Applied Surface Plasmon Resonance Research Articles

Antibody Profiling: Kinetics with Native Biomarkers for Diagnostic Assay and Drug Developments.

Despite remarkable progress in applied Surface Plasmon Resonance (SPR)-based methods, concise monitoring of kinetic properties for native biomarkers from patient samples is still lacking. Not only are low concentrations of native targets in patient samples, often in the pM range, a limiting and challenging factor, but body fluids as complex matrices furthermore complicate measurements. The here-described method enables the determination of kinetic constants and resulting affinities for native antigens from patients' cerebrospinal fluid (CSF) and sera binding to antibodies. Using a significantly extended target-enrichment step, we modified a common sandwich-assay protocol, based on a primary and secondary antibody. We successfully analyze antibody kinetics of native targets from a variety of origins, with consistent results, independent of their source. Moreover, native neurofilament light chain (NFL) was investigated as an exemplary biomarker. Obtained data reveal antibodies recognizing recombinant NFL with high affinities, while showing no, or only significantly weakened binding to native NFL. The indicated differences for recombinant vs. native material demonstrate another beneficial application. Our assay is highly suitable for gaining valuable insights into characteristics of native biomarkers, thus impacting on the binder development of diagnostic reagents or pharmaceutical drugs.

Method for screening influenza neutralizing antibodies in crude human plasma and its derivatives using SPR

We applied Surface Plasmon Resonance (SPR) technology to develop a method for potency screening and quantification of anti-influenza antibodies in minimally processed human plasma samples and intravenous immunoglobulin (IGIV) products. We found that specific antibodies in human plasma or IGIV capable of inhibiting binding of influenza hemagglutinin to receptor-analogous glycans do so in concentration-dependent manner. We ranked the inhibitory activity of plasma samples from multiple donors and found a good correlation (r = 0.87) of SPR assay measurements and conventional hemagglutination inhibition (HAI) assay results. This method was also applied to screen for specific anti-influenza antibodies in IGIV lots manufactured pre- and post-2009 H1N1 pandemic. The SPR method was also applied to study binding inhibition of the intact A/California/04/2009 H1N1 and B/Victoria/504/2000 influenza viruses to α2,6 or α2,3-linked synthetic glycans. In contrast to recombinant H1 hemagglutinin, which was found to interact primarily with α2,6-linked terminal sialic acids, intact H1N1 or influenza B virus recognized both types of receptor analogs with different observed dissociation rates and the inhibitory activity of plasma antibodies was dependent on the type of sialic acid link. The SPR method can provide a high-throughput, time-saving and semi-automated alternative to conventional assays such as HAI or microneutralization in situations where screening of large numbers of plasma donations to identify high titer units is needed to product highly potent immunoglobulins.

Vertebrate extracellular matrix protein hemicentin-1 interacts physically and genetically with basement membrane protein nidogen-2

Hemicentins are large proteins of the extracellular matrix that belong to the fibulin family and play pivotal roles during development and homeostasis of a variety of invertebrate and vertebrate tissues. However, bona fide interaction partners of hemicentins have not been described as yet. Here, applying surface plasmon resonance spectroscopy and co-immunoprecipitation, we identify the basement membrane protein nidogen-2 (NID2) as a binding partner of mouse and zebrafish hemicentin-1 (HMCN1), in line with the formerly described essential role of mouse HMCN1 in basement membrane integrity. We show that HMCN1 binds to the same protein domain of NID2 (G3) as formerly shown for laminins, but with an approximately 3.5-fold lower affinity and in a competitive manner. Furthermore, immunofluorescence and immunogold labeling revealed that HMCN1/Hmcn1 is localized close to basement membranes and in partial overlap with NID2/Nid2a in different tissues of mouse and zebrafish. Genetic knockout and antisense-mediated knockdown studies in zebrafish further show that loss of Nid2a leads to similar defects in fin fold morphogenesis as the loss of Laminin-α5 (Lama5) or Hmcn1. Finally, combined partial loss-of-function studies indicated that nid2a genetically interacts with both hmcn1 and lama5. Together, these findings suggest that despite their mutually exclusive physical binding, hemicentins, nidogens, and laminins tightly cooperate and support each other during formation, maintenance, and function of basement membranes to confer tissue linkage.

The Natural Compound Oblongifolin C Exhibits Anticancer Activity by Inhibiting HSPA8 and Cathepsin B In Vitro.

PPAPs (Polycyclic polyprenylated acylphloroglucinols) are a class of compounds with diverse bioactivities, including anticancer effects. Oblongifolin C (OC) is a PPAP isolated from the plant of Garcinia yunnanensis Hu. We previously discovered that OC induces apoptosis, inhibits autophagic flux, and attenuates metastasis in cancer cells. However, the protein targets and the detailed mechanism of action of OC remain unclear. To identify protein targets of OC, a non-labeled protein fishing assay was performed, and it was found that OC may interact with several proteins, including the heat shock 70 kDa protein 8 (HSPA8). Expanding on our previous studies on protein cathepsin B, this current study applied Surface Plasmon Resonance (SPR) and Isothermal Titration Calorimetry (ITC) to confirm the potential binding affinity between OC and two protein targets. This study highlights the inhibitory effect of OC on HSPA8 in cancer cells under heat shock stress, by specifically inhibiting the translocation of HSPA8. OC also enhanced the interaction between HSPA8, HSP90, and p53, upregulated the expression of p53 and significantly promoted apoptosis in cisplatin-treated cells. Additionally, a flow cytometry assay detected that OC sped up the apoptosis rate in HSPA8 knockdown A549 cells, while overexpression of HSPA8 delayed the OC-induced apoptosis rate. In summary, our results reveal that OC potentially interacts with HSPA8 and cathepsin B and inhibits HSPA8 nuclear translocation and cathepsin B activities, altogether suggesting the potential of OC to be developed as an anticancer drug.

Flow cytometry in rapid mycotoxin testing.

Flow cytometry in rapid mycotoxin testing.

Surface Plasmon Resonance Analysis of Histidine-Tagged F1-ATPase Surface Adsorption

Studies of the rotational activity of the enzymatic core (α3β3γ) of the F1-ATPase motor protein have relied on binding the enzyme to NTA-coated glass surfaces via polyhistidine tags engineered into the C-termini of each of the three α or β subunits. Those studies revealed the rotational motion of the central γ subunit by monitoring the motion of attached micron-long actin filaments or spherical nanoparticles. However, only a small percentage of the attached filaments or particles were observed to rotate, likely due, at least in part, to non-uniform surface attachment of the motor proteins. In this study, we have applied surface plasmon resonance to monitor the kinetics and affinity of binding of the His-tagged motor protein to NTA-coated gold sensor surfaces. The binding data, when fit to a heterogeneous binding model, exhibit two sets of adsorption–desorption rate constants with two dissociation constants of 4.0 × 10−9 M and 8.6 × 10−11 M for 6His-α3β3γ binding to the nickel ion-activated NTA surface. The data are consistent with mixed attachment of the protein via two (bimodal) and three (trimodal) NTA/Ni2+-His-tag interactions, respectively, with the less stable bimodal interaction dominating. The results provide a partial explanation for the low number of surface-attached F1 motors previously observed in rotation studies and suggest alternative approaches to uniform F1 motor surface attachment for future fabrication of motor-based nanobiodevices and materials.

Identification of Chondroitin Sulfate Linkage Region Glycopeptides Reveals Prohormones as a Novel Class of Proteoglycans

Vertebrates produce various chondroitin sulfate proteoglycans (CSPGs) that are important structural components of cartilage and other connective tissues. CSPGs also contribute to the regulation of more specialized processes such as neurogenesis and angiogenesis. Although many aspects of CSPGs have been studied extensively, little is known of where the CS chains are attached on the core proteins and so far, only a limited number of CSPGs have been identified. Obtaining global information on glycan structures and attachment sites would contribute to our understanding of the complex proteoglycan structures and may also assist in assigning CSPG specific functions. In the present work, we have developed a glycoproteomics approach that characterizes CS linkage regions, attachment sites, and identities of core proteins. CSPGs were enriched from human urine and cerebrospinal fluid samples by strong-anion-exchange chromatography, digested with chondroitinase ABC, a specific CS-lyase used to reduce the CS chain lengths and subsequently analyzed by nLC-MS/MS with a novel glycopeptide search algorithm. The protocol enabled the identification of 13 novel CSPGs, in addition to 13 previously established CSPGs, demonstrating that this approach can be routinely used to characterize CSPGs in complex human samples. Surprisingly, five of the identified CSPGs are traditionally defined as prohormones (cholecystokinin, chromogranin A, neuropeptide W, secretogranin-1, and secretogranin-3), typically stored and secreted from granules of endocrine cells. We hypothesized that the CS side chain may influence the assembly and structural organization of secretory granules and applied surface plasmon resonance spectroscopy to show that CS actually promotes the assembly of chromogranin A core proteins in vitro. This activity required mild acidic pH and suggests that the CS-side chains may also influence the self-assembly of chromogranin A in vivo giving a possible explanation to previous observations that chromogranin A has an inherent property to assemble in the acidic milieu of secretory granules.

Characterization of cross-reactive norovirus-specific monoclonal antibodies.

Noroviruses (NoVs) commonly cause acute gastroenteritis outbreaks. Broadly reactive diagnostic assays are essential for rapid detection of NoV infections. We previously generated a panel of broadly reactive monoclonal antibodies (MAbs). We characterized MAb reactivities by use of virus-like particles (VLPs) from 16 different NoV genotypes (6 from genogroup I [GI], 9 from GII, and 1 from GIV) coating a microtiter plate (direct enzyme-linked immunosorbent assay [ELISA]) and by Western blotting. MAbs were genotype specific or recognized multiple genotypes within a genogroup and between genogroups. We next applied surface plasmon resonance (SPR) analysis to measure MAb dissociation constants (Kd) as a surrogate for binding affinity; a Kd level of <10 nM was regarded as indicating strong binding. Some MAbs did not interact with the VLPs by SPR analysis. To further assess this lack of MAb-VLP interaction, the MAbs were evaluated for the ability to identify NoV VLPs in a capture ELISA. Those MAbs for which a Kd could not be measured by SPR analysis also failed to capture the NoV VLPs; in contrast, those with a measurable Kd gave a positive signal in the capture ELISA. Thus, some broadly cross-reactive epitopes in the VP1 protruding domain may be partially masked on intact particles. One MAb, NV23, was able to detect genogroup I, II, and IV VLPs from 16 genotypes tested by sandwich ELISA, and it successfully detected NoVs in stool samples positive by real-time reverse transcription-PCR when the threshold cycle (CT) value was <31. Biochemical analyses of MAb reactivity, including SPR analysis, identified NV23 as a broadly reactive ligand for application in norovirus diagnostic assays.

Dynamic identification of H2 epitopes from Leishmania (Leishmania) amazonensis cysteine proteinase B with potential immune activity during murine infection

Peptides from the COOH-terminal extension of cysteine proteinase B from Leishmania (Leishmania) amazonensis (cyspep) can modulate immune responses in vertebrate hosts. With this hypothesis as base, we used the online analysis tool SYFPEITHI to predict seven epitopes from this region with potential to bind H2 proteins. We performed proliferation tests and quantified reactive T lymphocytes applying a cytometry analysis, using samples from draining lymph node of lesions from L. (L.) amazonensis-infected mice. To define reactivity of T cells, we used complexes of DimerX (H2 D(b):Ig and H2 L(d):Ig) and the putative epitopes. Additionally, we applied surface plasmon resonance to verify real time interactions between the putative epitopes and DimerX proteins. Five peptides induced blastogenesis in BALB/c cells, while only two presented the same property in C57BL/6 mouse cells. In addition, our data indicate the existence of CD8+ T lymphocyte populations able to recognize each tested peptide in both murine strains. We observed an overlapping of results between the peptides that induced lymphocyte proliferation and those capable of binding to the DimerX in the surface plasmon resonance assays thus indicating that using these recombinant proteins in biosensing analyses is a promising tool to study real time molecular interactions in the context of major histocompatibility complex epitopes. The data gathered in this study reinforce the hypothesis that cyspep-derived peptides are important factors in the murine host infection by L. (L.) amazonensis.

Synthetic Oligonucleotide Probes for Detection of Autoimmune Antibodies

In this review, applications of synthetic oligonucleotide probes in diagnostics and studies of autoimmune antibodies against double-stranded DNA (anti-dsDNA) are described. As outlined herein, synthetic oligonucleotides and monoclonal antibodies provide appealing opportunities to develop standard simple assays for detection of antidsDNAs. Recent examples of anti-dsDNA detection using synthetic nucleic acid antigens include those applying surface plasmon resonance (SPR), antibody microarrays and homogeneous, or all-in-solution, detection with fluorescently-labelled probes. Since sequences of the applied nucleic acid antigens and monoclonal antibodies are known, the major benefit of these assays is the ability for the first time to clearly define the structural factors that govern the formation and stability of anti-dsDNA complexes. This is an essential first step toward understanding immune-complex mediated tissue injury in autoimmune conditions such as systemic lupus erythematosus (SLE) and arthritis, which involve production of pathogenic anti-dsDNAs. Moreover, synthetic nucleic acids and monoclonal antibodies have been demonstrated as key tools for the development of novel nucleic acid sensors for serotyping, along with studies of specificity and avidity of the antibody-dsDNA binding process. Among other antigens, fluorescent oligonucleotides prepared by click chemistry between novel alkyne-modified locked nucleic acid (LNA) strands and a series of fluorescent azides are proved to be very promising tools for efficient homogeneous detection of anti-dsDNAs.

HIV-2 and SIVmac Accessory Virulence Factor Vpx Down-regulates SAMHD1 Enzyme Catalysis Prior to Proteasome-dependent Degradation

SAMHD1, a dGTP-regulated deoxyribonucleoside triphosphate (dNTP) triphosphohydrolase, down-regulates dNTP pools in terminally differentiated and quiescent cells, thereby inhibiting HIV-1 infection at the reverse transcription step. HIV-2 and simian immunodeficiency virus (SIV) counteract this restriction via a virion-associated virulence accessory factor, Vpx (Vpr in some SIVs), which loads SAMHD1 onto CRL4-DCAF1 E3 ubiquitin ligase for polyubiquitination, programming it for proteasome-dependent degradation. However, the detailed molecular mechanisms of SAMHD1 recruitment to the E3 ligase have not been defined. Further, whether divergent, orthologous Vpx proteins, encoded by distinct HIV/SIV strains, bind SAMHD1 in a similar manner, at a molecular level, is not known. We applied surface plasmon resonance analysis to assess the requirements for and kinetics of binding between various primate SAMHD1 proteins and Vpx proteins from SIV or HIV-2 strains. Our data indicate that Vpx proteins, bound to DCAF1, interface with the C terminus of primate SAMHD1 proteins with nanomolar affinity, manifested by rapid association and slow dissociation. Further, we provide evidence that Vpx binding to SAMHD1 inhibits its catalytic activity and induces disassembly of a dGTP-dependent oligomer. Our studies reveal a previously unrecognized biochemical mechanism of Vpx-mediated SAMHD1 inhibition: direct down-modulation of its catalytic activity, mediated by the same binding event that leads to SAMHD1 recruitment to the E3 ubiquitin ligase for proteasome-dependent degradation.

The Peripheral Binding of 14-3-3γ to Membranes Involves Isoform-Specific Histidine Residues

Mammalian 14-3-3 protein scaffolds include seven conserved isoforms that bind numerous phosphorylated protein partners and regulate many cellular processes. Some 14-3-3-isoforms, notably γ, have elevated affinity for membranes, which might contribute to modulate the subcellular localization of the partners and substantiate the importance of investigating molecular mechanisms of membrane interaction. By applying surface plasmon resonance we here show that the binding to phospholipid bilayers is stimulated when 14-3-3γ is complexed with its partner, a peptide corresponding to the Ser19-phosphorylated N-terminal region of tyrosine hydroxylase. Moreover, membrane interaction is dependent on salts of kosmotropic ions, which also stabilize 14-3-3γ. Electrostatic analysis of available crystal structures of γ and of the non-membrane-binding ζ-isoform, complemented with molecular dynamics simulations, indicate that the electrostatic potential distribution of phosphopeptide-bound 14-3-3γ is optimal for interaction with the membrane through amphipathic helices at the N-terminal dimerization region. In addition, His158, and especially His195, both specific to 14-3-3γ and located at the convex lateral side, appeared to be pivotal for the ligand induced membrane interaction, as corroborated by site-directed mutagenesis. The participation of these histidine residues might be associated to their increased protonation upon membrane binding. Overall, these results reveal membrane-targeting motifs and give insights on mechanisms that furnish the 14-3-3γ scaffold with the capacity for tuned shuffling from soluble to membrane-bound states.

Design of ultra-sensitive biosensor applying surface plasmon resonance to a triangular resonator

We propose an ultra-sensitive integrated photonic sensor structure using an InP-based triangular resonator, in which a surface plasmon resonance (SPR) gold film is applied on a total internal reflection mirror. We have analyzed and optimized the triangular resonator sensor structure with an extremely small SPR mirror sensing area of 3.3 × 0.35 μm2. Due to the large phase shift in the SPR mirror, a significantly enhanced sensitivity of 930 nm/RIU (refractive index unit) and the maximum peak shift of half free spectral range have been obtained at the SPR angle of 24.125° with Au thickness of 33.4 nm for the change of the refractive index Δn = 1x10(-3). This value is larger than the previous largest value in micro resonator-type biosensors. Moreover, the proposed triangular resonator sensor can be easily made in a micro structure with optical source integration.

Multivalent Binding of Carbohydrates by the Human α-Defensin, HD5

Four of the six human alpha-defensins (human neutrophil peptides 1-3 and human alpha-defensin 5; HD5) have a lectin-like ability to bind glycosylated proteins. Using HD5 as a model, we applied surface plasmon resonance techniques to gain insights into this property. HD5 bound natural glycoproteins > neoglycoproteins based on BSA > nonglycosylated BSA >> free sugars. The affinity of HD5 for simple sugars covalently bound to BSA was orders of magnitude greater than its affinity for the same sugars in solution. The affinity of HD5 for protein-bound carbohydrates resulted from multivalent interactions which may also involve noncarbohydrate residues of the proteins. HD5 showed concentration-dependent self-association that began at submicromolar concentrations and proceeded to dimer and tetramer formation at concentrations below 5 microM. The (R9A, R28A) and (R13A, R32A) analogs of HD5 showed greatly reduced self-association as well as minimal binding to BSA and to BSA-affixed sugars. From this and other evidence, we conclude that the extensive binding of HD5 to (neo)glycoproteins results from multivalent nonspecific interactions of individual HD5 molecules with carbohydrate and noncarbohydrate moieties of the target molecule and that the primary binding events are magnified and enhanced by subsequent in situ assembly and oligomerization of HD5. Self-association and multivalent binding may play integral roles in the ability of HD5 to protect against infections caused by viruses and other infectious agents.

Surface Plasmon Resonance Study of Cooperative Interactions of Estrogen Receptor α and Transcriptional Factor Sp1 with Composite DNA Elements

We have applied surface plasmon resonance (SPR) spectroscopy to study the cooperative interactions of estrogen receptor alpha (ERalpha) and transcription factor Sp1 with a composite DNA element, containing an estrogen response element (ERE) half-site upstream of two adjacent Sp1 sites (+571 ERE/Sp1 composite site in promoter A of the human PR gene). Using nuclear extracts of MCF-7 breast cancer cells as sample, we have shown that Sp1 is associated with Sp1-binding sites only, whereas ERalpha can be recruited to DNA both through direct binding to the ERE half-site and/or through protein-protein interactions with DNA-bound Sp1. The ERE half-site and the proximal Sp1 site are only 4 bp apart, and our data suggests that one transcription factor bound to DNA constitutes a sterical hindrance of the accessibility of the binding site for the other transcription factor. Our data confirms previous observations that ERalpha increases the amount of Sp1 recruited to the composite binding site in a dose-dependent manner. Using recombinant proteins, we have unambiguously proved the formation of a ternary complex of ERalpha/Sp1-composite DNA, for which previously published electrophoretic mobility shift assay (EMSA) results are contradictive. With this study, we have demonstrated that the solid-liquid-phase SPR assay is a powerful alternative for studying multiprotein-DNA interactions and is superior to the EMSA experiments as it is capable of real-time measurements, can quantify the amount of protein bound, and can capture transient and weak binding interactions. The comprehensive characterization of the synergistic interactions between ERalpha-DNA, Sp1-DNA, and ERalpha-Sp1 contributes to the understanding of how ERalpha and Sp1 influence and activate gene transcription.

Applying Surface Plasmon Resonance to Monitor the IgE-Mediated Activation of Human Basophils

The histamine releasing test which detects histamine released from basophils in vitro is safe, sensitive and widely used for clinical examination in the field of allergy. However, basophils of certain individuals do not release histamine, because of dysfunctions in their intracellular signal transduction (non-responder). To overcome potential shortcomings of the histamine releasing test, we applied surface plasmon resonance (SPR) to detect the activation of basophils. Basophils of patients with allergy, and those of non-allergic volunteers were isolated from peripheral blood. A batch of basophils obtained from a healthy volunteer was treated with lactic acid and IgE of a patient with atopic dermatitis in order to replace their endogenous IgE. They were fixed on the sensor chip of the SPR apparatus, pretreated with or without various inhibitors for intracellular signal transduction, and exposed to the antigens or anti-IgE antibody. When basophils were sensitized with antigen specific IgE, they immediately caused the increase of resonance angle (AR) in response to either anti-IgE antibody or corresponding antigens, even when they did not release histamine. Moreover, the dose dependent reactions of basophils were reflected by the increase of AR as well as the release of histamine. The increase of AR in response to anti-IgE antibody was reduced by pre-treatment of basophils with inhibitors for intracellular signal transduction, but not more than the level for histamine release. SPR biosensors may be superior to the histamine release test for studying functions of human basophils including those not releasing histamine.

Surface plasmon resonance spectroscopy study of interfacial binding of thrombin to antithrombin DNA aptamers

We have applied surface plasmon resonance (SPR) spectroscopy, in combination with one-step direct binding, competition, and sandwiched assay schemes, to study thrombin binding to its DNA aptamers, with the aim to further the understanding of their interfacial binding characteristics. Using a 15-mer aptamer that binds thrombin primarily at the fibrinogen-recognition exosite as a model, we have demonstrated that introducing a DNA spacer in the aptamer enhances thrombin-binding capacity and stability, as similarly reported for hydrocarbon linkers. The bindings are aptamer surface coverage and salt concentration dependent. When free aptamers or DNA sequences complementary to the immobilized aptamer are applied after the formation of thrombin/aptamer complexes, bound thrombin is displaced to a certain extent, depending on the stability of the complexes formed under different conditions. When the 29-mer aptamer (specific to thrombin's heparin-binding exosite) is immobilized on the surface, its affinity to thrombin appears to be lower than the immobilized 15-mer aptamer, although the 29-mer aptamer is known to have a higher affinity in the solution phase. These findings underline the importance of aptamers' ability to fold into intermolecular structures and their accessibility for target capture. Using a sandwiched assay scheme followed by an additional signaling step involving biotin–streptavidin chemistry, we have observed the simultaneous binding of the 15- and 29-mer aptamers to thrombin protein at different exosites and have found that one aptamer depletes thrombin's affinity to the other when they bind together. We believe that these findings are invaluable for developing DNA aptamer-based biochips and biosensors.

Imaging of electrochemical enzyme sensor on gold electrode using surface plasmon resonance

Three types of imaging, namely layer structure, electrochemical reaction, and enzyme sensor response, were achieved by applying surface plasmon resonance (SPR) measurement to an electrochemical biosensor. We constructed glucose oxidase based mediator type sensors on a gold electrode by spotting the mediator that contained horseradish peroxidase and spin coating the glucose oxidase film. The layer structure of the sensor was imaged by means of angle scanning SPR measurement. The single sensor spot (about 1 mm in diameter) consisted of about 100×100 pixels and its spatial structure was imaged. The multilayer structure of the enzyme sensor had a complex reflectance–incident angle curve and this required us to choose a suitable incident angle for mapping the redox state. We chose an incident angle that provided the most significant reflection intensity difference by using data obtained from two angle scanning SPR measurements at different electrode potentials. At this incident angle, we controlled the electrochemical states of the spotted mediator in cyclic voltammetry and imaged the degree to which the charged site density changed. Finally, we mapped the enzymatic activity around the mediator spot by the enzymatic reoxidation of pre-reduced mediator in the presence of glucose.

Determinants of Ligand Specificity in Groups I and IV WW Domains as Studied by Surface Plasmon Resonance and Model Building

WW domains are universal protein modules for binding Pro-rich ligands. They are classified into four groups according to their binding specificity. Arg-14 and Arg-17, on the WW domain of Pin1, are thought to be important for the binding of Group IV ligands that have (Ser(P)/Thr(P))-Pro sequences. We have applied surface plasmon resonance to determine the ligand specificity of several WW domains containing Arg-14. Among these WW domains, Rsp5.2 and mNedd4.3 bound only to the Group I ligand containing Pro-Pro-Xaa-Tyr with K(D) values of 11 and 55 microm, respectively. The WW domains of hPin1, Caenorhabditis elegans Pin1 homologue (Y110), PinA, and SspI bound to Group IV ligands with K(D) values ranging from 22 to 700 microm. PinA and SspI do not have Arg-17, unlike Pin1 and Y110. The modeled structures of the WW domains of PinA and SspI revealed that the structure and the network of hydrogen bonds of Loop I, which are also formed in Pin1 and Y110, are conserved. We propose that this configuration of Loop I (referred to as the "p patch") is necessary for binding Group IV ligands and that it can be used to predict the specificity and functions of other WW domains.