Dynamic Behavior of DNA Replication Domains

Like many nuclear processes, DNA replication takes place in distinct domains that are scattered throughout the S-phase nucleus. Recently we have developed a fluorescent double-labeling procedure that allows us to visualize nascent DNA simultaneously with “newborn” DNA that had replicated earlier in the same nucleus during the same S-phase. Using this procedure we have shown that all DNA in a replication domain is replicated within 1 h (Manderset al.,1992,J. Cell Sci.103, 857–862). Here we extend these studies by analyzing the behavior of replication domains on a time scale of less than 1 h. We have carried out a series of double-labeling experiments in which we varied the time interval between nascent DNA and newborn DNA from 0 to 60 min. Subsequently, we determined from the confocal, 3D images the spatial position of replicated DNA domains and identified pairs of nearest neighbor domains containing newborn and nascent DNA, respectively. The distance between the centers of the two domains in a pair gradually increases. Accurate measurements show that domains containing nascent DNA and domains containing newborn DNA gradually separate from each other at a rate that is on the order of 0.5 μm/h. This indicates that either newly synthesized DNA moves away from sites of replication activity or the replication machinery is moving itself. This rate is essentially the same during early and late S-phase.     

Coarsening Dynamics of Domains in Lipid Membranes

We investigate isothermal diffusion and growth of micron-scale liquid domains within membranes of free-floating giant unilamellar vesicles with diameters between 80 and 250 μm. Domains appear after a rapid temperature quench, when the membrane is cooled through a miscibility phase transition such that coexisting liquid phases form. In membranes quenched far from a miscibility critical point, circular domains nucleate and then progress within seconds to late stage coarsening in which domains grow via two mechanisms 1), collision and coalescence of liquid domains, and 2), Ostwald ripening. Both mechanisms are expected to yield the same growth exponent, α = 1/3, where domain radius grows as time^α. We measure α = 0.28 ± 0.05, in excellent agreement. In membranes close to a miscibility critical point, the two liquid phases in the membrane are bicontinuous. A quench near the critical composition results in rapid changes in morphology of elongated domains. In this case, we measure α = 0.50 ± 0.16, consistent with theory and simulation.     

生物立方膜

脂质立方液晶在药物载体方面有着较为广泛的应用.然而在生物体内,有一种与之类似的结构,称为立方膜.具体而言,立方膜就是指含有脂蛋白的三维周期性脂质双分子单层、双层或多层的纳米曲面结构.亚细胞器中的这种生物立方膜结构可能也能作为药物载体,同时有抗氧化、紫外滤光等潜在作用.本文将主要介绍立方膜的研究进展、形成机理,以及在自然界中的存在情况,及其功能和潜在的应用价值.     

Biological Roles of Prion Domains

In vivo amyloid formation is a widespread phenomenon in eukaryotes. Self-perpetuating amyloids provide a basis for the infectious or heritable protein isoforms (prions). At least for some proteins, amyloid-forming potential is conserved in evolution despite divergence of the amino acid (aa) sequences. In some cases, prion formation certainly represents a pathological process leading to a disease. However, there are several scenarios in which prions and other amyloids or amyloid-like aggregates are either shown or suspected to perform positive biological functions. Proven examples include self/nonself recognition, stress defense and scaffolding of other (functional) polymers. The role of prion-like phenomena in memory has been hypothesized. As an additional mechanism of heritable change, prion formation may in principle contribute to heritable variability at the population level. Moreover, it is possible that amyloid-based prions represent by-products of the transient feedback regulatory circuits, as normal cellular function of at least some prion proteins is decreased in the prion state.Key Words: amyloid, amyloidosis, epigenetic, evolution, inheritance, mammals, misfolding, protein, stress, yeast     

Biological Roles of Prion Domains

In vivo amyloid formation is a widespread phenomenon in eukaryotes. Self-perpetuating amyloids provide a basis for the infectious or heritable protein isoforms (prions). At least for some proteins, amyloid-forming potential is conserved in evolution despite divergence of the amino acid (aa) sequences. In some cases, prion formation certainly represents a pathological process leading to a disease. However, there are several scenarios in which prions and other amyloids or amyloid-like aggregates are either shown or suspected to perform positive biological functions. Proven examples include self/nonself recognition, stress defense and scaffolding of other (functional) polymers. The role of prion-like phenomena in memory has been hypothesized. As an additional mechanism of heritable change, prion formation may in principle contribute to heritable variability at the population level. Moreover, it is possible that amyloid-based prions represent by-products of the transient feedback regulatory circuits, as normal cellular function of at least some prion proteins is decreased in the prion state.     

The Dipole Model and Phase Transitions in Biological Membranes

Assuming the dipole model for a membrane, approximate calculations are made which employ a dipole-dipole interaction energy. The calculations are based upon the assumption of cooperative coupling of membrane polar molecules and make use of the Bragg-Williams approximation. A theoretical estimate is made of the critical temperature at which phase changes might occur in certain biological membranes. Proposals are presented which explain how the dipole transition might relate to the sometimes observed thermal phase transitions in biological membranes.     

Mechanical Equilibrium of Biological Membranes

The nature of mechanical and electrical forces on biological membranes in relation to mechanical equilibrium is examined. The presence of a double layer of electric charge is shown to give rise to an effective pressure drop across a curved membrane of finite thickness. For certain geometric shapes of a membrane, the magnitude of the pressure drop due to electrostatic forces may set a limit on the hydrostatic pressure drop that the membrane can support without buckling. The results are applied to the equilibrium shape of the red blood cell.     

Domains and Rafts in Membranes – Hidden Dimensions of Selforganization

Both biomembranes and biomimetic membranes such as lipid bilayers withseveral components contain intramembrane domains and rafts.Macromolecules, which are anchored to the membrane but have no tendeney tocluster, induce curved nanodomains. Clustering of membrane componentsleads to larger domains which can grow up to a certain maximal size andthen undergo a budding process. The maximal domain size depends on theinterplay of spontaneous curvature, bending rigidity, and line tension.It is argued that this interplay governs the formation of bothclathrin-coated buds and caveolae. Finally, membrane adhesion often leadsto domain formation within the contact zone.     

Atomic Force Microscopy of Biological Membranes

Atomic force microscopy (AFM) is an ideal method to study the surface topography of biological membranes. It allows membranes that are adsorbed to flat solid supports to be raster-scanned in physiological solutions with an atomically sharp tip. Therefore, AFM is capable of observing biological molecular machines at work. In addition, the tip can be tethered to the end of a single membrane protein, and forces acting on the tip upon its retraction indicate barriers that occur during the process of protein unfolding. Here we discuss the fundamental limitations of AFM determined by the properties of cantilevers, present aspects of sample preparation, and review results achieved on reconstituted and native biological membranes.     

Fluctuations and Fractal Noise in Biological Membranes

Our understanding of cell structure and function derives from applications of a variety of physical and life science disciplines, methods and models to an important physiological process, namely, the exchange and transport of ions and molecules across biological membranes. We know that ion transport through membranes arises from a diversity of interrelated and interactive physical and chemical phenomena over a wide range of spatial and temporal scales. Among these phenomena common to all cellular structure and function include metabolism, kinetics of molecules, chemically mediated alteration of cell membrane electrical potential, membrane ion conductance, electrical signal propagation, and modulation by chemo- and mechanoreceptive mechanisms. This review focuses on the unique information contained in fluctuations in electrical properties associated with cell membrane ion transport. Received: 19 May 2000/Revised: 10 July 2000     

Bending Rigidities and Interdomain Forces in Membranes with Coexisting Lipid Domains

To precisely quantify the fundamental interactions between heterogeneous lipid membranes with coexisting liquid-ordered (Lo) and liquid-disordered (Ld) domains, we performed detailed osmotic stress small-angle x-ray scattering experiments by exploiting the domain alignment in raft-mimicking lipid multibilayers. Performing a Monte Carlo-based analysis allowed us to determine with high reliability the magnitude and functional dependence of interdomain forces concurrently with the bending elasticity moduli. In contrast to previous methodologies, this approach enabled us to consider the entropic undulation repulsions on a fundamental level, without having to take recourse to crudely justified mean-field-like additivity assumptions. Our detailed Hamaker-coefficient calculations indicated only small differences in the van der Waals attractions of coexisting Lo and Ld phases. In contrast, the repulsive hydration and undulation interactions differed significantly, with the latter dominating the overall repulsions in the Ld phase. Thus, alignment of like domains in multibilayers appears to originate from both, hydration and undulation repulsions.     

Molecular Mechanisms of Raft Organization in Biological Membranes

Russian Journal of Bioorganic Chemistry - This review analyzes and summarizes some actual models of raft organization as dynamic structural units in lipid membranes emphasizing the discrimination...     

Isotope Flows and Flux Ratios in Biological Membranes

Precise evaluation of permeability of biological tissues is often prevented by imprecise knowledge of operative forces. This problem has been approached by analysis of fluxes of isotopic species applied to opposite surfaces of a membrane. A simple and rather general flux ratio equation has been derived which may permit evaluation of membrane permeability, even without knowledge of forces, or of the nature of active transport processes. Permeability as thus defined should be insensitive to coupled flows, either of other species or of metabolism. In appropriate circumstances application of the equation may permit evaluation of the contributions of the various processes to the transport of the examined species. Composite series membranes would be expected to obey the unmodified general equation. Heterogeneous parallel pathways would alter the relation in a predictable manner. The effect of isotope interaction is specifically incorporated. The formulation is applied to consideration of energetics of active transport.     

p53蛋白质C端的三维结构及生物功能区

利用p53 C端118个氨基酸的mRNA二级结构和Chou-Fasman蛋白质二级结构预测原则,预测p53蛋白质C端289～325为卷曲肽段,368～393段包括两段螺旋结构: α₁ 368～373, α₂ 381～388.其中三段已知的蛋白质二级结构与此mRNA二级结构单元间有准确的对应关系.与四种以多重序列联配为基础的蛋白质二级结构预测方法（准确率均为73.20%左右）相对照,预测结果基本一致.结合单体聚合区31个氨基酸晶体结构,在SGI INDIGO²工作站上构建了p53 C端108个残基的三维结构.进一步揭示了p53 C端诸多生物功能区之间的空间构象关系.