Huadong Liu, Courtney K Voss, Chenggang Wu, Martin R Schiller, Shawn Shun-Cheng Li
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  ABSTRACT: Cellular functions require specific protein-protein interactions that are often mediated by modular domains that use binding pockets to engage particular sequence motifs in their partners. Yet, how different members of a domain family select for distinct sequence motifs is not fully understood. The human genome encodes 120 Src homology 2 (SH2) domains (in 110 proteins), which mediate protein-protein interactions by binding to proteins with diverse phosphotyrosine (pTyr)-containing sequences. The structure of the SH2 domain of BRDG1 bound to a peptide revealed a binding pocket that was blocked by a loop residue in most other SH2 domains. Analysis of 63 SH2 domain structures suggested that the SH2 domains contain three binding pockets, which exhibit selectivity for the three positions after the pTyr in a peptide, and that SH2 domain loops defined the accessibility and shape of these pockets. Despite sequence variability in the loops, we identified conserved structural features in the loops of SH2 domains responsible for controlling access to these surface pockets. We engineered new loops in an SH2 domain that altered specificity as predicted. Thus, selective blockage of binding subsites or pockets by surface loops provides a molecular basis by which the diverse modes of ligand recognition by the SH2 domain may have evolved and provides a framework for engineering SH2 domains and designing SH2-specific inhibitors.
  Science Signaling 01/2010; 3(120):ra34. · 7.50 Impact Factor
• Article: Crystallization and preliminary X-ray analysis of the stress-response PPM phosphatase RsbX from Bacillus subtilis.

  Masatoshi Suganuma, Aik Hong Teh, Masatomo Makino, Nobutaka Shimizu, Tomonori Kaneko, Kunio Hirata, Masaki Yamamoto, Takashi Kumasaka
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  ABSTRACT: RsbX from Bacillus subtilis is a manganese-dependent PPM phosphatase and negatively regulates the signal transduction of the general stress response by the dephosphorylation of RsbS and RsbR, which are activators of the alternative RNA polymerase sigma factor SigB. In order to elucidate the structural-functional relationship of its Ser/Thr protein-phosphorylation mechanism, an X-ray crystallographic diffraction study of RsbX was performed. Recombinant RsbX was expressed in Escherichia coli, purified and crystallized. Crystals were obtained using the sitting-drop vapour-diffusion method and X-ray diffraction data were collected to 1.06 angstrom resolution with an R(merge) of 8.1%. The crystals belonged to the triclinic space group P1, with unit-cell parameters a = 33.3, b = 41.7, c = 68.6 angstrom , alpha = 98.8, beta = 90.0, gamma = 108.4 degrees.
  Acta Crystallographica Section F Structural Biology and Crystallization Communications 11/2009; 65(Pt 11):1128-30. · 0.51 Impact Factor
• Article: Expression, crystallization and preliminary crystallographic analysis of the PAS domain of RsbP, a stress-response phosphatase from Bacillus subtilis.

  Masatomo Makino, Shinpei Kondo, Tomonori Kaneko, Seiki Baba, Kunio Hirata, Takashi Kumasaka
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  ABSTRACT: RsbP, a regulator of RNA polymerase sigma(B) activity in Bacillus subtilis, is a phosphatase containing a Per-Arnt-Sim (PAS) domain in its N-terminal region that is expected to sense energy stresses such as carbon, phosphate or oxygen starvation. Energy-stress signals are transmitted to the PAS domain and activate the C-terminal phosphatase domain of RsbP, leading to activation of the downstream anti-anti-sigma(B) factor RsbV. Finally, the general stress response is induced to protect the cells against further stresses. The recombinant PAS domain of RsbP was crystallized by the sitting-drop vapour-diffusion technique using 40% PEG 400 as a precipitant. The crystals belonged to space group P2(1), with unit-cell parameters a = 55.2, b = 71.7, c = 60.2 A, beta = 92.1 degrees . Diffraction data were collected to a resolution of 1.6 A.
  Acta Crystallographica Section F Structural Biology and Crystallization Communications 07/2009; 65(Pt 6):559-61. · 0.51 Impact Factor
• Article: The SH3 domain--a family of versatile peptide- and protein-recognition module.

  Tomonori Kaneko, Lei Li, Shawn S-C Li
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  ABSTRACT: Src homology 3 (SH3) domains were initially characterized as a prevalent protein module that recognizes proline-rich sequences, in particular those containing a PxxP motif. Recent studies have shown that the specificity and cellular function of SH3 domains are far more diverse than previously appreciated. Despite lacking distinguishing features, the ligand-binding surface of an SH3 domain can be molded to accommodate a variety of peptide ligands. Moreover, certain SH3 domains are capable of using surfaces distinct from the canonical ligand-binding site to engage a peptide or protein. The identification of novel motifs and domains recognized by the SH3 domain greatly expands the ligand pool and cellular function for this family. However, this also imposes the question as to how the specificity of the hundreds of human SH3 domains is regulated in a cell to ensure their proper functions. Here we review literature on the specificity of SH3 domains, with an emphasis on the structural basis of ligand recognition, and discuss mechanisms employed by SH3 domain-containing proteins to execute defined cellular functions through highly regulated SH3-ligand interactions.
  Frontiers in Bioscience 02/2008; 13:4938-52. · 3.52 Impact Factor
• Article: Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8.

  Ihsanawati, Takashi Kumasaka, Tomonori Kaneko, Chihiro Morokuma, Rie Yatsunami, Takao Sato, Satoshi Nakamura, Nobuo Tanaka
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  ABSTRACT: The crystal structure of xylanase 10B from Thermotoga maritima MSB8 (TmxB), a hyperthermostable xylanase, has been solved in its native form and in complex with xylobiose or xylotriose at 1.8 A resolution. In order to gain insight into the substrate subsite and the molecular features for thermal stability, we compared TmxB with family 10 xylanase structures from nine microorganisms. As expected, TmxB folds into a (beta/alpha)8-barrel structure, which is common among the glycoside hydrolase family 10. The enzyme active site and the environment surrounding the xylooligosaccharide of TmxB are highly similar to those of family 10 xylanases. However, only two xylose moieties were found in its binding pocket from the TmxB-xylotriose complex structure. This finding suggests that TmxB could be a potential biocatalyst for the large-scale production of xylobiose. The result of structural analyses also indicated that TmxB possesses some additional features that account for its thermostability. In particular, clusters of aromatic residues together with a lack of exposed hydrophobic residues are characteristic of the TmxB structure. TmxB has also a significant number of ion pairs on the protein surface that are not found in other thermophilic family 10 xylanases.
  Proteins Structure Function and Bioinformatics 01/2006; 61(4):999-1009. · 3.39 Impact Factor
• Article: Crystal structures of RsbQ, a stress-response regulator in Bacillus subtilis.

  Tomonori Kaneko, Nobuo Tanaka, Takashi Kumasaka
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  ABSTRACT: Growth-limiting stresses in bacteria induce the general stress response to protect the cells against future stresses. Energy stress caused by starvation conditions in Bacillus subtilis is transmitted to the sigma(B) transcription factor by stress-response regulators. RsbP, a positive regulator, is a phosphatase containing a PAS (Per-ARNT-Sim) domain and requires catalytic function of a putative alpha/beta hydrolase, RsbQ, to be activated. These two proteins have been found to interact with each other. We determined the crystal structures of RsbQ in native and inhibitor-bound forms to investigate why RsbP requires RsbQ. These structures confirm that RsbQ belongs to the alpha/beta hydrolase superfamily. Since the catalytic triad is buried inside the molecule due to the closed conformation, the active site is constructed as a hydrophobic cavity that is nearly isolated from the solvent. This suggests that RsbQ has specificity for a hydrophobic small compound rather than a macromolecule such as RsbP. Moreover, structural comparison with other alpha/beta hydrolases demonstrates that a unique loop region of RsbQ is a likely candidate for the interaction site with RsbP, and the interaction might be responsible for product release by operating the hydrophobic gate equipped between the cavity and the solvent. Our results support the possibility that RsbQ provides a cofactor molecule for the mature functionality of RsbP.
  Protein Science 03/2005; 14(2):558-65. · 2.80 Impact Factor
• Article: Structural insight into modest binding of a non-PXXP ligand to the signal transducing adaptor molecule-2 Src homology 3 domain.

  Tomonori Kaneko, Takashi Kumasaka, Tadashi Ganbe, Takao Sato, Keiji Miyazawa, Naomi Kitamura, Nobuo Tanaka
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  ABSTRACT: Although some exceptional motifs have been identified, it is well known that the PXXP motif is the motif of ligand proteins generally recognized by the Src homology 3 (SH3) domain. SH3-ligand interactions are usually weak, with ordinary KD approximately 10 microM. The structural basis for a tight and specific association (KD = 0.24 microm) between Gads SH3 and a novel motif, PX(V/I)(D/N)RXXKP, was revealed in a previous structural analysis of the complex formed between them. In this paper, we report the crystal structure of the signal transducing adaptor molecule-2 (STAM2) SH3 domain in complex with a peptide with a novel motif derived from a ligand protein, UBPY. The derived KD value for this complex is 27 microM. The notable difference in affinity for these parallel complexes may be explained because the STAM2 SH3 structure does not provide a specificity pocket for binding, whereas the Gads SH3 structure does. Instead, the structure of STAM2 SH3 is analogous to that of Grb2 SH3 which, in addition to normal PXXP ligands, has also been shown to moderately recognize the novel motif discussed herein. Thus, the extremely tight interaction observed between Gads SH3 and the novel motif is caused not by an innate ability of the novel motif but rather by an evolutionary change in the Gads SH3 domain. Instead, SH3 domains of STAM2 and Grb2 retain the moderate characteristics of recognizing their ligand proteins like other SH3 domains for appropriate transient interactions between signaling molecules.
  Journal of Biological Chemistry 12/2003; 278(48):48162-8. · 4.77 Impact Factor
• Article: Crystallization and preliminary X-ray studies of xylanase 10B from Thermotoga maritima.

  Ihsanawati, Takashi Kumasaka, Tomonori Kaneko, Chihiro Morokuma, Satoshi Nakamura, Nobuo Tanaka
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  ABSTRACT: Xylanases catalyze the hydrolysis of the beta-1,4-glycosidic bonds of xylan, which is the second most abundant component of plant cell walls after cellulose. The recombinant xylanase 10B from Thermotoga maritima MSB8 was prepared and crystallized by the sitting-drop vapour-diffusion method using 40 mM zinc acetate, 20 mM MES buffer pH 6.0 and 3% ethanol. Intensity data were collected to 2.5 A resolution at beamline BL26B2 of SPring-8. Preliminary X-ray analysis showed that the crystal belongs to space group P2(1)2(1)2, with unit-cell parameters a = 77.3, b = 80.6, c = 58.2 A and one molecule per asymmetric unit.
  Acta Crystallographica Section D Biological Crystallography 10/2003; 59(Pt 9):1659-61. · 12.62 Impact Factor
• Source

  Available from: ncbi.nlm.nih.gov

  Article: Wobble modification differences and subcellular localization of tRNAs in Leishmania tarentolae: implication for tRNA sorting mechanism.

  Tomonori Kaneko, Takeo Suzuki, Stephen T Kapushoc, Mary Anne Rubio, Jafar Ghazvini, Kimitsuna Watanabe, Larry Simpson, Tsutomu Suzuki
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  ABSTRACT: In Leishmania tarentolae, all mitochondrial tRNAs are encoded in the nuclear genome and imported from the cytosol. It is known that tRNA(Glu)(UUC) and tRNA(Gln)(UUG) are localized in both cytosol and mitochondria. We investigated structural differences between affinity-isolated cytosolic (cy) and mitochondrial (mt) tRNAs for glutamate and glutamine by mass spectrometry. A unique modification difference in both tRNAs was identified at the anticodon wobble position: cy tRNAs have 5-methoxycarbonylmethyl-2- thiouridine (mcm(5)s(2)U), whereas mt tRNAs have 5- methoxycarbonylmethyl-2'-O-methyluridine (mcm(5)Um). In addition, a trace portion (4%) of cy tRNAs was found to have 5-methoxycarbonylmethyluridine (mcm(5)U) at its wobble position, which could represent a common modification intermediate for both modified uridines in cy and mt tRNAs. We also isolated a trace amount of mitochondria-specific tRNA(Lys)(UUU) from the cytosol and found mcm(5)U at its wobble position, while its mitochondrial counterpart has mcm(5)Um. Mt tRNA(Lys) and in vitro transcribed tRNA(Glu) were imported much more efficiently into isolated mitochondria than the native cy tRNA(Glu) in an in vitro importation experiment, indicating that cytosol-specific 2-thiolation could play an inhibitory role in tRNA import into mitochondria.
  The EMBO Journal 03/2003; 22(3):657-67. · 9.20 Impact Factor
• Article: Evolving specificity from variability for protein interaction domains

  Tomonori Kaneko, Sachdev S. Sidhu, Shawn S.C. Li
  [show abstract] [hide abstract]
  ABSTRACT: An important question in modular domain–peptide interactions, which play crucial roles in many biological processes, is how the diverse specificities exhibited by different members of a domain family are encoded in a common scaffold. Analysis of the Src homology (SH) 2 family has revealed that its specificity is determined, in large part, by the configuration of surface loops that regulate ligand access to binding pockets. In a distinct manner, SH3 domains employ loops for ligand recognition. The PDZ domain, in contrast, achieves specificity by co-evolution of binding-site residues. Thus, the conformational and sequence variability afforded by surface loops and binding sites provides a general mechanism by which to encode the wide spectrum of specificities observed for modular protein interaction domains.
  Trends in Biochemical Sciences.