40．Study on the Release of B₁₂ form BtuF with Steered Molecular Dynamics Simulation

Cun-Xin Wang（王存新）, Ming Liu, Ting-Guang Sun, Wei-Zu Chen

北京工业大学 生命科学与生物工程学院

cxwang@bjut.edu.cn

BtuF is a periplasmic binding protein (PBP) that binds vitamin B₁₂ and delivers it to the periplasmic surface of BtuCD. PBP generally exhibits considerable conformational changes during ligand binding process. However, BtuF was found to be a closed structure for both monomer and complex structure with vitamin B₁₂ by X-ray experiment. In this work, the constant-velocity Steered Molecular Dynamics (cv-SMD) simulations were performed to understand the release process of B₁₂ form BtuF.

The complex structure of BtuF and B₁₂ was taken from the crystal structure (PDB entry: 1N4A), including 4008 solute atoms, 9503 water molecules, 9 ions (32526 atoms in total). In the cv-SMD procedure, a virtual spring was attached to the B₁₂ center of mass and was pulled along the minus z-axis with the constant velocity of 5×10^-4 nm/ps. The force constant of the virtual spring is 3500 pN/nm. The cv-SMD simulations were repeated four times with the same initial conditions for calculating the potential of mean force (PMF) employing Jarzynski’s equality. In every cv-SMD simulation, C_α atoms in the interconnection domain of BtuF were constrained (k = 5000 pN/nm) to prevent unexpected deformations. The B₁₂ molecule was slowly pulled out of the binding site along the minus z-axis for d = 1.8 nm (displacement). The simulation time of every cv-SMD simulation is 3.6 ns.

According to cv-SMD simulation data, a potential of mean force was calculated along the vitamin B₁₂ release pathway. The free energy change for B₁₂ unbinding is 113 kJ.mol^-1. This large free energy differences of the B₁₂ release process indicate that the affinity between BtuF and B₁₂ is very strong. From the principal component analysis for the complex of BtuF and B₁₂, it is found that shows clear opening-closing and twisting motion tendencies. These motion tendencies may facilitate the unbinding of B₁₂ from the binding pocket. The intrinsic flexibility of BtuF was also analyzed. It is found that Trp44-Gin45 pair located at the mouth of the B₁₂ binding pocket acts as a gate in the B₁₂ binding and unbinding process. All above results are helpful for us to understand the release process of B₁₂ form BtuF.

41．利用布朗动力学研究组蛋白与DNA的相互作用

王鹏业

中国科学院物理研究所，软物质物理实验室

pywang@aphy.iphy.ac.cn

利用布朗动力学模拟方法研究了核小体的形成动力学，提出了组蛋白八聚体旋转模型来解释DNA与组蛋白八聚体的作用过程。组成核小体的DNA在受到拉伸力时，组蛋白可被从核小体中剥离下来。我们模拟了这一拉伸的过程，得到了剥离过程的详细图像，给出了拉伸力与拉伸长度的关系和拉伸台阶。根据模拟结果提出了组蛋白的剥离模型。

通过可调的组蛋白手征性模型，模拟了核小体手征性的形成。发现DNA的缠绕方向强烈依赖于组蛋白的手征性。结果还显示出环境温度对核小体手征性有重要影响，提高温度可打破核小体的手征性。

我们模拟了由染色质重组复合体引起的DNA弯曲对组蛋白定向滑移的影响。结果表明，在核小体一边的DNA上产生一个弯曲环后，组蛋白八聚体会向这个弯曲环滑动，直至这个弯曲环消失。DNA弯曲环的大小是影响组蛋白八聚体会滑动的重要因素。

通过改变DNA与组蛋白八聚体之间的相互作用力，我们研究了组蛋白修饰（磷酸化、乙酰化、甲基化）对核小体结构的影响。布朗动力学结果显示核小体的结构稳定性很敏感地依赖于相互作用力的大小。DNA从修饰后的组蛋白八聚体上一圈一圈地解离下来。我们还研究了温度影响、DNA断点的影响以及修饰后的组蛋白八聚体与非修饰组蛋白八聚体的竞争效应。解释了DNA断点处的磷酸化核小体更容易解离的现象。

42．金属离子耦合的锌指蛋白折叠

王 炜

南京大学 物理系

wangwei@nju.edu.cn

金属离子一类重要的辅助因子，由于缺少一个合理的描述金属离子与蛋白质相互作用的理论模型，金属离子辅助的蛋白质折叠问题目前还仅仅局限于实验研究。通过将量子化学的计算结果整合到经典的分子动力学中，以及考虑金属离子诱导的去质子化等效应和金属离子诱导的极化效应。我们研究了典型的金属蛋白“锌指蛋白”的折叠过程，给出了金属离子与蛋白质结合的详细路径，以及金属离子的结合在蛋白质折叠中的作用。发现锌离子不仅可以稳定锌指蛋白的天然态结构，并且参与整个蛋白质折叠过程，调控蛋白质二级结构的折叠顺序与相对稳定性。这种金属离子在蛋白质二级结构折叠中的作用是由疏水核的形成所介导。同时，计算结果还表明锌指蛋白折叠过程中存在错误配位与配体交换现象。

43．Folding pathways of beta-hairpin

肖奕

华中科技大学物理系

yxiao@mail.hust.edu.cn

After ten-year investigations, the folding mechanisms of beta-hairpins are still under debate. Experiments strongly support zip-out pathway, while most simulations prefer the hydrophobic collapse model (including middle-out and zip-in pathways). We show that all pathways can occur during the folding of beta-hairpins but with different probabilities. The zip-out pathway is the most probable one. This is in agreement with the experimental results. We came to our conclusions by thirty-eight 100-ns room-temperature all-atom molecular dynamics simulations and 2700 20-ns United-Residue (UNRES) Langevin dynamics simulations of the beta-hairpin trpzip2. Our results may help to clarify the inconsistencies in the current pictures of β-hairpin folding mechanisms.

44．Single-Molecule Enzymology with Dynamic Disorder

薛晓川

清华大学高等研究中心

xuexc05@mails.tsinghua.edu.cn

The classic Michaelis-Menten equation describes the catalytic activities for ensembles of enzyme molecules very well. But recent single-molecule experiment showed that the waiting time distribution and other properties of single enzyme molecule were not consistent with the prediction based on the view point of ensemble. It has been contributed to the slow conformational changes of single enzyme in the catalytic processes. In this work we study the general dynamics of single enzyme in the presence of dynamic disorder. We find that, within the time separation regimes, i.e., the slow reaction and nondiffusion limits,

Michaelis-Menten equation exactly holds. Particularly, by employing the decoupling approximation we demonstrate analytically that the classic Michaelis-Menten equation is still an excellent approximation in the presence of general dynamic disorder. Especially, with this novel concept, we can understand the experimental results of a recent force-stretched single-molecule enzymatic reaction.

45．Experimental and theoretical studies of DNA micromechanics

严洁

National University of Singapore

phyyj@nus.edu.sg

The long DNA molecules are tightly compacted in cells, bacterial, and viruses. This tight folding is done at a cost of a huge DNA bending energy since DNA is rigid at short lengths. Using single-molecule manipulation and imaging methods, here we present our recent studies of the micromechanics of tightly bent DNAs. We show that local DNA defects may appear under above threshold bending curvature. Further investigations show that the defects are critical to understand recently reported anomalous DNA elasticity observed for short DNA under tight bending conditions. Our methods can be easily applied to the studies the micromechanics of other bio-molecules in cells.

46．A Logic-Based Technique that Characterizes the Class of Boolean Networks Producing a Given Biological Pathway

曾辰

George Washington University/华中科技大

chenz@gwu.edu

This talk considers Boolean models of biological networks as commonly applied to gene regulation. In such networks, any given start state leads deterministically to a sequence of states that end in an attractor or repeat in a cycle. Some recent work have constructed Boolean networks to explain particular biological pathways such as the cell cycle, in which the sequence of states is known to correspond to a particular biological function, and which raise interesting questions: how many networks produce a given sequence? What makes the naturally occurring network unique amongst these? This talk focuses on a logic-based technique to analyze such networks and, as a result, identifies an interesting property of the class of networks modeling the cell-cycle that helps address the latter question.

47．Local-majority-rule dynamics: Influence of network structure and dynamics-driven structural evolutions

周海军

中国科学院理论物理研究所

zhouhj@itp.ac.cn

The mutual influence of structure and dynamical processes in a complex networked system is an active yet challenging research topic. In the present report we approach this problem by studying a simple model system, namely the local majority-rule (LMR) dynamics on an evolving network. We first show analytically and by computer simulation that the structure of the network can have a qualitative influence on the typical relaxation time of the LMR dynamics, and that scale-free networks with decaying exponent $\gamma$ in the tiny range of $2< \gamma <2.5$ are particularly

efficient for the LMR process. Then we demonstrated that, under simple local rules of dynamics-structure feedback, the LMR dynamics can slowly drive the underlying network into a highly heterogeneous structure with high clustering coefficient and scale-free-like degree distributions. Most interestingly, a global hub emerges spontaneously in the network, which has direct interaction with a major fraction of all the other vertices of the network.

This work is done in collaboration with Reinhard Lipowsky and Zhen Shao.

References:

H. J. Zhou and R. Lipowsky, PNAS, 102 (2005), 10052-10057.

H. J. Zhou and R. Lipowsky, JSTAT, P01009 (2007).

Z. Shao and H. J. Zhou, arXiv: 0804.3181v1 (2008).

48．Effect of the Ordered Water on Protein Folding: An Off-Lattice Go-Like Model Study

左光宏

复旦大学物理系

ghzuo@fudan.edu.cn

Recent experiments have shown that the water molecules confined on the surfaces of some substrates, including the surfaces of cellular components in tissues and cells, form icelike ordered structures. Here, the effect of this ordered water on protein folding is studied quantitatively by using an off-lattice Go-like model. Our results show that the ordered water significantly promotes both the stability and the folding rate of proteins. Moreover, it is found that both the stability and the folding rate with respect to the size of the confined space can be characterized by negative exponential laws with close exponential parameters for different proteins.

49．Genome-Wide Identification and Evolutionary Analysis of the Plant Specific

SBP-box Transcription Factor Family

An-Yuan Guo, Qi-Hui Zhu, Xiaocheng Gu, Song Ge, Ji Yang, Jingchu Luo（罗静初）

北京大学生物信息中心

luojc@pku.edu.cn

We made genome-wide analyses to explore the evolutionary process of the SBP-box gene family. We identified 120 SBP-box genes from nine species representing the main green plant lineages: green alga, moss, lycophyte, gymnosperm and angiosperm. A maximum-likelihood phylogenetic tree was constructed using the protein sequences of the DNA-binding domain of SBP-box genes (SBP-domain). Our results revealed that all SBP-box genes of green alga clustered into a single clade (CR group), while all genes from land plants fell into two distinct groups. Group I had a single copy in each species except for poplar while group II had several members in each species and can be divided into several subgroups. The SBP-domain encoded by all SBP-box genes possesses two zinc fingers. The C-terminal zinc finger of both group I and group II had the same C2HC motif while their N-terminal zinc finger showed different signatures, C4 in group I and C3H in group II. The patterns of exon-intron structure in Arabidopsis and rice SBP-box genes were consistent with the phylogenetic results. A target site of microRNA miR156 was highly conserved among land plant SBP-box genes. Our results suggested that the SBP-box gene family might have originated from a common ancestor of green plants, followed by duplication and divergence in each lineage including exon-intron loss processes.

50．PlantTFDB: a comprehensive plant transcription factor database.

Guo AY, Chen X, Gao G, Zhang H, Zhu QH, Liu XC, Zhong YF, Gu X, He K, Luo J. （罗静初）

北京大学生物信息中心

luojc@pku.edu.cn

We made genome-wide analyses to explore the evolutionary process of the SBP-box gene family. We identified 120 SBP-box genes from nine species representing the main green plant lineages: green alga, moss, lycophyte, gymnosperm and angiosperm. A maximum-likelihood phylogenetic tree was constructed using the protein sequences of the DNA-binding domain of SBP-box genes (SBP-domain). Our results revealed that all SBP-box genes of green alga clustered into a single clade (CR group), while all genes from land plants fell into two distinct groups. Group I had a single copy in each species except for poplar while group II had several members in each species and can be divided into several subgroups. The SBP-domain encoded by all SBP-box genes possesses two zinc fingers. The C-terminal zinc finger of both group I and group II had the same C2HC motif while their N-terminal zinc finger showed different signatures, C4 in group I and C3H in group II. The patterns of exon-intron structure in Arabidopsis and rice SBP-box genes were consistent with the phylogenetic results. A target site of microRNA miR156 was highly conserved among land plant SBP-box genes. Our results suggested that the SBP-box gene family might have originated from a common ancestor of green plants, followed by duplication and divergence in each lineage including exon-intron loss processes.

51．Study of DNA bending elasticity by AFM Imaging of circular DNA

陈虎

新加坡国立大学物理系

phych@nus.edu.sg

Unusual DNA elasticity observed under tight bending conditions has been debated and has drawn great attentions from biologists and biophysicists. We present a new experimental evidence displaying unusual DNA bending elasticity by analyzing the shape distributions of DNA minicircles of size 189 and 378 base-pairs which are relaxed in 2D surface. The distributions are found different from the predictions by the canonical WLC model. The bending energy of DNA is smaller than WLC under the sharp bending conditions, which indicates that it is not so difficult to form sharp bending conformations as predicted by WLC model.Different non-linear bending elasticity models are discussed to explain all related experiments about DNA bending elasticity.

52．人类灵长类特有锌指蛋白ZNF480在肌管分化和形成过程中的多级调控作用

吴秀山

湖南师范大学心脏发育研究中心

Xiushanwu2003@yahoo.com.cn

灵长类特有锌指蛋白约占人类基因组中最大蛋白家族－Kruppel锌指蛋白的三分之一，至今尚无任何关于这些基因功能性研究的报道（Aaron T.等，2006）。我们选择小鼠C2C12细胞系模型，以灵长类特有锌指基因ZNF480为代表，研究该类蛋白的蛋白结合位点与功能的进化关系。研究结果表明，人类 ZNF480基因的mRNA 和蛋白表达水平随小鼠细胞模型的肌管分化和形成过程而上调，明显促进小鼠C2C12细胞系的肌管的生成，说明ZNF480尽管已进化为灵长类特有锌指基因，其调控哺乳类肌肉细胞分化的功能仍然得以保留。为了进一步探讨灵长类ZNF480蛋白调控哺乳类肌肉细胞分化的分子调控机制，我们研究了ZNF480蛋白与小鼠/人类myogenin启动子上的保守结合位点的关系，发现ZNF480蛋白能与小鼠/人类myogenin启动子的保守结合位点结合，表明ZNF480蛋白调控哺乳类肌肉细胞分化的功能是通过myogenin启动子的结合位点的保守性进化而实现的。同时，我们发现ZNF480蛋白和E12/MyoD蛋白在肌肉特异性基因MCK的启动子上形成了新的结合位点，ZNF480蛋白是与E12/MyoD蛋白形成复合体，结合在MCK启动子上的新结合位点上，共同增强MCK的转录活性，从而促进小鼠肌细胞分化和肌管的形成。这些结果证实了我们克隆的人类灵长类特有基因ZNF480在促进小鼠肌细胞分化和肌管形成中的多级调控作用，为解释灵长类特有锌指蛋白的功能进化提供了新的模型。

53．从衰老生化本质看“上医治未病”的科学道理

印大中

湖南师范大学生命科学学院

dazhongyin@hotmail.com

尽管“上医治未病”是中医对待疾病和健康问题的一个突出的思维优势，但解读其中隐含的科学原理却是中西医结合生命科学所面临的极大的难题。本专题以系统生物医学和老年医学的最新研究进展为基础，以（能量）代谢组学和蛋白质表达后在衰老过程中的生化变化规律及其相互作用的专业知识为启迪，将“中医治本”与生命在应激过程中出现的“亚健康”生理生化过程贯通思考，为传统中医体系中诸多“防重于治”的医疗措施和理论提出了现代科学的解释。

54．葡萄糖和RyR通道调控的胰腺β细胞

詹璇，贾亚

华中师范大学物理学院

zhanx@phy.ccnu.edu.cn

我们的主要工作是，首次将葡萄糖浓度和Ryanodine受体（RyR）通道引入到胰腺β细胞模型中，讨论了葡萄糖浓度和RyR通道对胰腺β细胞膜电位振荡形式的影响。结果表明细胞对葡萄糖浓度变化的响应比激活RyR通道时更加快速，而以上两种方法都可以使膜电位从超极化的静息态变成爆发式振荡的电活性。当葡萄糖浓度低于刺激值时适量的激活RyR通道也能使膜电位发生爆发式振荡以及引发细胞液内自由Ca^2＋平均浓度的增加。特别是，发现适当激活RyR通道时膜电位会出现一种复杂振荡，并且这种复杂振荡形式可能比一般的爆发式振荡能更有效的引发胰岛素分泌。我们还对模型进行动力学分析以帮助了解参数变化引发振荡形式变化的原因。

55．Intrinsic peroxidase-like activity of ferromagnetic nanoparticles and application in an immunoassay

阎锡蕴

中国科学院生物物理研究所

yanxy@sun5.ibp.ac.cn

Nanoparticles that contain magnetic materials, such as magnetite (Fe₃O₄), are particularly useful for imaging and separation techniques. Since these nanoparticles are generally considered to be biologically and chemically inert, they are typically coated with metal catalysts, antibodies or enzymes to increase their functionality as separation agents. Here, we report that magnetite nanoparticles in fact possess an intrinsic enzyme mimetic activity similar to that found in natural peroxidases, which are widely used to oxidize organic substrates in the treatment of wastewater or as detection tools. Based on this finding, we have developed a novel immunoassay in which antibody-modified magnetite nanoparticles provide three functions: capture, separation and detection. The stability, ease of production and versatility of these nanoparticles makes them a powerful tool for a wide range of potential applications in medicine, biotechnology and environmental chemistry.

56．A charge driven molecular water pump inspired by the structure of biological channels (aquaporins)

方海平

中国科学院上海应用物理研究所

Fanghaiping@sinap.ac.cn

Understanding and controlling the transport of water across nanochannels is of great importance for designing novel molecular devices, machines and sensors and has wide applications, including the desalination of seawater. Nano-pumps driven by electric or magnetic fields can transport ions and magnetic quanta, but water is charge-neutral and has no magnetic moment. On the basis of molecular dynamics simulations, we propose a design for a molecular water pump. The design uses a combination of charges positioned adjacent to a nanopore, and is inspired by the structure of channels in the cellular membrane that conduct water in and out of the cell (aquaporins). The remarkable pumping ability is attributed to the charge dipole-induced ordering of water confined in the nanochannels where water can be easily driven by external fields in a concerted fashion. These findings may provide possibilities for developing water transport devices that function without osmotic pressure or a hydrostatic pressure gradient.

57．单个RNA分子力致折叠和去折叠时间序列的Bayesian分析

柳飞

清华大学高等研究中心，北京

liufei@mail.tsinghua.edu.cn

单个RNA分子力致折叠和去折叠光阱实验可以获得大量的分子延展时间序列。从这些序列中推断出RNA分子内在物理参数是个相当有意义的生物物理学问题。在这个工作中我们理论考察了这种可能性。我们首先构建了该实验系统的一个粗粒化理论模型，并在此模型的基础上，提出了一个基于Monte Carlo Markov链的Bayesian分析方法。我们的计算表明，该方法在推断分子内在物理参数是相当有效和精确的。

58．Exact Shape Equation of Solid Lipid Monolayer Domain : A Primary Model for Raft Formation in Membranes

欧阳钟灿

中国科学院理论物理研究所

oy@itp.ac.cn

Solid lipid monolayer domain surround by a fluid phase is studied by the equilibrium between line tension and long range dipole-dipole interaction. An exact domain shape equation is derived in form without introducing an artificial cutoff distance between dipoles. By introducing a cut-off of interaction distance between molecular dipoles to prevent divergence of the terms relating electrostatic dipole-dipole energy we obtained a approximate shape equation. From the equation we have found its analytic solutions among which a kinked shape solution (i.e., a cusp appears in the boundary) is nicely confirmed in many experimental observations in lipid monolayer. It reveals that the electrostatic dipole-dipole energy, a double line integral same as the Neumann’s formula for self-inductance of a single coil, can be regarded as the formation mechanism of raft in membranes.

References:

[1] M. Iwamoto and Ou-Yang Zhong-can, Phys. Rev. Lett. 93, 206101 (2004)

[2] M. Iwamoto, Liu Fei, and Ou-Yang Zhong-can, J. Chem. Phys. 125, 224701 (2006)