Molecular-dynamics simulation methods for macromolecular crystallography.

It is investigated whether molecular-dynamics (MD) simulations can be used to enhance macromolecular crystallography (MX) studies. Historically, protein crystal structures have been described using a single set of atomic coordinates. Because conformational variation is important for protein function, researchers now often build models that contain multiple structures. Methods for building such models can fail, however, in regions where the crystallographic density is difficult to interpret, for example at the protein-solvent interface. To address this limitation, a set of MD-MX methods that combine MD simulations of protein crystals with conventional modeling and refinement tools have been developed. In an application to a cyclic adenosine monophosphate-dependent protein kinase at room temperature, the procedure improved the interpretation of ambiguous density, yielding an alternative water model and a revised protein model including multiple conformations. The revised model provides mechanistic insights into the catalytic and regulatory interactions of the enzyme. The same methods may be used in other MX studies to seek mechanistic insights.

Treatment Outcomes of Newly Diagnosed Epilepsy: A Systematic Review and Meta-analysis.

BACKGROUND AND OBJECTIVES: Understanding the multi-faceted treatment outcomes of newly diagnosed epilepsy is critical for developing rational therapeutic strategies. A meta-analysis was conducted to derive pooled estimates of a range of seizure outcomes in children and adults with newly diagnosed epilepsy commenced on antiseizure medication treatment, and to identify factors associated with different outcomes. METHODS: PubMed/EMBASE were screened for eligible articles between 1 January, 1995 and 1 May, 2021 to include unselected cohort studies with a ≥ 12-month follow-up of seizure outcomes. Proportions of patients seizure free at different follow-up timepoints and their characteristics at the study population level were extracted. The patients were group-wise aggregated using a random-effects model. Primary outcomes were proportions of patients with cumulative 1-year seizure freedom (C1YSF), and 1-year and 5-year terminal seizure freedom (T1YSF and T5YSF). Secondary outcomes included the proportions of patients with early sustained seizure freedom, drug-resistant epilepsy and seizure-free off antiseizure medication at the last follow-up (off antiseizure medications). A separate random-effects meta-analysis was performed for nine predictors of importance. RESULTS: In total, 39 cohorts (total n = 21,139) met eligibility criteria. They included 15 predominantly adult cohorts (n = 12,024), 19 children (n = 6569), and 5 of mixed-age groups (n = 2546). The pooled C1YSF was 79% (95% confidence interval [CI] 74-83). T1YSF was 68% (95% CI 63-72) and T5YSF was 69% (95% CI 62-75). Children had higher C1YSF (85% vs 68%, p < 0.001) and T1YSF than adult cohorts (74% vs 61%, p = 0.007). For secondary outcomes, 33% (95% CI 27-39) of patients achieved early sustained seizure freedom, 17% (95% CI 13-21) developed drug resistance, and 39% (95% CI 30-50) were off antiseizure medications at the last follow-up. Studies with a longer follow-up duration correlated with higher C1YSF (p < 0.001) and being off antiseizure medications (p = 0.045). Outcomes were not associated with study design (prospective vs retrospective), cohort size, publication year, or the earliest date of recruitment. Predictors of importance in newly diagnosed epilepsy include etiology, epilepsy type, abnormal diagnostics (neuroimaging, examination, and electroencephalogram findings), number of seizure types, and pre-treatment seizure burden. CONCLUSIONS: Seizure freedom is achieved with currently available antiseizure medications in most patients with newly diagnosed epilepsy, yet this is often not immediate, may not be sustainable, and has not improved over recent decades. Symptomatic etiology, abnormal neuro-diagnostics, and increased pre-treatment seizure burden and seizure types are important predictors for unfavorable outcomes in newly diagnosed epilepsy. The study findings may be used as a quantitative benchmark on the efficacy of future antiseizure medication therapy for this patient population.

A PKA inhibitor motif within SMOOTHENED controls Hedgehog signal transduction.

The Hedgehog (Hh) cascade is central to development, tissue homeostasis and cancer. A pivotal step in Hh signal transduction is the activation of glioma-associated (GLI) transcription factors by the atypical G protein-coupled receptor (GPCR) SMOOTHENED (SMO). How SMO activates GLI remains unclear. Here we show that SMO uses a decoy substrate sequence to physically block the active site of the cAMP-dependent protein kinase (PKA) catalytic subunit (PKA-C) and extinguish its enzymatic activity. As a result, GLI is released from phosphorylation-induced inhibition. Using a combination of in vitro, cellular and organismal models, we demonstrate that interfering with SMO-PKA pseudosubstrate interactions prevents Hh signal transduction. The mechanism uncovered echoes one used by the Wnt cascade, revealing an unexpected similarity in how these two essential developmental and cancer pathways signal intracellularly. More broadly, our findings define a mode of GPCR-PKA communication that may be harnessed by a range of membrane receptors and kinases.

PKA Cß: a forgotten catalytic subunit of cAMP-dependent protein kinase opens new windows for PKA signaling and disease pathologies.

3',5'-cyclic adenosine monophosphate (cAMP) dependent protein kinase or protein kinase A (PKA) has served as a prototype for the large family of protein kinases that are crucially important for signal transduction in eukaryotic cells. The PKA catalytic subunits are encoded by the two major genes PRKACA and PRKACB, respectively. The PRKACA gene encodes two known splice variants, the ubiquitously expressed Cα1 and the sperm-specifically expressed Cα2. In contrast, the PRKACB gene encodes several splice variants expressed in a highly cell and tissue-specific manner. The Cß proteins are called Cß1, Cß2, Cß3, Cß4 and so-called abc variants of Cß3 and Cß4. Whereas Cß1 is ubiquitously expressed, Cß2 is enriched in immune cells and the Cß3, Cß4 and their abc variants are solely expressed in neuronal cells. All Cα and Cß splice variants share a kinase-conserved catalytic core and a C-terminal tail encoded by exons 2 through 10 in the PRKACA and PRKACB genes, respectively. All Cα and Cß splice variants with the exception of Cα1 and Cß1 are hyper-variable at the N-terminus. Here, we will discuss how the PRKACA and PRKACB genes have developed as paralogs that encode distinct and functionally non-redundant proteins. The fact that Cα and Cß splice variant mutations are associated with numerous diseases further opens new windows for PKA-induced disease pathologies.

Germline and Mosaic Variants in PRKACA and PRKACB Cause a Multiple Congenital Malformation Syndrome.

PRKACA and PRKACB code for two catalytic subunits (Cα and Cß) of cAMP-dependent protein kinase (PKA), a pleiotropic holoenzyme that regulates numerous fundamental biological processes such as metabolism, development, memory, and immune response. We report seven unrelated individuals presenting with a multiple congenital malformation syndrome in whom we identified heterozygous germline or mosaic missense variants in PRKACA or PRKACB. Three affected individuals were found with the same PRKACA variant, and the other four had different PRKACB mutations. In most cases, the mutations arose de novo, and two individuals had offspring with the same condition. Nearly all affected individuals and their affected offspring shared an atrioventricular septal defect or a common atrium along with postaxial polydactyly. Additional features included skeletal abnormalities and ectodermal defects of variable severity in five individuals, cognitive deficit in two individuals, and various unusual tumors in one individual. We investigated the structural and functional consequences of the variants identified in PRKACA and PRKACB through the use of several computational and experimental approaches, and we found that they lead to PKA holoenzymes which are more sensitive to activation by cAMP than are the wild-type proteins. Furthermore, expression of PRKACA or PRKACB variants detected in the affected individuals inhibited hedgehog signaling in NIH 3T3 fibroblasts, thereby providing an underlying mechanism for the developmental defects observed in these cases. Our findings highlight the importance of both Cα and Cß subunits of PKA during human development.

New-onset epilepsy in the elderly.

People who are 60 years old and older have the highest incidence of developing new-onset epilepsy. The increase of the ageing population has resulted in a greater number of patients with new-onset epilepsy or at risk of developing the condition. Previously published review articles regarding epilepsy in older patients have had a broad focus, including people who were diagnosed with epilepsy in their childhood or middle age. The present review focuses on the causes, treatment, prognosis and psychosocial impact of new-onset epilepsy in people aged ≥60 years. Following a search of the medical electronic databases and relevant references, we identified 22 studies overall that met the inclusion criteria. Only four randomized clinical trials (RCTs) were identified that compared different antiepileptic drug treatments in this population, demonstrating that newer-generation antiepileptic drugs (e.g. lamotrigine and levetiracetam) were generally better tolerated. One uncontrolled study provided promising evidence of good outcomes and safety for surgical resection as a treatment for people with uncontrolled seizures. Five studies reported that people ≥60 years with new-onset epilepsy have significant cognitive impairments (e.g. memory loss) and psychological issues including depression, anxiety and fatigue. We found that there is limited evidence to guide treatment in people with Alzheimer's disease and epilepsy. The specific features of new-onset epilepsy in this target population significantly influences the choice of treatment. Cognitive and psychiatric screening before treatment may be useful for management. Two studies with proposed guidelines were identified but no formal clinical practice guidelines exist for this special population to assist with appropriate management. There is a need for more RCTs that investigate effective treatments with limited side effects. More research studies on the psychosocial effects of new-onset epilepsy, and long-term outcomes, for people aged ≥60 years are also required.

Factors influencing doctors' selection of dabigatran in non-valvular atrial fibrillation.

RATIONALE, AIMS AND OBJECTIVES: This study was designed to examine the factors that influence doctors' decision in initiating or switching from warfarin to dabigratran. METHOD: A survey questionnaire was sent to 181 doctors who were most likely to prescribe dabigatran (e.g. cardiologists and general internists) at the University of California, San Francisco Medical Center between November 2011 and February 2012. Survey participants were asked to complete an electronic or a paper version of the questionnaire, which consisted of 17 multiple-choice questions. Fisher's exact test and Cochran-Mantel-Haenszel test were used to compare survey responses between cardiologists and general internists. RESULTS: A total of 65 survey responses were received (35.9% response rate). There were 13 cardiologists and 51 general internists who participated in the study. Cost (25%), renal function (21%) and CHADS2 score (18%) were the three factors doctors considered most often to determine a patient's eligibility for dabigatran in warfarin-naïve patients. On the other hand, histories of unstable international normalized ratio (37%) and missed appointments (17%) along with cost (19%) were most often considered in patients on warfarin. Cardiologists had prescribed dabigatran more often and had a significantly higher level of comfort with prescribing the drug than general internists (P = 0.003; 77% vs. 27%). CONCLUSIONS: Cost was the most important factor influencing doctors' decision to prescribe dabigatran. Safety and effectiveness of dabigatran as well as patient preference were additional factors influencing their decision. General internists were less comfortable with prescribing dabigatran than cardiologists.