Molecular dynamics simulations give insight into the conformational change,complex formation,and electron transfer pathway for cytochrome P450 reductase

Cytochrome P450 reductase (CYPOR) undergoes a large conformational change to allow for an electron transfer to a redox partner to take place. After an internal electron transfer over its cofactors, it opens up to facilitate the interaction and electron transfer with a cytochrome P450. The open conformation appears difficult to crystallize. Therefore, a model of a human CYPOR in the open conformation was constructed to be able to investigate the stability and conformational change of this protein by means of molecular dynamics simulations. Since the role of the protein is to provide electrons to a redox partner, the interactions with cytochrome P450 2D6 (2D6) were investigated and a possible complex structure is suggested. Additionally, electron pathway calculations with a newly written program were performed to investigate which amino acids relay the electrons from the FMN cofactor of CYPOR to the HEME of 2D6. Several possible interacting amino acids in the complex, as well as a possible electron transfer pathway were identified and open the way for further investigation by site directed mutagenesis studies.     

Design,construction, and characterization of a second‐generation DARPin library with reduced hydrophobicity

Designed ankyrin repeat proteins (DARPins) are well‐established binding molecules based on a highly stable nonantibody scaffold. Building on 13 crystal structures of DARPin‐target complexes and stability measurements of DARPin mutants, we have generated a new DARPin library containing an extended randomized surface. To counteract the enrichment of unspecific hydrophobic binders during selections against difficult targets containing hydrophobic surfaces such as membrane proteins, the frequency of apolar residues at diversified positions was drastically reduced and substituted by an increased number of tyrosines. Ribosome display selections against two human caspases and membrane transporter AcrB yielded highly enriched pools of unique and strong DARPin binders which were mainly monomeric. We noted a prominent enrichment of tryptophan residues during binder selections. A crystal structure of a representative of this library in complex with caspase‐7 visualizes the key roles of both tryptophans and tyrosines in providing target contacts. These aromatic and polar side chains thus substitute the apolar residues valine, leucine, isoleucine, methionine, and phenylalanine of the original DARPins. Our work describes biophysical and structural analyses required to extend existing binder scaffolds and simplifies an existing protocol for the assembly of highly diverse synthetic binder libraries.     

The control of branching morphogenesis

Many organs of higher organisms are heavily branched structures and arise by an apparently similar process of branching morphogenesis. Yet the regulatory components and local interactions that have been identified differ greatly in these organs. It is an open question whether the regulatory processes work according to a common principle and how far physical and geometrical constraints determine the branching process. Here, we review the known regulatory factors and physical constraints in lung, kidney, pancreas, prostate, mammary gland and salivary gland branching morphogenesis, and describe the models that have been formulated to analyse their impacts.     

Dissecting the energy metabolism in Mycoplasma pneumoniae through genome‐scale metabolic modeling

Mycoplasma pneumoniae, a threatening pathogen with a minimal genome, is a model organism for bacterial systems biology for which substantial experimental information is available. With the goal of understanding the complex interactions underlying its metabolism, we analyzed and characterized the metabolic network of M. pneumoniae in great detail, integrating data from different omics analyses under a range of conditions into a constraint‐based model backbone. Iterating model predictions, hypothesis generation, experimental testing, and model refinement, we accurately curated the network and quantitatively explored the energy metabolism. In contrast to other bacteria, M. pneumoniae uses most of its energy for maintenance tasks instead of growth. We show that in highly linear networks the prediction of flux distributions for different growth times allows analysis of time‐dependent changes, albeit using a static model. By performing an in silico knock‐out study as well as analyzing flux distributions in single and double mutant phenotypes, we demonstrated that the model accurately represents the metabolism of M. pneumoniae. The experimentally validated model provides a solid basis for understanding its metabolic regulatory mechanisms.     

An in vivo control map for the eukaryotic mRNA translation machinery

Rate control analysis defines the in vivo control map governing yeast protein synthesis and generates an extensively parameterized digital model of the translation pathway. Among other non‐intuitive outcomes, translation demonstrates a high degree of functional modularity and comprises a non‐stoichiometric combination of proteins manifesting functional convergence on a shared maximal translation rate. In exponentially growing cells, polypeptide elongation (eEF1A, eEF2, and eEF3) exerts the strongest control. The two other strong control points are recruitment of mRNA and tRNA_i to the 40S ribosomal subunit (eIF4F and eIF2) and termination (eRF1; Dbp5). In contrast, factors that are found to promote mRNA scanning efficiency on a longer than‐average 5′untranslated region (eIF1, eIF1A, Ded1, eIF2B, eIF3, and eIF5) exceed the levels required for maximal control. This is expected to allow the cell to minimize scanning transition times, particularly for longer 5′UTRs. The analysis reveals these and other collective adaptations of control shared across the factors, as well as features that reflect functional modularity and system robustness. Remarkably, gene duplication is implicated in the fine control of cellular protein synthesis.     

Buchbesprechungen

Abstract

Schenk/Kolb: Grundriß der physiologischen Chemie, 6. überarbeitete Auflage. Erschienen im VEB Gustav Fischer Verlag Jena, 1971. Mit 116 Abb. und 237 Tab., Ganzleinen, Format 10,5 × 24,5 cm. Preis: 30,—M. Reviewed by H. Bergner.

H. Bergner: Energie — Leben — Leistung — Nahrung. Erschienen im Urania-Verlag Leipzig-Jena-Berlin 1971, 144 Seiten, mit 49 Abb. und 25 Tab., Ganzleinen, Format 14,5 × 21,5 cm, Preis: 9,80 M. Reviewed by H. Haenel.

G. Dirksen, W. Kaufmann und E. Pfeffer: Untersuchungen zur Verdauungs physiologie der Milchkuh mit der Umleitungstechnik am Duodenum. Erschienen im Verlag Paul Parey, Hamburg und Berlin 1972. 43 Seiten mit 10 Abb. und 22 Tab., kart., Format 16,5 × 25 cm, Preis: 22,00 DM (als Beiheft zur Z. Tierphys. Tierernähr. Futtermittelkd., für Bezicher der Zeitschrift 20,35 DM). Reviewed by H. Bergner.     

A stage-structured predator–prey model with distributed maturation delay and harvesting

ABSTRACT

A stage-structured predator–prey system with distributed maturation delay and harvesting is investigated. General birth and death functions are used. The local stability of each feasible equilibria is discussed. By using the persistence theory, it is proven that the system is permanent if the coexistence equilibrium exists. By using Lyapunov functional and LaSalle invariant principle, it is shown that the trivial equilibrium is globally stable when the other equilibria are not feasible, and that the boundary equilibrium is globally stable if the coexistence equilibrium does not exist. Finally, sufficient conditions are derived for the global stability of the coexistence equilibrium.     

Fat area and lipid droplet morphology of porcine oocytes during in vitro maturation with trans-10, cis-12 conjugated linoleic acid and forskolin

Lipid droplets (LD) in porcine oocytes form a dark mass reaching almost all cytoplasm. Herein we investigated changes in fat areas, cytoplasmic tone and LD morphology during in vitro maturation (IVM) of porcine oocytes cultured with 100 μM trans-10, cis-12 conjugated linoleic acid (t10,c12 CLA) or 10 μM forskolin at different time periods. Four groups were constituted: control, excipient, t10,c12 CLA and forskolin, with drugs being supplemented during 44 to 48 h and the initial 22 to 24 h in Experiments 1 and 2, respectively. In Experiment 3, forskolin was supplemented for the first 2 h. Matured oocytes were inseminated with frozen-thawed boar semen and cleavage rate recorded. Before and during IVM, samples of oocytes were evaluated for LD, total and fat areas and fat gray value or for meiotic progression. Results showed that forskolin supplementation during 44 to 48 h or 22 to 24 h inhibits oocyte maturation (exp. 1: forskolin = 5.1 ± 8.0%, control = 72.6 ± 5.0%; exp. 2: forskolin = 24.3 ± 7.4%, control = 71.6 ± 5.6%) and cleavage (exp. 1: forskolin = 0.0 ± 0.0%, control = 55.4 ± 4.1%; exp. 2: forskolin = 8.3 ± 3.3%, control = 54.5 ± 3.0%). Forskolin also reduced oocyte and fat areas. In Experiment 3, forskolin negative effect on oocyte maturation and cleavage disappeared, although minor (P ⩽ 0.03) LD and oocyte fat areas were identified at 22 to 24 h of IVM. Oocytes supplemented with t10,c12 CLA during 44 to 48 h presented a lighter (P ⩽ 0.04) colour tone cytoplasm than those of control and forskolin. In conclusion, t10,c12 CLA and forskolin were capable of modifying the distribution and morphology of cytoplasmic LD during porcine oocyte maturation, thus reducing its lipid content in a time-dependent manner.     

CT诊断用于胰腺癌侵犯胰周动静脉的临床价值分析

目的：探究CT诊断对于胰腺癌侵犯胰周动静脉的临床价值。方法：随机选取在我院就诊的64例胰腺癌患者,在他们进行手术前全在距离肿瘤边缘1cm内的血管进行分期和诊断进而进行螺旋CT检查。结果：经组织学术后病理切片染色发现胰周动脉29条,静脉48条。运用外科手术探查方法发现86条胰周动脉,89条胰周静脉。在这些血管中,有23条动脉、47条静脉经外科手术证实的确是肿瘤侵犯,并且经过CT诊断,我们最终断定为有25条动脉、46条静脉处于1～4级。结论：胰周动、静脉受到侵犯时,具有不同的CT表现特征,因此在利用CT方法判断胰周动、静脉遭受侵犯时应当根据不同情况不同对待。