Modeling the Correlation Functions of Conformational Motions in Proteins

Abstract

A first principles calculation of the correlation function for conformational motion (CM) in proteins is carried out within the framework of a microscopic model of a protein as a heterogeneous system. The fragments of the protein are assumed to be identical hard spheres undergoing the CM within their conformational potentials about some mean equilibrium positions assigned by the tertiary structure. The memory friction function (MFF) for the generalized Langevin equation describing the CM of the particle is obtained on the basis of the direct calculation which is feasible for the present model of the protein due to the existence of a natural large parameter, viz. the ratio of the minimal distance between the mean equilibrium positions of the particles (～7A) to the amplitude of their CM (<1A). A relationship between the MFF and the correlation functions of the CM of the particles is derived which makes their calculation to be a self-consistent mathematical problem. The general analysis of the MFF is exemplified by a simple model case in which the mean equilibrium positions of the particles form a regular lattice so that the correlation functions for all particles are the same. In this case the MFF is shown to be an infinite series of the powers of the auto-correlation function whose coefficients are independent on temperature. The latter is a result of the abstraction of the interaction potential by that of hard spheres which actually corresponds to the high temperature limit. On the examples of cubic and triangular lattices the coefficients are shown to be non-negative values which increase with the increase of the packing density of the particles and quickly tend to zero with the increase of their index. Thus the MFF can be approximated by a polynomial of the correlation function and the resulting mathematical equation is analogous to the one from the dynamic theory of liquids. The correlation function of the CM is obtained by numerical solution of the equation. At realistic packing densities for proteins it exhibits transparent non-exponential decay and includes two relaxation processes: the first one on the intermediate timescale (tens of picoseconds) and the second on the long timescale (its characteristic time is about tens of nanoseconds at small values of the friction coefficient and increases by orders of the magnitude with the increase of the latter). Thus the present approach provides the microscopic basis for previous phenomenologi- cal models of cooperative dynamics in proteins.     

Two- and Three-Dimensional Live Cell Imaging of DNA Damage Response Proteins

Double-strand breaks (DSBs) are the most deleterious DNA lesions a cell can encounter. If left unrepaired, DSBs harbor great potential to generate mutations and chromosomal aberrations¹. To prevent this trauma from catalyzing genomic instability, it is crucial for cells to detect DSBs, activate the DNA damage response (DDR), and repair the DNA. When stimulated, the DDR works to preserve genomic integrity by triggering cell cycle arrest to allow for repair to take place or force the cell to undergo apoptosis. The predominant mechanisms of DSB repair occur through nonhomologous end-joining (NHEJ) and homologous recombination repair (HRR) (reviewed in²). There are many proteins whose activities must be precisely orchestrated for the DDR to function properly. Herein, we describe a method for 2- and 3-dimensional (D) visualization of one of these proteins, 53BP1.The p53-binding protein 1 (53BP1) localizes to areas of DSBs by binding to modified histones^3,4, forming foci within 5-15 minutes⁵. The histone modifications and recruitment of 53BP1 and other DDR proteins to DSB sites are believed to facilitate the structural rearrangement of chromatin around areas of damage and contribute to DNA repair⁶. Beyond direct participation in repair, additional roles have been described for 53BP1 in the DDR, such as regulating an intra-S checkpoint, a G2/M checkpoint, and activating downstream DDR proteins^7-9. Recently, it was discovered that 53BP1 does not form foci in response to DNA damage induced during mitosis, instead waiting for cells to enter G1 before localizing to the vicinity of DSBs⁶. DDR proteins such as 53BP1 have been found to associate with mitotic structures (such as kinetochores) during the progression through mitosis¹⁰.In this protocol we describe the use of 2- and 3-D live cell imaging to visualize the formation of 53BP1 foci in response to the DNA damaging agent camptothecin (CPT), as well as 53BP1''s behavior during mitosis. Camptothecin is a topoisomerase I inhibitor that primarily causes DSBs during DNA replication. To accomplish this, we used a previously described 53BP1-mCherry fluorescent fusion protein construct consisting of a 53BP1 protein domain able to bind DSBs¹¹. In addition, we used a histone H2B-GFP fluorescent fusion protein construct able to monitor chromatin dynamics throughout the cell cycle but in particular during mitosis¹². Live cell imaging in multiple dimensions is an excellent tool to deepen our understanding of the function of DDR proteins in eukaryotic cells.     

Marked Point Process: Using Correlation Functions to Explore a Spatial Data Set

The relationship between the locations of the clumps of sprouts, some morphological characteristics of the clumps and the local soil environment in an old sweet chestnut coppice are studied. The theory of marked point process, which has not yet been used extensively in forestry studies, is shown to be adequate for the analysis of this type of spatial data. The marks correspond to morphological characteristics of the clumps: “diameter”, “number of sprouts”, “height at one year”, and “height at three years”. Several covariance functions are described which give a method for exploring the spatial relationships within the stand. Some of these functions are introduced for the first time in an actual statistical analysis. By using these functions, it is shown that the clumps are regularly distributed. The variables “diameter” and “number of sprouts” are strongly spatially negatively correlated, whereas the heights are slightly or not correlated. By categorising the individuals according to the mark values, it is shown that the small clumps tended to be aggregated in the gaps between medium and large clumps. Values of heights in the ties of the distribution are related as well as their spatial correlation to the local soil environment.     

MAR结合蛋白及其调控功能

核基质结合区 （MAR)是真核生物中能与核基质结合的DNA片段.MAR通过与特异的MAR结合蛋白相互作用,在提高转基因表达水平、降低转基因个体之间表达水平差异以及染色体包装等方面具有重要的调控作用.目前,已在不同物种分离MAR结合蛋白,分别为核基质成分、核仁蛋白、组蛋白、叶绿体蛋白等,它们在调控基因表达、细胞发育、细胞凋亡、染色体包装等方面具有重要的功能.本文综述了目前分离出的MAR结合蛋白及其功能,并对MAR-结合蛋白研究作一展望.     

Small GTP-binding Proteins and their Functions in Plants

Small GTP-binding proteins exist in eukaryotes from yeast to animals to plants and constitute a superfamily whose members function as molecular switches that cycle between “active” and “inactive” states. They regulate a wide variety of cell functions such as signal transduction, cell proliferation, cytoskeletal organization, intracellular membrane trafficking, and gene expression. In yeast and animals, this superfamily is structurally classified into at least five families: the Ras, Rho, Rab, Arf/Sar1, and Ran families. However, plants contain Rab, Rho, Arf, and Ran homologs, but no Ras. Small GTP-binding proteins have become an intensively studied group of regulators not only in yeast and animals but also in plants in recent years. In this article we briefly review the class and structure of small GTP-binding proteins. Their working modes and functions in animals and yeast are listed, and the functions of individual members of these families in plants are discussed, with the emphasis on the recently revealed plant-specific roles of these proteins, including their cross-talk with plant hormones and other signals, regulation of organogenesis (leaf, root, and embryo), polar growth, cell division, and involvement in various stress and defense responses.     

高等植物病原相关蛋白

在过去的三十年中,人们对诱导系统性抗性——这一普遍存在于高等植物抗病过程中的现象——进行了深入研究。被真菌、细菌或病毒侵染后,植物表现出广泛的、长时间的系统性抗性。在这一过程中,植物细胞壁组成成分发生改变,表达各种病原相关蛋白(PR蛋白),并合成多种植物抗毒素。本文就主要的PR蛋白家族的结构和功能特性,PR蛋白的发现和分类,及PR蛋白的应用作一综述。     

DCAF家族蛋白研究进展

DCAF (DDB1-and CUL4-associated factor)是一类新发现的含"WDXR"结构域的蛋白质家族,其可与CRL4-DDB1构成E3泛素连接酶,通过对靶蛋白进行泛素化修饰,实现对细胞生长、分化、凋亡等一系列生命活动的调控。DCAF蛋白的异常表达通常与肿瘤、发育障碍等疾病密切相关。本文主要根据目前的研究成果对DCAF家族蛋白的功能及机制展开论述。     

Functions of TET Proteins in Hematopoietic Transformation

DNA methylation is a well-characterized epigenetic modification that plays central roles in mammalian development, genomic imprinting, X-chromosome inactivation and silencing of retrotransposon elements. Aberrant DNA methylation pattern is a characteristic feature of cancers and associated with abnormal expression of oncogenes, tumor suppressor genes or repair genes. Ten-eleven-translocation (TET) proteins are recently characterized dioxygenases that catalyze progressive oxidation of 5-methylcytosine to produce 5-hydroxymethylcytosine and further oxidized derivatives. These oxidized methylcytosines not only potentiate DNA demethylation but also behave as independent epigenetic modifications per se. The expression or activity of TET proteins and DNA hydroxymethylation are highly dysregulated in a wide range of cancers including hematologic and non-hematologic malignancies, and accumulating evidence points TET proteins as a novel tumor suppressor in cancers. Here we review DNA demethylation-dependent and -independent functions of TET proteins. We also describe diverse TET loss-of-function mutations that are recurrently found in myeloid and lymphoid malignancies and their potential roles in hematopoietic transformation. We discuss consequences of the deficiency of individual Tet genes and potential compensation between different Tet members in mice. Possible mechanisms underlying facilitated oncogenic transformation of TET-deficient hematopoietic cells are also described. Lastly, we address non-mutational mechanisms that lead to suppression or inactivation of TET proteins in cancers. Strategies to restore normal 5mC oxidation status in cancers by targeting TET proteins may provide new avenues to expedite the development of promising anti-cancer agents.     

植物过敏性蛋白质及其生物学功能

在引起I型超敏反应的变应原中 ,植物的花粉、果实和汁液可以分别作为吸入性变应原 (inhalentallergen)、食入性变应原 (ingestentallergen)、接触性变应原 (contactentallergen)使过敏者患上鼻炎、哮喘、枯草热等疾病。而其中引起这些超敏反应的植物类蛋白质本身在植物体内亦行使着特定的生物学功能。对这些植物类过敏性蛋白质的研究不仅在植物学本身研究中具有一定意义 ,同时在变态反应性疾病的免疫治疗中亦具有重要的应用价值。目前 ,这类涉及植物学、免疫学和变态反应学的研究逐渐形成了一个新的交叉研究领域。     

植物营养贮存蛋白及其生物学功能研究进展

植物营养贮存蛋白（vegetative storage proteins）是广泛存在于植物营养组织且含量丰富的蛋白,最初是作为植物氮源的临时贮存形式而被人们认识。然而,不同植物中的营养贮存蛋白的生化来源和生物学特性并不相同,并且除了营养贮存功能外,更重要的是这类蛋白在植物防御中也承担着多种多样的重要角色,或具有抗虫活性,或能够抑制病原细菌和病原真菌的生长,或参与植物防御过程中的信号转导等。对植物营养贮存蛋白在植物防御中作用机制的深入研究将使这类蛋白在新型生物农药的开发和植物抗病基因工程中具有广阔的应用前景。     

植物营养贮存蛋白及其生物学功能研究进展

植物营养贮存蛋白(vegetative storage proteins )是广泛存在于植物营养组织且含量丰富的蛋白, 最初是作为植物氮源的临时贮存形式而被人们认识。然而, 不同植物中的营养贮存蛋白的生化来源和生物学特性并不相同, 并且除了营养贮存功能外, 更重要的是这类蛋白在植物防御中也承担着多种多样的重要角色, 或具有抗虫活性, 或能够抑制病原细菌和病原真菌的生长, 或参与植物防御过程中的信号转导等。对植物营养贮存蛋白在植物防御中作用机制的深入研究将使这类蛋白在新型生物农药的开发和植物抗病基因工程中具有广阔的应用前景。     

被膜蛋白糖基化在HIV感染中的作用

在HIV感染过程中,病毒被膜蛋白糖基化起着重要作用。它使病毒粒子具有高度糖基化的表面,帮助HIV逃避人体免疫细胞识别和攻击。在病毒入侵时,被膜糖蛋白与宿主细胞表面的受体结合,并进行一系列构象变化,使病毒粒子顺利地与宿主细胞膜融合。介绍近年来对被膜蛋白糖基化过程与HIV成熟、感染和逃避免疫应答等方面分子水平作用机理的深入了解,这些作用机理将会有助于艾滋病疫苗的研制和以“糖链为靶”药物的开发。     

Nuclear Trafficking and Functions of Endocytic Proteins Implicated in Oncogenesis

A subset of proteins predominantly associated with early endosomes or implicated in clathrin‐mediated endocytosis can shuttle between the cytoplasm and the nucleus. Although the endocytic functions of these proteins have been extensively studied, much less effort has been expended in exploring their nuclear roles. Membrane trafficking proteins can affect signalling and proliferation and this can be achieved either at a nuclear or endocytic level. Furthermore, some proteins, such as Huntingtin interacting protein 1, are known as cancer biomarkers. This review will highlight the limits of our understanding of their nuclear functions and the relevance of this to signalling and oncogenesis.     

解偶联蛋白及功能研究进展

解偶联蛋白(ucP,uncoupling protein)是一类线粒体内膜上的载体,属于线粒体载体超家族,可以将H^ 从线粒体内膜渗漏到线粒体基质中,减少ATP的合成并产生热能。已知UCPl在小鼠中有维持体温和能量稳态的重要作用。而UCP2和UCP3可控制活性氧(reactive oxygen species,ROS)产生、调节脂肪酸氧化,并且在肥胖和糖尿病发生中有重要作用。     

利用酵母双杂交技术筛选与hPOT1相互作用的新蛋白

目的:利用酵母双杂交系统筛选与人POT1(human protection of telomeres 1,hPOT1)相互作用的蛋白。方法:以hPOT1的300～634氨基酸片段为诱饵,在人乳腺cDNA文库中筛选能与hPOT1相互作用的蛋白质;运用营养缺陷型培养基和X-α-Gal实验排除假阳性,并对阳性克隆进行序列测定和比对。结果:经过酵母双杂交筛选,发现7个与hPOT1相互作用的蛋白;选取NM23B与hPOT1通过GST-pull down和免疫共沉淀进行进一步的验证,结果证明它们确实存在相互作用。结论:hPOT1能与NM23B发生相互作用,在此实验基础上可以进一步研究NM23B与hPOT1相互作用的生物学意义。