Visualizing the Induced Binding of SH2-Phosphopeptide.

Approximately 100 proteins in the human genome contain an SH2 domain recognizing small flexible phosphopeptides. It is therefore important to understand in atomistic detail the way these peptides bind and the conformational changes that take place upon binding. Here, we obtained several spontaneous binding events between the p56 lck SH2 domain and the pYEEI peptide within 2 Å RMSD from the crystal structure and with kinetic rates compatible with experiments using high-throughput molecular dynamics simulations. Binding is achieved in two phases, fast contacts of the charged phospho-tyrosine and then rearrangement of the ligand involving the stabilization of two important loops in the SH2 domain. These observations provide insights into the binding pathways and induced conformations of the SH2-phosphopeptide complex which, due to the characteristics of SH2 domains, should be relevant for other SH2 recognition peptides.

Immunolymphoscintigraphy for metastatic sentinel nodes: test of a model.

Aim. To develop a method and obtain proof-of-principle for immunolymphoscintigraphy for identification of metastatic sentinel nodes. Methods. We selected one of four tumour-specific antibodies against human breast cancer and investigated (1), in immune-deficient (nude) mice with xenograft human breast cancer expressing the antigen if specific binding of the intratumorally injected, radioactively labelled, monoclonal antibody could be scintigraphically visualized, and (2) transportation to and retention in regional lymph nodes of the radioactively labelled antibody after subcutaneous injection in healthy rabbits. Results and Conclusion. Our paper suggests the theoretical possibility of a model of dual isotope immuno-lymphoscintigraphy for noninvasive, preoperative, malignant sentinel node imaging.

High-throughput all-atom molecular dynamics simulations using distributed computing.

Although molecular dynamics simulation methods are useful in the modeling of macromolecular systems, they remain computationally expensive, with production work requiring costly high-performance computing (HPC) resources. We review recent innovations in accelerating molecular dynamics on graphics processing units (GPUs), and we describe GPUGRID, a volunteer computing project that uses the GPU resources of nondedicated desktop and workstation computers. In particular, we demonstrate the capability of simulating thousands of all-atom molecular trajectories generated at an average of 20 ns/day each (for systems of approximately 30 000-80 000 atoms). In conjunction with a potential of mean force (PMF) protocol for computing binding free energies, we demonstrate the use of GPUGRID in the computation of accurate binding affinities of the Src SH2 domain/pYEEI ligand complex by reconstructing the PMF over 373 umbrella sampling windows of 55 ns each (20.5 mus of total data). We obtain a standard free energy of binding of -8.7 +/- 0.4 kcal/mol within 0.7 kcal/mol from experimental results. This infrastructure will provide the basis for a robust system for high-throughput accurate binding affinity prediction.

HLA associations in insulin-dependent diabetes mellitus diagnosed during pregnancy.

Sixty out of 63 patients with insulin-dependent diabetes mellitus (IDDM) diagnosed during pregnancy in the Diabetes Centre at the Department of Obstetrics and Gynaecology, Rigshospitalet, Copenhagen, were re-examined 2-16 years after diagnosis. Fourty-six patients were currently insulin-treated and the remaining 14 patients were all severely glucose intolerant. HLA-typing was carried out in 41 of these patients. The HLA phenotype distribution showed a highly significant difference from that of non-diabetics but was similar to that seen in IDDM not related to pregnancy. Thus, pregnancy may constitute a special trigger mechanism for IDDM, but the subsequent pathogenic mechanisms are probably the same as those involved in other cases of IDDM.

Increased incidence of true type I diabetes acquired during pregnancy.

A longitudinal study was carried out of all patients with newly acquired insulin dependent diabetes during pregnancy (as distinct from non-insulin-dependent gestational diabetes) seen at the Copenhagen Centre for Diabetes and Pregnancy during 1966 to 1980. The series comprised 63 patients with a mean age of 27 (SEM 1) years. At diagnosis the mean fasting blood glucose concentration was 15.6 (1.3) mmol/l and mean maximal insulin dose 49 (3) IU/day. At a prospective follow up examination a mean of 8 (SEM 1) years after diagnosis 46 of 60 patients (77%) were being treated with insulin (35 (2) IU/day) and had a very low mean stimulated plasma C peptide value (0.12 (0.02) nmol/l) suggesting absent or nearly absent beta cell function. The remaining 14 patients (23%), not currently receiving insulin, appeared to be severely glucose intolerant, having a mean fasting blood glucose concentration of 13.4 (1.2) mmol/l. Thus most of these patients developing insulin dependent diabetes during pregnancy had true type I disease. Compared with the age specific incidence of type I diabetes in the background population of women the incidence was at least 70% higher in pregnant than non-pregnant women (p less than 0.001; chi 2 = 11.6; f = 1). This increased incidence occurred in the third trimester when the risk of developing type I diabetes was 3.8 times that of non-pregnant women (p less than 0.000001; chi 2 = 35.6; f = 1). Finally, the risk of developing insulin dependent diabetes during pregnancy was lower when conception occurred in the winter (p less than 0.05; chi 2 = 4.18; f = 1).

Glucose tolerance in early pregnancy.

The effect of pregnancy on oral glucose tolerance (50 g of glucose) and plasma insulin and glucagon responses to oral glucose was studied in weeks 10 and 32 of pregnancy and again 1 year post partum in 12 normal women. Already in week 10, fasting plasma glucose was decreased and the glucose-induced insulin secretion increased as compared with post partum. However, glucose tolerance was not affected at this time. In week 32, glucose tolerance had deteriorated, although the levels of both fasting and glucose-induced insulin were higher than those found in early pregnancy and post partum. At all investigations fasting plasma glucagon and the suppression of plasma glucagon after oral glucose were similar, indicating that glucagon is not implicated in the changes in glucose homeostasis seen in pregnancy. It is concluded that glucose tolerance is unaltered by pregnancy in week 10. Pregnancy has, however, at this very early stage already affected glucose homeostasis as seen by the decrease in fasting plasma glucose and the increase in the insulin response to glucose.

Insulin receptors in normal pregnant women and women with gestational diabetes.

In a serial study of insulin receptor binding to monocytes from normal pregnant women, a significant increase in insulin binding in mid pregnancy followed by a significant decrease in late pregnancy at tracer insulin concentration was found. No changes in the insulin concentration necessary to reduce tracer binding by 50% (ID50) were observed. At delivery, binding to isolated adipocytes was significantly lower in normal pregnant women than in non-pregnant normal controls while no difference in ID50 was observed. No differences in insulin binding at tracer insulin concentration to monocytes and adipocytes between normal weight women with gestational diabetes and healthy non-diabetic pregnant controls were found, but the ID50 was significantly lower in women with gestational diabetes diagnosed in late pregnancy than in pregnant controls at the same weeks of gestation.