Interaction domains: from simple binding events to complex cellular behavior

Surface-Induced Conformational Changes of α-Synuclein on Silica Nanoparticles of Varying Sizes Corresponding to Protein Structural Domains: Insights from Enhanced Sampling MD Simulations

Protein-nanoparticle interactions are crucial in a diverse array of biotechnology and biomedical applications. Variations in nanoparticle sizes can adjust surface interactions with proteins and biomolecules, thereby influencing their conformation and functionality. To achieve precise control over the nanoparticle sizes corresponding to the dimensions of protein structural domains (∼nm) and establish the relationship between nanoparticle curvature and protein conformational changes, we conduct well-tempered metadynamics simulations to explore the secondary structure changes and thermodynamic characteristics of α-synuclein (αS), an intrinsically disordered protein (IDP), adsorbed onto silicon dioxide (SiO2) nanoparticles of varying sizes (diameter, d = 0.5-2.5 nm). The analysis of αS's conformational landscapes and structural probabilities reveals that intermediate-sized SiO2 nanoparticles (d = 1.2-1.4 nm) effectively stabilize the native intrinsically disordered conformations of αS (with domain sizes of 1-2 nm). In contrast, excessively large or small SiO2 nanoparticles significantly enhance the likelihood of forming intramolecular β-sheet domains within αS chains, a process that is critical for subsequent aggregation of αS. This study is of significance to the development of nanoparticles that stabilize desired protein conformations, which may pave the way for in vivo penetration and distribution of nanoparticles as well as biomedicine therapeutic interventions aimed at targeting αS aggregation.

Lens-free on-chip 3D microscopy based on wavelength-scanning Fourier ptychographic diffraction tomography

Lens-free on-chip microscopy is a powerful and promising high-throughput computational microscopy technique due to its unique advantage of creating high-resolution images across the full field-of-view (FOV) of the imaging sensor. Nevertheless, most current lens-free microscopy methods have been designed for imaging only two-dimensional thin samples. Lens-free on-chip tomography (LFOCT) with a uniform resolution across the entire FOV and at a subpixel level remains a critical challenge. In this paper, we demonstrated a new LFOCT technique and associated imaging platform based on wavelength scanning Fourier ptychographic diffraction tomography (wsFPDT). Instead of using angularly-variable illuminations, in wsFPDT, the sample is illuminated by on-axis wavelength-variable illuminations, ranging from 430 to 1200 nm. The corresponding under-sampled diffraction patterns are recorded, and then an iterative ptychographic reconstruction procedure is applied to fill the spectrum of the three-dimensional (3D) scattering potential to recover the sample's 3D refractive index (RI) distribution. The wavelength-scanning scheme not only eliminates the need for mechanical motion during image acquisition and precise registration of the raw images but secures a quasi-uniform, pixel-super-resolved imaging resolution across the entire imaging FOV. With wsFPDT, we demonstrate the high-throughput, billion-voxel 3D tomographic imaging results with a half-pitch lateral resolution of 775 nm and an axial resolution of 5.43 μm across a large FOV of 29.85 mm2 and an imaging depth of >200 μm. The effectiveness of the proposed method was demonstrated by imaging various types of samples, including micro-polystyrene beads, diatoms, and mouse mononuclear macrophage cells. The unique capability to reveal quantitative morphological properties, such as area, volume, and sphericity index of single cell over large cell populations makes wsFPDT a powerful quantitative and label-free tool for high-throughput biological applications.

The permissive binding theory of cancer

The later stages of cancer, including the invasion and colonization of new tissues, are actively mysterious compared to earlier stages like primary tumor formation. While we lack many details about both, we do have an apparently successful explanatory framework for the earlier stages: one in which genetic mutations hold ultimate causal and explanatory power. By contrast, on both empirical and conceptual grounds, it is not currently clear that mutations alone can explain the later stages of cancer. Can a different type of molecular change do better? Here, I introduce the "permissive binding theory" of cancer, which proposes that novel protein binding interactions are the key causal and explanatory entity in invasion and metastasis. It posits that binding is more abundant at baseline than we observe because it is restricted in normal physiology; that any large perturbation to physiological state revives this baseline abundance, unleashing many new binding interactions; and that a subset of these cause the cellular functions at the heart of oncogenesis, especially invasion and metastasis. Significant physiological perturbations occur in cancer cells in very early stages, and generally become more extreme with progression, providing interactions that continually fuel invasion and metastasis. The theory is compatible with, but not limited to, causal roles for the diverse molecular changes observed in cancer (e.g. gene expression or epigenetic changes), as these generally act causally upstream of proteins, and so may exert their effects by changing the protein binding interactions that occur in the cell. This admits the possibility that molecular changes that appear quite different may actually converge in creating the same few protein complexes, simplifying our picture of invasion and metastasis. If correct, the theory offers a concrete therapeutic strategy: targeting the key novel complexes. The theory is straightforwardly testable by large-scale identification of protein interactions in different cancers.

Analysis of Host–Bacteria Protein Interactions Reveals Conserved Domains and Motifs That Mediate Fundamental Infection Pathways

Adhesion and colonization of host cells by pathogenic bacteria depend on protein–protein interactions (PPIs). These interactions are interesting from the pharmacological point of view since new molecules that inhibit host-pathogen PPIs would act as new antimicrobials. Most of these interactions are discovered using high-throughput methods that may display a high false positive rate. The absence of curation of these databases can make the available data unreliable. To address this issue, a comprehensive filtering process was developed to obtain a reliable list of domains and motifs that participate in PPIs between bacteria and human cells. From a structural point of view, our analysis revealed that human proteins involved in the interactions are rich in alpha helix and disordered regions and poorer in beta structure. Disordered regions in human proteins harbor short sequence motifs that are specifically recognized by certain domains in pathogenic proteins. The most relevant domain–domain interactions were validated by AlphaFold, showing that a proper analysis of host-pathogen PPI databases can reveal structural conserved patterns. Domain–motif interactions, on the contrary, were more difficult to validate, since unstructured regions were involved, where AlphaFold could not make a good prediction. Moreover, these interactions are also likely accommodated by post-translational modifications, especially phosphorylation, which can potentially occur in 25–50% of host proteins. Hence, while common structural patterns are involved in host–pathogen PPIs and can be retrieved from available databases, more information is required to properly infer the full interactome. By resolving these issues, and in combination with new prediction tools like Alphafold, new classes of antimicrobials could be discovered from a more detailed understanding of these interactions.

Protein Interaction Domains: Structural Features and Drug Discovery Applications (Part 2)

BACKGROUND

Proteins present a modular organization made up of several domains. Apart from the domains playing catalytic functions, many others are crucial to recruit interactors. The latter domains can be defined as "PIDs" (Protein Interaction Domains) and are responsible for pivotal outcomes in signal transduction and a certain array of normal physiological and disease-related pathways. Targeting such PIDs with small molecules and peptides able to modulate their interaction networks, may represent a valuable route to discover novel therapeutics.

OBJECTIVE

This work represents a continuation of a very recent review describing PIDs able to recognize post-translationally modified peptide segments. On the contrary, the second part concerns with PIDs that interact with simple peptide sequences provided with standard amino acids.

METHODS

Crucial structural information on different domain subfamilies and their interactomes was gained by a wide search in different online available databases (including the PDB (Protein Data Bank), the Pfam (Protein family), and the SMART (Simple Modular Architecture Research Tool)). Pubmed was also searched to explore the most recent literature related to the topic.

RESULTS AND CONCLUSION

PIDs are multifaceted: they have all diverse structural features and can recognize several consensus sequences. PIDs can be linked to different diseases onset and progression, like cancer or viral infections and find applications in the personalized medicine field. Many efforts have been centered on peptide/peptidomimetic inhibitors of PIDs mediated interactions but much more work needs to be conducted to improve drug-likeness and interaction affinities of identified compounds.

Protein Kinases in Hematological Disorders

Cell signaling is an important part of the complex system of molecular communication that governs basic cellular activities and coordinates cell cycle machinery. Pathological alterations in the cellular information processing may be responsible for the diseases such as cancer. Numerous diseases may be treated effectively via the pharmacological management of cellular signaling. Protein kinases (PK) have significantly important roles in the cell signal transduction process. Protein kinases phosphorylate serine, threonine, tyrosine and histidine amino acids in a wide variety of molecular networks. Two main PK groups are distinguished; serine/threonine kinase and tyrosine kinases. MAPK (mitogen-activated protein kinases), ERK, EGFR (epidermal growth factor receptor), src, abl, FAK (focal adesion kinase), and JAK (janus family kinase) are considered as the main PK molecular networks. Protein kinases are closely related to the pathobiology of hematologic neoplastic disorders. For instance; JAKV617F point mutation-causing polycythemia vera and essential thrombocytosis occur at the position 617 in the JH2 domain of the JAK2 gene. The protein kinase inhibitor drugs targeting specific kinase molecules have already been developed and widely used in the field of Clinical Hematology. The existence of a local renin-angiotensin system (RAS) specific to the hematopoietic bone marrow (BM) microenvironment had been proposed two decades ago. Local BM RAS is important in hematopoietic stem cell biology and microenvironment. There are interactions among the local BM RAS and PK. For example, ACE2-ang(1-7)-Mas axis inhibits p38 MAPK/NF-КB signaling pathway. The Local BM RAS may have a role in the effect on PK in this biological spectrum. The aim of this review is to outline the functions of PKs in the pathobiology of hematologic neoplastic disorders.

The Relevance of the SH2 Domain for c-Src Functionality in Triple-Negative Breast Cancer Cells

The role of Src family kinases (SFKs) in human tumors has been always associated with tyrosine kinase activity and much less attention has been given to the SH2 and SH3 adapter domains. Here, we studied the role of the c-Src-SH2 domain in triple-negative breast cancer (TNBC). To this end, SUM159PT and MDA-MB-231 human cell lines were employed as model systems. These cells conditionally expressed, under tetracycline control (Tet-On system), a c-Src variant with point-inactivating mutation of the SH2 adapter domain (R175L). The expression of this mutant reduced the self-renewal capability of the enriched population of breast cancer stem cells (BCSCs), demonstrating the importance of the SH2 adapter domain of c-Src in the mammary gland carcinogenesis. In addition, the analysis of anchorage-independent growth, proliferation, migration, and invasiveness, all processes associated with tumorigenesis, showed that the SH2 domain of c-Src plays a very relevant role in their regulation. Furthermore, the transfection of two different aptamers directed to SH2-c-Src in both SUM159PT and MDA-MB-231 cells induced inhibition of their proliferation, migration, and invasiveness, strengthening the hypothesis that this domain is highly involved in TNBC tumorigenesis. Therefore, the SH2 domain of c-Src could be a promising therapeutic target and combined treatments with inhibitors of c-Src kinase enzymatic activity may represent a new therapeutic strategy for patients with TNBC, whose prognosis is currently very negative.

Protein Interaction Domains and Post-Translational Modifications: Structural Features and Drug Discovery Applications

Background:

Many pathways regarding healthy cells and/or linked to diseases onset and progression depend on large assemblies including multi-protein complexes. Protein-protein interactions may occur through a vast array of modules known as protein interaction domains (PIDs).

Objective:

This review concerns with PIDs recognizing post-translationally modified peptide sequences and intends to provide the scientific community with state of art knowledge on their 3D structures, binding topologies and potential applications in the drug discovery field.

Method:

Several databases, such as the Pfam (Protein family), the SMART (Simple Modular Architecture Research Tool) and the PDB (Protein Data Bank), were searched to look for different domain families and gain structural information on protein complexes in which particular PIDs are involved. Recent literature on PIDs and related drug discovery campaigns was retrieved through Pubmed and analyzed.

Results and Conclusion:

PIDs are rather versatile as concerning their binding preferences. Many of them recognize specifically only determined amino acid stretches with post-translational modifications, a few others are able to interact with several post-translationally modified sequences or with unmodified ones. Many PIDs can be linked to different diseases including cancer. The tremendous amount of available structural data led to the structure-based design of several molecules targeting protein-protein interactions mediated by PIDs, including peptides, peptidomimetics and small compounds. More studies are needed to fully role out, among different families, PIDs that can be considered reliable therapeutic targets, however, attacking PIDs rather than catalytic domains of a particular protein may represent a route to obtain selective inhibitors.

Genome-wide inference of the Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairs

Apart from some model organisms, the interactome of most organisms is largely unidentified. High-throughput experimental techniques to determine protein-protein interactions (PPIs) are resource intensive and highly susceptible to noise. Computational methods of PPI determination can accelerate biological discovery by identifying the most promising interacting pairs of proteins and by assessing the reliability of identified PPIs. Here we present a first in-depth study describing a global view of the ant Camponotus floridanus interactome. Although several ant genomes have been sequenced in the last eight years, studies exploring and investigating PPIs in ants are lacking. Our study attempts to fill this gap and the presented interactome will also serve as a template for determining PPIs in other ants in future. Our C. floridanus interactome covers 51,866 non-redundant PPIs among 6,274 proteins, including 20,544 interactions supported by domain-domain interactions (DDIs), 13,640 interactions supported by DDIs and subcellular localization, and 10,834 high confidence interactions mediated by 3,289 proteins. These interactions involve and cover 30.6% of the entire C. floridanus proteome.

Cabozantinib (XL184) and R428 (BGB324) Inhibit the Growth of Esophageal Squamous Cell Carcinoma (ESCC)

Esophageal squamous cell carcinoma (ESCC) is a deadly disease for which no effective targeted therapeutic agent has been approved. Both AXL and c-MET have been reported to be independent prognostic factors for ESCC. Thus, inhibitors of AXL/c-MET might have great potential as targeted therapy for ESCC. In the current study, we evaluated the therapeutic potential of the AXL/c-MET selective inhibitors, R428 and cabozantinib, in cell and mouse xenograft models. We demonstrated that both R428 and cabozantinib significantly inhibited the growth of CE81T and KYSE-70 ESCC cells and showed by wound-healing assay that they both inhibited ESCC cell migration. In the animal model, ESCC xenograft models were established by injecting KYSE-70 cells with Matrigel into the upper back region of NOD-SCID male mice followed by treatment with vehicle control, R428 (50 mg/kg/day), cisplatin (1.0 mg/kg), or cabozantinib (30 mg/kg/day) for the indicated number of days. R428 alone significantly inhibited ESCC tumor growth compared to the vehicle; however, no synergistic effect with cisplatin was observed. Notably, the dramatic efficacy of cabozantinib alone was observed in the mouse xenograft model. Collectively, our study demonstrated that both cabozantinib and R428 inhibit ESCC growth in cell and xenograft models. The results reveal the great potential of using cabozantinib for targeted therapy of ESCC.

Free energy calculations on the stability of the 14-3-3ζ protein

Mutations of cysteine are often introduced to e.g. avoid formation of non-physiological inter-molecular disulfide bridges in in-vitro experiments, or to maintain specificity in labeling experiments. Alanine or serine is typically preferred, which usually do not alter the overall protein stability, when the original cysteine was surface exposed. However, selecting the optimal mutation for cysteines in the hydrophobic core of the protein is more challenging. In this work, the stability of selected Cys mutants of 14-3-3ζ was predicted by free-energy calculations and the obtained data were compared with experimentally determined stabilities. Both the computational predictions as well as the experimental validation point at a significant destabilization of mutants C94A and C94S. This destabilization could be attributed to the formation of hydrophobic cavities and a polar solvation of a hydrophilic side chain. A L12E, M78K double mutant was further studied in terms of its reduced dimerization propensity. In contrast to naïve expectations, this double mutant did not lead to the formation of strong salt bridges, which was rationalized in terms of a preferred solvation of the ionic species. Again, experiments agreed with the calculations by confirming the monomerization of the double mutants. Overall, the simulation data is in good agreement with experiments and offers additional insight into the stability and dimerization of this important family of regulatory proteins.

Extent of pre-translational regulation for the control of nucleocytoplasmic protein localization

Background

Appropriate protein subcellular localization is essential for proper cellular function. Central to the regulation of protein localization are protein targeting motifs, stretches of amino acids serving as guides for protein entry in a specific cellular compartment. While the use of protein targeting motifs is modulated in a post-translational manner, mainly by protein conformational changes and post-translational modifications, the presence of these motifs in proteins can also be regulated in a pre-translational manner. Here, we investigate the extent of pre-translational regulation of the main signals controlling nucleo-cytoplasmic traffic: the nuclear localization signal (NLS) and the nuclear export signal (NES).

Results

Motif databases and manual curation of the literature allowed the identification of 175 experimentally validated NLSs and 120 experimentally validated NESs in human. Following mapping onto annotated transcripts, these motifs were found to be modular, most (73 % for NLS and 88 % for NES) being encoded entirely in only one exon. The presence of a majority of these motifs is regulated in an alternative manner at the transcript level (61 % for NLS and 72 % for NES) while the remaining motifs are present in all coding isoforms of their encoding gene. NLSs and NESs are pre-translationally regulated using four main mechanisms: alternative transcription/translation initiation, alternative translation termination, alternative splicing of the exon encoding the motif and frameshift, the first two being by far the most prevalent mechanisms. Quantitative analysis of the presence of these motifs using RNA-seq data indicates that inclusion of these motifs can be regulated in a tissue-specific and a combinatorial manner, can be altered in disease states in a directed way and that alternative inclusion of these motifs is often used by proteins with diverse interactors and roles in diverse pathways, such as kinases.

Conclusions

The pre-translational regulation of the inclusion of protein targeting motifs is a prominent and tightly-regulated mechanism that adds another layer in the control of protein subcellular localization.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2854-4) contains supplementary material, which is available to authorized users.

Evolution of domain-peptide interactions to coadapt specificity and affinity to functional diversity

Evolution of complexity in eukaryotic proteomes has arisen, in part, through emergence of modular independently folded domains mediating protein interactions via binding to short linear peptides in proteins. Over 30 years, structural properties and sequence preferences of these peptides have been extensively characterized. Less successful, however, were efforts to establish relationships between physicochemical properties and functions of domain-peptide interactions. To our knowledge, we have devised the first strategy to exhaustively explore the binding specificity of protein domain-peptide interactions. We applied the strategy to SH3 domains to determine the properties of their binding peptides starting from various experimental data. The strategy identified the majority (∼70%) of experimentally determined SH3 binding sites. We discovered mutual relationships among binding specificity, binding affinity, and structural properties and evolution of linear peptides. Remarkably, we found that these properties are also related to functional diversity, defined by depth of proteins within hierarchies of gene ontologies. Our results revealed that linear peptides evolved to coadapt specificity and affinity to functional diversity of domain-peptide interactions. Thus, domain-peptide interactions follow human-constructed gene ontologies, which suggest that our understanding of biological process hierarchies reflect the way chemical and thermodynamic properties of linear peptides and their interaction networks, in general, have evolved.

The principle of conformational signaling

Specific conformations of signaling proteins can serve as “signals” in signal transduction by being recognized by receptors.

Quantitative analysis of protein-protein interactions

Numerous authors, including contributors to this volume, have described methods to detect protein-protein interactions. Many of these approaches are now accessible to the inexperienced investigator thanks to core facilities and/or affordable instrumentation. This chapter discusses some common design considerations that are necessary to obtain valid measurements, as well as the assumptions and analytical methods that are relevant to the quantitation of these interactions.

Genetic variants of EGF and VEGF predict prognosis of patients with advanced esophageal squamous cell carcinoma

PURPOSE

To investigate the association between genetic polymorphisms of growth factor-related genes and prognosis in patients with advanced esophageal squamous cell carcinoma (ESCC).

PATIENTS AND METHODS

A total of 334 ESCC patients with advanced tumor stages (stages IIB, III and IV) were enrolled in the study. The genotypes of 14 candidate single nucleotide polymorphisms (SNPs) involved in growth factor-related functions were analyzed using iPLEX Gold technology from the genomic DNA of peripheral leukocytes, and were correlated with the clinical outcome of patients. Serum levels of growth factors were examined by enzyme-linked immunosorbent assay (ELISA).

RESULTS

The genetic polymorphisms of EGF:rs4444903, EGF:rs2237051 and VEGF:rs2010963 showed significant associations with overall survival (OS) of advanced ESCC patients (A/A+ A/G vs. GG, [HR = 0.77, 95% CI = 0.60-0.99, P = 0.039 for rs4444903; A/G+ G/G vs. A/A, [HR = 0.74, 95% CI = 0.58-0.95, P = 0.019 for rs2237051; G/G+G/C vs. C/C, [HR] inves = 0.69, 95% CI = 0.50-0.95, P = 0.023 for rs2010963). EGFR:rs2227983 and 3 SNPs of PIK3CA also showed borderline significant correlation with OS of advanced ESCC patients (P = 0.058 for rs2227983; P = 0.069, 0.091 and 0.067 for rs6443624, rs7651265 and rs7621329 of PIK3CA respectively). According to cumulative effect analysis of multiple SNPs, patients carrying 4 unfavorable genotypes exhibited more than a 3-fold increased risk of mortality. Finally, both EGF and VEGF expression levels significantly associated with patient mortality.

CONCLUSION

The genetic variants and expression levels of EGF and VEGF can serve as prognostic predictors in patients with advanced ESCC, and thus provide more information for optimizing personalized therapies for patients with ESCC.

Distinct ubiquitin binding modes exhibited by SH3 domains: molecular determinants and functional implications

SH3 domains constitute a new type of ubiquitin-binding domains. We previously showed that the third SH3 domain (SH3-C) of CD2AP binds ubiquitin in an alternative orientation. We have determined the structure of the complex between first CD2AP SH3 domain and ubiquitin and performed a structural and mutational analysis to decipher the determinants of the SH3-C binding mode to ubiquitin. We found that the Phe-to-Tyr mutation in CD2AP and in the homologous CIN85 SH3-C domain does not abrogate ubiquitin binding, in contrast to previous hypothesis and our findings for the first two CD2AP SH3 domains. The similar alternative binding mode of the SH3-C domains of these related adaptor proteins is characterised by a higher affinity to C-terminal extended ubiquitin molecules. We conclude that CD2AP/CIN85 SH3-C domain interaction with ubiquitin constitutes a new ubiquitin-binding mode involved in a different cellular function and thus changes the previously established mechanism of EGF-dependent CD2AP/CIN85 mono-ubiquitination.

Multimeric and differential binding of CIN85/CD2AP with two atypical proline-rich sequences from CD2 and Cbl-b*

The CD2AP (CD2-associated protein) and CIN85 (Cbl-interacting protein of 85 kDa) adaptor proteins each employ three Src homology 3 (SH3) domains to cluster protein partners and ensure efficient signal transduction and down-regulation of tyrosine kinase receptors. Using NMR, isothermal titration calorimetry and small-angle X-ray scattering methods, we have characterized several binding modes of the N-terminal SH3 domain (SH3A) of CD2AP and CIN85 with two natural atypical proline-rich regions in CD2 (cluster of differentiation 2) and Cbl-b (Casitas B-lineage lymphoma), and compared these data with previous studies and published crystal structures. Our experiments show that the CD2AP-SH3A domain forms a type II dimer with CD2 and both type I and type II dimeric complexes with Cbl-b. Like CD2AP, the CIN85-SH3A domain forms a type II complex with CD2, but a trimeric complex with Cbl-b, whereby the type I and II interactions take place at the same time. Together, these results explain how multiple interactions among similar SH3 domains and ligands produce a high degree of diversity in tyrosine kinase, cell adhesion or T-cell signaling pathways.

The switches.ELM resource: a compendium of conditional regulatory interaction interfaces

Short linear motifs (SLiMs) are protein interaction sites that play an important role in cell regulation by controlling protein activity, localization, and local abundance. The functionality of a SLiM can be modulated in a context-dependent manner to induce a gain, loss, or exchange of binding partners, which will affect the function of the SLiM-containing protein. As such, these conditional interactions underlie molecular decision-making in cell signaling. We identified multiple types of pre- and posttranslational switch mechanisms that can regulate the function of a SLiM and thereby control its interactions. The collected examples of experimentally characterized SLiM-based switch mechanisms were curated in the freely accessible switches.ELM resource (http://switches.elm.eu.org). On the basis of these examples, we defined and integrated rules to analyze SLiMs for putative regulatory switch mechanisms. We applied these rules to known validated SLiMs, providing evidence that more than half of these are likely to be pre- or posttranslationally regulated. In addition, we showed that posttranslationally modified sites are enriched around SLiMs, which enables cooperative and integrative regulation of protein interaction interfaces. We foresee switches.ELM complementing available resources to extend our knowledge of the molecular mechanisms underlying cell signaling.

Peptide-binding domains: are limp handshakes safest?

Interactions between short peptides within proteins and peptide-binding domains can trigger many important cell signaling processes, and their interactions are typically of modest affinity. A study showed that this modest affinity appears to be favored by evolution. They used phage display selection to discover "superbinder" Src Homology 2 (SH2) domains, which bound peptides with much stronger affinity than naturally occurring SH2 domains. These superbinder domains had strong biological effects, such as blocking cell signaling. Although the superbinders had higher affinity, this did not appear to reduce their specificity. In contrast, SH2-binding peptides from bacterial pathogens have evolved to exhibit promiscuity of binding to multiple SH2 domains, carried within effector proteins that subvert signaling upon entry into the mammalian cell. Because there are many potential peptide binders of the SH2 domain found in numerous human proteins, modest affinity not only may optimize transient signaling mediated by reversible interactions but also may minimize off-target deleterious binding effects. The stage is set for a more thorough evaluation of the specificity and off-target impact of both naturally occurring and artificial domains and peptides. This may help define both targets and reagents for therapeutic intervention in key signaling processes mediated by short peptides.

Mixed-lineage kinase 3 phosphorylates prolyl-isomerase Pin1 to regulate its nuclear translocation and cellular function

Nuclear protein peptidyl-prolyl isomerase Pin1-mediated prolyl isomerization is an essential and novel regulatory mechanism for protein phosphorylation. Therefore, tight regulation of Pin1 localization and catalytic activity is crucial for its normal nuclear functions. Pin1 is commonly dysregulated during oncogenesis and likely contributes to these pathologies; however, the mechanism(s) by which Pin1 catalytic activity and nuclear localization are increased is unknown. Here we demonstrate that mixed-lineage kinase 3 (MLK3), a MAP3K family member, phosphorylates Pin1 on a Ser138 site to increase its catalytic activity and nuclear translocation. This phosphorylation event drives the cell cycle and promotes cyclin D1 stability and centrosome amplification. Notably, Pin1 pSer138 is significantly up-regulated in breast tumors and is localized in the nucleus. These findings collectively suggest that the MLK3-Pin1 signaling cascade plays a critical role in regulating the cell cycle, centrosome numbers, and oncogenesis.

A dynamic view of domain-motif interactions

Many protein-protein interactions are mediated by domain-motif interaction, where a domain in one protein binds a short linear motif in its interacting partner. Such interactions are often involved in key cellular processes, necessitating their tight regulation. A common strategy of the cell to control protein function and interaction is by post-translational modifications of specific residues, especially phosphorylation. Indeed, there are motifs, such as SH2-binding motifs, in which motif phosphorylation is required for the domain-motif interaction. On the contrary, there are other examples where motif phosphorylation prevents the domain-motif interaction. Here we present a large-scale integrative analysis of experimental human data of domain-motif interactions and phosphorylation events, demonstrating an intriguing coupling between the two. We report such coupling for SH3, PDZ, SH2 and WW domains, where residue phosphorylation within or next to the motif is implied to be associated with switching on or off domain binding. For domains that require motif phosphorylation for binding, such as SH2 domains, we found coupled phosphorylation events other than the ones required for domain binding. Furthermore, we show that phosphorylation might function as a double switch, concurrently enabling interaction of the motif with one domain and disabling interaction with another domain. Evolutionary analysis shows that co-evolution of the motif and the proximal residues capable of phosphorylation predominates over other evolutionary scenarios, in which the motif appeared before the potentially phosphorylated residue, or vice versa. Our findings provide strengthening evidence for coupled interaction-regulation units, defined by a domain-binding motif and a phosphorylated residue.

Domain-motif interactions are instrumental for many central cellular processes, and are therefore tightly regulated. Phosphorylation events are known modulators of protein-protein interactions in general, including domain-motif interactions. Here, we addressed the association of phosphorylation and domain-motif interaction taking a motif-centred view. We integrated human domain-motif interaction and phosphorylation data for four representative domains (SH2, WW, SH3 and PDZ), and showed that the adjacency between phosphorylation and domain-motif interactions is extensive, suggesting interesting functional links between them that extend the classical and widely studied phospho-regulation of SH2 or WW domain-motif interactions. Furthermore, we show that such interaction-regulation units may function as double switches, concurrently enabling interaction of the motif with one domain and disabling interaction with another domain. These latter interaction-regulation units are more conserved in evolution than the individual units comprising them. Assuming that the four analyzed domain-motif interaction types are reliable representatives of such interactions, our results support the existence of units comprising motifs and associated phosphorylation sites, in which the regulation of domain-motif interaction is inherent.

A human sterile alpha motif domain polymerizome

The sterile alpha motif (SAM) domain is one of the most common protein modules found in eukaryotic genomes. Many SAM domains have been shown to form helical polymer structures suggesting that SAM modules can be used to create large protein complexes in the cell. Because many polymeric SAM domains form heterogenous and insoluble aggregates that are experimentally intractable when isolated, it is likely that many polymeric SAM domains have gone uncharacterized. We, therefore, developed a method to maintain polymeric SAM domains in a soluble form that allowed rapid screening for potential SAM polymers. SAM domains were expressed as fusions to a super-negatively charged green fluorescent protein (negGFP). The negGFP imparts three useful properties to the SAM domains: (1) the charge helps to maintain solubility; (2) the charge leads to reliable migration toward the cathode on native gels; and (3) the fluorescence emission allows visualization in crude extracts. Using the negGFP-SAM fusions, we screened a large library of human SAM domains for polymerization using a native gel screen. A selected set of hSAM domains were then purified and examined for true polymer formation by electron microscopy. In this manner, we identified a set of new potential SAM polymers: ANKS3, Atherin, BicaudalC1, Caskin1, Caskin2, Kazrin, L3MBTL3, L3MBTL4, LBP, LiprinB1, LiprinB2, SAMD8, SAMD9, and STIM2. While further characterization will be necessary to verify that the SAM domains identified here truly form polymers, our results provide a much stronger working hypothesis for a large number of proteins that was possible from sequence analysis alone.

Domain-domain interactions underlying herpesvirus-human protein-protein interaction networks

Protein-domains play an important role in mediating protein-protein interactions. Furthermore, the same domain-pairs mediate different interactions in different contexts and in various organisms, and therefore domain-pairs are considered as the building blocks of interactome networks. Here we extend these principles to the host-virus interface and find the domain-pairs that potentially mediate human-herpesvirus interactions. Notably, we find that the same domain-pairs used by other organisms for mediating their interactions underlie statistically significant fractions of human-virus protein inter-interaction networks. Our analysis shows that viral domains tend to interact with human domains that are hubs in the human domain-domain interaction network. This may enable the virus to easily interfere with a variety of mechanisms and processes involving various and different human proteins carrying the relevant hub domain. Comparative genomics analysis provides hints at a molecular mechanism by which the virus acquired some of its interacting domains from its human host.

Importance of CH/π hydrogen bonds in recognition of the core motif in proline-recognition domains: an ab initio fragment molecular orbital study

We examined CH/π hydrogen bonds in protein/ligand complexes involving at least one proline residue using the ab initio fragment molecular orbital (FMO) method and the program CHPI. FMO calculations were carried out at the Hartree-Fock (HF)/6-31G*, HF/6-31G**, second-order Møller-Plesset perturbation (MP2)/6-31G*, and MP2/6-31G** levels for three Src homology 3 (SH3) domains and five proline-recognition domains (PRDs) complexed with their corresponding ligand peptides. PRDs use a conserved set of aromatic residues to recognize proline-rich sequences of specific ligands. Many CH/π hydrogen bonds were identified in these complexes. CH/π hydrogen bonds occurred, in particular, in the central part of the proline-rich motifs. Our results suggest that CH/π hydrogen bonds are important in the recognition of SH3 and PRDs by their ligand peptides and play a vital role in the signal transduction system. Combined use of the FMO method and CHPI analysis is a valuable tool for the study of protein/protein and protein/ligand interactions and may be useful in rational drug design.

Lentiviral vector-mediated siRNA knockdown and concurrent rescue of Murine CIN85

RNA interference (RNAi), an evolutionarily conserved process of gene silencing, is now a common tool in gene functional studies. However, potential "off-target effects" is one of major concerns in RNAi experiment associated with false positive results. Apart from continuing improvement in small interfering RNA (siRNA) designs, there is no method available to prevent the generation of "off-target effects" resulted from possible identity between siRNA and abundant cellular mRNA transcripts. In the present study, we have developed a lentiviral vector-mediated system that allows efficient siRNA silencing and concurrent rescue of targeted genes. While this approach does not eliminate potential "off-target effects," concurrent rescue of a target gene allows a definite judgment with regard to a phenotype change, either from expected siRNA silencing or "off-target effects." The system has been validated with murine CIN85 gene and may be generally applicable in molecular studies from broad fields.

Regulation of myocardial growth and death by NADPH oxidase

The NADPH oxidases (Nox) are transmembrane proteins dedicated to producing reactive oxygen species (ROS), including superoxide and hydrogen peroxide, by transferring electrons from NAD(P)H to molecular oxygen. Nox2 and Nox4 are expressed in the heart and play an important role in mediating oxidative stress at baseline and under stress. Nox2 is primarily localized on the plasma membrane, whereas Nox4 is found primarily on intracellular membranes, on mitochondria, the endoplasmic reticulum or the nucleus. Although Nox2 plays an important role in mediating angiotensin II-induced cardiac hypertrophy, Nox4 mediates cardiac hypertrophy and heart failure in response to pressure overload. Expression of Nox4 is upregulated by hypertrophic stimuli, and Nox4 in mitochondria plays an essential role in mediating oxidative stress during pressure overload-induced cardiac hypertrophy. Upregulation of Nox4 induces oxidation of mitochondrial proteins, including aconitase, thereby causing mitochondrial dysfunction and myocardial cell death. On the other hand, Noxs also appear to mediate physiological functions, such as erythropoiesis and angiogenesis. In this review, we discuss the role of Noxs in mediating oxidative stress and both pathological and physiological functions of Noxs in the heart.

Biophysical characterization of recombinant proteins: a key to higher structural genomics success

Hundreds of genomes have been successfully sequenced to date, and the data are publicly available. At the same time, the advances in large-scale expression and purification of recombinant proteins have paved the way for structural genomics efforts. Frequently, however, little is known about newly expressed proteins calling for large-scale protein characterization to better understand their biochemical roles and to enable structure-function relationship studies. In the Structural Genomics Consortium (SGC), we have established a platform to characterize large numbers of purified proteins. This includes screening for ligands, enzyme assays, peptide arrays and peptide displacement in a 384-well format. In this review, we describe this platform in more detail and report on how our approach significantly increases the success rate for structure determination. Coupled with high-resolution X-ray crystallography and structure-guided methods, this platform can also be used toward the development of chemical probes through screening families of proteins against a variety of chemical series and focused chemical libraries.

Oxygen-mediated endocytosis in cancer

Solid tumours invariably exhibit regions of hypoxia and up-regulation of receptor tyrosine kinases (RTKs) that trigger multiple signal pathways, including those that govern cell proliferation, survival and motility, ultimately contributing to oncogenesis. Although past studies have shown hypoxia-dependent transcriptional and translational induction of several RTK expression and their respective ligands, recent evidence suggests that hypoxia regulates RTK signalling through endocytosis, a major deactivation pathway of RTKs. Hypoxia-mediated endocytosis is also thought to modulate the activity of a growing list of other membrane-associated proteins such as integrins and Na,K-ATPase. These recent discoveries underscore the emergence of endocytosis as an important hypoxia-mediated regulatory process in cancer.

Characterization of thyrotropin receptor antibody-induced signaling cascades

The TSH receptor (TSHR) is constitutively active and is further enhanced by TSH ligand binding or by stimulating TSHR antibodies (TSHR-Abs) as seen in Graves' disease. TSH is known to activate the thyroid epithelial cell via both Galphas-cAMP/protein kinase A/ERK and Galphaq-Akt/protein kinase C coupled signaling networks. The recent development of monoclonal antibodies to the TSHR has enabled us to investigate the hypothesis that different TSHR-Abs may have unique signaling imprints that differ from TSH ligand itself. We have, therefore, performed sequential studies, using rat thyrocytes (FRTL-5, passages 5-20) as targets, to examine the signaling pathways activated by a series of monoclonal TSHR-Abs in comparison with TSH itself. Activation of key signaling molecules was estimated by specific immunoblots and/or enzyme immunoassays. Continuing constitutive TSHR activity in thyroid cells, deprived of TSH and serum for 48 h, was demonstrated by pathway-specific chemical inhibition. Under our experimental conditions, TSH ligand and TSHR-stimulating antibodies activated both Galphas and Galphaq effectors. Importantly, some TSHR-blocking and TSHR-neutral antibodies were also able to generate signals, influencing primarily the Galphaq effectors and induced cell proliferation. Most strikingly, antibodies that used the Galphaq cascades used c-Raf-ERK-p90RSK as a unique signaling cascade not activated by TSH. Our study demonstrated that individual TSHR-Abs had unique molecular signatures which resulted in sequential preferences. Because downstream thyroid cell signaling by the TSHR is both ligand dependent and independent, this may explain why TSHR-Abs are able to have variable influences on thyroid cell biology.

An integrative domain-based approach to predicting protein-protein interactions

Protein-protein interactions (PPIs) are intrinsic to almost all cellular processes. Different computational methods offer new chances to study PPIs. To predict PPIs, while the integrative methods use multiple data sources instead of a single source, the domain-based methods often use only protein domain features. Integration of both protein domain features and genomic/proteomic features from multiple databases can more effectively predict PPIs. Moreover, it allows discovering the reciprocal relationships between PPIs and biological features of their interacting partners. We developed a novel integrative domain-based method for predicting PPIs using inductive logic programming (ILP). Two principal domain features used were domain fusions and domain-domain interactions (DDIs). Various relevant features of proteins were exploited from five popular genomic and proteomic databases. By integrating these features, we constructed biologically significant ILP background knowledge of more than 278,000 ground facts. The experimental results through multiple 10-fold cross-validations demonstrated that our method predicts PPIs better than other computational methods in terms of typical performance measures. The proposed ILP framework can be applied to predict DDIs with high sensitivity and specificity. The induced ILP rules gave us many interesting, biologically reciprocal relationships among PPIs, protein domains, and PPI-related genomic/proteomic features. Supplementary material is available at (http://www.jaist.ac.jp/~s0560205/PPIandDDI/).

Structure, regulation and evolution of Nox-family NADPH oxidases that produce reactive oxygen species

NADPH oxidases of the Nox family exist in various supergroups of eukaryotes but not in prokaryotes, and play crucial roles in a variety of biological processes, such as host defense, signal transduction, and hormone synthesis. In conjunction with NADPH oxidation, Nox enzymes reduce molecular oxygen to superoxide as a primary product, and this is further converted to various reactive oxygen species. The electron-transferring system in Nox is composed of the C-terminal cytoplasmic region homologous to the prokaryotic (and organelle) enzyme ferredoxin reductase and the N-terminal six transmembrane segments containing two hemes, a structure similar to that of cytochrome b of the mitochondrial bc(1) complex. During the course of eukaryote evolution, Nox enzymes have developed regulatory mechanisms, depending on their functions, by inserting a regulatory domain (or motif) into their own sequences or by obtaining a tightly associated protein as a regulatory subunit. For example, one to four Ca(2+)-binding EF-hand motifs are present at the N-termini in several subfamilies, such as the respiratory burst oxidase homolog (Rboh) subfamily in land plants (the supergroup Plantae), the NoxC subfamily in social amoebae (the Amoebozoa), and the Nox5 and dual oxidase (Duox) subfamilies in animals (the Opisthokonta), whereas an SH3 domain is inserted into the ferredoxin-NADP(+) reductase region of two Nox enzymes in Naegleria gruberi, a unicellular organism that belongs to the supergroup Excavata. Members of the Nox1-4 subfamily in animals form a stable heterodimer with the membrane protein p22(phox), which functions as a docking site for the SH3 domain-containing regulatory proteins p47(phox), p67(phox), and p40(phox); the small GTPase Rac binds to p67(phox) (or its homologous protein), which serves as a switch for Nox activation. Similarly, Rac activates the fungal NoxA via binding to the p67(phox)-like protein Nox regulator (NoxR). In plants, on the other hand, this GTPase directly interacts with the N-terminus of Rboh, leading to superoxide production. Here I describe the regulation of Nox-family oxidases on the basis of three-dimensional structures and evolutionary conservation.

Reaction-diffusion modeling ERK- and STAT-interaction dynamics

The modeling of the dynamics of interaction between ERK and STAT signaling pathways in the cell needs to establish the biochemical diagram of the corresponding proteins interactions as well as the corresponding reaction-diffusion scheme. Starting from the verbal description available in the literature of the cross talk between the two pathways, a simple diagram of interaction between ERK and STAT5a proteins is chosen to write corresponding kinetic equations. The dynamics of interaction is modeled in a form of two-dimensional nonlinear dynamical system for ERK-and STAT5a -protein concentrations. Then the spatial modeling of the interaction is accomplished by introducing an appropriate diffusion-reaction scheme. The obtained system of partial differential equations is analyzed and it is argued that the possibility of Turing bifurcation is presented by loss of stability of the homogeneous steady state and forms dissipative structures in the ERK and STAT interaction process. In these terms, a possible scaffolding effect in the protein interaction is related to the process of stabilization and destabilization of the dissipative structures (pattern formation) inherent to the model of ERK and STAT cross talk.

Interaction networks for systems biology

Cellular functions are almost always the result of the coordinated action of several proteins, interacting in protein complexes, pathways or networks. Progress made in devising suitable tools for analysis of protein-protein interactions, have recently made it possible to chart interaction networks on a large-scale. The aim of this review is to provide a short overview of the most promising contributions of interaction networks to human biology, structural biology and human genetics.

Domains mediate protein-protein interactions and nucleate protein assemblies

Cell physiology is governed by an intricate mesh of physical and functional links among proteins, nucleic acids and other metabolites. The recent information flood coming from large-scale genomic and proteomic approaches allows us to foresee the possibility of compiling an exhaustive list of the molecules present within a cell, enriched with quantitative information on concentration and cellular localization. Moreover, several high-throughput experimental and computational techniques have been devised to map all the protein interactions occurring in a living cell. So far, such maps have been drawn as graphs where nodes represent proteins and edges represent interactions. However, this representation does not take into account the intrinsically modular nature of proteins and thus fails in providing an effective description of the determinants of binding. Since proteins are composed of domains that often confer on proteins their binding capabilities, a more informative description of the interaction network would detail, for each pair of interacting proteins in the network, which domains mediate the binding. Understanding how protein domains combine to mediate protein interactions would allow one to add important features to the protein interaction network, making it possible to discriminate between simultaneously occurring and mutually exclusive interactions. This objective can be achieved by experimentally characterizing domain recognition specificity or by analyzing the frequency of co-occurring domains in proteins that do interact. Such approaches allow gaining insights on the topology of complexes with unknown three-dimensional structure, thus opening the prospect of adopting a more rational strategy in developing drugs designed to selectively target specific protein interactions.

The social network of a cell: recent advances in interactome mapping

Proteins very rarely act in isolation. Biomolecular interactions are central to all biological functions. In human, for example, interference with biomolecular networks often lead to disease. Protein-protein and protein-metabolite interactions have traditionally been studied one by one. Recently, significant progresses have been made in adapting suitable tools for the global analysis of biomolecular interactions. Here we review this suite of powerful technologies that enable an exponentially growing number of large-scale interaction datasets. These new technologies have already contributed to a more comprehensive cartography of several pathways relevant to human pathologies, offering a broader choice for therapeutic targets. Genome-wide scale analyses in model organisms reveal general organizational principles of eukaryotic proteomes. We also review the biochemical approaches that have been used in the past on a smaller scale for the quantification of the binding constant and the thermodynamics parameters governing biomolecular interaction. The adaptation of these technologies to the large-scale measurement of biomolecular interactions in (semi-)quantitative terms represents an important challenge.

Activation of growth factor receptors in esophageal cancer--implications for therapy

Esophageal cancer is a highly aggressive disease and is the seventh most common cause of cancer-related death in the western world. Worldwide, it ranks as the sixth most frequent cause of cancer death. Despite advances in surgical techniques and treatment, the prognosis of esophageal cancer remains poor, with very few long-term survivors. The need for novel strategies to detect esophageal cancer earlier and to improve current therapy is urgent. It is well established that growth factors and growth factor receptor-mediated signaling pathways are important components of the transformation process in many forms of cancer, including esophageal cancer. With the recent advances in drug development, there are emerging possibilities to use growth factor signal transduction pathways in targeted therapy. This review provides a summary of the role of growth factors and their receptors in esophageal cancer and discusses their potential roles as biomarkers and as targets in therapy.

Structure and Function of the PB1 Domain, a Protein Interaction Module Conserved in Animals, Fungi, Amoebas, and Plants

Proteins containing the PB1 domain, a protein interaction module conserved in animals, fungi, amoebas, and plants, participate in diverse biological processes. The PB1 domains adopt a ubiquitin-like beta-grasp fold, containing two alpha helices and a mixed five-stranded beta sheet, and are classified into groups harboring an acidic OPCA motif (type I), the invariant lysine residue on the first beta strand (type II), or both (type I/II). The OPCA motif of a type I PB1 domain forms salt bridges with basic residues, especially the conserved lysine, of a type II PB1 domain, thereby mediating a specific PB1-PB1 heterodimerization, whereas additional contacts contribute to high affinity and specificity of the modular interaction. The canonical PB1 dimerization is required for the formation of complexes between p40(phox) and p67(phox) (for activation of the NADPH oxidase crucial for mammalian host defense), between the scaffold Bem1 and the guanine nucleotide exchange factor Cdc24 (for polarity establishment in yeasts), and between the polarity protein Par6 and atypical protein kinase C (for cell polarization in animal cells), as well as for the interaction between the mitogen-activated protein kinase kinase kinases MEKK2 or MEKK3 and the downstream target mitogen-activated protein kinase kinase MEK5 (for early cardiovascular development in mammals). PB1 domains can also mediate interactions with other protein domains. For example, an intramolecular interaction between the PB1 and PX domains of p40(phox) regulates phagosomal targeting of the microbicidal NADPH oxidase; the PB1 domain of MEK5 is likely responsible for binding to the downstream kinase ERK5, which lacks a PB1 domain; and the scaffold protein Nbr1 associates through a PB1-containing region with titin, a sarcomere protein without a PB1 domain. This Review describes various aspects of PB1 domains at the molecular and cellular levels.