Comparison between the nitric oxide reductase family and its aerobic relatives,the cytochrome oxidases

The denitrification pathway has been studied in the hyperthermophilic archaeon Pyrobaculum aerophilum. In contrast with Gram-negative bacteria, all four denitrification enzymes are membrane-bound. P. aerophilum is also the only denitrifyer identified so far in which menaquinol is the electron donor to all four denitrification reductases. The NO reductase (NOR) of P. aerophilum belongs to the superfamily of haem-copper oxidases and is of the qNOR (quinol-dependent) type. Three types of NOR have been purified so far: cNOR (cytochrome c/pseudoazurin-dependent), qNOR and qCu(A)NOR (qNOR that contains Cu(A) at the electron entry site). It is proposed that the NORs and the various cytochrome oxidases have evolved by modular evolution, in view of the structure of their electron donor sites. qNOR is further proposed to be the ancestor of all NORs and cytochrome oxidases belonging to the superfamily of haem-copper oxidases.     

The primary cilium of telocytes in the vasculature: electron microscope imaging

Blood vessels are highly organized and complex structure, which are far more than simple tubes conducting the blood to almost any tissue of the body. The fine structure of the wall of blood vessels has been studied previously using the electron microscope, but the presence the telocytes associated with vasculature, a specific new cellular entity, has not been studied in depth. Interestingly, telocytes have been recently found in the epicardium, myocardium, endocardium, human term placenta, duodenal lamina propria and pleura. We show the presence of telocytes located on the extracellular matrix of blood vessels (arterioles, venules and capillaries) by immunohistochemistry and transmission electron microscopy. Also, we demonstrated the first evidence of a primary cilium in telocytes. Several functions have been proposed for these cells. Here, the telocyte-blood vessels cell proximity, the relationship between telocytes, exosomes and nervous trunks may have a special significance.     

Ultrafast transient absorption studies on Photosystem I reaction centers from Chlamydomonas reinhardtii. 1. A new interpretation of the energy trapping and early electron transfer steps in Photosystem I

The energy transfer and charge separation kinetics in core Photosystem I (PSI) particles of Chlamydomonas reinhardtii has been studied using ultrafast transient absorption in the femtosecond-to-nanosecond time range. Although the energy transfer processes in the antenna are found to be generally in good agreement with previous interpretations, we present evidence that the interpretation of the energy trapping and electron transfer processes in terms of both kinetics and mechanisms has to be revised substantially as compared to current interpretations in the literature. We resolved for the first time i), the transient difference spectrum for the excited reaction center state, and ii), the formation and decay of the primary radical pair and its intermediate spectrum directly from measurements on open PSI reaction centers. It is shown that the dominant energy trapping lifetime due to charge separation is only 6-9 ps, i.e., by a factor of 3 shorter than assumed so far. The spectrum of the first radical pair shows the expected strong bleaching band at 680 nm which decays again in the next electron transfer step. We show furthermore that the early electron transfer processes up to approximately 100 ps are more complex than assumed so far. Several possibilities are discussed for the intermediate redox states and their sequence which involve oxidation of P700 in the first electron transfer step, as assumed so far, or only in the second electron transfer step, which would represent a fundamental change from the presently assumed mechanism. To explain the data we favor the inclusion of an additional redox state in the electron transfer scheme. Thus we distinguish three different redox intermediates on the timescale up to 100 ps. At this level no final conclusion as to the exact mechanism and the nature of the intermediates can be drawn, however. From comparison of our data with fluorescence kinetics in the literature we also propose a reversible first charge separation step which has been excluded so far for open PSI reaction centers. For the first time an ultrafast 150-fs equilibration process, occurring among exciton states in the reaction center proper, upon direct excitation of the reaction center at 700 nm, has been resolved. Taken together the data call for a fundamental revision of the present understanding of the energy trapping and early electron transfer kinetics in the PSI reaction center. Due to the fact that it shows the fastest trapping time observed so far of any intact PSI particle, the PSI core of C. reinhardtii seems to be best suited to further characterize the electron transfer steps and mechanisms in the reaction center of PSI.     

马传染性贫血病病毒结构模型的建立

通过电子显微镜多种技术的观察和研究,明确了马传染性贫血病病毒的典型形态结构,即呈球形,表面附有顶端带钮状物的纤突,病毒膜为三层(单位膜),病毒基质充填于病毒膜和核芯亮之间,核芯壳呈园锥形,核芯为螺旋结构。在此基础上建立了马传染性贫血病病毒的结构模型。这是国内外首次报道,为深入研究该病毒和其有关病毒的特性奠定了基础,并为该病毒的分类提供了形态学依据。     

Structural determination of the functional sites of E. coli elongation factor Tu

Recently, we have made significant progress in solving the structure of a nicked form of elongation factor (EF)-Tu complexed with GDP. The structure has been refined to an R factor of 19.2% at 2.6 A resolution, so that most of the structure is clearly visible in the electron density map. Here we describe what is known about functional sites of EF-Tu in terms of the structure, which still lacks amino acids 40-60.     

Trial comparison of mitochondrial cristae craters images obtained by the freeze-fracturing and ultrathin sections method

In two-folded lamina of the mitochondrial cristae occurs in mitochondria of spermatocytes large areas of the inner and outer halves in freeze-fracturing technique morphological observations suggest that in mitochondrial membrane there exist "crater-like' structures with internal diameter of approximately 18 nm. A question has come up why no mention has so far been found in the literature of the appearance of similar structure in mitochondrial cristae in specimens in transmission electron microscope (TEM) observed. Thus comparison of our findings obtained by the freeze-fracturing (FF) method with those achieved by TEM was made.     

The structure of human-plasma low-density lipoprotein B. An X-ray small-angle scattering study.

1. X-ray small-angle scattering of human plasma lipoprotein B of the low-density fraction (rho = 1.016--1.060 g.cm-3) has been recorded to high precision at different electron density contrasts. 2. The overall structure of the particles is characterized by a quasi-spherical shape and radial symmetry. A maximum diameter of 23 nm and a molecular weight of 2.4 X 10(6) have been determined. 3. The internal structure is described in terms of a model consisting of spherical layers with different electron densities indicating that the neutral lipids are arranged in the core of the molecule up to a radius of about 8 nm surrounded by a monolayer of free cholesterol, phospholipids and protein. The neural lipids are shown to be in an ordered, liquid crystalline state at 4 degrees C and to undergo a thermotropic transition into a disordered state at higher temperatures.     

Tubulin structure: insights into microtubule properties and functions

The structure of tubulin has recently been determined by electron crystallography, paving the way for a clearer understandin of the unique properties of tubulin that allow its varied functions within the cell. Some of the ongoing work on tubulin can be interpreted in terms of its structure, which can serve to guide future studies.     

Structure of the 50S ribosomal subunit from Escherichia coli. Investigation of the intact subunit and core particles by electron microscopy and analogue image processing.

Structures of 50S ribosomal subunits, CsCl and ethidium bromide core particles from these subunits have been investigated by electron microscopy and image processing by FAIRS. This method revealed structural details which are obscured in individual images, and enabled to distinguish six crown forms, different in their side protuberances, and two kidney forms. Crown forms were imaged as symmetrical or asymmetrical forms. The latter type was far more frequent in untreated populations than the first. The depletion of proteins by both agents caused stepwise degradation of the side protuberances in the crown forms thereby transforming asymmetrical to symmetrical forms. It is concluded from these findings that asymmetrical and symmetrical forms in untreated populations represent also structurally different particles. From the higher complexity in terms of component composition and structure it is concluded that the asymmetrical crown forms are more likely to represent the native structure of isolated 50S subunits than the symmetrical forms. Existing models for this subunit are discussed in terms of this finding.     

Presence and coding properties of 2'-O-methyl-5-carbamoylmethyluridine (ncm5Um) in the wobble position of the anticodon of tRNA(Leu) (U*AA) from brewer's yeast.

The unknown modified nucleoside U* has been isolated by enzymatic and HPLC protocols from tRNA(Leu) (U*AA) recently discovered in brewer's yeast. The pure U* nucleoside has been characterized by electron impact mass spectroscopy, and comparison of its chromatographic and UV-absorption properties with those of appropriate synthetic compounds. The structure of U* was established as 2'-O-methyl-5-carbamoylmethyluridine (ncm5Um). The yeast tRNA(Leu) (U*AA) is the only tRNA so far sequenced which has been shown to contain ncm5Um. The location of such a modified uridine at the first position of the anticodon restricts the decoding property to A of the leucine UUA codon.     

Studies on the Ultrastructure of the Genital Organs in Proseriata (Turbellaria). I. Cirrifera aculeata (Ax) (Coelogynoporidae)

The genital organs in adult specimens of Cirrifera aculeata have been studied by transmission electron microscopy. The male copulatory organ is of the conjuncta-duplex type provided with a spiny cirrus. The structure of the epithelia lining the different parts of the genital organs is described. The cirrus spines and the spines in the genital atrium are shown to be intracellular specializations. The structure and location of the cirrus spines in the Proseriata studied so far are discussed.     

Genetic testing,life insurance,and adverse selection.

Life insurance is a key element of the UK social structure in terms of family protection and house purchase; it thus needs to be viewed in this broad context, rather than solely as a commercial activity. Insurers have not so far actively requested genetic tests for life insurance, but have insisted on knowing of and being able to act on existing genetic test information. The main reason given for this has been to avoid serious adverse selection; however, this has never been adequately estimated. Review of the different major categories of Mendelian genetic disorders suggests that the scope for adverse selection is extremely limited and that insurers would lose little, and possibly gain more, by foregoing the disclosure and use of this information in relation to life insurance policies of ''normal'' size and nature. The likely future use in service of genetic tests based on susceptibility or population screening makes it especially important that the issue is rapidly resolved for Mendelian disorders; so far there is no sign that insurers are willing to achieve this.     

The stapes of the Goal Measures embolomere Pholiderpeton scutigerum Huxley (Amphibia: Anthracosauria) and otic evolution in early tetrapods

Middle ear structure has been of interest for a long time in studies of the origins and relationships of early tetrapod groups. The model of a dorsally-directed, rod-like stapes with a tympanum, thought common to labyrinthodont amphibians, was taken to be primitive for tetrapods. The stapes of embolomeres and other early anthracosaurs were assumed to be of this form, but difficulties resulted if the middle ear structure of fossil and living reptiles was considered ultimately derived from this source.
The embolomere stapes has been identified and does not conform to the predicted model. It most closely resembles that of Greererpeton , an early notchless temnospondyl. The stapes is compared with those of other tetrapods in terms of the theoretical five processes. An interpretation is put forward in which all but the opercular are seen as potentially present. The embolomere stapes is compared with that of Greererpeton in terms of recent theories of mechanical function and is seen to weaken them. They are then compared as part of a possible acoustic mechanism. The embolomere middle ear structure is reinterpreted as a receiver for low-frequency sound and the 'otic notch' is not considered to have housed a tympanum.
The resemblance between the stapes of these two animals seems best explained by their closeness to the plesiomorphic condition for tetrapods, a conclusion which forces the abandonment of the concept of a 'labyrinthodont middle ear'. The middle ear structure of later groups can be interpreted as having evolved from one similar to that seen in these two animals. The conclusion supports those reached in other recent papers that tympana were not primitive for tetrapods but have been independently derived in several groups.     

纽带蛋白及其与微丝和膜结合的研究

 用落球粘度计测量低剪切粘度的方法研究了纽带蛋白-肌动蛋白的相互作用。与以前关于纽带蛋白可使肌动蛋白粘度降低并推测它抑制微丝间相互作用的报道不同,10—50μg/ml的纽带蛋白引起肌动蛋白细丝溶液粘度略有增加。电镜观察表明,由于纽带蛋白的作用,肌动蛋白丝聚集成束。 远紫外圆二色谱显示,在pH7.0下,220和207nm处呈双负峰,190nm处有一正峰。按三波长法计算,其α螺旋和β折叠含量分别占41％和22％。研究了pH,磷脂和去垢剂对其构象的影响。疏水性结合的和水溶性的纽带蛋白相比,存在少量构象差别。联系这一蛋白处在细胞骨架与质膜相联系的特殊位置,推测在体内,纽带蛋白与脂结合后也可能发生类似的构象变化。     

Exploring biomolecular machines: energy landscape control of biological reactions

For almost 15 years, our Pathway model has been the most powerful model in terms of predicting the tunnelling mechanism for electron transfer (ET) in biological systems, particularly proteins. Going beyond the conventional Pathway models, we have generalized our method to understand how protein dynamics modulate not only the Franck-Condon factor, but also the tunnelling matrix element. We have demonstrated that when interference among pathways modulates the electron tunnelling interactions in proteins (particularly destructive interference), dynamical effects are of critical importance. Tunnelling can be controlled by protein conformations that lie far from equilibrium-those that minimize the effect of destructive interference during tunnelling, for example. In the opposite regime, electron tunnelling is mediated by one (or a few) constructively interfering pathway tubes and dynamical effects are modest. This new mechanism for dynamical modulation of the ET rate has been able to explain and/or predict several rates that were later confirmed by experiment. However, thermal fluctuations can also affect these molecular machines in many other ways. For example, we show how global transformations, which control protein functions such as allostery, may involve large-scale motion and possibly partial unfolding during the reaction event.     

Apomyoglobin mutants with single point mutations at Val10 can form amyloid structures at permissive temperature

Formation of amyloid-like protein aggregates in human organs and tissues underlies many serious diseases, therefore being in the focus of numerous biochemical, medical, and molecular biological studies. So far, formation of amyloids by globular proteins has been studied mostly under conditions that strongly destabilized their native structure. Here we present our results obtained at permissive temperature by thioflavin T fluorescence, far UV CD, IR spectroscopy, and electron microscopy. We used apomyoglobin and its mutants with Ala or Phe substituted for Val10 that are structurally close to wild type apomyoglobin. It is shown that at permissive temperature the ability of the protein to form amyloids depends on the extent of its structural destabilization, but not on hydrophobicity of the substituting residue. A possible difference between amyloids formed by strongly destabilized proteins and those yielded by proteins with a slightly fluctuating native structure, as well as the stroke and infarction effect on the ability of proteins to form amyloid structures, are discussed.     

Direct determination of crystallographic phases for diffraction data from phospholipid multilamellar arrays.

Direct determination of crystallographic phases based on probabilistic of sigma 1 and sigma 2 "triplet" structure invariants has been found to be an effective technique for structure analysis with lamellar x-ray or electron diffraction intensity data from phospholipids. In many cases, nearly all phase values are determined, permitting a structure density (electron density for x-ray diffraction; electrostatic potential for electron diffraction) map to be calculated, which is directly interpretable in terms of known bilayer lipid structure. The major source of error is found to be due to the distortion of observed electron diffraction intensity data by incoherent multiple scattering, which can significantly affect the appearance of the electrostatic potential map, but not the success of the phase determination, as long as the observed Patterson function can be interpreted.     

The atomic structure of crystalline porcine pancreatic elastase at 2.5 A resolution: comparisons with the structure of alpha-chymotrypsin

Three isomorphous heavy-atom derivatives have been used to calculate a 2.5 Å resolution electron density map of tosyl-elastase at pH 5.0, from which an accurate atomic model has been constructed. Atomic co-ordinates measured from this model have been refined using model building, real-space refinement and energy minimization programs. The three-dimensional conformation of the polypeptide chain is described in terms of conformational angles, hydrogen-bonding networks and the environment of different types of amino acid side-chain.Difference Fourier calculation of the high resolution structure of native elastase at pH 5.0 shows it to be virtually identical to that of the tosyl derivative, except near the tosyl group. The conformation of the catalytically important residues in native elastase is very similar to that of native α-chymotrypsin, except for the orientation of the active centre serine oxygen. The significance of important structural similarities and differences between these two enzymes is discussed.Elastase contains 25 internal water molecules which play an important role in stabilizing the active conformation of the enzyme. Many of these water molecules are in identical positions to those found in the interior of α-chymotrypsin     

Atomic force microscopy of the myosin molecule.

Atomic force microscopy (AFM) has been used to study the structure of rabbit skeletal muscle myosin deposited onto a mica substrate from glycerol solution. Images of the myosin molecule have been obtained using contact mode AFM with the sample immersed in propanol. The molecules have two heads at one end of a long tail and have an appearance similar to those prepared by glycerol deposition techniques for electron microscopy, except that the separation of the two heads is not so well defined. The average length of the tail (155 +/- 5 nm) agrees well with previous studies. Bends in the myosin tail have been observed at locations similar to those observed in the electron microscope. By raising the applied force, it has been possible locally to separate the two strands of the alpha-helical coiled-coil tail. We conclude that the glycerol-mica technique is a useful tool for the preparation of fibrous proteins for examination by scanning probe microscopy.     

Ultrastructure of Spermiogenesis in Hyla japonica (Anura,Amphibia)

Spermiogenesis in Hyla japonica was examined using transmission electron microscopy. Features which have not been reported previously during spermiogenesis of anurans include: (1) the neck of pericentriolar material is well developed, (2) the perforatorium contains many microtubules, (3) the tail is composed of axoneme and axial rod, but has no undulating membrane. Such a structure has not been described in amphibians, although it occurs in fish and mammals, and (4) the modified microtubules have one to two long projections. So far they have not been observed in any species except Gerris and Aphyosemion. With the exception of the above characteristics, the spermatozoa of Hyla japonica are remarkably similar to those of Bufo sp.