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Apurinic/apyrimidinic sites (AP sites) which represent one of the most abundantly generated DNA lesions in the cell are generally repaired by base excision repair (BER) pathway. Multifunctional protein YB-1 is known to participate in cellular response to genotoxic stress and was shown to interact with several components of BER - DNA glycosylases NTH1, NEIL2, DNA polymerase β and DNA ligase III. Therefore, it is of great interest to investigate the influence of YB-1 on one of the major BER enzymes, responsible for AP site cleavage, AP endonuclease APE1, and on tyrosyl phosphodiesterase Tdp1, participating in APE1 independent pathway of AP site repair. Aim. Effect of multifunctional protein YB-1 on the AP site cleavage by the activities of APE1 and Tdp1 was studied. Methods. Gel-mobility shift assays and enzyme activity tests. Results. YB-1 was shown to inhibit the cleavage of AP site located in single-stranded DNA by both APE1 and Tdp1. Stimulation of APE1 activity on protruding double-stranded DNA in the presence of YB-1 was observed, whereas no effect on Tdp1-mediated cleavage of AP site in double-stranded DNA was found. Conclusions. YB-1 can modulate the repair of AP sites in DNA by both positively stimulating APE1 during the classic BER of AP sites and avoiding a possible generation of doublestrand breaks, arising from the cleavage of single-stranded portion of DNA substrate already used by different DNA-processing pathway. [ABSTRACT FROM AUTHOR]

Abstract: This study addresses the influence of three different land use systems (continuous maize, pasture/maize rotation, permanent pasture) on the relationships between earthworm populations and the number of earthworm burrows quantified in a soil profile. Quantified burrows were limited to those observable by the naked eye (i.e. >2mm in diameter) and enumerated earthworms were limited to those which could have created the observable burrows (i.e. >0.3g). The results were combined with data from the literature coming from different geographical regions. This study showed that earthworm abundance decreased with the increasing land management intensity (maize crop vs. pasture), while the number of burrows could be higher or similar under maize compared to pasture. Under maize, despite lower earthworm abundance and the annual destruction of the burrows by tillage, the number of burrows was almost as high as under pasture. This absence of a relationship between burrow numbers and earthworm abundance was observed in the soil profile and for each layer of the profile for each land use system. Furthermore, the burrow number/m−2 per earthworm strongly varied depending on land use and was far higher under maize when compared to pasture (74 vs. 7). Therefore, a power-law type relationship was clearly established between burrow number/m−2 per earthworm and earthworm abundance. This power type relationship was also observed when including data from the literature although it followed a different mathematical model. These results were explained by (i) increased earthworm burrowing activity (i.e. an increase in the number of burrows produced by each earthworm) under maize, and (ii) the dynamics of burrow number under pasture (i.e. decreased burrowing activity and burrow destruction process); both results of food accessibility combined with inter-individual competition. The results of the study suggest that farmers should not use the number of pores as an indicator of earthworm abundance, but as an indicator of earthworm activity, which could be integrated in an indicator of soil quality. [Copyright &y& Elsevier]

Abstract: Poorly documented yet spectacularly thick and extensive outcrops of calcrete hardpan occur on gneiss in the semiarid region of Coimbatore, South India. The hardpan caps a series of residual plateaux forming the present-day continental divide and grades into large expanses of Vertisols. Characteristic calcrete and Vertisol profiles were logged along toposequences and sampled for macro- and micromorphological study, and for chemical and mineralogical composition. Strontium isotopic analyses revealed that the calcrete is derived from in situ weathering of Ca-bearing primary minerals of the saprolite, which is rich in ankerite, Ca-amphiboles and Ca-plagioclase. The macroscale analysis revealed a range of facies developed within the gneiss saprolite, but in terms of relative chronology the nodular hardpan has the longest history. Two evolutionary pathways leading to nodular hardpan formation have been established. The first occurs entirely within a vadose environment, whereas the second begins within a phreatic environment before continuing to develop in vadose conditions. The ability to identify and map these generic categories of calcrete constitutes a potential tool for reconstructing paleotopography and paleogroundwater levels. The bedrock-weathering-derived nodular hardpan is blanketed by a laminar facies that correlates with an eolian event with marine Sr signatures. This suggests influx of Ca dust from the Arabian Sea continental shelf during a Pleistocene sea-level low-stand. It defines an important benchmark in the chronology of the area and highlights the potential antiquity of the thick calcrete profiles. [Copyright &y& Elsevier]

So far, soil-landscape models have been based on soil surface topographic information only. However, hillslope hydrology that affects soil distribution is also controlled by sub-surface flow pathways that may not entirely be explained by surface terrain features. This paper compares the accuracy of a model for predicting the spatial variations of the hydromorphic index (HI) using the surface topography with that of a model that uses the sub-surface topography. The study was conducted in an agricultural hillslope of the Armorican Massif (Western France) where two DEMs were generated from observations of the surface topography and the topography of the saprolite upper boundary. For both DEMs, the best correlations with HI occurred for altitude, elevation above the stream bank, and compound topographic index. Predictions of HI using the sub-surface topography greatly decreased prediction errors, especially for intermediary HI values at middleslope position. Finally, the use of subsurface topography as a novel approach to enhance existing techniques in new applications is discussed. [Copyright &y& Elsevier]

Pedogenic carbonates (calcretes) have often been proposed as possible markers of the pedogenetic processes in soils under semi-arid climate. However, precise chronological constraints on their formation are required in order to investigate the climatic and paleo-environmental conditions that prevailed during and after their formation, and to improve our understanding of the physical and chemical conditions that promoted their development and preservation. Moreover, these authigenic calcium carbonate precipitates provide us with an interesting test of the U–Th radioactive disequilibrium dating method, the reliability of which has been demonstrated extensively in aragonitic corals and calcitic continental speleothems, but which remains much more questionable in highly porous, chemically and mineralogically complex media such as soil profiles. We report here 238 U– 234 U– 230 Th radioactive disequilibrium analyses measured by Thermo-Ionization Mass Spectrometry in calcretes from two sites in southwest India. Since calcretes are impure carbonates mixed with various amounts of parent rock and weathered minerals, all ages must be computed using the isochron technique, involving the extraction of several coeval subsamples from the same soil horizon and U–Th analyses after total dissolution (TSD) method, in order to correct for the detrital component. 232 Th is usually used as index of the detrital contamination, and the isochron age is derived from the isotopic composition ( 230 Th/ 238 U; 234 U/ 238 U) of the pure authigenic carbonate end-member of the mixing line. Our results show that each set of samples taken from decimetric blocks is characterized by a well-defined isochron line in a 3-D Osmond diagram ( 232 Th/ 238 U; 230 Th/ 238 U; 234 U/ 238 U). The regression lines obtained for most of the samples show probabilities of fit satisfying the mathematical assumptions of the isochron model (in most cases ≫ 0.05), and mean square weighted deviations (MSWD) values around 1. The compositions of the end-members are highly variable between the different isochrons, both for the carbonate phase, indicating various ages of cristallisation, and for the detrital phase, indicating various origins and compositions. Notably, our data demonstrate that the detrital component is in all cases out of secular equilibrium, by contrast with the standard paradigm of “dirty carbonate” dating, which is based on the assumption of average continental crust Th/U elemental ratio, and secular equilibrium values of the ( 230 Th/ 238 U) and ( 234 U/ 238 U) ratios. At the first site (Coimbatore), we obtain U–Th ages between 304 ± 38 ka and 44 ± 2.9 ka (2σ) from the base to the top of the profile. These suggest discontinuous precipitation of the different facies in good agreement with micromorphological observations. At the second study site (Gundlupet), the carbonate nodules sampled from two different profiles, yield consistent ages of 200 ka, which suggests that precipitation of nodular carbonate occurred across the entire pediment toposequence during a single event. Surprisingly, in mere contradiction with the standard model of impure carbonate dating, two puzzling samples display “vertical isochrons”, i.e., variable 232 Th/ 238 U without any variation of the 230 Th/ 238 U and 234 U/ 238 U ratios. Such patterns require extremely high 232 Th/ 238 U ratios, in an as yet unidentified detrital phase. Taken at face value, these results suggest that no clear correlation can be inferred between the precipitation of these pedogenic carbonates and major orbitally-driven climate variations recorded in other archives during the last glacial/interglacial cycles. [ABSTRACT FROM AUTHOR]

TRAM domain proteins present in A rchaea and Bacteria have a β-barrel shape with anti-parallel β-sheets that form a nucleic acid binding surface; a structure also present in cold shock proteins ( Csps). Aside from protein structures, experimental data defining the function of TRAM domains is lacking. Here, we explore the possible functional properties of a single TRAM domain protein, Ctr3 ( cold-responsive TRAM domain protein 3) from the Antarctic archaeon M ethanococcoides burtonii that has increased abundance during low temperature growth. Ribonucleic acid ( RNA) bound by Ctr3 in vitro was determined using RNA-seq. Ctr3-bound M . burtonii RNA with a preference for transfer (t) RNA and 5S ribosomal RNA, and a potential binding motif was identified. In t RNA, the motif represented the C loop; a region that is conserved in t RNA from all domains of life and appears to be solvent exposed, potentially providing access for Ctr3 to bind. Ctr3 and Csps are structurally similar and are both inferred to function in low temperature translation. The broad representation of single TRAM domain proteins within A rchaea compared with their apparent absence in B acteria, and scarcity of Csps in A rchaea but prevalence in B acteria, suggests they represent distinct evolutionary lineages of functionally equivalent RNA-binding proteins. [ABSTRACT FROM AUTHOR]

Abstract: Calcrete profiles developed on Precambrian silicate rocks in south peninsular India are studied and compared in terms of mineralogical, chemical and isotopic composition. The aim of this study is to determine the origin of calcium and the processes governing the development of a minor economic deposit in different geomorphic settings. The investigation integrates observations from an outcrop to a microfabric scale and reveals that the origin of calcium is local and linked with the weathering of the minerals of the surrounding rocks. The CaCO3 precipitation occurs after vertical and lateral translocation in the slope system. [Copyright &y& Elsevier]

The objective of this study was to assess Lebanese population exposure to trace elements (TEs) via white pita consumption. A survey of white pita consumption was achieved among one thousand Lebanese individuals, grouped into adults (above 15 years old, men, and women) and young people (6-9 and 10-14 years old). The most consumed pita brands, labeled B1, B2, and B3, were selected. Levels of TEs (i.e., As, Cd, Co, Cr, Hg, Ni, and Pb) in B1, B2, B3 pitas were measured. The highest contents of TEs in pitas were: Ni (1292 µg/kg) and Co (91 µg/kg) in B1; As (400 µg/kg) and Cd (< 15 µg/kg) in B2; Cr (363 µg/kg), Pb (260 µg/kg), and Hg (0.89 µg/kg) in B3. The pita brand B3 was the source of the highest TEs exposure, except for Ni for which it was B1. Daily exposures to TEs due to the fact of pita consumption were compared to safety levels. There were no safety concerns for Hg, Cd, Cr or Co (except the 95th percentile of 6-9 years old). An excess of the Ni tolerable daily intake was observed for the most exposed populations. The very low margins of exposure for As and Pb suggest a worrying risk for the Lebanese population.

Alteration of axonal transport has emerged as a common precipitating factor in several neurodegenerative disorders including Human Spastic Paraplegia (HSP). Mutations of the SPAST (SPG4) gene coding for the spastin protein account for 40% of all autosomal dominant uncomplicated HSP. By cleaving microtubules, spastin regulates several cellular processes depending on microtubule dynamics including intracellular membrane trafficking. Axonal transport is fundamental for the viability of motor neurons which often have very long axons and thus require efficient communication between the cell body and its periphery. Here we found that the anterograde velocity of VAMP7 vesicles, but not that of VAMP2, two vesicular-SNARE proteins implicated in neuronal development, is enhanced in SPG4-KO neurons. We showed that this effect is associated with a slight increase of the level of acetylated tubulin in SPG4-KO neurons and correlates with an enhanced activity of kinesin-1 motors. Interestingly, we demonstrated that an artificial increase of acetylated tubulin by drugs reproduces the effect of Spastin KO on VAMP7 axonal dynamics but also increased its retrograde velocity. Finally, we investigated the effect of microtubule targeting agents which rescue axonal swellings, on VAMP7 and microtubule dynamics. Our results suggest that microtubule stabilizing agents, such as taxol, may prevent the morphological defects observed in SPG4-KO neurons not simply by restoring the altered anterograde transport to basal levels but rather by increasing the retrograde velocity of axonal cargoes., (Copyright © 2017 Elsevier B.V. All rights reserved.)

The human YB-1 protein plays multiple cellular roles, of which many are dictated by its binding to RNA and DNA through its Cold Shock Domain (CSD). Using molecular dynamics simulation approaches validated by experimental assays, the YB1 CSD was found to interact with nucleic acids in a sequence-dependent manner and with a higher affinity for RNA than DNA. The binding properties of the YB1 CSD were close to those observed for the related bacterial Cold Shock Proteins (CSP), albeit some differences in sequence specificity. The results provide insights in the molecular mechanisms whereby YB-1 interacts with nucleic acids.

Energy transfer between chromophores in photosynthesis proceeds with near-unity quantum efficiency. Understanding the precise mechanisms of these processes is made difficult by the complexity of the electronic structure and interactions with different vibrational modes. Two-dimensional spectroscopy has helped resolve some of the ambiguities and identified quantum effects that may be important for highly efficient energy transfer. Many questions remain, however, including whether the coherences observed are electronic and/or vibrational in nature and what role they play. We utilize a two-color, four-wave mixing experiment with control of the wavelength and polarization to selectively excite specific coherence pathways. For the light-harvesting complex PC645, from cryptophyte algae, we reveal and identify specific contributions from both electronic and vibrational coherences and determine an excited-state structure based on two strongly coupled electronic states and two vibrational modes. Separation of the coherence pathways also uncovers the complex evolution of these coherences and the states involved.

Observations of long-lived coherences in photosynthetic light-harvesting complexes utilize short pulses with broad spectral bandwidths to coherently excite multiple transitions and coherent superpositions. In order to identify the role that such quantum effects might play in efficient energy transfer, however, an alternative approach is required. We have developed a technique for two-color photon echo spectroscopy to selectively excite the pathway of interest and measure its evolution in the absence of any other excitation. We use this technique to excite a coherence pathway in phycocyanin-645 from cryptophyte algae and measure the dynamics of this coherence. A decoherence time of 500 fs was measured, and clear signatures for strong coupling between the electronic states and phonon modes were observed, allowing coherent coupling between otherwise nonresonant transitions. This provides detailed experimental evidence of the long-lived coherences and the nature of the quantum mechanical interactions between electronic states and phonon modes in phycocyanin-645 from cryptophyte marine algae.

We report the NMR assignment of the PN2-3 subdomain of the CPAP protein. It has been previously shown that this motif interacts with tubulin, inhibits microtubule nucleation from the centrosome and depolymerizes taxol-stabilized microtubules.

Bacterial polysulfide reductase (PsrABC) is an integral membrane protein complex responsible for quinone-coupled reduction of polysulfide, a process important in extreme environments such as deep-sea vents and hot springs. We determined the structure of polysulfide reductase from Thermus thermophilus at 2.4-A resolution, revealing how the PsrA subunit recognizes and reduces its unique polyanionic substrate. The integral membrane subunit PsrC was characterized using the natural substrate menaquinone-7 and inhibitors, providing a comprehensive representation of a quinone binding site and revealing the presence of a water-filled cavity connecting the quinone binding site on the periplasmic side to the cytoplasm. These results suggest that polysulfide reductase could be a key energy-conserving enzyme of the T. thermophilus respiratory chain, using polysulfide as the terminal electron acceptor and pumping protons across the membrane via a previously unknown mechanism.

Stathmin is a ubiquitous microtubule destabilizing protein that is believed to play an important role linking cell signaling to the regulation of microtubule dynamics. Here we show that stathmin strongly destabilizes microtubule minus ends in vitro at steady state, conditions in which the soluble tubulin and microtubule levels remain constant. Stathmin increased the minus end catastrophe frequency approximately 13-fold at a stathmin:tubulin molar ratio of 1:5. Stathmin steady-state catastrophe-promoting activity was considerably stronger at the minus ends than at the plus ends. Consistent with its ability to destabilize minus ends, stathmin strongly increased the treadmilling rate of bovine brain microtubules. By immunofluorescence microscopy, we also found that stathmin binds to purified microtubules along their lengths in vitro. Co-sedimentation of purified microtubules polymerized in the presence of a 1:5 initial molar ratio of stathmin to tubulin yielded a binding stoichiometry of 1 mol of stathmin per approximately 14.7 mol of tubulin in the microtubules. The results firmly establish that stathmin can increase the steady-state catastrophe frequency by a direct action on microtubules, and furthermore, they indicate that an important regulatory action of stathmin in cells may be to destabilize microtubule minus ends.

Stathmin family proteins interact with tubulin and negatively regulate its assembly in microtubules. One stathmin molecule forms a complex with two alphabeta tubulin heterodimers in an interaction that is weakened upon stathmin phosphorylation. The X-ray structure of crystals of the complex reveals a head-to-tail arrangement of the two tubulins which are connected by a long stathmin alpha helix. By holding tubulins in a curved complex that is not incorporated in microtubules, stathmin lowers the pool of "assembly competent" tubulin. An alternate mechanism has been also proposed to account for the stathmin action in vivo; it involves a direct interaction of stathmin with microtubule (+) ends. More experiments are needed to evaluate the relative contribution of this alternative mechanism to the regulation of tubulin assembly by stathmin.

The Sm/Lsm proteins associate with small nuclear RNA to form the core of small nuclear ribonucleoproteins, required for processes as diverse as pre-mRNA splicing, mRNA degradation and telomere formation. The Lsm proteins from archaea are likely to represent the ancestral Sm/Lsm domain. Here, we present the crystal structure of the Lsm alpha protein from the thermophilic archaeon Methanobacterium thermoautotrophicum at 2.0 A resolution. The Lsm alpha protein crystallizes as a heptameric ring comprised of seven identical subunits interacting via beta-strand pairing and hydrophobic interactions. The heptamer can be viewed as a propeller-like structure in which each blade consists of a seven-stranded antiparallel beta-sheet formed from neighbouring subunits. There are seven slots on the inner surface of the heptamer ring, each of which is lined by Asp, Asn and Arg residues that are highly conserved in the Sm/Lsm sequences. These conserved slots are likely to form the RNA-binding site. In archaea, the gene encoding Lsm alpha is located next to the L37e ribosomal protein gene in a putative operon, suggesting a role for the Lsm alpha complex in ribosome function or biogenesis., (Copyright 2001 Academic Press.)

We live on a cold planet where more than 80% of the biosphere is permanently below 5 degrees C, and yet comparatively little is known about the genetics and physiology of the microorganisms inhabiting these environments. Based on molecular probe and sequencing studies, it is clear that Archaea are numerically abundant in diverse low-temperature environments throughout the globe. In addition, non-low-temperature-adapted Archaea are commonly exposed to sudden decreases in temperature, as are other microorganisms, animals, and plants. Considering their ubiquity in nature, it is perhaps surprising to find that there is such a lack of knowledge regarding low-temperature adaptation mechanisms in Archaea, particularly in comparison to what is known about archaeal thermophiles and hyperthermophiles and responses to heat shock. This review covers what is presently known about adaptation to cold shock and growth at low temperature, with a particular focus on Antarctic Archaea. The review highlights the similarities and differences that exist between Archaea and Bacteria and eukaryotes, and addresses the potentially important role that protein synthesis plays in adaptation to the cold. By reviewing the present state of the field, a number of important areas for future research are identified.

Phosphoproteins of the stathmin family interact with the alphabeta tubulin heterodimer (tubulin) and hence interfere with microtubule dynamics. The structure of the complex of GDP-tubulin with the stathmin-like domain of the neural protein RB3 reveals a head-to-tail assembly of two tubulins with a 91-residue RB3 alpha helix in which each copy of an internal duplicated sequence interacts with a different tubulin. As a result of the relative orientations adopted by tubulins and by their alpha and beta subunits, the tubulin:RB3 complex forms a curved structure. The RB3 helix thus most likely prevents incorporation of tubulin into microtubules by holding it in an assembly with a curvature very similar to that of the depolymerization products of microtubules.

The advantages of the organism Dictyostelium discoideum as an expression host for recombinant glycoproteins have been exploited for the production of an isotopically labeled cell surface protein for NMR structure studies. Growth medium containing [(15)N]NH(4)Cl and [(13)C]glycerol was used to generate isotopically labeled Escherichia coli, which was subsequently introduced to D. discoideum cells in simple Mes buffer. A variety of growth conditions were screened to establish minimal amounts of nitrogen and carbon metabolites for a cost-effective protocol. Following single-step purification by anion-exchange chromatography, 8 mg of uniformly (13)C,(15)N-labeled protein secreted by approximately 10(10) D. discoideum cells was isolated from 3.3 liters of supernatant. Mass spectrometry showed the recombinant protein of 16 kDa to have incorporated greater than 99.9% isotopic label. The two-dimensional (1)H-(13)C HSQC spectrum confirms (13)C labeling of both glycan and amino acid residues of the glycoprotein. All heteronuclear NMR spectra showed a good dispersion of cross-peaks essential for high-quality structure determination., (Copyright 2000 Academic Press.)

d-Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) catalyses the central CO(2)-fixing reaction of photosynthesis in a complex, multiple-step process. Several structures of rubisco complexed with substrate analogues, inhibitors and products have been determined by X-ray crystallography. The structures fall into two well-defined and distinct states. The active site is either "open" or "closed". The timing and mechanism of the transition between these two states have been uncertain. We solved the crystal structure of unactivated (metal-free) rubisco from tobacco with only inorganic phosphate bound and conclude that phosphate binding per se does not trigger closure, as it does in the similarly structured enzyme, triosephosphate isomerase. Comparison of all available rubisco structures suggests that, instead, the distance between the terminal phosphates (P1 and P2) of the bisphosphate ligand is the trigger: if that distance is less than 9.1 A, then the active site closes; if it is greater than 9.4 A then the enzyme remains open. Shortening of the inter-phosphate distance results from the ligand binding in a more curved conformation when O atoms of the ligand's sugar backbone interact either with the metal, if it is present, or with charged groups in the metal-binding site, if the metal is absent. This shortening brings the P1 phosphate into hydrogen bonding contact with Thr65. Thr65 exists in two discrete states related by a rotation of the backbone psi torsion angle. This rotation is coupled to domain rotation and hence to active site closure. Rotation of the side-chain of Thr65 also affects the C-terminal strand of large subunit which packs against Loop 6 after closure. The position of the C-terminal strand in the closed state is stabilised by multiple polar interactions with a distinctive highly-charged latch site involving the side-chain of Asp473. In the open state, this latch site may be occupied instead by phosphorylated anions., (Copyright 2000 Academic Press.)

Stathmin, also referred to as Op18, is a ubiquitous cytosolic phosphoprotein, proposed to be a small regulatory protein and a relay integrating diverse intracellular signaling pathways involved in the control of cell proliferation, differentiation and activities. It interacts with several putative downstream target and/or partner proteins. One major action of stathmin is to interfere with microtubule dynamics, by inhibiting the formation of microtubules and/or favoring their depolymerization. Stathmin (S) interacts directly with soluble tubulin (T), which results in the formation of a T2S complex which sequesters free tubulin and therefore impedes microtubule formation. However, it has been also proposed that stathmin's action on microtubules might result from the direct promotion of catastrophes, which is still controversial. Phosphorylation of stathmin regulates its biological actions: it reduces its affinity for tubulin and hence its action on microtubule dynamics, which allows for example progression of cells through mitosis. Stathmin is also the generic element of a protein family including the neural proteins SCG10, SCLIP and RB3/RB3'/RB3". Interestingly, the stathmin-like domains of these proteins also possess a tubulin binding activity in vitro. In vivo, the transient expression of neural phosphoproteins of the stathmin family leads to their localization at Golgi membranes and, as previously described for stathmin and SCG10, to the depolymerization of interphasic microtubules. Altogether, the same mechanism for microtubule destabilization, that implies tubulin sequestration, is a common feature likely involved in the specific biological roles of each member of the stathmin family.

Cryptophytes are unicellular photosynthetic algae that use a lumenally located light-harvesting system, which is distinct from the phycobilisome structure found in cyanobacteria and red algae. One of the key components of this system is water-soluble phycoerythrin (PE) 545 whose expression is enhanced by low light levels. The crystal structure of the heterodimeric alpha(1)alpha(2)betabeta PE 545 from the marine cryptophyte Rhodomonas CS24 has been determined at 1.63-A resolution. Although the beta-chain structure is similar to the alpha and beta chains of other known phycobiliproteins, the overall structure of PE 545 is novel with the alpha chains forming a simple extended fold with an antiparallel beta-ribbon followed by an alpha-helix. The two doubly linked beta50/beta61 chromophores (one on each beta subunit) are in van der Waals contact, suggesting that exciton-coupling mechanisms may alter their spectral properties. Each alpha subunit carries a covalently linked 15,16-dihydrobiliverdin chromophore that is likely to be the final energy acceptor. The architecture of the heterodimer suggests that PE 545 may dock to an acceptor protein via a deep cleft and that energy may be transferred via this intermediary protein to the reaction center.

Thermal stability of mutant proteins has been investigated using temperature dependent molecular dynamics (MD) simulations in vacuo. The numerical modeling was aimed at mimicking protein expansion upon heating. After the conditions for an expanding protein accessible surface area were established for T4 lysozyme and barnase wild-type proteins, MD simulations were carried out under the same conditions using the crystal structures of several mutant proteins. The computed thermal expansion of the accessible surface area of mutant proteins was found to be strongly correlated with their experimentally measured stabilities. A similar, albeit weaker, correlation was observed for model mutant proteins. This opens the possibility of obtaining stability information directly from protein structure.

Stathmin is a ubiquitous cytosolic phosphoprotein participating in the relay and integration of diverse intracellular signaling pathways involved in the control of cell proliferation, differentiation, and activities. It is phosphorylated in response to diverse extracellular signals including hormones and growth factors, and it is highly expressed during development and in diverse tumoral cells and tissues. Stathmin interacts with tubulin and other potential protein partners such as BiP, KIS, CC1 and CC2/tsg101. In our present search for further functional partners of stathmin, we identified proteins in the Hsp70 family, and in particular Hsc70, as interacting with stathmin in vitro. Hsc70 is among the proteins coimmunoprecipitated with stathmin, and it is the main protein retained specifically on stathmin-Sepharose beads identified by one- and two-dimensional electrophoresis and immunoblots. Bovine serum albumin (BSA)-Sepharose did not bind Hsc70, and anti-stathmin antisera specifically inhibited the interaction of Hsc70 with stathmin-Sepharose. The binding of Hsc70 to stathmin is dependent on the phosphorylation status of stathmin, as it did not occur with a "pseudophosphorylated" mutant form of stathmin. This interaction is further dependent on the ATP status of Hsc70. It was inhibited in the presence of ATP-Mg++ but not in the presence of ATP-Mg++ and ethylenediaminetetraacetic acid (EDTA) or of ADP. Our results suggest that the interaction of stathmin with Hsc70 is specific in both proteins and most likely biologically relevant in the context of their functional implication in the control of numerous intracellular signaling and regulatory pathways, and hence of normal cell growth and differentiation.

Background: Plasminogen activator inhibitor 2 (PAI-2) is a member of the serpin family of protease inhibitors that function via a dramatic structural change from a native, stressed state to a relaxed form. This transition is mediated by a segment of the serpin termed the reactive centre loop (RCL); the RCL is cleaved on interaction with the protease and becomes inserted into betasheet A of the serpin. Major questions remain as to what factors facilitate this transition and how they relate to protease inhibition., Results: The crystal structure of a mutant form of human PAI-2 in the stressed state has been determined at 2.0 A resolution. The RCL is completely disordered in the structure. An examination of polar residues that are highly conserved across all serpins identifies functionally important regions. A buried polar cluster beneath betasheet A (the so-called 'shutter' region) is found to stabilise both the stressed and relaxed forms via a rearrangement of hydrogen bonds., Conclusions: A statistical analysis of interstrand interactions indicated that the shutter region can be used to discriminate between inhibitory and non-inhibitory serpins. This analysis implied that insertion of the RCL into betasheet A up to residue P8 is important for protease inhibition and hence the structure of the complex formed between the serpin and the target protease.

Large intragenic deletions of the TSG101/CC2 gene were recently reported in seven of 15 primary metastatic breast cancers. Although the number of samples was small, this observation suggested that TSG101/CC2 alterations were a major event in breast carcinogenesis. To study the frequency of these deletions in invasive breast cancers we analysed 189 primary invasive breast tumours and 59 breast cancer metastases. We detected intragenic rearrangements in only three samples (two primary tumours and one metastasis). Northern blot analysis of 43 tumours without rearrangements failed to detect any abnormalities. Furthermore, we studied TSG101/CC2 in 11 human breast adenocarcinoma cell lines by Southern blot, RT-PCR and sequencing of the entire coding region of the gene, and detected no abnormalities. These results show that genetic alteration of TSG101/CC2 is a rare event in breast cancer.

Prespore-specific antigen (PsA) is a putative cell-adhesion molecule of the cellular slime mould Dictyostelium discoideum, which has a similar molecular architecture to several mammalian cell-surface proteins. It has an N-terminal globular domain presented to the extracellular environment on an O-glycosylated stem (glycopeptide) that is attached to the cell membrane through a glycosyl-PtdIns anchor. The sequence of PsA suggests that PsA may belong to a new family of cell-surface molecules and here we present information on the structure of the N-terminal globular domain and determine the reducing-terminal linkage of the O-glycosylation. To obtain a sufficient amount of pure protein, a secreted recombinant form of PsA (rPsA), was expressed in D. discoideum and characterised. 1H-NMR spectra of rPsA contained features consistent with a high degree of beta-sheet in the N-terminal globular domain, a feature commonly observed in cell-adhesion proteins. Solid-phase Edman degradation of the glycopeptide of rPsA indicated that 14 of the 15 threonines and serines in the spacer region were glycosylated. The chemical structures of the O-glycosylations were determined to be single N-acetylglucosamine residues.

Cross-strand pair correlations are calculated for residue pairs in anti-parallel beta-sheet for two cases: pairs whose backbone atoms are hydrogen bonded together (H-bonded site) and pairs which are not (non-H-bonded site). The statistics show that this distinction is important. When glycine is located on the edge of a sheet, it shows a 3:1 preference for the H-bonded site. The strongest observed correlations are for pairs of disulfide-bonded cystines, many of which adopt a close-packed conformation with each cystine in a spiral conformation of opposite chirality to its partner. It is likely that these pairs are a signature for the family of small, cystine-rich proteins. Most other strong positive and negative correlations involve charged and polar residues. It appears that electrostatic compatibility is the strongest factor affecting pair correlation. Significant correlations are observed for beta- and gamma-branched residues in the non-H-bonded site. An examination of the structures shows a directionality in side chain packing. There is a correlation between (1) the directionality in the packing interactions of non-H-bonded beta- and gamma-branched residue pairs, (2) the handedness of the observed enantiomers of chiral beta-branched side chains, and (3) the handedness of the twist of beta-sheet. These findings have implications for the formation of beta-sheets during protein folding and the mechanism by which the sheet becomes twisted.

Stathmin, a ubiquitous cytosolic phosphoprotein which may play a role in integrating the effects of diverse signals regulating proliferation, differentiation and other cell functions, was found to be phosphorylated rapidly and stoichiometrically by mitogen-activated protein (MAP) kinase in vitro. Ser-25 was identified as the major site and Ser-38 as a minor site of phosphorylation, while the p42 and p44 isoforms of MAP kinase were the only significant stathmin kinases detected in PC12 cells after stimulation by nerve growth factor (NGF). The results suggest that MAP kinases are the enzymes responsible for increasing the level of phosphorylation of Ser-25, which has been observed previously in PC12 cells following stimulation by NGF.

The crystal structure of activated tobacco rubisco, complexed with the reaction-intermediate analogue 2-carboxy-arabinitol 1,5-bisphosphate (CABP) has been determined by molecular replacement, using the structure of activated spinach rubisco (Knight, S., Andersson, I., & Brändén, C.-I., 1990, J. Mol. Biol. 215, 113-160) as a model. The R-factor after refinement is 21.0% for 57,855 reflections between 9.0 and 2.7 A resolution. The local fourfold axis of the rubisco hexadecamer coincides with a crystallographic twofold axis. The result is that the asymmetric unit of the crystals contains half of the L8S8 complex (molecular mass 280 kDa in the asymmetric unit). The activated form of tobacco rubisco is very similar to the activated form of spinach rubisco. The root mean square difference is 0.4 A for 587 equivalent C alpha atoms. Analysis of mutations between tobacco and spinach rubisco revealed that the vast majority of mutations concerned exposed residues. Only 7 buried residues were found to be mutated versus 54 residues at or near the surface of the protein. The crystal structure suggests that the Cys 247-Cys 247 and Cys 449-Cys 459 pairs are linked via disulfide bridges. This pattern of disulfide links differ from the pattern of disulfide links observed in crystals of unactivated tobacco rubisco (Curmi, P.M.G., et al., 1992, J. Biol. Chem. 267, 16980-16989) and is similar to the pattern observed for activated spinach tobacco.

The structure of the unactivated form of ribulose-1,5-bisphosphate carboxylase/oxygenase was refined at a resolution of 2.0 A to an R-factor of 17.1%. The previous model (Chapman et al., 1988) was extensively rebuilt, and the small subunit was retraced. The refined model consists of residues 22-63 and 69-467 of the large subunit and the complete small subunit. A striking feature of the model is that several loops have very high B-factors, probably representing mobile regions of the molecule. An examination of the intersubunit contacts shows that the L8S8 hexadecamer is composed of four L2 dimers. The dominant contacts between these L2 dimers are formed by the small subunits. This suggests that the small subunits may be essential for maintaining the integrity of the L8S8 structure. The active site shows differences between the unactivated form and the quaternary complex. In particular, Lys334 has moved out of the active site by about 10A. This residue lies on loop 6 of the alpha beta barrel, which is a particularly mobile loop. The site of ribulose-1,5-bisphosphate carboxylase/oxygenase activation is well ordered in the absence of the carbamylation of Lys201 and Mg2+ binding. The residues are held poised by a network of hydrogen bonds. In the unactivated state, the active site is accessible to substrate binding.

The crystal structure of the diphtheria toxin dimer at 2.5 A resolution reveals a Y-shaped molecule of three domains. The catalytic domain, called fragment A, is of the alpha + beta type. Fragment B actually consists of two domains. The transmembrane domain consists of nine alpha-helices, two pairs of which are unusually apolar and may participate in pH-triggered membrane insertion and translocation. The receptor-binding domain is a flattened beta-barrel with a jelly-roll-like topology. Three distinct functions of the toxin, each carried out by a separate structural domain, can be useful in designing chimaeric proteins, such as immunotoxins, in which the receptor-binding domain is substituted with antibodies to target other cell types.

Relative 125I-albumin concentration was measured in vivo in the aortic media of sham-operated (n = 10) and hypertensive (two-kidney, one clip) rats, untreated (n = 8) or treated (n = 10) by an angiotensin converting enzyme inhibitor (CEI, Trandolapril). Blood pressure was acutely lowered to a normal level at the time of the experiment in hypertensive rats (n = 7) to separate the direct effect of increased pressure from the effect of pressure-induced structural changes. Relative tissue concentration profiles of labeled albumin across the media were obtained using a serial frozen-sectioning technique. In hypertensive rats, the mean medial albumin concentration decreased by 35% in the ascending arch and 32% in the descending arch (p less than 0.01). When blood pressure was acutely lowered in hypertensive animals, this value decreased further by 56% in the ascending arch, 48% in the descending arch (p less than 0.01), and 22% in the thoracic aorta (p less than 0.05) as compared with controls. The medial thickness in hypertensive rats was significantly increased (more in the ascending arch than in the rest of the aorta). Four-week CEI treatment reversed hypertension and medial thickening, but the mean medial albumin concentration remained significantly lower in the arch (by 36% in the ascending part and 40% in the descending part, p less than 0.01). The collagen content in the thoracic aorta was significantly increased in hypertensive rats (by 40%, p less than 0.01) and remained increased (by 29%, p less than 0.01) after CEI treatment. These results suggested that the hypertension-induced structural changes might reduce the medial distribution volume for albumin, whereas elevated blood pressure per se tended to enhance albumin concentration within the media. However, the net result of chronic hypertension was a reduction of the mean medial albumin concentration. The aortic arch appeared to be more affected than the rest of the aorta. Fiber content, more than medial thickness, might be responsible for the observed differences in albumin concentration. Lowering of blood pressure seemed to be insufficient to restore normal albumin concentration profiles and perhaps those of other macromolecules. This finding may be relevant in evaluating some of the complications associated with hypertension.

We have presented two applications of the method of neutron scattering utilizing selective deuteration of actin. In these experiments the actin was rendered effectively invisible to neutrons by matching the scattering-length densities of deuterated actin and the solvent. The scattering of neutrons by myosin S1 and by Tm bound to this actin was studied. For free chymotrypsin-generated S1 it was found that Rg = 4.0 +/- 0.15 nm, while for papain-generated S1 it was found that Rg = 4.6 +/- 0.2 nm. Upon binding of papain-generated S1 to actin at low NS1/N actin ratios, the change in Rg in difference experiments was delta Rg = 0.05 +/- 0.15 nm. This lack of significant change in Rg in the very low-s domain confirms and extends our earlier neutron scattering work in the higher-s domain. The longest chords of S1, as well as shorter ones, are not significantly altered upon actin binding. These results indicate that muscle contraction does not occur as a result of large-scale changes in S1 structure. In actin-Tm complexes, a measurement of the mean cross-helix separation, d, of Tm molecules has been made using neutron scattering. With deuterated actin matched out in 93% D2O buffer, it was found that d = 7.9 +/- 0.3 nm. This value is in good agreement with a model based on Tm crystallography and also with recent electron microscopy results. These experiments demonstrate the feasibility and value of neutron diffraction and scattering techniques in the study of muscle contraction and its control. One can expect that the further employment of emerging cell biology techniques for generating deuterated proteins will aid our understanding of muscle in the future.

Neutron scattering has been used to compare the structure of myosin S1 that is free in solution to that when it is bound to F-actin. To achieve this, deuterated actin was obtained from D. discoideum that had been fed deuterated E. coli. This deuterated actin was rendered "invisible" to neutrons when dissolved in 94% D2O. The neutron scattering patterns obtained from S1 bound to deuterated actin were identical to those of free S1 except for oscillations due to S1's bound to the same actin filament. At low S1 to actin stoichiometries, these oscillations diminish and the patterns become indistinguishable. The apparent radius of gyration of S1 bound to actin is identical to that of free S1 when the stoichiometry is low. Thus, no changes in the structure of S1 were observed to a resolution of 2.5 nm. Computer modelling studies were used to evaluate the compatibility of models for the mechanism of force generation with the neutron data. These studies show that for powerstrokes greater than 5.0 nm, the data are consistent with more than 80% of the crossbridge maintaining a rigid conformation during force generation.

To investigate the effect of hyperpressure on the transport of LDL and albumin in the arterial wall, we measured in vitro the uptake of both 131I-LDL and 125I-albumin in intact rabbit thoracic aorta, held at in vivo length and pressurized to 70 or 160 mmHg. Arteries were incubated for 2 h at 70 mmHg, and for 5 min, 30 min, 1 h and 2 h at 160 mmHg. The transmural distribution of the relative concentrations of LDL (CLDL) and albumin (CAlb) across the wall was determined using a serial frozen sectioning technique. At 70 mmHg, the mean medial CLDL and CAlb values were 0.0018 +/- 0.0007 and 0.0039 +/- 0.0013, respectively. At 160 mmHg, CLDL and CAlb were markedly increased. The distribution of labeled albumin was almost uniform across the media and reached a steady state after 30 min, whereas labeled LDL accumulated in the first inner layers, a steady state being achieved after 1 h. The 1-hour values of CLDL in the first and second luminal sections (0.24 +/- 0.03 and 0.13 +/- 0.05, respectively) were much higher than those of CAlb, the CLDL/CAlb ratios being 4.12 +/- 0.94 and 2.34 +/- 0.42 (p less than 0.01), respectively. In the subsequent sections, the CLDL markedly decreased and became much lower than the CAlb, the CLDL/CAlb ratio averaging 0.2 in the two thirds outer media. To investigate whether LDL was trapped at high pressure in the inner layers, vessels were exposed to a tracer-free intraluminal solution for 30 min, following a 30-minute incubation with tracers.(ABSTRACT TRUNCATED AT 250 WORDS)

NMR and UV spectroscopy reveal that the tetravalent thorium ion interacts with actin in an identical fashion to the trivalent lanthanide ions. UV spectra and viscometry data suggest that the actin-bound Th4+ has an ionic radius of about 110 pm. Th4+ also contributes to the formation of crystalline actin tubes under appropriate conditions. The factors governing whether tubes form appear to be cationic radius and total charge on the actin monomer, rather than the valency of the ion per se.

The structure of subfragment 1 (S1) bound to F-actin has been compared to the structure of free S1 using neutron scattering. The F-actin was rendered "invisible" to neutrons by selective deuteration and solvent contrast matching. Highly deuterated actin was purified from the slime mold Dictyostelium discoideum, which was fed deuterated Escherichia coli. The properties of this actin were found to be similar to those of protonated actin. The neutron-scattering pattern of S1 bound to this "invisible" actin was compared to that of free S1. At near-physiological ionic strength, a strong interference effect was observed, which arose from pairs of S1 molecules cross-linking actin filaments. However, at low ionic strength the only differences that could be observed were attributed to interference effects between neutrons scattered from S1s bound randomly to equivalent sites on an actin filament. These effects became negligible as the fraction of actin sites occupied by S1 approached zero. Thus, we conclude that the scattering by S1 attached to F-actin is identical with that of free S1, to a resolution of about 2.5 nm. The difference in apparent radii of gyration is less than 0.05 nm. Modeling calculations have been carried out to determine the sensitivity of neutron scattering to possible S1 deformations. The calculations showed that deformations of the structure of S1 that are large enough ultimately to produce a powerstroke of 5 nm or greater are only consistent with the data if they involve at most about 20% of the S1 mass. These results restrict the class of plausible models describing force generation in muscle contraction.

In an attempt to investigate the effects of transmural pressure on LDL transport and distribution across the arterial wall, uptake of labeled LDL has been measured in excised rabbit thoracic aorta, held at in vivo length and pressurized to 70 or 160 mmHg. The transmural distribution of LDL concentration across the wall was determined by examining serial frozen sections cut parallel to the luminal surface at 20 microns intervals from the intima to adventitia. The LDL concentration observed in the first luminal section at 160 mmHg was 20-fold higher than that obtained at 70 mmHg. The LDL concentrations decreased in the subsequent sections of the first half of the media and became similar, in the outer half of the media, to the values observed under normal pressure. These results might provide an account of one of the mechanisms involved in the deleterious effects of hypertension in atherogenesis.

The effect of the trivalent cations scandium (Sc3+) and yttrium (Y3+) on the conformation of G-actin was examined using ultraviolet difference and high resolution 1H-NMR spectroscopy. A comparison was made with data obtained previously with the trivalent lanthanide cations (Ln3+). These results indicate that the first and subsequent Y ions (ionic radius 101.9 pm) behave exactly like Ln3+. Sc3+ is a smaller ion (87 pm) than any of the Ln3+. The first Sc3+ binds to a site on actin that is inaccessible to Mg2+, Y3+ and Ln3+. However, the second Sc3+ to bind behaves like an Ln3+. On replacing the native divalent cation (Mg2+), both Y3+ and Sc3+ mobilize the adenine ring of ATP bound to actin, thus exposing underlying residues to the solvent. When Y3+ and Sc3+ saturate their binding sites on actin, and when the ionic strength is raised to 0.1 M with KCl at pH 6.9, the actin aggregates. Y3+ binds to actin with a ratio of 6 : 1 and induces the aggregation of actin into crystalline actin tubes, whilst Sc3+ binds with a ratio of 8 : 1 and induces amorphous actin aggregates. These results are consistent with the suggestion that actin tubes are induced by trivalent cations, principally on the basis of their binding stoichiometry, which is determined by ionic radius.

There have been several reports which describe a conformational change of G-actin monomer in the presence of 0.1 M KCl. This altered monomer has been variously named, depending on whether the authors believed that it resembles G-actin, F-actin or has a conformation of its own. In this report we re-examine the experimental evidence for these proposals. The techniques include measurements of the rates of proteolytic digestion as well as near and far ultraviolet difference spectroscopy of actin in the presence and absence of KCl. We conclude that there is no compelling evidence for proposing a novel form of actin monomer.

The three-dimensional structure of ribulose-1,5-biphosphate carboxylase-oxygenase (RuBisCO), has been determined at 2.6 A resolution. This enzyme initiates photosynthesis by combining carbon dioxide with ribulose bisphosphate to form two molecules of 3-phosphoglycerate. In plants, RuBisCO is built from eight large (L) and eight small (S) polypeptide chains, or subunits. Both S chains and the NH2-terminal domain (N) of L are antiparallel beta, "open-face-sandwich" domains with four-stranded beta sheets and flanking alpha helices. The main domain (B) of L is an alpha/beta barrel containing most of the catalytic residues. The active site is in a pocket at the opening of the barrel that is partly covered by the N domain of a neighboring L chain. The domain contacts of the molecule and its conserved residues are discussed in terms of this structure.

The presence of bound Ln ions gives rise to changes in the ultraviolet absorbance of G-actin. Previously, Ln ions have been shown to mobilize the adenosine moiety of ATP bound to the actin monomer. The changes in ultraviolet absorbance appear to be fully attributable to this mobilization. Any structural changes induced in G-actin by the substitution of Ln ions for Ca2+ must be small enough so as not to perturb the environment of any aromatic chromophores other than those exposed by the mobility of the nucleotide. This conclusion is supported by measurements of the rates of proteolytic digestion of actin with and without bound Ln ions. The effect of Ln ions on the actin-bound nucleotide is not simply due to the increase in positive charge on the actin monomer. This is demonstrated by the absence of any ultraviolet spectral changes on the addition of a fivefold excess of Ca2+. Analysis of the ultraviolet difference spectrum obtained when Ln ions bind to G-actin indicates that at least one tryptophan residue is partially exposed to the solvent coincident with mobilization of the nucleotide. Tb3+ luminescence enhancement studies indicate that there are no Trp, Tyr or Phe residues in the vicinity of the high-affinity cation site. These results suggest that the exposed Trp may be close to the nucleotide.

Calcium antagonists have been shown to have an antiatherogenic effect. We investigated the effect of nicardipine and verapamil on the albumin transport across the media of excised rabbit thoracic aorta. The effect of nicardipine was also tested in deendothelialized arteries. The vessels were incubated for 90 minutes in oxygenated Krebs or 80 mM KCl solutions at in vivo length and at a transmural pressure of 70 mm Hg. The transmural concentration profiles of 125I-albumin across the media were measured by a frozen serial sectioning technique. In deendothelialized arteries, K+ decreased the mean medial uptake of labeled albumin, whereas 10(-7) M nicardipine in Krebs increased the uptake and 10(-9) M nicardipine had no effect. In a K+-rich solution, containing 10(-7) or 10(-9) M nicardipine, the medial uptake was lower than, but not significantly different from, that in Krebs. In intact K+-treated vessels, the wall concentrations near the lumen were increased and concentration gradients across the media were observed, possibly due to an increase in endothelial permeability following K+-induced contraction of the endothelial cells. This effect was reversed by the addition of 10(-7) M nicardipine, but not by 10(-7) M verapamil. Nicardipine and verapamil (10(-7) M) in Krebs solution enhanced the albumin uptake by the media of intact arteries. This effect on the permeability of the media may be related to the antiatherogenic effect of calcium antagonists.

Crystalline tubular aggregates of actin spontaneously assemble in the presence of certain of the lanthanide ions. These tubes are now known to contain a high degree of structural order and it has been suggested that they may be sensitive to small changes in the primary sequence. However, there have been no detailed studies of the effects of solution conditions associated with their formation. In this report we systematically examine the effects of lanthanide ion concentration, ionic radius, adenosine nucleotide concentration, divalent cation concentration, pH, KCl concentration and incubation time. The stringent control of these parameters leads to a high degree of predictability of the structural parameters of the tubes and will thus be of use in identifying actin isozymes.