Detection of an intermediate during the unfolding process of the dimeric ketosteroid isomerase

Failure to detect the intermediate in spite of its existence often leads to the conclusion that two-state transition in the unfolding process of the protein can be justified. In contrast to the previous equilibrium unfolding experiment fitted to a two-state model by circular dichroism and fluorescence spectroscopies, an equilibrium unfolding intermediate of a dimeric ketosteroid isomerase (KSI) could be detected by small angle X-ray scattering (SAXS) and analytical ultracentrifugation. The sizes of KSI were determined to be 18.7A in 0M urea, 17.3A in 5.2M urea, and 25.1A in 7M urea by SAXS. The size of KSI in 5.2M urea was significantly decreased compared with those in 0M and 7M urea, suggesting the existence of a compact intermediate. Sedimentation velocity as obtained by ultracentrifugation confirmed that KSI in 5.2M urea is distinctly different from native and fully-unfolded forms. The sizes measured by pulse field gradient nuclear magnetic resonance (NMR) spectroscopy were consistent with those obtained by SAXS. Discrepancy of equilibrium unfolding studies between size measurement methods and optical spectroscopies might be due to the failure in detecting the intermediate by optical spectroscopic methods. Further characterization of the intermediate using (1)H NMR spectroscopy and Kratky plot supported the existence of a partially-folded form of KSI which is distinct from those of native and fully-unfolded KSIs. Taken together, our results suggest that the formation of a compact intermediate should precede the association of monomers prior to the dimerization process during the folding of KSI.     

Choosing between two conflicting scientific hypotheses: The orce dilemmas

How may we choose between conflicting hypotheses when doing a scientific test? Bayesian theory of decision offers a tool to analyse what choosing actually is, preventing us either from giving too much value to rational compounds or from putting aside the scientists’ personal interests and prejudices. Gieres’ cognitive approach to the problem defines the Minimally Open-Minded Scientist’s approach as the right one to dial with the choice dilemma. This approach is used here to give an opinion on the status of the “Orce Man”.     

Exploring synonymous codon usage preferences of disulfide-bonded and non-disulfide bonded cysteines in the E. coli genome

High-quality data about protein structures and their gene sequences are essential to the understanding of the relationship between protein folding and protein coding sequences. Firstly we constructed the EcoPDB database, which is a high-quality database of Escherichia coli genes and their corresponding PDB structures. Based on EcoPDB, we presented a novel approach based on information theory to investigate the correlation between cysteine synonymous codon usages and local amino acids flanking cysteines, the correlation between cysteine synonymous codon usages and synonymous codon usages of local amino acids flanking cysteines, as well as the correlation between cysteine synonymous codon usages and the disulfide bonding states of cysteines in the E. coli genome. The results indicate that the nearest neighboring residues and their synonymous codons of the C-terminus have the greatest influence on the usages of the synonymous codons of cysteines and the usage of the synonymous codons has a specific correlation with the disulfide bond formation of cysteines in proteins. The correlations may result from the regulation mechanism of protein structures at gene sequence level and reflect the biological function restriction that cysteines pair to form disulfide bonds. The results may also be helpful in identifying residues that are important for synonymous codon selection of cysteines to introduce disulfide bridges in protein engineering and molecular biology. The approach presented in this paper can also be utilized as a complementary computational method and be applicable to analyse the synonymous codon usages in other model organisms.     

Kolmogorov complexity of epithelial pattern formation: The role of regulatory network configuration

The tissues of multicellular organisms are made of differentiated cells arranged in organized patterns. This organization emerges during development from the coupling of dynamic intra- and intercellular regulatory networks. This work applies the methods of information theory to understand how regulatory network structure both within and between cells relates to the complexity of spatial patterns that emerge as a consequence of network operation. A computational study was performed in which undifferentiated cells were arranged in a two dimensional lattice, with gene expression in each cell regulated by identical intracellular randomly generated Boolean networks. Cell–cell contact signalling between embryonic cells is modeled as coupling among intracellular networks so that gene expression in one cell can influence the expression of genes in adjacent cells. In this system, the initially identical cells differentiate and form patterns of different cell types. The complexity of network structure, temporal dynamics and spatial organization is quantified through the Kolmogorov-based measures of normalized compression distance and set complexity. Results over sets of random networks that operate in the ordered, critical and chaotic domains demonstrate that: (1) ordered and critical networks tend to create the most information-rich patterns; (2) signalling configurations in which cell-to-cell communication is non-directional mostly produce simple patterns irrespective of the internal network domain; and (3) directional signalling configurations, similar to those that function in planar cell polarity, produce the most complex patterns, but only when the intracellular networks function in non-chaotic domains.     

Systematic development of computational models for the catalytic site in galactose oxidase: impact of outer-sphere residues on the geometric and electronic structures

A systematic in silico approach has been employed to generate sound, experimentally validated active-site models for galactose oxidase (GO) using a hybrid density functional, B(38HF)P86. GO displays three distinct oxidation states: oxidized [Cu(II)-Y*]; semireduced [Cu(II)-Y]; and reduced [Cu(I)-Y]. Only the [Cu(II)-Y*] and the [Cu(I)-Y] states are assumed to be involved in the catalytic cycle, but their structures have not yet been determined. We have developed several models (1-7) for the [Cu(II)-Y*] state that were evaluated by comparison of our computational results with experimental data. An extended model system (6) that includes solvent molecules and second coordination sphere residues (R330, Y405, and W290) is essential to obtain an experimentally correct electronic structure of the active site. The optimized structure of 6 resulted in a five-coordinate Cu site with a protein radical centered on the Tyr-Cys cofactor. We further validated our converged model with the largest model (7) that included additional outer-sphere residues (Q406, H334, Y329, G513, and T580) and water molecules. Adding these residues did not affect significantly the active site's electronic and geometric structures. Using both 6 and 7, we explored the redox dependence of the active-site structure. We obtained four- and three-coordinate Cu sites for [Cu(II)-Y] and [Cu(I)-Y] states, respectively, that corroborate well with the experimental data. The relative energies of these states were validated by a comparison with experimental redox potentials. Collectively, our computational GO models well reproduce the physicochemical characteristics of the individual states, including their redox behaviors.     

基于潜意识理论的青少年网络成瘾研究

本文综述了青少年网络成瘾的预防和戒除方法,坚持了"习惯说",保留了对"疾病说"的看法。基于潜意识理论,将网络成瘾视为心理亚健康状态,分析了青少年网络成瘾的发生机理、提出了其预防和戒除原则。青少年网络成瘾的成因是心理上的缺失感,与青少年自我防护意识差、自我控制能力小、心理弹性弱,以及潜意识具有反复影响才可改变的特点有关。戒除网络成瘾的原则是淡化评判试测的标准、分散注意力、培养成就感、增强自信心、坚持以心治心等。     

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes

Enzyme catalysis evolved in an aqueous environment. The influence of solvent dynamics on catalysis is, however, currently poorly understood and usually neglected. The study of water dynamics in enzymes and the associated thermodynamical consequences is highly complex and has involved computer simulations, nuclear magnetic resonance (NMR) experiments, and calorimetry. Water tunnels that connect the active site with the surrounding solvent are key to solvent displacement and dynamics. The protocol herein allows for the engineering of these motifs for water transport, which affects specificity, activity and thermodynamics. By providing a biophysical framework founded on theory and experiments, the method presented herein can be used by researchers without previous expertise in computer modeling or biophysical chemistry. The method will advance our understanding of enzyme catalysis on the molecular level by measuring the enthalpic and entropic changes associated with catalysis by enzyme variants with obstructed water tunnels. The protocol can be used for the study of membrane-bound enzymes and other complex systems. This will enhance our understanding of the importance of solvent reorganization in catalysis as well as provide new catalytic strategies in protein design and engineering.     

松墨天牛对不同生理状态黑松挥发物的触角电生理和行为反应

用水蒸气蒸馏法结合气相色谱以及气相色谱-质谱联用技术(GC-MS)分析了黑松的健康木和松材线虫危害木中的挥发性物质,并利用触角电位和嗅觉仪测定技术比较分析了松墨天牛对黑松健康木和被害木挥发物的触角电生理和行为反应特点及其对健康木挥发物的日龄变化规律.结果表明,未交配天牛对健康木挥发物的EAG反应值大于被害木,已交配天牛对被害木EAG反应值显著大于健康木;15日龄前的EAG反应值随日龄的增加而升高.在“Y”型嗅觉仪中,未交配天牛对健康木挥发物表现为正趋性,对被害木挥发物表现为负趋性;而已交配天牛对被害木挥发物表现为正趋性,对健康木挥发物表现为负趋性;雌天牛随着日龄的增加对健康木挥发物的正趋性逐渐增强,在15日龄时达到最大,雄天牛在9日龄时正趋性最强.说明不同发育时期的松墨天牛成虫对不同生理状态的黑松具有不同的敏感性和选择性.     

The end of the adaptive landscape metaphor?

The concepts of adaptive/fitness landscapes and adaptive peaks are a central part of much of contemporary evolutionary biology; the concepts are introduced in introductory texts, developed in more detail in graduate-level treatments, and are used extensively in papers published in the major journals in the field. The appeal of visualizing the process of evolution in terms of the movement of populations on such landscapes is very strong; as one becomes familiar with the metaphor, one often develops the feeling that it is possible to gain deep insights into evolution by thinking about the movement of populations on landscapes consisting of adaptive valleys and peaks. But, since Wright first introduced the metaphor in 1932, the metaphor has been the subject of persistent confusion, from equivocation over just what the features of the landscape are meant to represent to how we ought to expect the landscapes to look. Recent advances—conceptual, empirical, and computational—have pointed towards the inadequacy and indeed incoherence of the landscapes as usually pictured. I argue that attempts to reform the metaphor are misguided; it is time to give up the pictorial metaphor of the landscape entirely and rely instead on the results of formal modeling, however difficult such results are to understand in ‘intuitive’ terms.

免疫球蛋白重链可变段和T细胞受体可变段的分子进化研究

为阐明免疫球蛋白(Ig)和T细胞受体(TCR)在抗体多样性产生机理上的异同,作者比较了Ig重链可变段(Ig V_H)和TCR可变段(TCR V)的密码子替代率和协同进化,并分析异同的原因。共搜集8种鼠和3种人的TCR α链可变段(V_α),11种鼠和1种人的TCRβ链可变段(V_β),以及2种鼠和4种人的T细胞γ链可变段;同时搜集11种鼠、3种人、3种南美鳄鱼和1种鲨鱼的Ig V_(H_(o))研究结果揭示:(1)对编码蛋白质的密码子来说,TCR V(包括V_α和V_β)的核苷酸替代率为Ig V_H的2.4倍,说明前者有更高的替代率。(2)以协同进化而言,TCR V和Ig V_H的基因重复率分别为1.7×10~(-6)和1.6×10~(-6)/基因年。两者几乎相同,均系低速保持者。TCR V的数目(V_α为100,V_β为30)远少于Ig V_H(数目为300),原因是前者受到主要组织相容性复合体的制约,即受到负选择,这与中性学说观点相一致。文章还讨论了体细胞突变和DNA重排对两类抗体多样性产生上的作用,并探讨了IgV_H和TCR V的假基因问题。