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.     

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.     

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。     

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。     

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。     

Multiple Functions of BCL-2 Family Proteins

BCL-2 family proteins are the regulators of apoptosis, but also have other functions. This family of interacting partners includes inhibitors and inducers of cell death. Together they regulate and mediate the process by which mitochondria contribute to cell death known as the intrinsic apoptosis pathway. This pathway is required for normal embryonic development and for preventing cancer. However, before apoptosis is induced, BCL-2 proteins have critical roles in normal cell physiology related to neuronal activity, autophagy, calcium handling, mitochondrial dynamics and energetics, and other processes of normal healthy cells. The relative importance of these physiological functions compared to their apoptosis functions in overall organismal physiology is difficult to decipher. Apoptotic and noncanonical functions of these proteins may be intertwined to link cell growth to cell death. Disentanglement of these functions may require delineation of biochemical activities inherent to the characteristic three-dimensional shape shared by distantly related viral and cellular BCL-2 family members.     

O-GlcNAc修饰蛋白质的生理功能和研究方法

氧连N-乙酰葡糖胺（O-GlcNAc）修饰是与磷酸化相类似的蛋白质翻译后修饰方式,它主要发生在细胞核和细胞质中的蛋白质上．与细胞信号通路密切相关,成为近年来的研究热点。该文主要从O-GlcNAc修饰蛋白质的生理功能和研究方法两方面介绍该领域近年来的研究成果。     

Five Hierarchical Levels of Sequence-Structure Correlation in Proteins

This article reviews recent work towards modelling protein folding pathways using a bioinformatics approach. Statistical models have been developed for sequence-structure correlations in proteins at five levels of structural complexity: (i) short motifs; (ii) extended motifs; (iii) nonlocal pairs of motifs; (iv) 3-dimensional arrangements of multiple motifs; and (v) global structural homology. We review statistical models, including sequence profiles, hidden Markov models (HMMs) and interaction potentials, for the first four levels of structural detail. The I-sites (folding Initiation sites) Library models short local structure motifs. Each succeeding level has a statistical model, as follows: HMMSTR (HMM for STRucture) is an HMM for extended motifs; HMMSTR-CM (Contact Maps) is a model for pairwise interactions between motifs; and SCALI-HMM (HMMs for Structural Core ALIgnments) is a set of HMMs for the spatial arrangements of motifs. The parallels between the statistical models and theoretical models for folding pathways are discussed in this article; however, global sequence models are not discussed because they have been extensively reviewed elsewhere. The data used and algorithms presented in this article are available at http://www.bioinfo.rpi.edu/~bystrc/ (click on "servers" or "downloads") or by request to bystrc@rpi.edu .     

高等植物微管组织中心及其相关蛋白

就高等植物微管组织中心及其相关蛋白质的研究进展作了简要介绍.     

Rab11的结构特征、效应因子与功能

Rab11是Rab小分子GTP酶家族的成员.在细胞内膜泡再循环途径中,Rab11作为重要调节因子,介导膜泡从内体向质膜的运输.近年来随着对Rab11研究的深入,人们发现该蛋白质在多种细胞生命活动中发挥着关键作用.现对Rab11的结构、效应蛋白及功能等方面进行了综述.     

间隙连接分子Cx43相关蛋白及其功能研究进展

间隙连接是细胞间直接进行信息交流的唯一膜通道结构。Cx43是构成间隙连接中分布最广、研究最多的间隙连接分子,目前运用免疫共沉淀、免疫荧光共定位、pull-down以及酵母双杂交等多种方法研究发现了众多的Cx43相关蛋白。这些蛋白通过与Cx43相互作用在间隙连接蛋白的组装、运输、膜定位,间隙连接通道的形成以及对间隙连接通讯的调控等一系列过程中均发挥十分重要的作用。本文就目前已经研究发现的Cx43相关蛋白及其最新的功能研究进展进行综述。     

Heat Shock Proteins: Functions and Role in Adaptation to Hyperthermia

The results are generalized of many-year studies into the adaptive role of heat shock proteins in different animals, including the representatives of cold- and warm-blooded species that inhabit regions with different thermal conditions. Adaptive evolution of the response to hyperthermia can lead to different results depending on the species. The thermal threshold of induction of the heat shock proteins in desert thermophylic species is, as a rule, higher than in the moderate climate species. In addition, thermoresistant species are often characterized by a certain level of heat shock proteins in cells even at a physiologically normal temperature. Although adaptation to hyperthermia is achieved in most cases without changes in the number of heat shock genes, they can be amplified in some cases in termophylic species. The role of mobile elements in evolution of the heat shock genes was shown and approach was developed for directional introduction of mutations in the promoter regions of these genes.__________Translated from Ontogenez, Vol. 36, No. 4, 2005, pp. 265–273.Original Russian Text Copyright © 2005 by Evgen’ev, Garbuz, Zatsepina.     

胰岛再生源蛋白(Reg)在组织修复中的功能和调控机制

胰岛再生源蛋白(regenerating islet-derived protein,Reg)是一个多功能分子,在多种生理、病理活动中发挥重要作用。该文主要综述Reg蛋白在组织损伤后促进细胞增殖、抑制炎症因子过表达、调控细胞凋亡和抑制病原微生物生长和扩散的功能及调控机制,为治疗组织损伤提供新思路和新途径。     

Proteinase Inhibitors as Antistress Proteins in Higher Plants

Physicochemical and functional characteristics of plant protein proteinase inhibitors as antistress biopolymers were studied to determine the mechanisms for plant resistance to phytopathogens and to obtain disease-resistant cereal and leguminous cultures. The activity of trypsin, chymotrypsin, and subtilisin inhibitors varied in monocotyledonous and dicotyledonous cultures. Study varieties of leguminous and cereal cultures were shown to contain endogenous inhibitors specific to proteinases of phytopathogenic fungi Fusarium, Colletotrichum, Helminthosporium, and Botrytis. These inhibitors were characterized by species specificity and variety specificity. Protease inhibitors from buckwheat seeds inhibited proteases of fungal pathogens and suppressed germination of spores and growth of the fungal mycelium. Our results suggest that proteinaceous inhibitors of proteinases are involved in the protective reaction of plants under stress conditions.__________Translated from Prikladnaya Biokhimiya i Mikrobiologiya, Vol. 41, No. 4, 2005, pp. 392–396.Original Russian Text Copyright © 2005 by Dunaevskii, Tsybina, Belyakova, Domash, Sharpio, Zabreiko, Belozerskii.