PI3K SH3 Domain Research Articles

Amyloid fibril formation kinetics of low-pH denatured bovine PI3K-SH3 monitored by three different NMR techniques.

Introduction: Misfolding of amyloidogenic proteins is a molecular hallmark of neurodegenerative diseases in humans. A detailed understanding of the underlying molecular mechanisms is mandatory for developing innovative therapeutic approaches. The bovine PI3K-SH3 domain has been a model system for aggregation and fibril formation. Methods: We monitored the fibril formation kinetics of low pH-denatured recombinantly expressed [U-13C, 15N] labeled bovine PI3K-SH3 by a combination of solution NMR, high-resolution magic angle spinning (HR-MAS) NMR and solid-state NMR spectra. Solution NMR offers the highest sensitivity and, therefore, allows for the recording of two-dimensional NMR spectra with residue-specific resolution for individual time points of the time series. However, it can only follow the decay of the aggregating monomeric species. In solution NMR, aggregation occurs under quiescent experimental conditions. Solid-state NMR has lower sensitivity and allows only for the recording of one-dimensional spectra during the time series. Conversely, solid-state NMR is the only technique to detect disappearing monomers and aggregated species in the same sample by alternatingly recoding scalar coupling and dipolar coupling (CP)-based spectra. HR-MAS NMR is used here as a hybrid method bridging solution and solid-state NMR. In solid-state NMR and HR-MAS NMR the sample is agitated due to magic angle spinning. Results: Good agreement of the decay rate constants of monomeric SH3, measured by the three different NMR methods, is observed. Moderate MAS up to 8kHz seems to influence the aggregation kinetics of seeded fibril formation only slightly. Therefore, under sufficient seeding (1% seeds used here), quiescent conditions (solution NMR), and agitated conditions deliver similar results, arguing against primary nucleation induced by MAS as a major contributor. Using solid-state NMR, we find that the amount of disappeared monomer corresponds approximately to the amount of aggregated species under the applied experimental conditions (250µM PI3K-SH3, pH 2.5, 298K, 1% seeds) and within the experimental error range. Data can be fitted by simple mono-exponential conversion kinetics, with lifetimes τ in the 14-38h range. Atomic force microscopy confirms that fibrils substantially grew in length during the aggregation experiment. This argues for fibril elongation as the dominant growth mechanism in fibril mass (followed by the CP-based solid-state NMR signal). Conclusion: We suggest a combined approach employing both solution NMR and solid-state NMR, back-to-back, on two aliquots of the same sample under seeding conditions as an additional approach to follow monomer depletion and growth of fibril mass simultaneously. Atomic force microscopy images confirm fibril elongation as a major contributor to the increase in fibril mass.

The Osmolyte TMAO Modulates Protein Folding Cooperativity by Altering Global Protein Stability

The folding of many globular proteins from the unfolded (U) to the native (N) state appears to be describable by a two-state N ↔ U model, which has led to the general belief that protein folding occurs in a highly cooperative manner. One reason for the widespread belief in "two-state folding" is that protein folding reactions are invariably studied by ensemble averaging probes and not by probes that can distinguish as well as quantify the multiple conformations that may be present. Consequently, how cooperativity is affected by protein stability, protein sequence, and solvent conditions is poorly understood. In this study, hydrogen exchange coupled to mass spectrometry (HX-MS) of the PI3K SH3 domain was carried out in the presence of a stabilizing osmolyte, trimethylamine N-oxide (TMAO). By showing that HX occurs under the EX1 regime even in the presence of 2 M TMAO, we were able to examine the temporal evolution of the populations of the different conformations present together. A strong link between protein folding cooperativity and protein stability is revealed. Increasing stability is accompanied by an increase in the ruggedness of the free energy landscape as well as diminished cooperativity; the number of amide sites simultaneously opening up their structure decreases with an increase in TMAO concentration. A comparison of the effect of TMAO to that of urea on the intrinsic dynamics of the PI3K SH3 domain indicates that TMAO counteracts the effect of urea not only on protein stability but also on protein folding cooperativity.

Modulation of the Extent of Cooperative Structural Change During Protein Folding by Chemical Denaturant.

Protein folding and unfolding reactions invariably appear to be highly cooperative reactions, but the structural and sequence determinants of cooperativity are poorly understood. Importantly, it is not known whether cooperative structural change occurs throughout the protein, or whether some parts change cooperatively and other parts change noncooperatively. In the current study, hydrogen exchange mass spectrometry has been used to show that the mechanism of unfolding of the PI3K SH3 domain is similar in the absence and presence of 5 M urea. The data are well described by a four state N ↔ IN ↔ I2 ↔ U model, in which structural changes occur noncooperatively during the N ↔ IN and IN ↔ I2 transitions, and occur cooperatively during the I2 ↔ U transition. The nSrc-loop and RT-loop, as well as β strands 4 and 5 undergo noncooperative unfolding, while β strands 1, 2, and 3 unfold cooperatively in the absence of urea. However, in the presence of 5 M urea, the unfolding of β strand 4 switches to become cooperative, leading to an increase in the extent of cooperative structural change. The current study highlights the relationship between protein stability and cooperativity, by showing how the extent of cooperativity can be varied, using chemical denaturant to alter protein stability.

Integrated in silico-in vitro characterization, identification and disruption of the intermolecular interaction between SH3 domain-containing protein kinases and human pituitary tumor-transforming gene 1.

The human pituitary tumor-transforming gene-1 (hPTTG1) has been found to be overexpressed in various cancers. Accumulated evidences implicate that some of protein kinases can specifically recognize two PXXP motifs at hPTTG1 C-terminus through their Src homology (SH3) domain and then phosphorylate the protein by their catalytic domain. Here, we integrate in silico analysis and in vitro assay to characterize the intermolecular interaction between the two hPTTG1 motif peptides 161LGPPSPVK168 (M1P) and 168KMPSPPWE175 (M2P) and the SH3 domains of Ser/Thr-specific protein kinases MAP3K and PI3K. It is identified that the two peptides bind to MAP3K SH3 domain with a moderate affinity, but cannot form stable complexes with PI3K SH3 domain. Long time scale molecular dynamics (MD) simulations reveal that the M1P peptide can fold into a standard poly-proline II helix that is bound in the peptide-binding pocket of MAP3K SH3 domain, while the M2P peptide gradually moves out of the pocket during the simulations and finally forms a weak, transient encounter complex with the domain. All these suggest that the MAP3K M1P site is a potential interacting partner of MAP3K SH3 domain, which may mediate the intermolecular recognition between hPTTG1 and MAP3K.

Critical Evaluation of the Two-State Model Describing the Equilibrium Unfolding of the PI3K SH3 Domain by Time-Resolved Fluorescence Resonance Energy Transfer

It appears that equilibrium unfolding transitions of many small proteins can be described as two-state transitions, because the probes commonly used to measure such transitions cannot detect the underlying heterogeneity inherent in protein folding and unfolding reactions. Time-resolved fluorescence or Forster resonance energy transfer (TRFRET) measurements have the potential to uncover such heterogeneity and to test the cooperativity of protein folding reactions. Here, TRFRET measurements have been used to study the equilibrium unfolding of the SH3 domain of PI3 kinase. The single tryptophan residue (W53) was used as the FRET donor, and a covalently attached thionitrobenzoate moiety at either of two sites (C17 and C70) was used as the FRET acceptor. The individual lifetime and amplitude components estimated from fitting the fluorescence decay kinetics to the sum of three or four exponentials were determined over a range of denaturant concentrations. The equilibrium unfolding transitions reported by these components were found to be noncoincident, suggesting the presence of multiple conformations in equilibrium during the course of unfolding. Fluorescence lifetime distributions were also generated by the model-free maximum entropy method of analysis. Different segments of the protein were found to show differences in the expansion of the native state at low denaturant concentrations, suggestive of gradual structural transitions. The unfolded protein was found to swell at increasingly high denaturant concentrations. The evolution of the fluorescence lifetime distributions with increasing denaturant concentration was also found to be incompatible with a two-state equilibrium unfolding model.

Correction to “Transient Helical Structure during PI3K and Fyn SH3 Domain Folding”

Correction to “Transient Helical Structure during PI3K and Fyn SH3 Domain Folding”

Molecular and structural characterization of the SH3 domain of AHI‐1 in regulation of cellular resistance of BCR‐ABL+ chronic myeloid leukemia cells to tyrosine kinase inhibitors

ABL tyrosine kinase inhibitor (TKI) therapy induces clinical remission in chronic myeloid leukemia (CML) patients but early relapses and later emergence of TKI-resistant disease remain problematic. We recently demonstrated that the AHI-1 oncogene physically interacts with BCR-ABL and JAK2 and mediates cellular resistance to TKI in CML stem/progenitor cells. We now show that deletion of the SH3 domain of AHI-1 significantly enhances apoptotic response of BCR-ABL(+) cells to TKIs compared to cells expressing full-length AHI-1. We have also discovered a novel interaction between AHI-1 and Dynamin-2, a GTPase, through the AHI-1 SH3 domain. The crystal structure of the AHI-1 SH3 domain at 1.53-Å resolution reveals that it adopts canonical SH3 folding, with the exception of an unusual C-terminal α helix. PD1R peptide, known to interact with the PI3K SH3 domain, was used to model the binding pattern between the AHI-1 SH3 domain and its ligands. These studies showed that an "Arg-Arg-Trp" stack may form within the binding interface, providing a potential target site for designing specific drugs. The crystal structure of the AHI-1 SH3 domain thus provides a valuable tool for identification of key interaction sites in regulation of drug resistance and for the development of small molecule inhibitors for CML.

Four-State Folding of a SH3 Domain: Salt-Induced Modulation of the Stabilities of the Intermediates and Native State

Unstable intermediates on the folding pathways of proteins can be stabilized sufficiently so that they accumulate to detectable extents by the addition of a suitable cosolute. Here, the effect of sodium sulfate (Na(2)SO(4)) on the folding of the SH3 domain of PI3 kinase was investigated in the presence of guanidine hydrochloride (GdnHCl) using intrinsic tyrosine fluorescence and 1-anilinonaphthalene-8-sulfonate (ANS) binding. The free energy of unfolding in water of the native state (N) increases linearly with Na(2)SO(4) concentration, indicating stabilization via the Hofmeister effect. The addition of 0.5 M Na(2)SO(4) causes accumulation of an early intermediate L, which manifests itself as (1) a sub-millisecond change in tyrosine and ANS fluorescence and (2) a curvature in the chevron plot. It is shown that L is a specific structural component of the initially collapsed ensemble. An intermediate, M, also accumulates in unfolding studies conducted in the presence of 0.5 M Na(2)SO(4) and manifests itself by causing a curvature in the unfolding arm of the chevron. M is shown to be a wet molten globule that binds to ANS under unfolding conditions and is stabilized to the same extent as N in the presence of Na(2)SO(4). A four-state U ↔ L ↔ M ↔ N scheme satisfactorily modeled the kinetic data. Thus, the folding of the PI3K SH3 domain in the presence of salt commences via the formation of a structured intermediate ensemble L, which accumulates before the rate-limiting step of folding. L subsequently proceeds to N via the late intermediate M that forms after the rate-limiting transition of folding.

Molecular and Structural Characterization of the SH3 Domain of AHI-1 in Regulation of Cellular Resistance of BCR-ABL+ Chronic Myeloid Leukemia Cells to Tyrosine Kinase Inhibitors

Abstract 966Chronic myeloid leukemia (CML) is a clonal multilineage myeloproliferative disorder characterized by the presence of the fusion gene BCR-ABL with increased tyrosine kinase activity. Imatinib mesylate (IM) and other BCR-ABL tyrosine kinase inhibitors (TKIs), including dasatinib (DA) and nilotinib (NL), have been introduced into clinical practice with remarkable effects on chronic phase CML. However, early relapses, acquired drug resistance, and persistence of leukemic stem cells remain problematic. Improved treatment approaches to target other key molecular elements active in CML stem/progenitor cells are needed. One candidate is AHI-1 (Abelson helper integration site 1), an oncogene that is highly deregulated in CML leukemic stem cells. It harbors two key domains, SH3 and WD40-repeat, which are known important mediators of protein-protein interactions. We recently demonstrated that AHI-1 physically interacts with BCR-ABL and JAK2 in CML cells and this interaction complex mediates transforming activity and TKI response/resistance of CML stem/progenitor cells. We have also shown that AHI-1 interacts independently with JAK2 and BCR-ABL via different binding sites to mediate their activities. In this study, we have characterized the biological and structural functions of the SH3 domain of AHI-1. To determine roles of the SH3 domain in regulation of cell proliferation and TKI response/resistance, several mutant forms, including SH3 domain deletion (SH3Δ), double WD40-repeat and SH3 domain deletion (SH3WD40Δ) and N-terminal deletion (N-terΔ, containing SH3 and WD40-repeat domains) were generated and stably transduced into BCR-ABL inducible BaF3 cells, in which the level of expression of BCR-ABL can be down-regulated by exposure to doxycycline. Overexpression of full-length Ahi-1 in BCR-ABL inducible cells resulted in fewer Annexin V+ apoptotic cells with doxycyclin (suppression of BCR-ABL) compared to BCR-ABL inducible cells (3 and 29% v.s.10 and 60% after 24 or 48 hours). Cells expressing the SH3Δ mutant and the SH3WD40D mutant displayed dramatically increased Annexin V+ cells (10, 77% and 34, 90% v.s.3 and 29%), while cells expressing the N-terΔ mutant had similar numbers of Annexin V+ cells compared to BCR-ABL inducible cells (6 and 41% v.s.10 and 60%). Similarly, BCR-ABL+ cells transduced with SH3Δ and SH3WD40D mutants displayed significantly increased apoptotic cells compared to cells transduced with full-length Ahi-1 in the presence of 2 μM IM (57, 87 vs. 26%), 2μM NL (65, 87 vs. 25%) and 150 nM DA (63, 96 vs. 34%) after 24 hour treatment. BCR-ABL+ cells transduced with the N-terδ mutant also showed more sensitivity to the drug treatments compared to the cells with the full-length Ahi-1(36% for IM, 40% for NL and 40% for DA), but with lower sensitivity than cells carrying the Ahi-1 SH3 domain deletion mutants, indicating that the SH3 domain of Ahi-1 plays a role in the mediation of TKI resistance. The crystal structure of the AHI-1 SH3 domain at 1.32-Å resolution revealed that the AHI-1SH3 domain adopts a canonical SH3 folding, but with an unusual C-terminal α helix. There are three large negatively charged patches, which are constructed by the n-Src loop, the end of the RT loop and the C-terminal helix, and this special feature may be involved in binding selectivity and specificity. PD1R peptide, known to interact with the PI3K SH3 domain, was used to model the binding pattern between AHI-1 SH3 domain and its ligands, and there may be formation of an “Arg-Arg-Trp” stack within the binding interface, which could be a targeting site for designing specific drugs. Moreover, using the AHI-1 SH3 domain as protein ‘bait’ in immunoprecipitation/mass spectrometry, Dynamin-2 was identified as a potential interacting partner of AHI-1; both AHI-1 and Dynamin-2 are involved in trafficking and signaling processes. In conclusion, the investigation of the structure of AHI-1 SH3 domain and its interacting proteins will thus provide invaluable insight in identification of key interaction sites in regulation of drug resistance and may be utilized for development of small molecule inhibitors for CML. Disclosures:No relevant conflicts of interest to declare.

Better biomolecule thermodynamics from kinetics

Protein stability is measured by denaturation: When solvent conditions are changed (e.g., temperature, denaturant concentration, or pH) the protein population switches between thermodynamic states. The resulting denaturation curves have baselines. If the baselines are steep, nonlinear, or incomplete, it becomes difficult to characterize protein denaturation. Baselines arise because the chromophore probing denaturation is sensitive to solvent conditions, or because the thermodynamic states evolve structurally when solvent conditions are changed, or because the barriers are very low (downhill folding). Kinetics can largely eliminate such baselines: Relaxation of chromophores, or within thermodynamic states, is much faster than the transition over activation barriers separating states. This separation of time scales disentangles population switching between states (desired signal) from chromophore or population relaxation within states (baselines). We derive simple formulas to extract unfolding thermodynamics from kinetics. The formulas are tested with model data and with a difficult experimental test case: the apparent two-state folder PI3K SH3 domain. Its melting temperature T(m) can be extracted reliably by our "thermodynamics from kinetics approach," even when conventional fitting is unreliable.

1P-038 Structural change of PI3K SH3 domain at acidic pH(Protein:Property, The 47th Annual Meeting of the Biophysical Society of Japan)

1P-038 Structural change of PI3K SH3 domain at acidic pH(Protein:Property, The 47th Annual Meeting of the Biophysical Society of Japan)

HCN, A Triple-Resonance NMR Technique for Selective Observation of Histidine and Tryptophan Side Chains in13C/15N-Labeled Proteins

HCN, a new 3D NMR technique for stepwise coherence transfer from1H to13C to15N and reverse through direct spin couplings1JCHand1JCN, is presented as a method for detection and assignment of histidine and tryptophan side-chain1H,13C, and15N resonances in uniformly13C/15N-labeled proteins. Product-operator calculations of cross-peak volumes vs adjustable delay τ3were employed for determination of optimal τ3. For the phosphatidylinositol 3-kinase (PI3K SH3 domain, MW = 9.6 kD) at pH 6, H(C)N, the1H/15N projection, produced observable cross peaks within 20 min. and was completely selective for the single tryptophan and single histidine. The 3D HCN experiment yielded well-defined cross peaks in 20 h for the13C/15N-labeled origin-specific DNA binding domain from simian virus 40 T-antigen (T-ag-OBD131–259, MW = 15.4 kD) at pH 5.5. Resonances from all six histidines in T-ag-OBD were observed, and 11 of the 121H and13C chemical shifts and 10 of the 1215N chemical shifts were determined. The13C dimension proved essential in assignment of the multiply overlapping1H and15N resonances. From the spectra recorded at a single pH, three of the imidazoles were essentially neutral and the other three were partially protonated (22–37%). HCN yielded strong cross peaks after 18 h on a 2.0 mMsample of phenylmethanesulfonyl fluoride (PMSF)-inhibited α-lytic protease (MW = 19.8 kD) at pH 4.4. No spectra have been obtained, however, of native or boronic acid-inhibited α-lytic protease after 18 h at various temperatures ranging from 5 to 55°C, probably due to efficient relaxation of active-site imidazole1H and/or15N nuclei.

1H and 15N assignments and secondary structure of the PI3K SH3 domain

The sequential 1H and 15N assignments of the SH3 domain of human phosphatidyl inositol 3'-kinase (PI3K) were determined by a combination of homonuclear and heteronuclear NMR experiments. With the exception of several protons belonging to lysine and proline residues, all proton and proton-bearing amide nitrogen resonances were assigned. Based on the sequential nuclear Overhauser effects (NOEs), 3 J NH-CαH coupling constants and locations of slowly exchanging amide protons, we determined that the secondary structures of the protein consists of six β-strands, two β-turns and four short helices. Additional long range NOEs indicate that these β-strands form two antiparallel β-sheets. The topology of secondary structural elements of the PI3K SH3 domain is similar to those of the SH3 domains from c-Src and α-spectrin, suggesting that the SH3 family has a common tertiary structural motif.