Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease

The emergence of compensatory drug-resistant mutations in HIV-1 protease challenges the common view of the reaction mechanism of this enzyme. Here, we address this issue by performing classical and ab initio molecular dynamics simulations (MD) on a complex between the enzyme and a peptide substrate. The classical MD calculation reveals large-scale protein motions involving the flaps and the cantilever. These motions modulate the conformational properties of the substrate at the cleavage site. The ab initio calculations show in turn that substrate motion modulates the activation free energy barrier of the enzymatic reaction dramatically. Thus, the catalytic power of the enzyme does not arise from the presence of a pre-organized active site but from the protein mechanical fluctuations. The implications of this finding for the emergence of drug-resistance are discussed.     

Prediction of human protein function from post-translational modifications and localization features

We have developed an entirely sequence-based method that identifies and integrates relevant features that can be used to assign proteins of unknown function to functional classes, and enzyme categories for enzymes. We show that strategies for the elucidation of protein function may benefit from a number of functional attributes that are more directly related to the linear sequence of amino acids, and hence easier to predict, than protein structure. These attributes include features associated with post-translational modifications and protein sorting, but also much simpler aspects such as the length, isoelectric point and composition of the polypeptide chain.     

Functional aspects of strepsirrhine lumbar vertebral bodies and spinous processes

The relationship between form and function in the lumbar vertebral column has been well documented among platyrrhines and especially catarrhines, while functional studies of postcranial morphology among strepsirrhines have concentrated predominantly on the limbs. This morphometric study investigates biomechanically relevant attributes of the lumbar vertebral morphology of 20 species of extant strepsirrhines. With this extensive sample, our goal is to address the influence of positional behavior on lumbar vertebral form while also assessing the effects of body size and phylogenetic history. The results reveal distinctions in lumbar vertebral morphology among strepsirrhines in functional association with their habitual postures and primary locomotor behaviors. In general, strepsirrhines that emphasize pronograde posture and quadrupedal locomotion combined with leaping (from a pronograde position) have the relatively longest lumbar regions and lumbar vertebral bodies, features promoting sagittal spinal flexibility. Indrids and galagonids that rely primarily on vertical clinging and leaping with orthograde posture share a relatively short (i.e., stable and resistant to bending) lumbar region, although the length of individual lumbar vertebral bodies varies phylogenetically and possibly allometrically. The other two vertical clingers and leapers, Hapalemur and Lepilemur, more closely resemble the pronograde, quadrupedal taxa. The specialized, suspensory lorids have relatively short lumbar regions as well, but the lengths of their lumbar regions are influenced by body size, and Arctocebus has dramatically longer vertebral bodies than do the other lorids. Lumbar morphology among galagonids appears to reflect a strong phylogenetic signal superimposed on a functional one. In general, relative length of the spinous processes follows a positively allometric trend, although lorids (especially the larger-bodied forms) have relatively short spinous processes for their body size, in accordance with their positional repertoire. The results of the study broaden our understanding of postcranial adaptation in primates, while providing an extensive comparative database for interpreting vertebral morphology in fossil primates.     

冈崎姬小蜂生物学特性的研究

 对美洲斑潜蝇幼虫寄生蜂──冈崎姬小蜂Neochrysocharis okazakii Kamijo生物学特 性的研究结果表明：（1）补充蜜汁能显著延长成蜂寿命;（2）在20～33℃范围内各虫 态发育速率与温度呈线性相关,发育起点温度81℃,完成一个世代需要1887日·度的积 温;成蜂寿命与温度呈负线性相关,产卵量在30℃时达到最大;内禀增长率与温度呈线性相 关。     

Mutation in collagen gene induces cardiomyopathy in transgenic mice

In many remodeling tissues, such as the heart, collagen degradation to provide new integrin-binding sites is required for survival. However, complete loss of integrin signaling due to disconnection from extracellular matrix (ECM) leads to apoptosis and dilatation. To test the hypothesis that a mutation in type I collagen gene induces cardiomyopathy, we employed a metalloproteinase-resistant collagen mutant homozygous transgenic male (B6,129-Colla-1) and compared with age-sex matched wildtype C57BL/J6 control mice. At the age of 38-42 weeks, aortic and left ventricle (LV) pressure were measured. The LV wall thickness and diameter were measured by a digital micrometer. The levels of matrix metalloproteinase-2 (MMP-2) activity and cardiospecific tissue inhibitor of metalloproteinase-4 (TIMP-4) were measured by zymography and Western blot analyses, respectively. The levels of collagenolysis were measured by Western blot using anti-collagen antibody. In transgenic and wildtype mice, end-diastolic pressure (EDP) was 8.3 +/- 1.7 and 6.5 +/- 1.1 mmHg; LV diameter was 3.43 +/- 0.07 and 2.94 +/- 0.05 mm; wall thickness was 1.18 +/- 0.03 and 1.28 +/- 0.04 mm; end-diastolic wall stress was 600 +/- 158 and 347 +/- 49 dynes/cm(2), respectively. The increase in LV wall stress was associated with increased MMP-2 activity, increased collagenolysis, and decreased levels of TIMP-4. This leads to reduced elastic compliance in collagen mutant transgenic mice. The occurrence of cardiomyopathy in adult Colla-1 mice may be a significant confounding factor as it may be indicative of increased basal levels of ECM disruption. This phenotype is what would be expected if collagen degradation normally supplies integrin ligands during cardiac muscle remodeling.     

Multi-compartmental modelling and experimental design for glucose transport studies in insulin-resistant rats

Many pathologies are associated with abnormalities of glucose metabolism or with perturbations of its transport (type 2 diabetes or insulin-resistance). The pre-diabetic state is characterised by a state of insulin-resistance, in others words a defect of glucose transport in insulin-sensible tissues, such as muscles and adipose tissues. The mathematical modelling of experimental data can be an excellent method to explore the mechanisms implied in the studied biological phenomenon. Thus, starting from a symbolic formulation like the compartmental modelling, it can be possible to develop a theoretical basis for the observation and to consider the best-adapted experiments for the study. We showed with mathematical models that [123I]-6-deoxy-6-iodo-D-glucose (6-DIG), shown as a tracer of glucose transport in vitro, could point out this transport abnormality. To quantify the insulin resistance, we estimated the fractional transfer coefficients of 6-DIG from the blood to the organs. We realised many studies to lead to a satisfying model; special attention has been paid to the precision of the parameter to select the best model. The results showed that by associating experimental data obtained with 6-DIG activities and an adapted mathematical model, discriminating parameters (in and out fractional transfer coefficients) between the two groups (control and insulin-resistant rats) could be pointed out.     

Pelvic and hindlimb musculature of Tyrannosaurus rex (Dinosauria: Theropoda)

In this article, we develop a new reconstruction of the pelvic and hindlimb muscles of the large theropod dinosaur Tyrannosaurus rex. Our new reconstruction relies primarily on direct examination of both extant and fossil turtles, lepidosaurs, and archosaurs. These observations are placed into a phylogenetic context and data from extant taxa are used to constrain inferences concerning the soft-tissue structures in T. rex. Using this extant phylogenetic bracket, we are able to offer well-supported inferences concerning most of the hindlimb musculature in this taxon. We also refrain from making any inferences for certain muscles where the resulting optimizations are ambiguous. This reconstruction differs from several previous attempts and we evaluate these discrepancies. In addition to providing a new and more detailed understanding of the hindlimb morphology of T. rex--the largest known terrestrial biped--this reconstruction also helps to clarify the sequence of character-state change along the line to extant birds.     

Functional-adaptive analysis of the hindlimb anatomy of extant marsupials and the paleobiology of the Paleocene marsupials Mayulestes ferox and Pucadelphys andinus

This article analyzes the adaptations of the hindlimb of two Early Paleocene marsupials, Mayulestes ferox and Pucadelphys andinus. This analysis is based on detailed comparisons with various extant marsupials, both South American and Australian. In the case of the South American opossums, original myological data were collected and osteological-myological associations were related to their locomotor behavior. The use of Australian genera helped to improve the appraisal of the locomotory habits of the fossil taxa. Several features are indicative of the ability of Mayulestes to climb or walk on uneven surfaces (e.g., very mobile hip joint, astragalocalcaneal joint pattern), and some other features emphasize a relative agility (e.g., strongly everted iliac blades, morphology of the distal epiphysis of the femur, medially stabilized cruroastragalar joint). Pucadelphys exhibits a hindlimb relatively similar morphologically to that of Mayulestes, but with features indicating slightly increased agility and a terrestrial component that is more emphasized than in Mayulestes. The Tiupampa fossils were therefore more agile than most living didelphids and resembled the condition observed in living dasyurids more. These conclusions complement a previous study performed on the forelimb of these fossils.