BuildBeta—A system for automatically constructing beta sheets

We describe a method that can thoroughly sample a protein conformational space given the protein primary sequence of amino acids and secondary structure predictions. Specifically, we target proteins with β‐sheets because they are particularly challenging for ab initio protein structure prediction because of the complexity of sampling long‐range strand pairings. Using some basic packing principles, inverse kinematics (IK), and β‐pairing scores, this method creates all possible β‐sheet arrangements including those that have the correct packing of β‐strands. It uses the IK algorithms of ProteinShop to move α‐helices and β‐strands as rigid bodies by rotating the dihedral angles in the coil regions. Our results show that our approach produces structures that are within 4–6 Å RMSD of the native one regardless of the protein size and β‐sheet topology although this number may increase if the protein has long loops or complex α‐helical regions. Proteins 2010. © Published 2009 Wiley‐Liss, Inc.     

Postnatal handling reverses social anxiety in serotonin receptor 1A knockout mice

Mice lacking the serotonin receptor 1A (Htr1a knockout, Htr1a ^KO ) show increased innate and conditioned anxiety. This phenotype depends on functional receptor activity during the third through fifth weeks of life and thus appears to be the result of long-term changes in brain function as a consequence of an early deficit in serotonin signaling. To evaluate whether this phenotype can be influenced by early environmental factors, we subjected Htr1a knockout mice to postnatal handling, a procedure known to reduce anxiety-like behavior and stress responses in adulthood. Offspring of heterozygous Htr1a knockout mice were separated from their mother and exposed 15 min each day from postnatal day 1 (PD1) to PD14 to clean bedding. Control animals were left undisturbed. Maternal behavior was observed during the first 13 days of life. Adult male offspring were tested in the open field, social approach and resident–intruder tests and assessed for corticosterone response to restraint stress. Knockout mice showed increased anxiety in the open field and in the social approach test as well as an enhanced corticosterone response to stress. However, while no effect of postnatal handling was seen in wild-type mice, handling reduced anxiety-like behavior in the social interaction test and the corticosterone response to stress in knockout mice. These findings extend the anxiety phenotype of Htr1a ^KO mice to include social anxiety and demonstrate that this phenotype can be moderated by early environmental factors.     

Redox potential of the Rieske iron-sulfur protein: Quantum-chemical and electrostatic study

Quantum-chemical study of structures, energies, and effective partial charge distribution for several models of the Rieske protein redox center is performed in terms of the B3LYP density functional method in combination with the broken symmetry approach using three different atomic basis sets. The structure of the redox complex optimized in vacuum differs markedly from that inside the protein. This means that the protein matrix imposes some stress on the active site resulting in distortion of its structure. The redox potentials calculated for the real active site structure are in a substantially better agreement with the experiment than those calculated for the idealized structure. This shows an important role of the active site distortion in tuning its redox potential. The reference absolute electrode potential of the standard hydrogen electrode is used that accounts for the correction caused by the water surface potential. Electrostatic calculations are performed in the framework of the polarizable solute model. Two dielectric permittivities of the protein are employed: the optical permittivity for calculation of the intraprotein electric field, and the static permittivity for calculation of the dielectric response energy. Only this approach results in a reasonable agreement of the calculated and experimental redox potentials.     

Association of permanent arterial hypertension with the renin-angiotensin and kinin-bradykinin system genes in children

A new approach, based on scoring, was proposed for a more objective estimation of the contribution of several genetic variants to a multifactorial disease. Two variants of the approach—genotype scoring and unfavorable factor scoring—were tested by analyzing the polymorphisms of REN (I9–83G>A), AGT (M235T), ACE (I/D), AGTR1 (1166A>C), ATGR2 (3123C>A), and BKR2 (?58T>C and I/D) in children with arterial hypertension (AH). Each of the two variants reported that the genes of the renin-angiotensin and kinin-brady-kinin systems play an important role in permanent AH in girls.     

Model-free analysis of binding at lipid membranes employing micro-calorimetric measurements

Based on universal thermodynamic principles (Schwarz in Biophys Chem 86:119–129, 2000) it is shown how measured enthalpy changes can be utilized to determine the relevant binding isotherm as well as the variation of the molar enthalpy change. This is carried out in a novel way involving multiple titration experiments whose evaluation requires no beforehand assumptions or models whatever. An appropriate specific model mechanism may be discussed afterwards and developed in view of the given experimental results. The pertinent procedure is demonstrated using micro-calorimetric data obtained in the case of the local anesthetic dibucaine as it associates with POPC liposomes. Mutual interactions of the bound ligand molecules could be described in terms of repulsive enthalpic and entropic activity coefficients. Apparently these are induced by electrostatic forces and by the finite size of binding sites, respectively.     

A P system and a constructive membrane-inspired DNA algorithm for solving the Maximum Clique Problem

We present a P system with replicated rewriting to solve the Maximum Clique Problem for a graph. Strings representing cliques are built gradually. This involves the use of inhibitors that control the space of all generated solutions to the problem. Calculating the maximum clique for a graph is a highly relevant issue not only on purely computational grounds, but also because of its relationship to fundamental problems in genomics. We propose to implement the designed P system by means of a DNA algorithm. This algorithm is then compared with two standard papers that addressed the same problem and its DNA implementation in the past. This comparison is carried out on the basis of a series of computational and physical parameters. Our solution features a significantly lower cost in terms of time, the number and size of strands, as well as the simplicity of the biological implementation.     

Sample size reestimation by Bayesian prediction

We review a Bayesian predictive approach for interim data monitoring and propose its application to interim sample size reestimation for clinical trials. Based on interim data, this approach predicts how the sample size of a clinical trial needs to be adjusted so as to claim a success at the conclusion of the trial with an expected probability. The method is compared with predictive power and conditional power approaches using clinical trial data. Advantages of this approach over the others are discussed.     

Steady-state analysis of metabolic pathways: comparing the double modulation method and the lin-log approach

The increasing interest in studying enzyme kinetics under in vivo conditions requires practical methods to estimate control parameters from experimental data. In contrast to currently established approaches of dynamic modelling, this paper addresses the steady-state analysis of metabolic pathways. Within the framework of metabolic control analysis (MCA), elasticity coefficients are used to describe the control properties of a local enzyme reaction. The double modulation method is one of the first experimental approaches to estimate elasticity coefficients from measurements of steady-state flux rates and metabolite concentrations. We propose a generalized form of the double modulation method and compare it to the recently developed linear-logarithmic approach.     

Systemic Neurochemical Alterations in Schizophrenic Brain: Glutamate Metabolism in Focus

We have used a systemic approach to establish a relationship between enzyme measures of glial glutamate and energy metabolism (glutamine synthetase and glutamine synthetase-like protein, glutamate dehydrogenase isoenzymes, brain isoform creatine phosphokinase) and two major glial proteins (glial fibrillary acidic protein and myelin basic protein) in autopsied brain samples taken from patients with schizophrenia (SCH) and mentally healthy subjects (23 and 22 cases, respectively). These biochemical parameters were measured in tissue extracts in three brain areas (prefrontal cortex, caudate nucleus, and cerebellum). Significant differences in the level of at least one of the glutamate metabolizing enzymes were observed between two studied groups in all studied brain areas. Different patterns of correlative links between the biochemical parameters were found in healthy and schizophrenic brains. These findings give a new perspective to our understanding of the impaired regulation of enzyme levels in the brain in SCH.     

A taxonomic survey of lactic acid bacteria isolated from wheat (Triticum durum) kernels and non-conventional flours

In order to explore the correspondence between raw material- and mature sourdough-lactic acid bacterial (LAB) communities, 59 Italian wheat (Triticum durum) grain samples, one bran and six non-conventional flour samples were analyzed through a culture-dependent approach. The highest cell count by an agar medium specific for LAB was 2.16 log CFU/g. From about 2300 presumptive LAB (Gram-positive and catalase-negative) colonies collected, a total of 356 isolates were subjected to identification by a genetic polyphasic strategy consisting of RAPD-PCR analysis, partial 16S rRNA gene sequencing, species-specific and multiplex PCRs. The isolates were recognized as 137 strains belonging to Aerococcus, Enterococcus, Lactobacillus, Lactococcus and Pediococcus genera and a phylogram based on partial 16S rRNA genes was constructed. The species most frequently found were Enterococcus faecium, Enterococcus mundtii and Lactobacillus graminis, which are not generally reported to be typical in mature sourdoughs.