Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro.

In addition to its essential role in viral polyprotein processing, the SARS-CoV-2 3C-like protease (3CLpro) can cleave human immune signaling proteins, like NF-κB Essential Modulator (NEMO) and deregulate the host immune response. Here, in vitro assays show that SARS-CoV-2 3CLpro cleaves NEMO with fine-tuned efficiency. Analysis of the 2.50 Å resolution crystal structure of 3CLpro C145S bound to NEMO226-234 reveals subsites that tolerate a range of viral and host substrates through main chain hydrogen bonds while also enforcing specificity using side chain hydrogen bonds and hydrophobic contacts. Machine learning- and physics-based computational methods predict that variation in key binding residues of 3CLpro-NEMO helps explain the high fitness of SARS-CoV-2 in humans. We posit that cleavage of NEMO is an important piece of information to be accounted for, in the pathology of COVID-19.

Identification of Small-Molecule Inhibitors of Fibroblast Growth Factor 23 Signaling via In Silico Hot Spot Prediction and Molecular Docking to α-Klotho.

Fibroblast growth factor 23 (FGF23) is a therapeutic target for treating hereditary and acquired hypophosphatemic disorders, such as X-linked hypophosphatemic (XLH) rickets and tumor-induced osteomalacia (TIO), respectively. FGF23-induced hypophosphatemia is mediated by signaling through a ternary complex formed by FGF23, the FGF receptor (FGFR), and α-Klotho. Currently, disorders of excess FGF23 are treated with an FGF23-blocking antibody, burosumab. Small-molecule drugs that disrupt protein/protein interactions necessary for the ternary complex formation offer an alternative to disrupting FGF23 signaling. In this study, the FGF23:α-Klotho interface was targeted to identify small-molecule protein/protein interaction inhibitors since it was computationally predicted to have a large fraction of hot spots and two druggable residues on α-Klotho. We further identified Tyr433 on the KL1 domain of α-Klotho as a promising hot spot and α-Klotho as an appropriate drug-binding target at this interface. Subsequently, we performed in silico docking of ∼5.5 million compounds from the ZINC database to the interface region of α-Klotho from the ternary crystal structure. Following docking, 24 and 20 compounds were in the final list based on the lowest binding free energies to α-Klotho and the largest number of contacts with Tyr433, respectively. Five compounds were assessed experimentally by their FGF23-mediated extracellular signal-regulated kinase (ERK) activities in vitro, and two of these reduced activities significantly. Both these compounds were predicted to have favorable binding affinities to α-Klotho but not have a large number of contacts with the hot spot Tyr433. ZINC12409120 was found experimentally to disrupt FGF23:α-Klotho interaction to reduce FGF23-mediated ERK activities by 70% and have a half maximal inhibitory concentration (IC50) of 5.0 ± 0.23 µM. Molecular dynamics (MD) simulations of the ZINC12409120:α-Klotho complex starting from in silico docking poses reveal that the ligand exhibits contacts with residues on the KL1 domain, the KL1-KL2 linker, and the KL2 domain of α-Klotho simultaneously, thereby possibly disrupting the regular function of α-Klotho and impeding FGF23:α-Klotho interaction. ZINC12409120 is a candidate for lead optimization.

Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro.

In addition to its essential role in viral polyprotein processing, the SARS-CoV-2 3C-like (3CLpro) protease can cleave human immune signaling proteins, like NF-κB Essential Modulator (NEMO) and deregulate the host immune response. Here, in vitro assays show that SARS-CoV-2 3CLpro cleaves NEMO with fine-tuned efficiency. Analysis of the 2.14 Å resolution crystal structure of 3CLpro C145S bound to NEMO 226-235 reveals subsites that tolerate a range of viral and host substrates through main chain hydrogen bonds while also enforcing specificity using side chain hydrogen bonds and hydrophobic contacts. Machine learning- and physics-based computational methods predict that variation in key binding residues of 3CLpro- NEMO helps explain the high fitness of SARS-CoV-2 in humans. We posit that cleavage of NEMO is an important piece of information to be accounted for in the pathology of COVID-19.

Continuous Prophylactic Antiretrovirals/Antiretroviral Therapy Since Birth Reduces Seeding and Persistence of the Viral Reservoir in Children Vertically Infected With Human Immunodeficiency Virus.

BACKGROUND: Early antiretroviral therapy (ART) restricts the size of the human immunodeficiency virus (HIV) reservoir in infants. However, whether antiretroviral (ARV) prophylaxis given to exposed vertically infected children exerts similar effects remains unknown. METHODS: We measured total and integrated HIV DNA, as well as the frequency of CD4 T cells producing multiply spliced RNA (msRNA) after stimulation (inducible reservoir) in vertically infected Thai infants. Eighty-five infants were followed longitudinally for up to 3 years. We compared the size of the reservoir in children who received continuous ARV prophylaxis since birth vs those who never received or discontinued prophylaxis before initiating ART. We used samples from a cross-sectional cohort of 37 Thai children who had initiated ART within 6 months of life to validate our findings. RESULTS: Before ART, levels of HIV DNA and the frequencies of cells producing msRNA were significantly lower in infants who received continuous ARV prophylaxis since birth compared to those in whom ARV prophylaxis was discontinued or never initiated (P < .020 and P < .001, respectively). Upon ART initiation, total and integrated HIV DNA levels decayed significantly in both groups (P < .01 in all cases). Interestingly, the initial differences in the frequencies of infected cells persisted during 3 years on ART. The beneficial effect of prophylaxis on the size of the HIV reservoir was confirmed in the cross-sectional study. Importantly, no differences were observed between children who discontinued prophylactic ARVs before starting ART and those who delayed ART initiation without receiving prior prophylaxis. CONCLUSIONS: Neonatal ARV prophylaxis with direct transition to ART durably limits the size of the HIV reservoir.

Combining Three-Dimensional Modeling with Artificial Intelligence to Increase Specificity and Precision in Peptide-MHC Binding Predictions.

The reliable prediction of the affinity of candidate peptides for the MHC is important for predicting their potential antigenicity and thus influences medical applications, such as decisions on their inclusion in T cell-based vaccines. In this study, we present a rapid, predictive computational approach that combines a popular, sequence-based artificial neural network method, NetMHCpan 4.0, with three-dimensional structural modeling. We find that the ensembles of bound peptide conformations generated by the programs MODELLER and Rosetta FlexPepDock are less variable in geometry for strong binders than for low-affinity peptides. In tests on 1271 peptide sequences for which the experimental dissociation constants of binding to the well-characterized murine MHC allele H-2Db are known, by applying thresholds for geometric fluctuations the structure-based approach in a standalone manner drastically improves the statistical specificity, reducing the number of false positives. Furthermore, filtering candidates generated with NetMHCpan 4.0 with the structure-based predictor led to an increase in the positive predictive value (PPV) of the peptides correctly predicted to bind very strongly (i.e., K d < 100 nM) from 40 to 52% (p = 0.027). The combined method also significantly improved the PPV when tested on five human alleles, including some with limited data for training. Overall, an average increase of 10% in the PPV was found over the standalone sequence-based method. The combined method should be useful in the rapid design of effective T cell-based vaccines.

Feasibility and Acceptability of Inpatient Palliative Care E-Family Meetings During COVID-19 Pandemic.

Family meetings are fundamental to the practice of palliative medicine and serve as a cornerstone of intervention on the inpatient palliative care consultation service. The COVID-19 pandemic disrupted the structure and process of in-patient family meetings, owing to necessary but restrictive visitor policies that did not allow families to be present in the hospital. We describe implementation of telemedicine to facilitate electronic family (e-family) meetings to facilitate in-patient palliative care. Of 67 scheduled meetings performed by the palliative care service, only two meetings were aborted for a 97% success rate of scheduled meetings occurring. On a five-point Likert-type scale, the average clinician rating of the e-family meeting overall quality was 3.18 (SD, .96). Of the 10 unique family participants who agreed to be interviewed, their overall ratings of the e-family meetings were high. Over 80% of respondent families participants reported that they agreed or strongly agreed that they were able to ask all of their questions, felt comfortable expressing their thoughts and feelings with the clinical team, felt like they understood the care their loved one received, and that the virtual family meeting helped them trust the clinical team. Of patients who were able to communicate, 50% of family respondents reported that the e-family meeting helped them understand their loved one's thoughts and wishes.

Prediction of peptide binding to MHC using machine learning with sequence and structure-based feature sets.

Selecting peptides that bind strongly to the major histocompatibility complex (MHC) for inclusion in a vaccine has therapeutic potential for infections and tumors. Machine learning models trained on sequence data exist for peptide:MHC (p:MHC) binding predictions. Here, we train support vector machine classifier (SVMC) models on physicochemical sequence-based and structure-based descriptor sets to predict peptide binding to a well-studied model mouse MHC I allele, H-2Db. Recursive feature elimination and two-way forward feature selection were also performed. Although low on sensitivity compared to the current state-of-the-art algorithms, models based on physicochemical descriptor sets achieve specificity and precision comparable to the most popular sequence-based algorithms. The best-performing model is a hybrid descriptor set containing both sequence-based and structure-based descriptors. Interestingly, close to half of the physicochemical sequence-based descriptors remaining in the hybrid model were properties of the anchor positions, residues 5 and 9 in the peptide sequence. In contrast, residues flanking position 5 make little to no residue-specific contribution to the binding affinity prediction. The results suggest that machine-learned models incorporating both sequence-based descriptors and structural data may provide information on specific physicochemical properties determining binding affinities.

Screening for Opioid Misuse in the Nonhospitalized Seriously Ill Patient.

Background: Responding to an epidemic of opioid-related deaths, guidelines and laws have been implemented to promote safe opioid prescribing practices. Objective: This study evaluates differences in screening practices and knowledge of laws between oncologists and cardiologists who prescribe opiates. Design: Surveys regarding screening practices and knowledge of opioid prescribing laws were distributed in March 2017 to oncology and congestive heart failure (CHF) clinicians at the University of Virginia. Chi-square and Wilcoxon rank sum tests were used. Results: Forty-six of 129 (35.6%) oncology providers and 7 of 14 (50%) CHF providers reported prescribing opiates in their clinic with usable survey results. The majority of oncology (65.22%) and cardiology (85.71%) providers report screening for substance abuse "when indicated" (p = 0.053). Only 19.6% of oncologists reported always using the prescription monitoring program (PMP), while 71.43% of cardiologists reported using it always (p = 0.014). Of the oncology providers, 66.67% report never using the urine drug screen (UDS), while 86.7% of cardiologists reported using it "when indicated" (p = 0.0086). Up to 34.78% of the oncologists and 57.14% of the cardiologists reported of never screening the family members for misuse (p = 0.317). Knowledge of laws was similar between groups, with 14.29% of cardiology and 17.39% of oncology providers reporting no knowledge of opioid prescribing laws (p = 0.2869). Conclusions: Routine screening for substance misuse risk was uncommon for both groups, but cardiology providers were more likely to use the PMP or UDS. Knowledge gaps regarding Virginia laws were noted in both groups. Improved education regarding best practices and laws, as well as programs to promote screening, is needed for all providers.

Dying on Hospice in the Midst of an Opioid Crisis: What Should We Do Now?

The current opioid crisis in the United States is a major problem facing health-care providers, even at the end of life. Opioids continue to be the mainstay treatment for pain at the end of life, with the prevalence of pain reported in up to 80% of patients and tends to increase as one gets closer toward the end of life. In the past year, 20.2 million Americans had a substance use disorder (SUD) and SUDs are disabling disorders that largely go untreated. In addition, the coexistence of both a mental health and SUD is very common with the use of opioids often as a means of chemical coping. Most hospice programs do not have standardized SUD policies/guidelines in place despite the increasing concerns about substance abuse within the United States. The goal of this article is to review the literature on this topic and offer strategies on how to manage pain in patients who have active SUD or who are at risk for developing SUD in those dying on hospice.

Oral Vitamin C (500 mg/d) to Pregnant Smokers Improves Infant Airway Function at 3 Months (VCSIP). A Randomized Trial.

Rationale: We reported a randomized trial demonstrating daily supplemental vitamin C to pregnant smokers significantly improved newborn pulmonary function tests. The current study tests these results in a new cohort using infant pulmonary function tests. Objectives: To determine if infants of pregnant smokers randomized to daily supplemental vitamin C would have improved forced expiratory flows (FEFs) at 3 months of age compared with those randomized to placebo, and to investigate the association of the α5 nicotinic acetylcholine receptor. Methods: A randomized, double-blind, placebo-controlled trial was conducted at three centers. Two hundred fifty-one pregnant smokers were randomized at 13-23 weeks of gestation: 125 randomized to vitamin C (500 mg/d) and 126 to placebo. Measurements and Main Results: The primary outcome was FEF75 at 3 months of age performed with the raised volume rapid thoracic compression technique (Jaeger/Viasys). FEF50 and FEF25-75 obtained from the same expiratory curves were prespecified secondary outcomes. The infants of pregnant smokers randomized to vitamin C (n = 113) had the following FEFs at 3 months of age compared with those randomized to placebo (n = 109) as measured by FEF75 (200.7 vs. 188.7 ml/s; adjusted 95% confidence interval [CI] for difference, -3.33 to 35.64; P = 0.10), FEF50 (436.7 vs. 408.5 ml/s; adjusted 95% CI for difference, 6.10-61.30; P = 0.02), and FEF25-75 (387.4 vs. 365.8 ml/s; adjusted 95% CI for difference, 0.92-55.34; P = 0.04). Infant FEFs seemed to be negatively associated with the maternal risk alleles for the α5 nicotinic acetylcholine receptor (rs16969968). Conclusions: Although the primary outcome of FEF75 was not improved after vitamin C supplementation to pregnant smokers, the predetermined secondary outcomes FEF50 and FEF25-75 were significantly improved. These results extend our previous findings and demonstrate improved airway function (FEF50 and FEF25-75) at 3 months of age in infants after vitamin C supplementation to pregnant smokers. Clinical trial registered with www.clinicaltrials.gov (NCT01723696).

Vitamin C to Decrease the Effects of Smoking in Pregnancy on Infant Lung Function (VCSIP): Rationale, design, and methods of a randomized, controlled trial of vitamin C supplementation in pregnancy for the primary prevention of effects of in utero tobacco smoke exposure on infant lung function and respiratory health.

Despite strong anti-smoking efforts, at least 12% of American women cannot quit smoking when pregnant resulting in >450,000 smoke-exposed infants born yearly. Smoking during pregnancy is the largest preventable cause of childhood respiratory illness including wheezing and asthma. Recent studies have shown a protective effect of vitamin C supplementation on the lung function of offspring exposed to in utero smoke in a non-human primate model and an initial human trial. Vitamin C to Decrease the Effects of Smoking in Pregnancy on Infant Lung Function (VCSIP) is a randomized, double-blind, placebo-controlled trial to evaluate pulmonary function at 3months of age in infants delivered to pregnant smokers randomized to 500mg/day of vitamin C versus placebo during pregnancy. Secondary aims evaluate the incidence of wheezing through 12months and pulmonary function testing at 12months of age. Women are randomized between 13 and 23weeks gestation from clinical sites in Portland, Oregon at Oregon Health & Science University and PeaceHealth Southwest Medical Center and in Indianapolis, Indiana at Indiana University and Wishard Hospital. Vitamin C supplementation occurs from randomization to delivery. Monthly contact with participants and monitoring of medical records is performed to document medication adherence, changes in smoking and medical history, and adverse events. Pulmonary function testing of offspring occurs at 3 and 12months of age and incidence of wheezing and respiratory illness through 12months is captured via at least quarterly questionnaires. Ancillary studies are investigating the impact of vitamin C on placental blood flow and DNA methylation.

Variations in mRNA and protein levels of Ikaros family members in pediatric T cell acute lymphoblastic leukemia.

BACKGROUND: Pediatric T cell acute lymphoblastic leukemia (T-ALL) is a highly heterogeneous disease in which the cells share phenotypic characteristics with normal human thymocytes. The Ikaros family of transcription factors includes five members that are required for normal T cell development and are implicated in leukemogenesis. The goal of this work was to correlate the pattern of expression of Ikaros family members with the phenotype of the T-ALL cells. METHODS: We obtained twenty-four samples from pediatric T-ALL patients and used multi-parameter flow cytometry to characterize each sample, comparing the phenotype of the leukemic cells with normal human thymocytes. Then, we defined the expression levels of each Ikaros family member to determine whether the mRNA levels or splicing or protein levels were similar to the normal patterns seen during human T cell development. RESULTS: Multi-parameter analysis of the phenotype of T-ALL cells revealed that each patient's cells were unique and could not be readily correlated with stages of T cell development. Similarly, the pattern of Ikaros expression varied among patients. In most patients, Ikaros mRNA was the dominant family member expressed, but some patients' cells contained mostly Helios, Aiolos, or Eos mRNA. Despite that most patients had elevated mRNA levels of Ikaros family members and unique patterns of mRNA splicing, most patients had significantly reduced protein levels of Ikaros and Aiolos. CONCLUSIONS: Our analysis of the cell phenotype and Ikaros expression levels in T-ALL cells revealed the extent of heterogeneity among patients. While it is rarely possible to trace leukemic cells to their developmental origin, we found distinct patterns of Ikaros family mRNA levels in groups of patients. Further, mRNA and protein levels of Ikaros and Aiolos did not correlate, indicating that mRNA and protein levels are regulated via distinct mechanisms.

Breast Cancer Screening and Prevention.

This issue provides a clinical overview of breast cancer screening and prevention, focusing on risk assessment, screening, prevention, and practice improvement. The content of In the Clinic is drawn from the clinical information and education resources of the American College of Physicians (ACP), including MKSAP (Medical Knowledge and Self-Assessment Program). Annals of Internal Medicine editors develop In the Clinic in collaboration with the ACP's Medical Education and Publishing divisions and with the assistance of additional science writers and physician writers.

A Mouthful of Anomalies.

Isolated bilateral macrodontia of the mandibular second premolars is a rare condition. We believe that the case reported here is the first in which isolated bilateral macrodontia of the mandibular second premolars presents with numerous dental anomalies affecting other teeth. A 14-year-old boy was referred to the Paediatric Dental Department of King's College Hospital with a partially erupted mandibular left second premolar. Clinical and radiographic examination subsequently revealed macrodontia of both mandibular second premolar teeth and multiple other dental anomalies. This report discusses the presentation and multidisciplinary management of this case. Clinical relevance: This case report describes an already rare condition made even more extraordinary owing to its presentation with multiple other dental anomalies.

Smoke-free outdoor areas: supporting local government to introduce tobacco control policies.

OBJECTIVES: To ascertain the proportion of councils with smoke-free outdoor areas (SFOA) policies in New South Wales (NSW), Australia and to explore the enablers and barriers to local governments introducing such policies. METHODS: A structured survey of council staff at NSW councils was conducted by telephone in 2011. Participants were asked about the existence of any SFOA policy, and enablers and barriers of the policy. RESULTS: The study was completed by 148 of 152 NSW councils. Eighty five (57%) councils had an SFOA policy, with playgrounds most likely to be covered by the policy. The most frequently cited enabler for the introduction of SFOA policy was direct advocacy letters, while the most commonly mentioned barrier was a lack of resources. CONCLUSION AND IMPLICATIONS: In the absence of state or federal legislation, local government or councils may respond to community expectations for smoke-free outdoor areas by introducing policy. Advocacy and support from non-government health organisations can increase the likelihood of this occurring and address barriers facing councils, with rural councils most likely to benefit from such support. Interest from councils can influence the adoption of state-wide smoke-free outdoor areas legislation.

Health and economic effects from linking bedside and outpatient tobacco cessation services for hospitalized smokers in two large hospitals: study protocol for a randomized controlled trial.

BACKGROUND: Extended smoking cessation follow-up after hospital discharge significantly increases abstinence. Hospital smoke-free policies create a period of 'forced abstinence' for smokers, thus providing an opportunity to integrate tobacco dependence treatment, and to support post-discharge maintenance of hospital-acquired abstinence. This study is funded by the National Heart, Lung, and Blood Institute (1U01HL1053231). METHODS/DESIGN: The Inpatient Technology-Supported Assisted Referral study is a multi-center, randomized clinical effectiveness trial being conducted at Kaiser Permanente Northwest (KPNW) and at Oregon Health & Science University (OHSU) hospitals in Portland, Oregon. The study assesses the effectiveness and cost-effectiveness of linking a practical inpatient assisted referral to outpatient cessation services plus interactive voice recognition (AR + IVR) follow-up calls, compared to usual care inpatient counseling (UC). In November 2011, we began recruiting 900 hospital patients age ≥18 years who smoked ≥1 cigarettes in the past 30 days, willing to remain abstinent postdischarge, have a working phone, live within 50 miles of the hospital, speak English, and have no health-related barriers to participation. Each site will randomize 450 patients to AR + IVR or UC using a 2:1 assignment strategy. Participants in the AR + IVR arm will receive a brief inpatient cessation consult plus a referral to available outpatient cessation programs and medications, and four IVR follow-up calls over seven weeks postdischarge. Participants do not have to accept the referral. At KPNW, UC participants will receive brief inpatient counseling and encouragement to self-enroll in available outpatient services. The primary outcome is self-reported thirty-day smoking abstinence at six months postrandomization for AR + IVR participants compared to usual care. Additional outcomes include self-reported and biochemically confirmed seven-day abstinence at six months, self-reported seven-day, thirty-day, and continuous abstinence at twelve months, intervention dose response at six and twelve months for AR + IVR recipients, incremental cost-effectiveness of AR + IVR intervention compared to usual care at six and twelve months, and health-care utilization and expenditures at twelve months for AR + IVR recipients compared to UC. DISCUSSION: This study will provide important evidence for the effectiveness and cost-effectiveness of linking hospital-based tobacco treatment specialists' services with discharge follow-up care. TRIAL REGISTRATION: ClinicalTrials.gov: NCT01236079.

The Meaning-Making intervention (MMi) appears to increase meaning in life in advanced ovarian cancer: a randomized controlled pilot study.

OBJECTIVE: This pilot study aimed to provide supportive evidence for the acceptability and usefulness of the Meaning-Making intervention (MMi) in patients newly diagnosed with Stage III or IV ovarian cancer, and to provide estimates of parameters needed to design a full-scale study. METHODS: A randomized controlled trial with 24 patients (12 experimental and 12 control) was conducted. Existential well-being (primary outcome), overall quality of life, distress, anxiety, depression and self-efficacy were measured. RESULTS: Compared to the control group, patients in the experimental group had a better sense of meaning in life at one and three months post-intervention. CONCLUSION: The MMi seems a promising intervention for advanced cancer patients, and a full randomized controlled trial is warranted to further investigate its efficacy.

Enhanced weight loss with pramlintide/metreleptin: an integrated neurohormonal approach to obesity pharmacotherapy.

The neurohormonal control of body weight involves a complex interplay between long-term adiposity signals (e.g., leptin), and short-term satiation signals (e.g., amylin). In diet-induced obese (DIO) rodents, amylin/leptin combination treatment led to marked, synergistic, fat-specific weight loss. To evaluate the weight-lowering effect of combined amylin/leptin agonism (with pramlintide/metreleptin) in human obesity, a 24-week, randomized, double-blind, active-drug-controlled, proof-of-concept study was conducted in obese or overweight subjects (N = 177; 63% female; 39 +/- 8 years; BMI 32.0 +/- 2.1 kg/m(2); 93.3 +/- 13.2 kg; mean +/- s.d.). After a 4-week lead-in period with pramlintide (180 microg b.i.d. for 2 weeks, 360 microg b.i.d. thereafter) and diet (40% calorie deficit), subjects achieving 2-8% weight loss were randomized 1:2:2 to 20 weeks of treatment with metreleptin (5 mg b.i.d.), pramlintide (360 microg b.i.d.), or pramlintide/metreleptin (360 microg/5 mg b.i.d.). Combination treatment with pramlintide/metreleptin led to significantly greater weight loss from enrollment to week 20 (-12.7 +/- 0.9%; least squares mean +/- s.e.) than treatment with pramlintide (-8.4 +/- 0.9%; P < 0.001) or metreleptin (-8.2 +/- 1.3%; P < 0.01) alone (evaluable, N = 93). The greater reduction in body weight was significant as early as week 4, and weight loss continued throughout the study, without evidence of a plateau. The most common adverse events with pramlintide/metreleptin were injection site events and nausea, which were mostly mild to moderate and decreased over time. These results support further development of pramlintide/metreleptin as a novel, integrated neurohormonal approach to obesity pharmacotherapy.

TRP1 interacting PDZ-domain protein GIPC forms oligomers and is localized to intracellular vesicles in human melanocytes.

PDZ proteins coordinate assembly of protein complexes that participate in diverse biological processes. GIPC is a multifunctional PDZ protein that interacts with several soluble and membrane proteins. Unlike most PDZ proteins, GIPC contains single PDZ domain and the mechanisms by which GIPC mediates its actions remain unclear. We investigated the possibility that in lieu of multiple PDZ domains, GIPC forms multimers. Here, we demonstrate that GIPC can bind to itself and that the PDZ domain is involved in GIPC-GIPC interaction. Gel filtration, sucrose gradient centrifugation and chemical cross-linking showed that whereas bulk of cytosolic GIPC was present as monomer, oligomers with an estimated molecular mass corresponding to GIPC homotrimer were readily detectable in the membrane fraction. Modeling of GIPC PDZ domain showed feasibility of trimerization. Immunogold electron microscopy showed that GIPC is present in clusters near vesicles. Our data suggest that oligomers of GIPC mediate its functions in melanocytes.

Disruption of shape-complementarity markers to create cytotoxic variants of ribonuclease A.

Onconase (ONC), an amphibian member of the bovine pancreatic ribonuclease A (RNase A) superfamily, is in phase III clinical trials as a treatment for malignant mesothelioma. RNase A is a far more efficient catalyst of RNA cleavage than ONC but is not cytotoxic. The innate ability of ONC to evade the cytosolic ribonuclease inhibitor protein (RI) is likely to be a primary reason for its cytotoxicity. In contrast, the non-covalent interaction between RNase A and RI is one of the strongest known, with the RI.RNase A complex having a K(d) value in the femtomolar range. Here, we report on the use of the fast atomic density evaluation (FADE) algorithm to identify regions in the molecular interface of the RI.RNase A complex that exhibit a high degree of geometric complementarity. Guided by these "knobs" and "holes", we designed variants of RNase A that evade RI. The D38R/R39D/N67R/G88R substitution increased the K(d) value of the pRI.RNase A complex by 20 x 10(6)-fold (to 1.4 microM) with little change to catalytic activity or conformational stability. This and two related variants of RNase A were more toxic to human cancer cells than was ONC. Notably, these cytotoxic variants exerted their toxic activity on cancer cells selectively, and more selectively than did ONC. Substitutions that further diminish affinity for RI (which has a cytosolic concentration of 4 microM) are unlikely to produce a substantial increase in cytotoxic activity. These results demonstrate the utility of the FADE algorithm in the examination of protein-protein interfaces and represent a landmark towards the goal of developing chemotherapeutics based on mammalian ribonucleases.