PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank.

The Protein Data Bank (PDB) is the global repository for public-domain experimentally determined 3D biomolecular structural information. The archival nature of the PDB presents certain challenges pertaining to updating or adding associated annotations from trusted external biodata resources. While each Worldwide PDB (wwPDB) partner has made best efforts to provide up-to-date external annotations, accessing and integrating information from disparate wwPDB data centers can be an involved process. To address this issue, the wwPDB has established the PDB Next Generation (or NextGen) Archive, developed to centralize and streamline access to enriched structural annotations from wwPDB partners and trusted external sources. At present, the NextGen Archive provides mappings between experimentally determined 3D structures of proteins and UniProt amino acid sequences, domain annotations from Pfam, SCOP2 and CATH databases and intra-molecular connectivity information. Since launch, the PDB NextGen Archive has seen substantial user engagement with over 3.5 million data file downloads, ensuring researchers have access to accurate, up-to-date and easily accessible structural annotations. Database URL: http://www.wwpdb.org/ftp/pdb-nextgen-archive-site.

Community recommendations on cryoEM data archiving and validation.

In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for the deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and the resulting consensus recommendations. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.

Community recommendations on cryoEM data archiving and validation: Outcomes of a wwPDB/EMDB workshop on cryoEM data management, deposition and validation.

In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and consensus recommendations resulting from the workshop. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.

PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank.

While the Protein Data Bank (PDB) contains a wealth of structural information on ligands bound to macromolecules, their analysis can be challenging due to the large amount and diversity of data. Here, we present PDBe CCDUtils, a versatile toolkit for processing and analysing small molecules from the PDB in PDBx/mmCIF format. PDBe CCDUtils provides streamlined access to all the metadata for small molecules in the PDB and offers a set of convenient methods to compute various properties using RDKit, such as 2D depictions, 3D conformers, physicochemical properties, scaffolds, common fragments, and cross-references to small molecule databases using UniChem. The toolkit also provides methods for identifying all the covalently attached chemical components in a macromolecular structure and calculating similarity among small molecules. By providing a broad range of functionality, PDBe CCDUtils caters to the needs of researchers in cheminformatics, structural biology, bioinformatics and computational chemistry.

Cardiac reverse remodelling by imaging parameters with recent changes to guideline medical therapy in heart failure.

Recently established heart failure therapies, including sodium glucose co-transporter 2 inhibitors, angiotensin-neprilysin inhibitors, and cardiac resynchronization therapy, have led to both clinical and structural improvements. Reverse remodelling describes the structural and functional responses to therapy and has been shown to correlate with patients' clinical response, acting as a biomarker for treatment success. The introduction of these new therapeutic agents in addition to advances in non-invasive cardiac imaging has led to an expansion in the evaluation and the validation of cardiac reverse remodelling. Methods including volumetric changes as well as strain and myocardial work have all been shown to be non-invasive end-points of reverse remodelling, correlating with clinical outcomes. Our review summarizes the current available evidence on reverse remodelling in heart failure by the non-invasive cardiac imaging techniques, in particular transthoracic echocardiography.

Cardiac sarcoma presenting as paraneoplastic arthritis and clubbing: a case report and literature review.

BACKGROUND: Cardiac tumours are rare, and clinical manifestations depend on the anatomical location. Symptoms can be the result of cardiac outflow anomalies, constitutional features such as fever, loss of weight, and/or paraneoplastic manifestations such as arthritis. To date, there has only been one other case report in the literature of cardiac sarcoma presenting as paraneoplastic arthropathy. CASE PRESENTATION: A 52-year-old woman presented with acute onset corticosteroid-resistant inflammatory polyarthralgia, clubbing and a systolic murmur. Transthoracic echocardiogram revealed a dilated left atrium with an echogenic mass and brain magnetic resonance imaging revealed multiple embolic infarcts. Histopathology following emergency resection showed a Grade 3 left atrial intimal sarcoma. The polyarthralgia and clubbing resolved soon after tumour removal. The patient went on to receive chemotherapy and remains in remission. CONCLUSIONS: This case highlights the rare paraneoplastic association of cardiac sarcoma and arthropathy.

Unified access to up-to-date residue-level annotations from UniProtKB and other biological databases for PDB data.

More than 61,000 proteins have up-to-date correspondence between their amino acid sequence (UniProtKB) and their 3D structures (PDB), enabled by the Structure Integration with Function, Taxonomy and Sequences (SIFTS) resource. SIFTS incorporates residue-level annotations from many other biological resources. SIFTS data is available in various formats like XML, CSV and TSV format or also accessible via the PDBe REST API but always maintained separately from the structure data (PDBx/mmCIF file) in the PDB archive. Here, we extended the wwPDB PDBx/mmCIF data dictionary with additional categories to accommodate SIFTS data and added the UniProtKB, Pfam, SCOP2, and CATH residue-level annotations directly into the PDBx/mmCIF files from the PDB archive. With the integrated UniProtKB annotations, these files now provide consistent numbering of residues in different PDB entries allowing easy comparison of structure models. The extended dictionary yields a more consistent, standardised metadata description without altering the core PDB information. This development enables up-to-date cross-reference information at the residue level resulting in better data interoperability, supporting improved data analysis and visualisation.

PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education.

The archiving and dissemination of protein and nucleic acid structures as well as their structural, functional and biophysical annotations is an essential task that enables the broader scientific community to conduct impactful research in multiple fields of the life sciences. The Protein Data Bank in Europe (PDBe; pdbe.org) team develops and maintains several databases and web services to address this fundamental need. From data archiving as a member of the Worldwide PDB consortium (wwPDB; wwpdb.org), to the PDBe Knowledge Base (PDBe-KB; pdbekb.org), we provide data, data-access mechanisms, and visualizations that facilitate basic and applied research and education across the life sciences. Here, we provide an overview of the structural data and annotations that we integrate and make freely available. We describe the web services and data visualization tools we offer, and provide information on how to effectively use or even further develop them. Finally, we discuss the direction of our data services, and how we aim to tackle new challenges that arise from the recent, unprecedented advances in the field of structure determination and protein structure modeling.

Pregnancy-related cardiovascular conditions and outcomes in a United States Medicaid population.

OBJECTIVE: This study aims to examine the incidence of pregnancy-related cardiometabolic conditions and severe cardiovascular outcomes, and their relationship in US Medicaid-funded women. METHODS: Medicaid is a government-sponsored health insurance programme for low-income families in the USA. We report the incidence of pregnancy-related cardiometabolic conditions (hypertensive disorders and diabetes in, or complicated by, pregnancy) and severe cardiovascular outcomes (myocardial infarction, stroke, acute heart failure, cardiomyopathy, cardiac arrest, ventricular fibrillation, ventricular tachycardia, aortic dissection/aneurysm and peripheral vascular disease) among Medicaid-funded women with a birth (International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM) diagnosis code O80 or O82) over the period January 2015-June 2019, from the states of Georgia, Ohio and Indiana. In this cross-sectional cohort, we examined the relationship between pregnancy-related cardiometabolic conditions and severe cardiovascular outcomes from pregnancy through to 60 days after birth using multivariable models. RESULTS: Among 74 510 women, mean age 26.4 years (SD 5.5), the incidence per 1000 births of pregnancy-related cardiometabolic conditions was 224.3 (95% CI 221.3 to 227.3). The incidence per 1000 births of severe cardiovascular conditions was 10.8 (95% CI 10.1 to 11.6). Women with pregnancy-related cardiometabolic conditions were at greater risk of having a severe cardiovascular condition with an age-adjusted OR of 3.1 (95% CI 2.7 to 3.5). CONCLUSION: This US cohort of Medicaid-funded women have a high incidence of severe cardiovascular conditions during pregnancy. Cardiometabolic conditions of pregnancy conferred threefold higher odds of severe cardiovascular outcomes.

LV non-compaction in patients with coarctation of the aorta: prevalence and effects on cardiac function.

BACKGROUND: Left ventricular non-compaction has been associated with heart failure, arrhythmia, thromboembolism and sudden death. The prevalence of non-compaction in patients with coarctation of the aorta and its clinical significance remains unknown, although obstructive left heart disease is common in patients with non-compaction. We sought to evaluate the prevalence of left ventricular non-compaction in patients with repaired aortic coarctation as well as its effect on left ventricular size and systolic function. METHODS AND RESULTS: In total, 268 patients (Mean age 26 (inter-quartile range 21-37) years, 63% male) undergoing cardiac magnetic resonance imaging for clinical follow-up were included from three tertiary centres for adult congenital heart disease. Clinical data was obtained from medical records and correlated with ventricular volumes and function. Left ventricular non-compaction was defined as a diastolic non-compacted:compacted dimension ratio >2.3 in the worst affected segment on a long-axis view. Left ventricular non-compaction was present in 8.2% of patients with repaired coarctation. Left ventricular end-diastolic volumes and stroke volumes were significantly higher in patients with non-compaction compared to those without. There were no significant differences in ventricular mass or ejection fraction in these two groups. CONCLUSIONS: Left ventricular non-compaction is relatively common in patients with repaired coarctation of the aorta and correlates with increased left ventricular end-diastolic volumes.

Long term clinical outcomes associated with CMR quantified isolated left ventricular non-compaction in adults.

BACKGROUND: Left ventricular non-compaction (LVNC) is a complex clinical condition with several diagnostic criteria but no diagnostic gold standard. We aimed to evaluate our thresholding technique in a group of patients with LVNC and assess the risk of major adverse cardiovascular and cerebrovascular events (MACCE). METHODS: We retrospectively analyzed cardiac magnetic resonance (CMR) scans of patients with Petersen criteria LVNC and quantified noncompacted myocardial mass. We assessed the association of noncompacted myocardial mass, CMR derived LV volumetric parameters and late gadolinium enhancement (LGE) to MACCE including cardiac death, cardiac transplantation, sustained ventricular tachycardia/ventricular fibrillation (VT/VF) and ischemic stroke. Patients with known genetic mutations and cardiovascular disease were excluded. RESULTS: 98 patients with LVNC were included (55 males,56.7%); 17(17.3%) patients had impaired LV function and five (5.1%) had LGE. Patients with impaired LV function had more end-systolic noncompacted mass (61.9 g±22.4 vs. 38.1 g±15.8, p < 0.001) and larger end-systolic noncompacted to total myocardial mass (44%±9 vs. 36%±12, p = 0.003). At 78 months follow-up [interquartile range(IQR) 66-90], MACCE occurred in 11(11.3%) patients; nine(81.8%) had impaired LV function and two(18.2%) had LGE. Impaired LV function and LV LGE were predictors of MACCE (HR = 35.6, 95% CI = 7.65-165.21, p < 0.001 and HR = 16.2, 95% CI = 4.54-57.84, p < 0.001) whereas noncompacted mass were not. CONCLUSION: Noncompacted mass was not an independent predictor of major adverse events but in patients with impaired LV function and/or LV LGE, the risk of MACCE was high. These results highlight the importance of including LV volumetrics and scar in the assessment of patients with LV noncompaction.

The role of multimodality imaging in the diagnosis of left ventricular noncompaction.

Left ventricular noncompaction (LVNC) is a heterogeneous entity and, in reality, a likely spectrum of disease which is clinically associated with arrhythmia, thromboembolic complications and sudden cardiac death. With the emergence of cardiac MRI (cMRI), the phenotype is increasingly more prevalent, resulting in clinical uncertainty regarding prognosis and management. The currently accepted hypothesis suggests an early embryonic arrest of the normal, sequential myocardial compaction process. LVNC is observed in isolation or in association with congenital heart disease, neuromuscular disease or a vast array of genetic cardiomyopathies. Definition of the entity varies among international society guidelines with differences both within and between imaging modalities, predominantly echocardiography and cMRI. Long-term prognostic data are emerging but due to the intrinsic variability in reported prevalence, selection bias and lack of pathological to prognostic correlation, there are many uncertainties regarding clinical management. This review seeks to clarify the role of multimodality imaging in diagnosis and management of the disease. We discuss the sensitivity and specificity of the current diagnostic criteria, as well as the nuances in diagnosis using the available imaging modalities.

Left ventricular non-compaction in patients with single ventricle heart disease.

OBJECTIVE: Left ventricular non-compaction is an architectural abnormality of the myocardium, associated with heart failure, systemic thromboembolism, and arrhythmia. We sought to assess the prevalence of left ventricular non-compaction in patients with single ventricle heart disease and its effects on ventricular function. METHODS: Cardiac MRI of 93 patients with single ventricle heart disease (mean age 24 ± 8 years; 55% male) from three tertiary congenital centres was retrospectively reviewed; 65 of these had left ventricular morphology and are the subject of this report. The presence of left ventricular non-compaction was defined as having a non-compacted:compacted (NC:C) myocardial thickness ratio >2.3:1. The distribution of left ventricular non-compaction, ventricular volumes, and function was correlated with clinical data. RESULTS: The prevalence of left ventricular non-compaction was 37% (24 of 65 patients) with a mean of 4 ± 2 affected segments. The distribution was apical in 100%, mid-ventricular in 29%, and basal in 17% of patients. Patients with left ventricular non-compaction had significantly higher end-diastolic (128 ± 44 versus 104 ± 46 mL/m2, p = 0.047) and end-systolic left ventricular volumes (74 ± 35 versus 56 ± 35 mL/m2, p = 0.039) with lower left ventricular ejection fraction (44 ± 11 versus 50 ± 9%, p = 0.039) compared to those with normal compaction. The number of segments involved did not correlate with ventricular function (p = 0.71). CONCLUSIONS: Left ventricular non-compaction is frequently observed in patients with left ventricle-type univentricular hearts, with predominantly apical and mid-ventricular involvement. The presence of non-compaction is associated with increased indexed end-diastolic volumes and impaired systolic function.

PDBe: improved findability of macromolecular structure data in the PDB.

The Protein Data Bank in Europe (PDBe), a founding member of the Worldwide Protein Data Bank (wwPDB), actively participates in the deposition, curation, validation, archiving and dissemination of macromolecular structure data. PDBe supports diverse research communities in their use of macromolecular structures by enriching the PDB data and by providing advanced tools and services for effective data access, visualization and analysis. This paper details the enrichment of data at PDBe, including mapping of RNA structures to Rfam, and identification of molecules that act as cofactors. PDBe has developed an advanced search facility with ∼100 data categories and sequence searches. New features have been included in the LiteMol viewer at PDBe, with updated visualization of carbohydrates and nucleic acids. Small molecules are now mapped more extensively to external databases and their visual representation has been enhanced. These advances help users to more easily find and interpret macromolecular structure data in order to solve scientific problems.

A simple measure of the extent of Ebstein valve rotation with cardiovascular magnetic resonance gives a practical guide to feasibility of surgical cone reconstruction.

BACKGROUND: Once surgical management is indicated, variation of Ebstein valve morphology affects surgical strategy. This study explored practical, easily measureable, cardiovascular magnetic resonance (CMR)-derived attributes that may contribute to the complexity and risk of cone reconstruction. METHODS: A retrospective assessment was performed of Ebstein anomaly patients older than 12 years age, with pre-operative CMR, undergoing cone surgical reconstruction by one surgeon. In addition to clinical data, the CMR-derived Ebstein valve rotation angle (EVRA), area ratios of chamber size, indexed functional RV (RVEDVi) and left ventricular (LV) volumes, tricuspid valve regurgitant fraction (TR%) and other valve attributes were related to early surgical outcome; including death, significant residual TR% or breakdown of repair. RESULTS: Of 26 operated patients older than 12 years age, since program start, 20 had pre-op CMR and underwent surgery at median (range) age 20 (14-57) years. TR% was improved in all patients. Four of the 20 CMR patients (20%) experienced early surgical dehiscence of the paravalve tissue, with cone-shaped tricuspid valve intact; one of whom died. A larger EVRA correlated with Carpentier category and was significantly related to dehiscence. If EVRA >60o, relative risk of dehiscence was 3.2 (CI 1.3-4.9, p = 0.03). Those with dehiscence had thickened, more tethered anterior leaflet edges (RR 17, CI 3-100, p < 0.01), smaller pre-operative functional RVEDVi; (132 vs 177 mL/m2, p = 0.04), and were older (median 38 vs 19 years, p = 0.01). TR %, chamber area ratios and LV parameters were not different. CONCLUSIONS: Comprehensive CMR assessment characterizes patients prior to cone surgical reconstruction of Ebstein anomaly. Pragmatic observation of larger EVRA, smaller RVEDVi and leaflet thickening, suggests risk of repair tension and dehiscence, and may require specific modification of cone surgical technique, such as leaflet augmentation.

Persistent reduction in global longitudinal strain in the longer term after radiation therapy in patients with breast cancer.

BACKGROUND: More than 80% of breast cancer patients receive radiotherapy (RT). However, RT can lead to cardiotoxicity, which usually develops insidiously over years, making diagnosis difficult. It is also unknown whether early identification of at-risk patients might improve long-term outcome. We have previously described subclinical alterations, detected by two-dimensional speckle tracking strain echocardiography, in left ventricular (LV) function immediately following RT in breast cancer. HYPOTHESIS: Subclinical myocardial alterations in LV function consequent to RT cardiotoxicity, observed early, persist at 12 months. METHODS: 40 chemotherapy naive women with left-sided breast cancer, treated with surgery and adjuvant breast RT, were prospectively recruited from two tertiary hospitals. Transthoracic echocardiography was performed at baseline (pre-RT), 6 weeks post-RT, and 12 months post-RT. RESULTS: An increase in LV end diastolic and end systolic volumes was seen from baseline, consistent with persistent LV remodelling; however, due to the increase in both systolic and diastolic volumes over time, no change in LV ejection fraction (EF) was observed. Global longitudinal strain (GLS) and S' velocity remained significantly lower at 12 months post-RT. GLS dropped by >10% in 16 patients and by >20% in 4 patients compared to baseline. CONCLUSIONS: Subclinical cardiac dysfunction using strain analysis, evident early, persists one year after RT, despite unchanged conventional indices such as LVEF. Persistent GLS reduction may be of particular importance in breast cancer patients receiving concomitant chemotherapy. Longer term prospective studies are required to determine if reductions in strain post-RT are associated with future adverse cardiovascular events.

CSmetaPred: a consensus method for prediction of catalytic residues.

BACKGROUND: Knowledge of catalytic residues can play an essential role in elucidating mechanistic details of an enzyme. However, experimental identification of catalytic residues is a tedious and time-consuming task, which can be expedited by computational predictions. Despite significant development in active-site prediction methods, one of the remaining issues is ranked positions of putative catalytic residues among all ranked residues. In order to improve ranking of catalytic residues and their prediction accuracy, we have developed a meta-approach based method CSmetaPred. In this approach, residues are ranked based on the mean of normalized residue scores derived from four well-known catalytic residue predictors. The mean residue score of CSmetaPred is combined with predicted pocket information to improve prediction performance in meta-predictor, CSmetaPred_poc. RESULTS: Both meta-predictors are evaluated on two comprehensive benchmark datasets and three legacy datasets using Receiver Operating Characteristic (ROC) and Precision Recall (PR) curves. The visual and quantitative analysis of ROC and PR curves shows that meta-predictors outperform their constituent methods and CSmetaPred_poc is the best of evaluated methods. For instance, on CSAMAC dataset CSmetaPred_poc (CSmetaPred) achieves highest Mean Average Specificity (MAS), a scalar measure for ROC curve, of 0.97 (0.96). Importantly, median predicted rank of catalytic residues is the lowest (best) for CSmetaPred_poc. Considering residues ranked ≤20 classified as true positive in binary classification, CSmetaPred_poc achieves prediction accuracy of 0.94 on CSAMAC dataset. Moreover, on the same dataset CSmetaPred_poc predicts all catalytic residues within top 20 ranks for ~73% of enzymes. Furthermore, benchmarking of prediction on comparative modelled structures showed that models result in better prediction than only sequence based predictions. These analyses suggest that CSmetaPred_poc is able to rank putative catalytic residues at lower (better) ranked positions, which can facilitate and expedite their experimental characterization. CONCLUSIONS: The benchmarking studies showed that employing meta-approach in combining residue-level scores derived from well-known catalytic residue predictors can improve prediction accuracy as well as provide improved ranked positions of known catalytic residues. Hence, such predictions can assist experimentalist to prioritize residues for mutational studies in their efforts to characterize catalytic residues. Both meta-predictors are available as webserver at: http://14.139.227.206/csmetapred/ .

Structural and electrical cardiac abnormalities are prevalent in asymptomatic adults with myotonic dystrophy.

OBJECTIVE: Cardiac disease accounts for a large burden of premature mortality and morbidity in patients with type 1 myotonic dystrophy (MD). However, little is known about structural cardiac abnormalities particularly in asymptomatic patients with MD. We sought to describe the prevalence and extent of structural cardiac abnormalities in patients with MD and to assess their association with functional, electrical, biochemical and genetic disturbances. METHODS: In this case-control study, 40 adults with MD who had no contraindications to cardiac MRI (CMR) were identified from the Grampian region genetic database. Forty-one age-and-gender-matched healthy volunteers were also recruited. All subjects underwent detailed assessment including CMR, echocardiography, electrocardiography, signal-averaged electrocardiography, Holter monitoring and quantification of serum B-type natriuretic peptide (BNP). Genetic testing of patients with MD was performed with quantification of CTG trinucleotide repeat sequences. Results of clinical, electrical, genetic and biochemical investigations were correlated with cardiac structural and functional abnormalities detected on CMR. RESULTS: Electrical disturbances including prolongation of PR (187±29 vs 156±23 ms, p<0.001) and QRS intervals (99±11 vs 89±9 ms, p<0.001) were the most prevalent abnormality. Patients with MD had a significantly lower left ventricular (LV) mass (142±44 vs 172±73 g, p=0.03) and lower right ventricular (RV) ejection fraction (46±9 vs 50±7%, p=0.02) compared with controls, although LV ejection fraction was similar between the groups (58±8 vs 59±6%, p=0.34). LV non-compaction was also significantly more prevalent in the MD cohort (35% vs 12%, p=0.019). Late gadolinium enhancement was present in 13% of patients with MD. Muscular disability scores correlated with electrical changes (r=0.529, p<0.001); however, the number of CTG repeat sequences did not correlate with either electrical or structural abnormalities. CONCLUSIONS: Patients with MD have a high prevalence of both electrical and structural abnormalities. These include reduced LV mass, impaired RV contractility, a high prevalence of LV non-compaction and myocardial fibrosis. These findings illustrate the potential utility of CMR detecting subclinical disease in otherwise asymptomatic patients with MD.

Patient selection essential for computed tomography coronary angiography.

OBJECTIVE: Computed tomography coronary angiography (CTCA) has become a commonly used imaging modality in patients with suspected anginal symptoms but also in asymptomatic populations. This practice has raised concerns due to potential high radiation exposure in terms of adequate benefit to risk profile. DESIGN: Demographics and CTCA scan details were collected from a consecutive series of 586 patients referred to a single community radiology practice for a CTCA. RESULTS: Of the 586 patients, 271 (46.2%) were women. Mean age was 58.3 standard deviation (SD) 12.2, range 15-90 years, body mass index (BMI) 28.6 SD 5.9 kg/m(2), and heart rate 60 SD 10 beats per minute. Mean total radiation was 4.79 SD 3.45 mSv (range 0.64-31.34). The mean radiation exposure in the lowest quartile of BMI and heart rate were 3.01 SD 1.84 mSv and 3.95 SD 2.72 mSv, compared to the highest 7.32 SD 3.51 mSv and 6.20 SD 4.38 mSv (p for trend <0.0001 in both). CONCLUSION: The radiation exposure in this consecutive series of patients is low in general but patient selection for CTCA imaging appears to be paramount. Patients with a high BMI and especially with high heart rate receive a higher dose of radiation.