Excluded volume as a determinant of macromolecular structure and reactivity

The effect of excluded volume on the thermodynamic activity of globular macromolecules and macromolecular complexes in solution is studied in the hard-particle approximation. Activity coefficients are calculated as a function of the fraction of total volume occupied by macromolecules using relations obtained from scaled particle and lattice models. Significant and readily observable effects are predicted to occur as the fraction of volume occupied by globular macromolecules increases, including the following: (i) Compact quasi-spherical macromolecular conformations become increasingly energetically favored over extended anisometric conformations. (ii) Self- and heteroassociation processes are enhanced, particularly those leading to the formation of compact quasi-spherical aggregates. (iii) Depending upon the details of the reaction mechanism, the rate of an enzyme-catalyzed reaction may monotonically decrease, go through a maximum, or exhibit more complex behavior. A given degree of volume occupancy by larger macromolecules is predicted to have less effect on the structure and self-association of smaller macromolecules than the same degree of volume occupancy by smaller macromolecules has on the structure and self-association of larger macromolecules.     

Turnover of cell-surface macromolecules in cultured dog tracheal epithelial cells

We studied the metabolism of sulfated cell-surface macromolecules in dog tracheal epithelial cells in primary culture. To examine the time-course and rate of appearance of sulfated macromolecules at the cell surface, the cells were pulsed with 35SO4 for short periods (5-15 min), and the incubation medium was sampled for spontaneously released macromolecules (basal secretions) and for release induced by trypsin (trypsin-accessible secretions). Trypsin-accessible 35S-labeled macromolecules appeared on the cell surface within 5-10 min, increased linearly, and plateaued by 40 min; the median transit time for 35S-labeled macromolecules to reach the cell surface was 21 min. 35S-labeled macromolecules in basal secretions increased with a similar time-course, reaching a plateau by 40 min. Incorporation of [3H]serine into the protein moiety of trypsin-accessible macromolecules occurred more slowly; trypsin-accessible 3H-labeled macromolecules were barely detectable at 1 h and increased to a maximum after 2 h, suggesting the presence of a preformed pool of nonsulfated core protein. Pretreatment with cycloheximide, an inhibitor of protein synthesis, decreased trypsin-accessible 35S-labeled macromolecules log-linearly depending on the duration of pretreatment providing an estimate of the rate of depletion of the core protein pool (t1/2 = 32 min). During continuous exposure to 35SO4, 35S-labeled macromolecules accumulated on the cell surface (trypsin-accessible compartment) for 16 h, at which point the cell-surface pool was saturated (t1/2 = 7.5 h). After pulse-labeling the cells with 35SO4 for 15 min, the 35S-labeled macromolecules disappeared continuously from the cell surface (t1/2 = 4.6 h), and 79% of the radioactivity was recovered in the medium as nondialyzable macromolecules. Release of the 35S-labeled macromolecules from the cell surface was abolished at 4 degrees C, indicative of an energy-dependent process, but multiple proteinase inhibitors did not affect the release. We conclude that sulfate is metabolized rapidly into epithelial cell-surface macromolecules, which accumulate continuously into a relatively large cell-surface pool, before they are released by an undefined energy-dependent mechanism.     

生物大分子质谱电离技术的突破及核磁共振三维结构测定方法的建立——2002年诺贝尔化学奖简介

2002年诺贝尔化学奖授予了质谱和核磁共振领域的三位科学家以表彰他们对生物大分子鉴定及结构分析方法做出的贡献．其中两位科学家J．B．Fenn和K．Tanaka分别发展了生物大分子质谱分析的软解吸电离方法;另一科学家K．Wüthrich则将核磁共振技术成功地应用于生物大分子如蛋白质的溶液三维结构测定．他们的研究成果已使质谱和核磁共振技术成为生物大分子强有力的研究手段,极大地促进了生物大分子的研究进程,必将对整个生命科学研究产生深远的影响．     

Nanoscale amphiphilic macromolecules as lipoprotein inhibitors: the role of charge and architecture

A series of novel amphiphilic macromolecules composed of alkyl chains as the hydrophobic block and poly(ethylene glycol) as the hydrophilic block were designed to inhibit highly oxidized low density lipoprotein (hoxLDL) uptake by synthesizing macromolecules with negatively charged moieties (ie, carboxylic acids) located in the two different blocks. The macromolecules have molecular weights around 5,500 g/mol, form micelles in aqueous solution with an average size of 20-35 nm, and display critical micelle concentration values as low as 10(-7) M. Their charge densities and hydrodynamic size in physiological buffer solutions correlated with the hydrophobic/ hydrophilic block location and quantity of the carboxylate groups. Generally, carboxylate groups located in the hydrophobic block destabilize micelle formation more than carboxylate groups in the hydrophilic block. Although all amphiphilic macromolecules inhibited unregulated uptake of hoxLDL by macrophages, inhibition efficiency was influenced by the quantity and location of the negatively charged-carboxylate on the macromolecules. Notably, negative charge is not the sole factor in reducing hoxLDL uptake. The combination of smaller size, micellar stability and charge density is critical for inhibiting hoxLDL uptake by macrophages.     

Effects of Hydration on Steric and Electric Charge-Induced Interstitial Volume Exclusion—a Model

The presence of collagen and charged macromolecules like glycosaminoglycans (GAGs) in the interstitial space limits the space available for plasma proteins and other macromolecules. This phenomenon, known as interstitial exclusion, is of importance for interstitial fluid volume regulation. Physical/mathematical models are presented for calculating the exclusion of electrically charged and neutral macromolecules that equilibrate in the interstitium under various degrees of hydration. Here, a central hypothesis is that the swelling of highly electrically charged GAGs with increased hydration shields parts of the neutral collagen of the interstitial matrix from interacting with electrically charged macromolecules, such that exclusion of charged macromolecules exhibits change due to steric and charge effects. GAGs are also thought to allow relatively small neutral, but also charged macromolecules neutralized by a very high ionic strength, diffuse into the interior of GAGs, whereas larger macromolecules may not. Thus, in the model, relatively small electrically charged macromolecules, such as human serum albumin, and larger neutral macromolecules such as IgG, will have quite similar total volume exclusion properties in the interstitium. Our results are in agreement with ex vivo and in vivo experiments, and suggest that the charge of GAGs or macromolecular drugs may be targeted to increase the tissue uptake of macromolecular therapeutic agents.     

Mathematical model of molecular transport and recycling of membrane receptors in a cell

A mathematical model for analysing dynamics of receptor-mediated endocytosis (RME) for bivalent macromolecules is presented. The results suggest that RME bivalent macromolecules and the recycling of its receptor(s) involve regulation mechanisms of many cell functions, including proliferation, differentiation adhesion etc.     

荧光能量转移技术在生物学研究中的应用

荧光能量转移(FRET)是指两个携带不同荧光基团的大分子在相互间距离足够近时(10～100A)所发生的能量非放射性地由一个荧光基团向另一个荧光基团转移的现象。结合绿色荧光蛋白的发现,FRET技术可用于检测生物大分子中不同亚基的位置和生物大分子间的相互作用。近年来,FRET技术在生物学研究中的突破性进展是在活体细胞中实时监测生物大分子之间的相互作用。本文就绿色荧光蛋白的发现,FRET技术的原理、研究进展和应用前景作简要综述。     

Developmental changes in the tracheal mucociliary system in neonatal sheep

We studied the postnatal development of the tracheal epithelium and mucociliary system in neonatal sheep. Secretion of macromolecules (radiolabeled with 35SO4 and [3H]-threonine), unidirectional fluxes of Cl-, Na+, and water (measured with radioactive tracers), and ciliary beat frequency (CBF) were measured in tracheal tissues in vitro. Tracheal mucus transport velocity (TMV) was measured in vivo. Sheep were studied at 0, 2, 4, 8, and greater than 24 (adult) wk after birth. In newborn sheep trachea, secretion of macromolecules was significantly elevated (cf. adults), and there was basal net secretion of Cl- under short-circuit and open-circuit conditions. This induced open-circuit secretion of Na+. Secretion of macromolecules decreased rapidly by 2 wk (by 40-50%) and was not different from adult values by 4 wk. Active Na+ absorption developed rapidly, and from 2 wk onward it predominated under open-circuit conditions, inducing net Cl- absorption. These changes in secretory function were associated with an age-related increase in TMV, whereas inherent tracheal CBF was unchanged. In sheep, therefore, the newborn's trachea has elevated secretion of macromolecules and secretes Cl- and liquid under basal conditions. Normal secretory function (a reduction in secretion of macromolecules coupled with net absorption of ions and presumably of liquid also) approaches adult function by 2-4 wk of age.     

Increase of poly(L-lysine) uptake but not fluid phase endocytosis in neuraminidase pretreated Madin-Darby canine kidney (MDCK) cells

The uptake of Poly(L-lysine) conjugates in cultured cells has been used as a model for non-specific adsorptive endocytosis of cationic macromolecules. To study the effect of glycocalyx desialylation on the uptake of cationic macromolecules in epithelial cells, Madin-Darby canine kidney (MDCK) cell monolayers were treated with neuraminidase and incubated with Poly(L-lysine) conjugates. Neuraminidase pretreatment of MDCK cells resulted in a 40% increase in the uptake of Poly(L-lysine) whereas trypsin pretreatment did not. Neuraminidase pretreatment did not increase the endocytosis of fluid phase markers in MDCK cells, nor the uptake of Poly(L-lysine) in L929 fibroblasts. These results suggest that the negative charges, rather than the glycoprotein matrices of glycocalyx, play an important role in the control of the uptake of cationic macromolecules in epithelial cells.     

Incorporation of fucose and glucosamine into cell bound and medium released macromolecules.

(1) Determinations were carried out on the incorporation of fucose-6-(3H) and glucosamine-6-(3H) into trichloracetic acid insoluble macromolecules which remained bound to the cells or were released into the medium of chick embryo muscle cell cultures. The radioactivity determined in the medium was corrected for unspecific binding of label to components of the medium. (2) During an incorporation period of six hours the incorporation per microgram DNA with fucose as label into cell bound macromolecules is about twice as high as the incorporation into macromolecules released into medium. With glucosamine about twice as much is incorporated into medium released into the cell bound macromolecules. (3) The incorporation per microgram DNA increased during a culture period of three days but the increase ceases at different times during this culture period when determined with fucose or glucosamine or for cell bound and medium released material. (4) An increase in cell density increases the incorporation per DNA of fucose and to a much slighter extent that of glucosamine. Reduction of cell density by addition of cytosine arabinoside to the medium does not increase the incorporation per microgram DNA. (5) The effect of changes of fibroblast/myoblast ratios on the incorporation of fucose and glucosamine were examined. No significant effect was observed for a ratio of 10-30% fibroblasts when control cultures or cultures after cell sedimentation were maintained in complete medium. Marked changes were observed after culture in medium without protein components. Under these conditions an increase in the fibroblast/myoblast ratios were observed as well as an increase in the incorporation of label into medium released and a decrease into cell bound macromolecules.     

Glomerular permselection: shape and flow

The selective permeability of the glomerular basement membrane to macromolecules is a function of the size and charge of the macromolecule. Evidence suggests that shape may also be a factor. The orientation of macromolecules in solution is dependent on their size, shape, and frictional interactions with moving solvent molecules. The spaces between the glomerular visceral epithelial cells (slit pores) may produce a non-uniform distribution of fluid flow within the basement membrane, and this non-uniformity may increase during disease. This report is of a model that relates the filtration of rigid prolate ellipsoidal (cigar) shaped macromolecules to the size and shape of the filter and to the velocity of solvent flow. The calculations, using published macromolecular and glomerular parameters correspond well to published data. The glomerular visceral epithelial cell, by altering the number, size and distribution of the intercellular spaces, may regulate the passage of ellipsoidal shaped macromolecules, such as albumin and IgG, into and through glomerular structures.     

Better Cryo-EM Specimen Preparation: How to Deal with the Air–Water Interface?

Cryogenic electron microscopy (cryo-EM) is now one of the most powerful and widely used methods to determine high-resolution structures of macromolecules. A major bottleneck of cryo-EM is to prepare high-quality vitrified specimen, which still faces many practical challenges. During the conventional vitrification process, macromolecules tend to adsorb at the air–water interface (AWI), which is known unfriendly to biological samples. In this review, we outline the nature of AWI and the problems caused by it, such as unpredictable or uneven particle distribution, protein denaturation, dissociation of complex and preferential orientation. We review and discuss the approaches and underlying mechanisms to deal with AWI: 1) Additives, exemplified by detergents, forming a protective layer at AWI and thus preserving the native folds of target macromolecules. 2) Fast vitrification devices based on the idea to freeze in-solution macromolecules before their touching of AWI. 3) Thin layer of continuous supporting films to adsorb macromolecules, and when functionalized with affinity ligands, to specifically anchor the target particles away from the AWI. Among these supporting films, graphene, together with its derivatives, with negligible background noise and mechanical robustness, has emerged as a new generation of support. These strategies have been proven successful in various cases and enable us a better handling of the problems caused by the AWI in cryo-EM specimen preparation.     

Transmission of the quantum interaction of erythrocytes

The previously demonstrated long-range quantum mechanical interaction between human erythrocytes suspended in plasma also occurs with artificial media. Certain macromolecules dissolved in phosphate-buffered saline will transmit the interaction provided their concentration is above a minimum. Extended macromolecules transmit the interaction, whereas a compact macromolecule (albumin) does not.     

Diffusion of macromolecules in agarose gels: comparison of linear and globular configurations.

The diffusion coefficients (D) of different types of macromolecules (proteins, dextrans, polymer beads, and DNA) were measured by fluorescence recovery after photobleaching (FRAP) both in solution and in 2% agarose gels to compare transport properties of these macromolecules. Diffusion measurements were conducted with concentrations low enough to avoid macromolecular interactions. For gel measurements, diffusion data were fitted according to different theories: polymer chains and spherical macromolecules were analyzed separately. As chain length increases, diffusion coefficients of DNA show a clear shift from a Rouse-like behavior (DG congruent with N0-0.5) to a reptational behavior (DG congruent with N0-2.0). The pore size, a, of a 2% agarose gel cast in a 0.1 M PBS solution was estimated. Diffusion coefficients of the proteins and the polymer beads were analyzed with the Ogston model and the effective medium model permitting the estimation of an agarose gel fiber radius and hydraulic permeability of the gels. Not only did flexible macromolecules exhibit greater mobility in the gel than did comparable-size rigid spherical particles, they also proved to be a more useful probe of available space between fibers.     

Further studies on the extrusion of cytosol macromolecules by cultured chick embryo fibroblast cells

The RNA and lipid-associated macromolecules extruded by chick embryo fibroblast cells have been analysed by chromatography. The results taken with those previously obtained suggest that cultured chick embryo fibroblasts excrete a wide range of cytosol macromolecules into the surrounding medium. As previously found with DNA and protein, the chromatographic patterns found with supernatant and cell cytosol preparations were closely similar, suggesting that the media supernatant macromolecules are cytosal derived. A proportion of the RNA and lipid associated material elutes at the same position as the previously observed for DNA and protein on gel exclusion chromatography, suggesting that cell cytosol contains a discrete DNA-RNA-protein lipid complex (size approx 5 X 10(5) dalton) which is extruded by cultured cells.     

Macromolecular crowding in biological systems: hydrodynamics and NMR methods

Most biologically relevant environments involve highly concentrated macromolecular solutions and most biological processes involve macromolecules that diffuse and interact with other macromolecules. Macromolecular crowding is a general phenomenon that strongly affects the transport properties of macromolecules (rotational and translational diffusion) as well as the position of their equilibria. NMR methods can provide information on molecular interactions, as well as on translational and rotational diffusion. In fact, rotational diffusion, through its determinant role in NMR relaxation, places a practical limit on the systems that can be studied by NMR. While in dilute solutions of non-aggregating macromolecules this limit is set by macromolecular size, in crowded solutions excluded volume effects can have a strong effect on the observed diffusion rates. Hydrodynamic theory offers some insight into the magnitude of crowding effects on NMR observable parameters.     

A pathway separate from the central channel through the nuclear pore complex for inorganic ions and small macromolecules

Nuclear pore complexes (NPCs) are supramolecular nanomachines that mediate the exchange of macromolecules and inorganic ions between the nucleus and the cytosol. Although there is no doubt that large cargo is transported through the centrally located channel, the route of ions and small molecules remains debatable. We thus tested the hypothesis that there are two separate pathways by imaging NPCs using atomic force microscopy, NPC electrical conductivity measurements, and macromolecule permeability assays. Our data indicate a spatial separation between the active transport of macromolecules through the central channel and the passive transport of ions and small macromolecules through the pore periphery.     

Evidence that dipicolinic acid is covalently bound to specific macromolecules in spores of Bacillus subtilis

Abstract Two dipicolinic acid (DPA)-binding macromolecules with molecular masses of about 440 kDa and 230 kDa were detected in the soluble fractions of dormant and germinated spores of Bacillus subtilis using native PAGE and an immunological technique. In SDS-PAGE, only one band with the molecular mass of about 50 kDa was found. Proteinase K partially digested the 440-kDa macromolecule of dormant spores to convert it into a 230-kDa one, and completely digested both the 440-kDa and 230-kDa bands of germinated spores. DNase I did not affect either DPA-binding macromolecules. This suggests that the two DPA-binding macromolecules are of similar origin, their main component is protein and a conformational change may occur during germination. DPA was not dissociated from the DPA-binding macromolecules by extensive dialysis and SDS treatment, suggesting the presence of a covalent bonding.     

Nuclear estradiol receptors in several "non-target" organs of rats]

Some properties of the macromolecules of the KCl-extracts of the nuclei of the uterus, kidney, liver, testis and prostate, specifically binding estradiol (E2), were studied. These macromolecules of the uterus and the liver were found to be maximally extracted from chromatin by the 0.6 M KCl concentration. The capacity of the macromolecules of the uterine, kidney and liver nuclear extracts to bind E2 specifically is destroyed completely by pronase, but not by RNA-ASe and DNA-ase, pointing to the protein nature of these macromolecules. Only estrogenic compounds, but not testosterone, 5alpha-dihydrotestosterone, progesterone or corticosterone were capable to compete with H3--E2 for the E2--binding sites of the macromolecules of the nuclear extracts of all the organs investigaeted. It is assumed that macromolecules of the nuclei of the investigated nontarget organs specifically binding E2 are estrogen receptors.     

Respective roles of high and low molecular weight serum growth factors in the metabolism of proteoglycans and other cartilage macromolecules

35S radiolabeling allowed an evaluation to be made of neosynthesized macromolecules in chick embryo cartilage cultures. Activities for growth factors of high (serum retentate) or low (ultrafiltrate below 1,000) molecular weight (MW) were assessed in pelvic cartilage explants and in corresponding incubation media. In the absence of growth factor, 35S was mostly incorporated in glycosaminoglycans (GAGs) as regards the medium and for cartilage, in guanidinium chloride unextractable material. In retentate-enriched medium, 35S incorporation was enhanced in all cartilage GAGs while in the medium, stimulation essentially occurred in macromolecules other than GAGs. Low MW growth factors exclusively enhanced cartilage levels of macromolecules which were insoluble in guanidinium chloride. In the medium, these factors did not display any significant effect. These results indicate that human serum growth factors with high and low MW possess different metabolic targets at the cellular level.