Residue packing in globular and intrinsically disordered proteins

Intrinsically disordered proteins (IDPs)/regions do not have well-defined secondary and tertiary structures, however, they are functional and it is critical to gain a deep understanding of their residue packing. The shape distributions methodology, which is usually utilized in pattern recognition, clustering, and classification studies in computer science, may be adopted to study the residue packing of the proteins. In this study, shape distributions of the globular proteins and IDPs were obtained to shed light on the residue packing of their structures. The shape feature that was used is the sphericity of tetrahedra obtained by Delaunay Tessellation of points of C? coordinates. Then the sphericity probability distributions were compared by using Principal Component Analysis. This computational structural study shows that the set of IDPs constitute a more diverse set than the set of globular proteins in terms of the geometrical properties of their network structures. © 2018 Wiley Periodicals, Inc.Authors appreciate the kind support and suggestions from Turkan Haliloglu

Heterotopic pancreatic tissue located in the gallbladder wall. A case report

PubMed: 21386642Context Heterotopia of the pancreas can be defined as the presence of pancreatic tissue in an abnormal location without any continuity with the main body of the pancreas. Heterotopic pancreatic tissue located in the gallbladder is a rare entity. Despite being a congenital condition, it takes years for heterotopic pancreas to become symptomatic. Case report An 80-year-old male patient presented to our hospital with a two-week history of abdominal pain, nausea and vomiting aggravated after meals. Abdominal ultrasonography revealed minimal wall edema and small grain-sized gallstones in the gallbladder. The patient was hospitalized and laparoscopic cholecystectomy was performed for acute cholecystitis. Pathologic examination showed a 6 mm nodular mass of pancreatic tissue in the gallbladder wall, comprised mainly of ductal and acinic structures and a few endocrine cells. Conclusion We found this case of pancreatic heterotopia worth reporting because of its rare incidence

Bistability in Apoptosis: Roles of Bax, Bcl-2, and Mitochondrial Permeability Transition Pores

We propose a mathematical model for mitochondria-dependent apoptosis, in which kinetic cooperativity in formation of the apoptosome is a key element ensuring bistability. We examine the role of Bax and Bcl-2 synthesis and degradation rates, as well as the number of mitochondrial permeability transition pores (MPTPs), on the cell response to apoptotic stimuli. Our analysis suggests that cooperative apoptosome formation is a mechanism for inducing bistability, much more robust than that induced by other mechanisms, such as inhibition of caspase-3 by the inhibitor of apoptosis (IAP). Simulations predict a pathological state in which cells will exhibit a monostable cell survival if Bax degradation rate is above a threshold value, or if Bax expression rate is below a threshold value. Otherwise, cell death or survival occur depending on initial caspase-3 levels. We show that high expression rates of Bcl-2 can counteract the effects of Bax. Our simulations also demonstrate a monostable (pathological) apoptotic response if the number of MPTPs exceeds a threshold value. This study supports our contention, based on mathematical modeling, that cooperativity in apoptosome formation is critically important for determining the healthy responses to apoptotic stimuli, and helps define the roles of Bax, Bcl-2, and MPTP vis-à-vis apoptosome formation