GalaxyDomDock: An Ab Initio Domain–domain Docking Web Server for Multi-domain Protein Structure Prediction

A significant proportion of proteins comprise multiple domains. Domain–domain docking is a tool that predicts multi-domain protein structures when individual domain structures can be accurately predicted but when domain orientations cannot be predicted accurately. GalaxyDomDock predicts an ensemble of domain orientations from given domain structures by docking. Such information would also be beneficial in elucidating the functions of proteins that have multiple states with different domain orientations. GalaxyDomDock is an ab initio domain–domain docking method based on GalaxyTongDock, a previously developed protein–protein docking method. Infeasible domain orientations for the given linker are effectively screened out from the docked conformations by a geometric filter, using the Dijkstra algorithm. In addition, domain linker conformations are predicted by adopting a loop sampling method FALC. The proposed GalaxyDomDock outperformed existing ab initio domain–domain docking methods, such as AIDA and Rosetta, in performance tests on the Rosetta benchmark set of two-domain proteins. GalaxyDomDock also performed better than or comparable to AIDA on the AIDA benchmark set of two-domain proteins and two-domain proteins containing discontinuous domains, including the benchmark set in which each domain of the set was modeled by the recent version of AlphaFold. The GalaxyDomDock web server is freely available as a part of GalaxyWEB at http://galaxy.seoklab.org/domdock.     

Low serum PON1 activity: An independent risk factor for coronary artery disease in North–West Indian type 2 diabetics

The paraoxonase (PON1) gene polymorphisms are known to affect the PON1 activity and coronary artery disease (CAD) risk. Studies done so far have given conflicting results. In the present study, we determined the role of PON1 genetic variants and PON1 activity in the development of CAD in North–West Indian Punjabis, a distinct ethnic group, having high incidence of both CAD and type 2 diabetes. 300 angiographically proven CAD with type 2 diabetics and 250 type 2 diabetics with no clinically evident CAD were enrolled. Serum PON1 activity and genotyping of coding (Q192R, L55M) and promoter (− 909G/C, − 162A/G, − 108C/T) region polymorphisms were carried out and haplotypes were determined using PHASE software.     

An RNA interference based study for the role of ALDH1 in keratinocytes: DNA microarray,antibody–chip array and bioinformatics approaches

The role of acetaldehyde dehydrogenase 1 (ALDH1) has been probed in several diseases, especially in various types of cancers. However, the role of ALDH1 in skin cells has not been well elucidated. In this study, we aimed to identify critical factors associated with ALDH1 in keratinocytes through gene and protein expression profiling approaches. To this end, we conducted serial OMICS studies, including DNA microarray analysis, integrated antibody–chip arrays, and the implementation of bioinformatics algorithms designed to integrate siRNA data upon ALDH1 silencing. Cumulatively, these approaches identified several novel genes and proteins in keratinocytes associated with the downregulation of ALDH1. These novel genes and proteins included CYP1A1, a member of the cytochrome family of enzymes; extracellular matrix genes; and cytokines and chemokines, which are believed to play important roles in ALDH1-associated skin diseases such as atopic dermatitis. By integrating the datasets obtained from these complementary high-throughput OMICS studies and utilizing the strengths of each method, we obtained new insights into the functional role of ALDH1 in skin cells. The approach used here could help contribute to our clinical understanding of ALDH1-associated diseases, and may also be broadly applicable to a wider range of diseases.     

An RNA Phage Lab: MS2 in Walter Fiers’ Laboratory of Molecular Biology in Ghent, from Genetic Code to Gene and Genome, 1963–1976

The importance of viruses as model organisms is well-established in molecular biology and Max Delbrück’s phage group set standards in the DNA phage field. In this paper, I argue that RNA phages, discovered in the 1960s, were also instrumental in the making of molecular biology. As part of experimental systems, RNA phages stood for messenger RNA (mRNA), genes and genome. RNA was thought to mediate information transfers between DNA and proteins. Furthermore, RNA was more manageable at the bench than DNA due to the availability of specific RNases, enzymes used as chemical tools to analyse RNA. Finally, RNA phages provided scientists with a pure source of mRNA to investigate the genetic code, genes and even a genome sequence. This paper focuses on Walter Fiers’ laboratory at Ghent University (Belgium) and their work on the RNA phage MS2. When setting up his Laboratory of Molecular Biology, Fiers planned a comprehensive study of the virus with a strong emphasis on the issue of structure. In his lab, RNA sequencing, now a little-known technique, evolved gradually from a means to solve the genetic code, to a tool for completing the first genome sequence. Thus, I follow the research pathway of Fiers and his ‘RNA phage lab’ with their evolving experimental system from 1960 to the late 1970s. This study illuminates two decisive shifts in post-war biology: the emergence of molecular biology as a discipline in the 1960s in Europe and of genomics in the 1990s.     

Is Metabolic Syndrome Predictive of Prevalence,Extent, and Risk of Coronary Artery Disease beyond Its Components? Results from the Multinational Coronary CT Angiography Evaluation for Clinical Outcome: An International Multicenter Registry (CONFIRM)

Although metabolic syndrome is associated with increased risk of cardiovascular disease and events, its added prognostic value beyond its components remains unknown. This study compared the prevalence, severity of coronary artery disease (CAD), and prognosis of patients with metabolic syndrome to those with individual metabolic syndrome components. The study cohort consisted of 27125 consecutive individuals who underwent ≥64-detector row coronary CT angiography (CCTA) at 12 centers from 2003 to 2009. Metabolic syndrome was defined as per NCEP/ATP III criteria. Metabolic syndrome patients (n=690) were matched 1:1:1 to those with 1 component (n=690) and 2 components (n=690) of metabolic syndrome for age, sex, smoking status, and family history of premature CAD using propensity scoring. Major adverse cardiac events (MACE) were defined by a composite of myocardial infarction (MI), acute coronary syndrome, mortality and late target vessel revascularization. Patients with 1 component of metabolic syndrome manifested lower rates of obstructive 1-, 2-, and 3-vessel/left main disease compared to metabolic syndrome patients (9.4% vs 13.8%, 2.6% vs 4.5%, and 1.0% vs 2.3%, respectively; p<0.05), while those with 2 components did not (10.5% vs 13.8%, 2.8% vs 4.5% and 1.3% vs 2.3%, respectively; p>0.05). At 2.5 years, metabolic syndrome patients experienced a higher rate of MACE compared to patients with 1 component (4.4% vs 1.6%; p=0.002), while no difference observed compared to individuals with 2 components (4.4% vs 3.2% p=0.25) of metabolic syndrome. In conclusion, Metabolic syndrome patients have significantly greater prevalence, severity, and prognosis of CAD compared to patients with 1 but not 2 components of metabolic syndrome.