Geometric and Statistical Properties of the Mean-Field HP Model, the LS Model and Real Protein Sequences

Lattice models, for their coarse-grained nature, are best suited for the study of the ``designability problem'', the phenomenon in which most of the about 16,000 proteins of known structure have their native conformations concentrated in a relatively small number of about 500 topological classes of conformations. Here it is shown that on a lattice the most highly designable simulated protein structures are those that have the largest number of surface-core switchbacks. A combination of physical, mathematical and biological reasons that causes the phenomenon is given. By comparing the most foldable model peptides with protein sequences in the Protein Data Bank, it is shown that whereas different models may yield similar designabilities, predicted foldable peptides will simulate natural proteins only when the model incorporates the correct physics and biology, in this case if the main folding force arises from the differing hydrophobicity of the residues, but does not originate, say, from the steric hindrance effect caused by the differing sizes of the residues.Comment: 12 pages, 10 figure

Mean-Field HP Model, Designability and Alpha-Helices in Protein Structures

Analysis of the geometric properties of a mean-field HP model on a square lattice for protein structure shows that structures with large number of switch backs between surface and core sites are chosen favorably by peptides as unique ground states. Global comparison of model (binary) peptide sequences with concatenated (binary) protein sequences listed in the Protein Data Bank and the Dali Domain Dictionary indicates that the highest correlation occurs between model peptides choosing the favored structures and those portions of protein sequences containing alpha-helices.Comment: 4 pages, 2 figure

The role of visfatin in pathogenesis of gestational diabetes (GDM)

Gestational diabetes (GDM) is defined as a glucose intolerance of varying severity with onset or first recognition during pregnancy. Two major metabolic disorders: insulin resistance and β-cells dysfunction, play currently major role in pathogenesis of GDM. Adipose tissue is an organ involved in production of adipokines, which have various influence on metabolism of glucose and lipids. Visfatin is an adipokine mainly produced and secreted by the fat tissue. It exerts an insulin-like effect by binding to the insulin receptor-1 and have hypoglycemic effect. Visfatin appears to be an important factor in the pathophysiology of GDM. The aim of this article is to review the literature concerning the relationship between the adipokine mentioned above and GDM, and to clarify its role in the pathophysiology of GDM

Serferzy trzeciego wieku

The Library of Cracow University of Technology is working closely with the University of the Third Age of of Cracow University of Technology  for two years. As a part of the "Internet Week" program, workshops are organized. Participants are learning how to effectively search for data and information.Biblioteka Politechniki Krakowskiej od dwóch lat ściślej współpracuje z Uniwersytetem Trzeciego Wieku Politechniki Krakowskiej. W ramach kampanii „Tygodnia z Internetem” realizowane są warsztaty z wyszukiwania informacji

Sprawozdanie z seminarium „Otwieranie nauki – praktyka i perspektywy”

The report from a conference which took place in Cracow in 2016.Sprawozdanie z konferencji, która odbyła się w Krakowie we wrześniu 2016 roku

VII Bałtycka Konferencja „Zarządzanie i Organizacja Bibliotek” - sprawozdanie z konferencji

Sprawozdanie z VII Bałtyckiej Konferencji „Zarządzanie i Organizacja Bibliotek

Handicap-Recover Evolution Leads to a Chemically Versatile, Nucleophile-Permissive Protease.

Mutation of the tobacco etch virus (TEV) protease nucleophile from cysteine to serine causes an approximately ∼104 -fold loss in activity. Ten rounds of directed evolution of the mutant, TEVSer , overcame the detrimental effects of nucleophile exchange to recover near-wild-type activity in the mutant TEVSer X. Rather than respecialising TEV to the new nucleophile, all the enzymes along the evolutionary trajectory also retained the ability to use the original cysteine nucleophile. Therefore the adaptive evolution of TEVSer is paralleled by a neutral trajectory for TEVCys , in which mutations that increase serine nucleophile reactivity hardly affect the reactivity of cysteine. This apparent nucleophile permissiveness explains how nucleophile switches can occur in the phylogeny of the chymotrypsin-like protease PA superfamily. Despite the changed key component of their chemical mechanisms, the evolved variants TEVSer X and TEVCys X have similar activities; this could potentially facilitate escape from adaptive conflict to enable active-site evolution.We acknowledge financial support from the Biotechnology and Biological Sciences Research Council and MedImmune. F. H. is an ERC Starting Investigator.This is the final version of the article. It first appeared from Wiley at http://dx.doi.org/10.1002/cbic.20150029

Serum homocysteine and vitamin B12 levels in women with gestational diabetes mellitus

Objectives: Gestational diabetes mellitus (GDM) is described as a glucose intolerance of variable severity which begun or was firstly recognized during gravidity. Two major metabolic disorders, insulin resistance and β-cell dysfunction, currently play major role in pathogenesis of GDM. Our intention was to investigate total serum homocysteine and vitamin B12 levels in pregnant women with GDM and non-diabetic gravid women. Material and methods: Serum homocysteine and vitamin B12 levels were prospectively measured in a total of 79 pregnant women, 60 of whom were diagnosed with GDM, and 19 of whom were healthy controls. Serum homocysteine levels were analyzed by ELISA. Vitamin B12 concentrations were determined by chemiluminescent immunoassay, and lipids were determined enzymatically. Results: GDM and control groups did not differ in terms of the serum homocysteine levels (median 7.24 vs 7.97 umol/L, respectively, p = 0.15). Nor did we find any association between serum homocysteine levels and BMI (r = 0.06, p = 0.55, respectively). There was no correlation between serum homocysteine and fasting serum glucose (r = 0.3, p = 0.8, respectively). There was no relationship between serum homocysteine concentrations and glycosylated hemoglobin (HgbA1c) levels (r = 0.06, p = 0.67, respectively). Serum vitamin B12 concentrations did not differ between the GDM and control groups (median 286 vs 262 pg/mL, respectively, p = 0.17). We found that levels of Vitamin B12 correlated inversely with fasting serum glucose concentrations (r = -0.44, p = 0.0009). Vitamin B12 concentrations increased along with LDL (r = 0.27, p = 0.043) and HDL (r = 0.38, p = 0.004) levels, however were inversely correlated with serum triglycerides (r = -0.34, p = 0.009). Conclusions: GDM patients with low Vitamin B12 values tend to have higher fasting serum glucose and altered lipid profiles (high triglycerides, low HDL and LDL). In women with GDM, serum homocysteine levels are not associated with HbA1c level, fasting glycemia, or BMI