Structural analyses of a hypothetical minimal metabolism

By integrating data from comparative genomics and large-scale deletion studies, we previously proposed a minimal gene set comprising 206 protein-coding genes. To evaluate the consistency of the metabolism encoded by such a minimal genome, we have carried out a series of computational analyses. Firstly, the topology of the minimal metabolism was compared with that of the reconstructed networks from natural bacterial genomes. Secondly, the robustness of the metabolic network was evaluated by simulated mutagenesis and, finally, the stoichiometric consistency was assessed by automatically deriving the steady-state solutions from the reaction set. The results indicated that the proposed minimal metabolism presents stoichiometric consistency and that it is organized as a complex power-law network with topological parameters falling within the expected range for a natural metabolism of its size. The robustness analyses revealed that most random mutations do not alter the topology of the network significantly, but do cause significant damage by preventing the synthesis of several compounds or compromising the stoichiometric consistency of the metabolism. The implications that these results have on the origins of metabolic complexity and the theoretical design of an artificial minimal cell are discussed.     

High-throughput modeling and analysis of protein structural dynamics

Protein function is a dynamic property closely related to the conformational mechanisms of protein structure in its physiological environment. To understand and control the function of target proteins, it becomes increasingly important to develop methods and tools for predicting collective motions at the molecular level. In this article, we review computational methods for predicting conformational dynamics and discuss software tools for data analysis. In particular, we discuss a high-throughput, web-based system called iGNM for protein structural dynamics. iGNM contains a database of protein motions for more than 20 000 PDB structures and supports online calculations for newly deposited PDB structures or user-modified structures. iGNM allows dynamics analysis of protein structures ranging from enzymes to large complexes and assemblies, and enables the exploration of protein sequence-structure-dynamics-function relations.     

不同培养方式对细菌纤维素产量和结构性质的影响

考察了自行筛选的Acetobacter xylinum NUST4.2在静置培养和发酵罐培养获得的细菌纤维素(BC)的产量、基本结构和性能的差异。结果表明:静置培养时产纤维素7.5g/L,产率为0.052g/L/h,在机械搅拌发酵罐中培养3d产量达3.13g/L,产率达0.043g/L/h;SEM分析显示静置培养和发酵罐培养得到的纤维素均具有网状结构,但静置获得的纤维素丝带相互缠绕且层状重叠,更加致密,丝带更细;FT-IR分析知搅拌不改变纤维素的化学结构,但能减弱分子间氢键,和XRD结合分析可知静置培养的纤维素具有更高结晶指数,更高Iα含量和更大晶粒尺寸,但不改变晶型,仍为纤维素I型,说明搅拌会干扰纤维素初始纤丝的结晶,有利于形成更小的晶粒和较Iα稳定的Iβ。与棉纤维素相比,静置培养获得的纤维素的热稳定性更好,而发酵罐培养获得的纤维素则阻燃性更好。     

A new method of biosensing with 1 microl of Escherichia coli suspension using atomic force microscopy

We developed a new method for detecting bacterial cells from 1-mul samples with atomic force microscopy (AFM). The use of a parafilm surface as a sample palette was effective for reacting small amounts of samples with an AFM probe. This was due to the parafilm's hydrophobic, semitransparent, and nonadhesive surface. In this way, all processes, such as the surface functionalization of a cantilever and the adhesion of Escherichia coli cells to a cantilever, were easily completed. In addition, we succeeded in detecting cell adsorption on the same AFM cantilever by both the drive mode and the thermal mode. The resonance frequency shift caused by cell adhesion was clearly detected by the two modes for the first time. Our data indicated the potential of applying AFM nanobiosensing to extremely small amounts of samples.     

Effects of organic and inorganic polyamine cations on the structure of human serum albumin

The presence of several high affinity binding sites on human serum albumin (HSA) makes it a possible target for many organic and inorganic molecules. Organic polyamines are widely distributed in living cells and their biological roles have been associated with their physical and chemical interactions with proteins, nucleic acids, and lipids. This study is designed to examine the effects of spermine, spermidine, putrescine, and cobalt [Co(III)]-hexamine cations on the solution structure of HSA using Fourier transform IR, UV-visible, and circular dichroism (CD) spectroscopic methods. The spectroscopic results show that polyamine cations are located along the polypeptide chains with no specific interaction. The order of perturbations is associated with the number of positive charges of the polyamine cation: spermine > Co(III)-hexamine > spermidine > putrescine. The overall binding constants are 1.7 x 10(4), 1.1 x 10(4), 5.4 x 10(3), and 3.9 x 10(3)M(-1), respectively. The protein conformation is altered (IR and CD data) with reductions of alpha helices from 60 to 55% for free HSA to 50-40% and with increases of beta structures from 22 to 15% for free HSA to 33-23% in the presence of polyamine cations.     

Constraints on the morphological evolution of marsupial shoulder girdles

Throughout their evolutionary histories, marsupial mammals have been taxonomically and morphologically less diverse than their sister taxa the placentals. Because of this, it has been proposed that the evolution of marsupials has been constrained by the functional requirements of their mode of reproduction. Marsupials give birth after short gestation times to immature neonates that immediately crawl, under the power of their precociously developed shoulder girdles, to the teat where they attach and complete their early development. Using a novel approach incorporating adult and embryological morphological data, this study is the first to both: (1) statistically support adult patterns of morphological divergence consistent with the constraint hypothesis, and (2) identify ontogenetic patterns of morphological change that demonstrate that the constraint was responsible, at least in part, for their formation. As predicted by the marsupial constraint, the shoulder girdles of adult marsupials are less diverse than those of adult placentals, and adult marsupial scapulae are less morphologically diverse than adult marsupial pelves. Furthermore, marsupials that complete an extensive crawl to the teat are restricted to a common pattern of ontogenetic scapular shape change, strongly supporting the hypothesis that the morphological development of the marsupial scapula has been limited evolutionarily by its obligate role in the crawl to the teat. Because this study establishes that ontogenetic and evolutionary morphological change is correlated within mammalian scapulae, it is probable that the marsupial constraint also restricted the morphological divergence of the scapula over evolutionary time by limiting ontogenetic change in the scapula. These findings, coupled with the importance of the shoulder girdle in mammalian locomotor specialization, support the conclusion that the low morphological diversity of marsupial forms over evolutionary time could be directly due to the constraint on marsupial morphological evolution caused by the functional requirements of the crawl to the teat.     

Intercellular calcium signalling in cultured renal epithelia: a theoretical study of synchronization mode and pacemaker activity

We investigate a two-dimensional lattice model representation of intercellular Ca²⁺ signalling in a population of epithelial cells coupled by gap junctions. The model is based on and compared with Ca²⁺ imaging data from globally bradykinin-stimulated MDCK-I (Madin-Darby canine kidney)-I cell layers. We study large-scale synchronization of relevance to our laboratory experiments. The system is found to express a wealth of dynamics, including quasiperiodic, chaotic and multiply-periodic behaviour for intermediate couplings. We take a particular interest in understanding the role of pacemaker cells in the synchronization process. It has been hypothesized that a few highly hormone-sensitive cells control the collective frequency of oscillation, which is close to the natural frequencies (without coupling) of these cells. The model behaviour is consistent with the conjectures of the pacemaker cell hypothesis near the critical coupling where the cells lock onto a single frequency. However, the simulations predict that the frequency in globally connected systems decreases with increasing coupling. It is found that a pacemaker is not defined by its natural frequency alone, but that other intrinsic or local factors must be considered. Inclusion of partly sensitized cells that do not oscillate autonomously in the cell layer increases the coupling necessary for global synchronization. For not excessively high coupling, these cells oscillate irregularly and with distinctive lower frequencies. In summary, the present study shows that the frequency of synchronized oscillations is not dictated by one or few fast-responding cells. The collective frequency is the result of a two-way communication between the phase-advanced pacemaker and its environment.     

Novel Properties of a Mouse γ-Aminobutyric Acid Transporter (GAT4)

We expressed the mouse gamma-aminobutyric acid (GABA) transporter GAT4 (homologous to rat/ human GAT-3) in Xenopus laevis oocytes and examined its functional and pharmacological properties by using electrophysiological and tracer uptake methods. In the coupled mode of transport (Na+/ Cl-/GABA cotransport), there was tight coupling between charge flux and GABA flux across the plasma membrane (2 charges/GABA). Transport was highly temperature-dependent with a temperature coefficient (Q10) of 4.3. The GAT4 turnover rate (1.5 s(-l); -50 mV, 21 degrees C) and temperature dependence suggest physiological turnover rates of 15-20 s(-1). No uncoupled current was observed in the presence of Na+. In the absence of external Na+, GAT4 exhibited two distinct uncoupled currents. (i) A Cl- leak current (ICl(leak)) was observed when Na+ was replaced with choline or tetraethylammonium. The reversal potential of (ICl(leak)) followed the Cl- Nernst potential. (ii) A Li+ leak current (ILi(leak)) was observed when Na+ was replaced with Li+. Both leak currents were inhibited by Na+, and both were temperature-independent (Q10 approximately 1). The two leak modes appeared not to coexist, as Li+ inhibited (ICl(leak)). The results suggest the existence of cation- and anion-selective channel-like pathways in GAT4. Flufenamic acid inhibited GAT4 Na+/Cl-/GABA cotransport, ILi(leak), and ICl(leak), (Ki approximately 30 microM), and the voltage-induced presteady-state charge movements (Ki approximately 440 microM). Flufenamic acid exhibited little or no selectivity for GAT1, GAT2, or GAT3. Sodium and GABA concentration jicroumps revealed that slow Na+ binding to the transporter is followed by rapid GABA-induced translocation of the ligands across the plasma membrane. Thus, Na+ binding and associated conformational changes constitute the rate-limiting steps in the transport cycle.     

Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model

In order to systematically analyze functionally relevant dynamical correlations within macromolecular complexes, we have developed computational methods based on the normal mode analysis of an elastic network model. First, we define two types of dynamical correlations (fluctuation-based and density-based), which are computed by summing up contributions from all low-frequency normal modes up to a given cutoff. Then we use them to select dynamically important "hinge residues" whose elastic distortion affects the fluctuations of a large number of residues. Second, in order to clarify long-range dynamical correlations, we decompose the dynamical correlations to individual normal modes to identify the most relevant modes. We have applied these methods to the analysis of the motor domain of Dictyostelium myosin and have obtained the following three interesting results that shed light on its mechanism of force generation: first, we find the hinge residues are distributed over several key inter-subdomain joints (including the nucleotide-binding pocket, the relay helix, the SH1 helix, the strut between the upper 50 kDa and the lower 50 kDa subdomains), which is consistent with their hypothesized roles in modulating functionally relevant inter-subdomain conformational changes; second, a single mode 7 (for structure 1VOM) is found to dominate the fluctuation-based correlations between the converter/strut and the nucleotide-binding pocket, revealing a surprising simplicity for their intriguing roles in the force generation mechanism; finally, we find a negative density-based correlation between the strut and the nucleotide-binding pocket, which is consistent with the hypothesized signaling pathway that links the actin-binding site's opening/closing with the nucleotide-binding pocket's closing/opening.     

Admixed sexual and facultatively asexual aphid lineages at mating sites

Cyclically parthenogenetic organisms may have facultative asexual counterparts. Such organisms, including aphids, are therefore interesting models for the study of ecological and genetic interactions between lineages differing in reproductive mode. Earlier studies on aphids have revealed major differences in the genetic outcomes of populations that are possibly resulting mostly either from sexual or from asexual reproduction. Besides, notable gene flow between sexual and asexual derivatives has been suspected, which could lead to the emergence of new asexual lineages. The present study examines the interplay between these lineages and is based on analyses of population structure of individuals that may contribute to the pool of sexual reproductive forms in the host alternating aphid Rhopalosiphum padi. Using a Bayesian assignment method, we first show that the sexual forms of R. padi on mating sites encompass two genetically distinct clusters of individuals in the western part of France. The first cluster included unique genotypes of sexual lineages, while the second cluster included facultatively asexual lineages in numerous copies, the reproductive mode of the two clusters being confirmed by reference clones. Sexual reproductive forms produced by sexual and facultatively asexual lineages are thus admixed at mating sites which gives a large opportunity for the two clusters to mate with each other. Nevertheless, this study also highlights, as previously demonstrated, that the two clusters retained high genetic differentiation. Possible explanations for the inferred limited genetic exchanges are advanced in the discussion, but further dedicated investigations are required to solve this paradox.