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Dissection of the Zipping-and-Assembly Mechanism for Folding of Model Proteins

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Chinese physics Letters 2010年第3期27卷 332-335页

作者：孙理王骏王炜 Nanjing National Laboratory of Microstructure and Department of physics Nanjing University Nanjing 210093

Zipping-and-assembly mechanism （ZAM） is a new mechanism describing the kinetics of protein folding. To dissect the validity of this mechanism for various protein-like systems, a prediction test based on three-dimensional HP lattice models is carried out. It is found that only the native structures of a part of protein-like models could be predicted with a ZAM-based method. The detailed comparisons between the model proteins which are predicted or failed with the ZAM-based method suggest that the ZAM is likely to be applicable for the model proteins with the weak hydrophobicity, the low contact order for native conformations, and the large separation between the energies of native state and denatured states. These observations bring us more information about the protein-like systems for which the ZAM could be applied.

关键词： biological physics

Directivity of Spherical Polyhedron Sound Source Used in Near-Field HRTF Measurements

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Chinese physics Letters 2010年第12期27卷 109-112页

作者：余光正谢菠荪饶丹 Acoustic Laboratory Department of Physics School of Science South China University of Technology Guangzhou 510641 State Key Laboratory of Subtropical Building Science South China University of Technology Guangzhou 510641

The omnidirectional character is one of important requirements for the sound source used in near-field head- related transfer function （HRTF） measurements. Based on the analysis on the radiation sound pressure and directivity character of various spherical polyhedron sound sources, a spherical dodecahedral sound source with radius of O. 035 m is proposed and manufactured. Theoretical and measured results indicate that the sound source is approximately omnidirectional below the frequency of 8 kHz. In addition, the sound source has reasonable magnitude response from 350Hz to 20 kHz and linear phase characteristics. Therefore, it is suitable for the near-field HRTF measurements.

关键词： Medical physics biological physics

Pseudo-Spin Model for the Cytoskeletal Microtubule Surface

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Chinese physics Letters 2004年第11期21卷 2313-2315页

作者：陈莹邱锡钧李儒新 Departmentofphysics ShanghaiUniversityShanghai200436 ShanghaiInstituteofOpticsandFineMechanics ChineseAcademyofSciencesShanghai201800

Due to the inherent symmetry structures and the electric properties in the microtubule (MT), we treat the MT as a one-dimensional ferroelectric system and describe the nonlinear dynamics of dimer electric dipoles in one protofilament of the MT by virtue of the double-well potential. Consequently, the physical problem has been mapped onto the pseudo-spin system, and the mean-field approximation has been taken to obtain some physical results, including the expression for the phase transition temperature Tc and the estimated value of Tc (about 312 K).

关键词： biological physics

Water in the Neck-Zipper Region of Kinesin

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Chinese physics Letters 2009年第7期26卷 376-379页

作者：黄艳宾潘章张辉安莉孔德信纪青 School of Science Hebei University of Engineering Handan 056038 School of Science Hebei University of Technology Tianjin 300130 Basic Courses Department Tangshan College Tangshan 063000 Shandong Provincial Research Center for Bioinformatlc Engineering and Technique Center for Advanced Study Shandong University of Technology Zibo 255049

Neck linker （NL） is one of the most important mechanical elements of kinesin motors. The zipping up process of the neck-zipper （NZ） formed by NL and the related secondary structure elements is one of the major parts of kinesin＇s power stroke. All the weak interactions that are responsible for the formation of NZ are sensitive to or dependent on water. To investigate the role of water in the NZ region, a molecular dynamics （MD） model is set up with a crystal structure of kinesin 2KIN surrounded by a 10 A water layer, and minimization is performed to determine the positions of hydrogen atoms and other atoms. It is revealed that water molecules can assist the docking process of NL by forming hydrogen bonds at those positions where direct hydrogen bonding between the two sides of NZ is hindered and then acts as a constructive component of NZ at the docked state of NL. This result may improve the understanding of the mechanism for the docking of NL of kinesin wherein the function of water has not been comprehended sufficiently.

关键词： biological physics

An RNA Base Discrete State Model toward Tertiary Structure Prediction

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Chinese physics Letters 2010年第11期27卷 201-204页

作者：张建张玉洁王炜 National Laboratory of Solid State Microstructure Department of Physics Nanjing University Nanjing 210093

We report a new ribonucleic acid （RNA） base discrete state model, which was first developed in our lab and designed to provide an efficient and accurate way of representing RNA structures toward RNA three-dimensional structure predictions. Since RNA free energy is largely determined by base pairs and base stackings instead of backbone trajectories, we directly model the RNA base configurations with respect to its previous one along the sequence. This is in sharp contrast with all previous works where the backbone trace was represented. To test how faithfully the discrete model can reproduce the chain trace in continuous space, we randomly select partial chains from the native structure of 23S ribosome RNA and re-grow them. The rms distance of the re-grown structures from the native ones is ～1.7 ？ for an optimized 16-state discrete model and gradually increases to ～3.3 ？ for long chains of length 50. The efficiency is also good, e.g. the program will finish within several tens of second for long loops of length 50. Our model may facilitate the RNA three-dimensional structure predictions in the near future when combined with appropriate free energy evaluation methods.

关键词： biological physics

Effects of CRAC Channel on Spatiotemporal Ca2＋ Patterns in T Cells

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Chinese physics Letters 2010年第2期27卷 311-314页

作者：李丛鑫陈晓芳王鹏业王渭池 Chinese Acad Sci Inst Phys Beijing Natl Lab Condensed Matter Phys Lab Soft Matter Phys Beijing 100190 Peoples R China

A reaction-diffusion model is built to investigate the temporal and spatial patterns of cytoplasmic Ca2＋ dynamics under the effects of Ca2＋-release activated Ca2＋（CRAC） channels in T cells. Simulation results show a strong dependence of the modulation mode of Ca2＋ oscillation and dynamic patterns of Ca2＋ wave on the influx rate through the CRAC channel （ksoc）. When ksoc is small, cytoplasmic Ca2＋ is modulated as a frequency-modulation （FM） signal, whereas it shows an amplitude modulation （AM） mode after ksoc passes through a critical value. The heterogeneity in spatial Ca2＋ distribution is mostly arising from the influx through CRAC channels in both FM and AM modes. During each Ca2＋ spike, a more sustained cytoplasmic Ca2＋ gradient is maintained in the AM mode rather than in the FM mode.

关键词： biological physics

A Method to Design Synthetic Cell-Cycle Networks

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Chinese physics Letters 2009年第7期26卷 236-239页

作者：缪可可 National Laboratory of Solid State Microstructures Nanjing University Nanjing 210093

The interactions among proteins, DNA and RNA in an organism form elaborate cell-cycle networks which govern cell growth and proliferation. Understanding the common structure of cell-cycle networks will be of great benefit to science research. Here, inspired by the importance of the cell-cycle regulatory network of yeast which has been studied intensively, we focus on small networks with 11 nodes, equivalent to that of the cell-cycle regulatory network used by Li et al. [Proc. Natl. Acad. Sci. USA 101（2004）4781] Using a Boolean model, we study the correlation between structure and function, and a possible common structure. It is found that cascade-like networks with a great number of interactions between nodes are stable. Based on these findings, we are able to construct synthetic networks that have the same functions as the cell-cycle regulatory network.

关键词： biological physics

Geometrical Constraint Equations and Geometrically Permissible Condition for Vesicles

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Chinese physics Letters 2004年第10期21卷 2057-2058页

作者：殷雅俊尹杰 SchoolofAerospace DepartmentofEngineeringMechanicsTsinghuaUniversityBeijing100084

The application of a geometrical constraint equation for lipid bilayer vesicles is investigated. First, both the physical meaning and the mathematical formulation for the spontaneous curvature of vesicles are clarified. Second, the geometrically permissible conditions and phase diagrams for vesicles, from which the criteria for the formation, existence and disintegration of vesicles may be determined, are revealed.

关键词： biological physics

Growth and Form in Biology： Generation of the Plant Morphology by Spontaneous Symmetry Breaking Based on a Pressure Field

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Chinese physics Letters 2004年第1期21卷 211-214页

作者：翁羽翔 LaboratoryofSoftMatterphysics InstituteofPhysicsandCenter/'orCondensedMatterPhysicsChineseAcademyofSciencesBeijing100080

Considering the role of mechanical forces playing in the morphogenetic pattern formation, we propose a second-order differential equation for the growth and form of plants based on the turgor pressure field at the organ and cellular level. The solutions can well describe various kinds of morphological features of flowers under certain hypotheses. The plant morphology is considered as the spontaneous symmetry breaking of a circular growing boundary, while the employed hypotheses are subjected to further experimental confirmation.

关键词： biological physics