Improving SH3 domain ligand selectivity using a non-natural scaffold

BACKGROUND

Src homology 3 (SH3) domains bind sequences bearing the consensus motif PxxP (where P is proline and x is any amino acid), wherein domain specificity is mediated largely by sequences flanking the PxxP core. This specificity is limited, however, as most SH3 domains show high ligand cross-reactivity. We have recently shown that diverse N-substituted residues (peptoids) can replace the prolines in the PxxP motif, yielding a new source of ligand specificity.

RESULTS

We have tested the effects of combining multiple peptoid substitutions with specific flanking sequences on ligand affinity and specificity. We show that by varying these different elements, a ligand can be selectively tuned to target a single SH3 domain in a test set. In addition, we show that by making multiple peptoid substitutions, high-affinity ligands can be generated that completely lack the canonical PxxP motif. The resulting ligands can potently disrupt natural SH3-mediated interactions.

CONCLUSIONS

Peptide-peptoid hybrid scaffolds yield SH3 ligands with markedly improved domain selectivity, overcoming one of the principal challenges in designing inhibitors against these domains. These compounds represent important leads in the search for orthogonal inhibitors of SH3 domains, and can serve as tools for the dissection of complex signaling pathways.

Reciprocal regulation of Hck activity by phosphorylation of Tyr(527) and Tyr(416). Effect of introducing a high affinity intramolecular SH2 ligand

The Src family tyrosine kinase Hck possesses two phosphorylation sites, Tyr(527) and Tyr(416), that affect the catalytic activity in opposite ways. When phosphorylated, Tyr(527) and residues C-terminal to it are involved in an inhibitory intramolecular interaction with the SH2 domain. However, this sequence does not conform to the sequence of the high affinity SH2 ligand, pYEEI. We mutated this sequence to YEEI and show that this mutant form of Hck cannot be activated by exogenous SH2 ligands. The SH3 domain of Hck is also involved in an inhibitory interaction with the catalytic domain. The SH3 ligand Nef binds to and activates YEEI-Hck mutant in a similar manner to wild-type Hck, indicating that disrupting the SH3 interaction overrides the strengthened SH2 interaction. The other phosphorylation site, Tyr(416), is the autophosphorylation site in the activation loop. Phosphorylation of Tyr(416) is required for Hck activation. We mutated this residue to alanine and characterized its catalytic activity. The Y416A mutant shows a higher K(m) value for peptide and a lower V(max) than autophosphorylated wild-type Hck. We also present evidence for cross-talk between the activation loop and the intramolecular binding of the SH2 and SH3 domains.

Acute biliary disease: initial CT and follow-up US versus initial US and follow-up CT

PURPOSE

To evaluate the utility of ultrasonography (US) versus that of computed tomography (CT) for assessment of acute biliary disease.

MATERIALS AND METHODS

Radiologic reports and clinical charts were reviewed in all patients who underwent US and CT within 48 hours of each other for evaluation of acute right upper quadrant pain. Radiologic findings and clinical outcome were correlated.

RESULTS

CT was the initial imaging study in 57 patients, and CT findings resulted in underdiagnosis or misdiagnosis of acute biliary disease in eight of 11 patients. Follow-up US results were suggestive of the correct diagnosis and provided additional clinical information in seven of these eight patients. US findings resulted in altered clinical treatment in six of 11 patients with acute biliary disease. US was the initial study in 66 patients, and US findings were suggestive of biliary disease or the correct diagnosis in seven of seven patients with acute biliary disease. Follow-up CT did not result in changes in clinical treatment in any patient with acute biliary disease.

CONCLUSION

Initial US is better than initial CT in patients suspected of having acute biliary disease. Follow-up CT provides no additional information regarding the biliary system, and its use should be limited to those patients with a wider differential diagnosis or with confusing clinical symptoms and signs.

Autonomous folding of a C-terminal inhibitory fragment of Escherichia coli isoleucine-tRNA synthetase

We previously reported that C-terminal fragments of Escherichia coli Ile-tRNA synthetase, a monomeric enzyme of 939 amino acids, act as dominant negative inhibitors of the wild-type enzyme in vivo and in vitro. Our experiments suggested that it is possible to block the functional assembly of a monomeric protein by interfering with the folding pathway. We postulated that the inhibitory C-terminal fragments fold autonomously, and in the presence of full-length Ile-tRNA synthetase, trap the N-terminal portion of polypeptide in an unproductive complex. Here, we report the results of experiments aimed at understanding the mechanism of dominant negative inhibition. We have carried out biophysical experiments on fragment 585-939 of Ile-tRNA synthetase, which we previously determined to be the minimal inhibitory unit. Circular dichroism and fluorescence spectroscopy indicate that this fragment forms a compact and stable structure in solution. The secondary structure of this fragment is predominantly alpha-helical, consistent with the crystal structure of Ile-tRNA synthetase from another organism. The C-terminal fragment is capable of forming native-like secondary and tertiary structure after refolding from guanidine HCl. Taken together, the results are consistent with the hypothesis that the inhibitory fragment of Ile-tRNA synthetase forms an independent folding unit.

Identification of residues involved in v-Src substrate recognition by site-directed mutagenesis

To study the role of the catalytic domain in v-Src substrate specificity, we engineered three site-directed mutants (Leu-472 to Tyr or Trp and Thr-429 to Met). The mutant forms of Src were expressed in Sf9 cells and purified. We analyzed the substrate specificities of wild-type v-Src and the mutants using two series of peptides that varied at residues C-terminal to tyrosine. The peptides contained either the YMTM motif found in insulin receptor substrate-1 (IRS-1) or the YGEF motif identified from peptide library experiments to be the optimal sequence for Src. Mutations at positions Leu-472 or Thr-429 caused changes in substrate specificity at positions P+1 and P+3 (i.e. one or three residues C-terminal to tyrosine). This was particularly evident in the case of the L-472W mutant, which had pronounced alterations in its preferences at the P+1 position. The results suggest that residue Leu-472 plays a role in P+1 substrate recognition by Src. We discuss the results in the light of recent work on the roles of the SH2, SH3 and catalytic domains of Src in substrate specificity.

Cross-sectional imaging of Kikuchi disease

PURPOSE

The purpose of this work was to characterize the cross-sectional imaging features of Kikuchi disease.

METHOD

A search of our hospital records yielded three patients with pathologically proven Kikuchi disease. CT, MR, and ultrasound examinations of these patients were reviewed to characterize the imaging features of Kikuchi disease.

RESULTS

MRI of the neck in one patient, CT of the chest and abdomen in another, and CT and MRI of the abdomen in the third demonstrated uniformly enhancing small lymph nodes in larger than normal numbers in the submandibular, axillary, gastrohepatic, celiac, periportal, paraaortic, retrocrural, mesenteric, and inguinal regions. Lymph node diameter was usually <10 mm and was always <18 mm.

CONCLUSION

Many small clustered lymph nodes may be a characteristic imaging feature of Kikuchi disease. The abdominal extent of disease may be underreported if cross-sectional imaging is not performed.

Advanced emphysema: preoperative chest radiographic findings as predictors of outcome following lung volume reduction surgery

PURPOSE

To determine whether preoperative chest radiographic findings alone can reliably predict which patients will achieve the best functional outcome of lung volume reduction surgery.

MATERIALS AND METHODS

The preoperative chest radiographs obtained in 57 patients who had undergone lung volume reduction surgery were retrospectively scored by five blinded readers for severity and distribution of emphysema, evidence of lung compression, disease heterogeneity, and other features. Comparisons were made with the 3-6-month postoperative functional outcome for each patient.

RESULTS

High disease heterogeneity (score > 2) and unequivocal lung compression (score 1) both were 100% predictive of a favorable outcome (FEV1 increase, > or = 30%). Low heterogeneity (score < 1) was 94% predictive of an unfavorable outcome (FEV1 increase < 30%), as was a lack of lung compression, which was 92% predictive of an unfavorable outcome. These two features also correlated with an improved 6-minute walk test result, although this correlation was weaker.

CONCLUSION

Chest radiography alone may be sufficient for initial screening. High disease heterogeneity and lung compression on chest radiographs are highly predictive of a favorable functional outcome.

Thickening of the diaphragm: a new computed tomography sign of diaphragm injury

Computed tomography examination is becoming a standard method of evaluating injury in blunt trauma. This report describes a previously unreported computed tomography sign of diaphragmatic injury. A retrospective review of imaging findings was performed on eight patients with surgically proven traumatic diaphragmatic rupture. Thickening of the diaphragm was present on computed tomography in six of eight patients with surgically proven diaphragm rupture. Two patients demonstrated previously established computed tomography signs of diaphragm rupture and two patients had no findings to suggest diaphragm injury. Diaphragm thickening is associated with diaphragm rupture and may be a useful diagnostic sign in the evaluation of patients with blunt trauma.

Engineering the substrate specificity of the Abl tyrosine kinase

c-Abl is a non-receptor tyrosine kinase that is involved in a variety of signaling pathways. Activated forms of c-Abl are associated with some forms of human leukemia. Presently, no high resolution structure of the tyrosine kinase domain of Abl is available. We have developed a structural homology model of the catalytic domain of Abl based on the crystal structure of the insulin receptor tyrosine kinase. Using this model as a guide, we selected residues near the active site predicted to play a role in peptide/protein substrate recognition. We expressed and purified 15 mutant forms of Abl with single amino acid substitutions at these positions and tested their peptide substrate specificity. We report here the identification of seven residues involved in recognition of the P-1, P+1, and P+3 positions of bound peptide substrate. Mutations in these residues cause distinct changes in substrate specificity. The results suggest features of Abl substrate recognition that may be relevant to related tyrosine kinases.

The right inferior supraazygous recess: a cause of upper esophageal pseudomass on double-contrast esophagography

OBJECTIVE

Our purpose was to characterize the radiographic features of a pseudomass impression on the upper thoracic esophagus, to determine the frequency of such a pseudomass both on double-contrast esophagography and on CT, and to elucidate the anatomic basis for this finding.

MATERIALS AND METHODS

Our study group consisted of 135 patients whose double-contrast esophagograms were reviewed retrospectively for the presence or absence of an extrinsic indentation on the right posterolateral wall of the upper thoracic esophagus. In another patient group, 50 CT scans of the chest were also reviewed for the presence or absence of a prominent right inferior supraazygous recess and an associated indentation on the upper thoracic esophagus.

RESULTS

Thirteen (9.6%) of the 135 barium studies revealed a smooth, gently sloping indentation on the right posterolateral wall of the upper thoracic esophagus. The indentations ranged from 5 to 10 cm in length and extended inferiorly from the thoracic inlet to or just below the aortic arch. Twenty-four (48%) of the 50 CT scans revealed a prominent right inferior supraazygous recess projecting behind the esophagus. In five cases (10%), this recess also caused a smooth indentation on the upper thoracic esophagus.

CONCLUSION

A pseudomass impression was seen on double-contrast radiography as a smooth, gently sloping indentation on the right posterolateral wall of the upper thoracic esophagus in approximately 10% of patients. The indentation probably represents a normal anatomic variant (i.e., an unusually prominent right inferior supraazygous recess) that should not be mistaken for adenopathy or other masses in the mediastinum impinging on the esophagus.

Intramolecular regulatory interactions in the Src family kinase Hck probed by mutagenesis of a conserved tryptophan residue

Intramolecular interactions between the Src homology domains (SH2 and SH3) and the catalytic domains of Src family kinases result in repression of catalytic activity. The crystal structure of the Src family kinase Hck, with its regulatory domains intact, has been solved. It predicts that a conserved residue, Trp260, at the end of the linker between the SH2 and the catalytic domains plays an important role in regulation by the SH3 and SH2 domains. We have mutated this residue and compared the activities of C-terminally phosphorylated wild type Hck and W260A Hck. The W260A mutant has a higher specific activity than wild type Hck. The W260A mutant requires autophosphorylation at Tyr416 for full activity, but it is not activated by ligand binding to the SH3 or SH2 domains. This mutation also changes the accessibility of the SH2 and SH3 domains to their cognate peptide ligands. Our results indicate that Trp260 plays a critical role in the coupling of the regulatory domains to the catalytic domain, as well as in positioning the ligand binding surfaces.

Thoracic CT in the intensive care unit: assessment of clinical usefulness

PURPOSE

To determine the clinical usefulness of thoracic computed tomography (CT) in patients in a general intensive care unit (ICU).

MATERIALS AND METHODS

Images obtained in 108 consecutive thoracic CT examinations and the associated bedside chest radiographs and medical records in 85 patients (55 men, 30 women; age range, 19-92 years) in the ICU of an institution were retrospectively reviewed. CT findings were compared with concurrent bedside chest radiographic findings. The clinical importance of each CT finding was determined by reviewing the clinical record.

RESULTS

Of the 232 chest radiographic findings, 199 (86%) were confirmed at CT; when disagreement about mild congestive heart failure was excluded, there was a 93% agreement (199 of 213 findings). However, only CT demonstrated 250 (52%) of the 482 total findings (232 + 250 findings). Although many of these new findings were not clinically important, 32 (30%) of the 108 CT examinations had at least one new clinically important finding. These important new findings most often were (a) abscesses or postoperative fluid collections in the mediastinum, chest wall, or retroperitoneum; (b) malignancies that were detected, staged, or evaluated; (c) unsuspected pneumonia; or (d) pleural effusions. The CT findings resulted in changes in clinical management in 24 (22%) of the 108 examinations.

CONCLUSION

CT of the thorax is clinically useful in selected situation in patients in ICUs.

Mycobacterial infection in immunocompromised patients

Mycobacterial infection, including both tuberculosis and nontuberculous mycobacterial infection, is an important cause of morbidity and mortality in immunocompromised patients, particularly those who are infected with the human immunodeficiency virus. When these patients have active tuberculosis, apical, often cavitary, opacities characteristic of postprimary tuberculosis remain among the more common radiographic presentations. However, unusual radiographic manifestations of tuberculosis are more common in immunocompromised patients than in the general population. Nontuberculous mycobacterial infection in immunocompromised patients is frequently hematogenously disseminated, and the appearance on chest radiography is varied. Among patients infected with the human immunodeficiency virus, unifocal or multifocal alveolar infiltrates and mediastinal lymphadenopathy are the most common manifestations.

Phosphorylation and activation of cGMP-dependent protein kinase by Src

Using information obtained from experiments with peptide substrates of v-Src, a motif within the cGMP-binding domain of cGMP-dependent protein kinase (cGK) was identified as a potential phosphorylation site for v-Src. Here we show that the purified Ialpha isozyme of cGK is phosphorylated stoichiometrically and in a time-dependent manner by purified Src in vitro. The kinase activity of cGK is elevated approximately 4-fold (relative to autophosphorylated cGK) or 10-fold (relative to unphosphorylated cGK) upon tyrosine phosphorylation by Src. Phosphorylation of cGK by v-Src produces modest effects on the cGMP-binding properties and dissociation rates of cGK, and reduces the kact for cGMP. We hypothesize that the mechanism of activation may involve coupling of the cGMP binding domain to the catalytic domain.

Reperfusion edema after thromboendarterectomy: radiographic patterns of disease

In patients with chronic pulmonary embolism, pulmonary thromboendarterectomy may result in a unique form of noncardiogenic pulmonary edema termed reperfusion edema. This report reviews the authors' experience after pulmonary thromboendarterectomy with particular emphasis on the radiographic manifestations of reperfusion edema. The clinical and radiographic record of 25 patients who underwent pulmonary thromboendarterectomy at the University of Pennsylvania from 1985 through 1995 were reviewed. The zonal distribution of radiographic opacity, time to maximal opacity, and the time to clearance of reperfusion edema were determined. The relationship of these radiographic manifestations to clinical severity of disease and clinical outcome was examined. Reperfusion edema, characterized by patchy bilateral perihilar alveolar opacities, occurred in all but one patient. There is a lower lung zone predominance of opacities, but in individual cases, striking unilateral or haphazard arrangements of opacities may be seen. In this small sample of patients, no association between preoperative pulmonary arterial pressures and radiographic appearance or clinical outcome was found. However, severity of radiographic opacities, as measured by the extent of involved lung, correlated with disease severity, as measured by time to extubation and time to discharge. Pneumonia, defined as a radiographic opacity that evolves discordantly with the reperfusion edema opacities, occurred in 20% of cases. Reperfusion edema is a common consequence of pulmonary thromboendarterectomy. The severity of radiographic manifestations and clinical severity of disease are related. This characteristically appears as perihilar alveolar opacities.

Enhanced phosphorylation of Src family kinase substrates containing SH2 domain binding sites

Src family protein-tyrosine kinases possess several modular domains important for regulation of catalytic activity and interaction with potential substrates. Here, we explore interactions between the SH2 domain of Hck, a Src family kinase, and substrates containing SH2 domain-binding sites. We have synthesized a series of peptide substrates containing a high affinity SH2 domain binding site, (phospho)Tyr-Glu-Glu-Ile. We show that the presence of this sequence in a peptide results in a dramatic increase in the phosphorylation rate of a second tyrosine located at the N terminus. Enhanced phosphorylation is not a consequence of stimulation of enzymatic activity by C-terminal tail displacement but is imparted instead by a 10-fold reduction in the Km of the phosphotyrosine-containing peptide when compared with a control. The isolated catalytic domain of the non-receptor tyrosine kinase Abl does not show a preference for the pYEEI motif-containing peptide; however, the preference is restored when the SH2 domain of Src is introduced into Abl. Furthermore, enhanced phosphorylation is dependent on the distance between SH2 domain-binding site and phosphorylatable tyrosine, with the minimum distance requirement being seven amino acids. Reversing the orientation of the pYEEI motif with respect to the substrate sequence decreases phosphorylation by down-regulated Hck, but both orientations are utilized equally well by activated Hck. We discuss the possible implications of these results for processive phosphorylation of substrates in vivo by Src family kinases.