New Methodology for Computer-Aided Modelling of Biomolecular Structure and Dynamics 2. Local Deformations and Cycles

Abstract

A new methodology for the conformational modelling of biomolecular systems (1) is extended to local deformations of chain molecules and to flexible molecular rings. It is shown that these two cases may be reduced to considering an equivalent molecular model with a regular tree-like topology. A simple procedure is developed to analyze any flexible rings (the five- and six-membered suguar rings of carbohydrates and nucleic acids, in particular) and local deformation regions by energy minimization. Dynamic equations are also derived for such molecular systems. As a result, a unified approach is proposed for the efficient energy minimization and simulation of dynamic behavior of multimolecular systems having any set of variable internal coordinates, local deformation regions and cycles. Advantages and domains of applicability of the approach are discussed.     

Large-Scale Analysis of Kinase Signaling in Yeast Pseudohyphal Development Identifies Regulation of Ribonucleoprotein Granules

Yeast pseudohyphal filamentation is a stress-responsive growth transition relevant to processes required for virulence in pathogenic fungi. Pseudohyphal growth is controlled through a regulatory network encompassing conserved MAPK (Ste20p, Ste11p, Ste7p, Kss1p, and Fus3p), protein kinase A (Tpk2p), Elm1p, and Snf1p kinase pathways; however, the scope of these pathways is not fully understood. Here, we implemented quantitative phosphoproteomics to identify each of these signaling networks, generating a kinase-dead mutant in filamentous S. cerevisiae and surveying for differential phosphorylation. By this approach, we identified 439 phosphoproteins dependent upon pseudohyphal growth kinases. We report novel phosphorylation sites in 543 peptides, including phosphorylated residues in Ras2p and Flo8p required for wild-type filamentous growth. Phosphoproteins in these kinase signaling networks were enriched for ribonucleoprotein (RNP) granule components, and we observe co-localization of Kss1p, Fus3p, Ste20p, and Tpk2p with the RNP component Igo1p. These kinases localize in puncta with GFP-visualized mRNA, and KSS1 is required for wild-type levels of mRNA localization in RNPs. Kss1p pathway activity is reduced in lsm1Δ/Δ and pat1Δ/Δ strains, and these genes encoding P-body proteins are epistatic to STE7. The P-body protein Dhh1p is also required for hyphal development in Candida albicans. Collectively, this study presents a wealth of data identifying the yeast phosphoproteome in pseudohyphal growth and regulatory interrelationships between pseudohyphal growth kinases and RNPs.     

A survey of toxicity of cyanobacterial blooms in Lake Ladoga and adjacent water bodies

Twentyfive cyanobacterial blooms in Lake Ladoga and adjacent water bodies were studied in the summer of 1990–1992. Toxicity of the water bloom material for mice was detected in 9 cases. The maximal tolerable doses (MTD) of the material extracted from biomass varied within 3–30 mg kg^–1 mouse body weight; 50% lethal doses (LD₅₀) were within 45–125 mg kg^–1. Toxic water blooms were registered in Karelian lakes and in the Neva Bay, Gulf of Finland. Cyanobacterial samples collected on the eastern coast of Lake Ladoga proved to be non-toxic. The species identified in toxic bloom material included Anabaena circinalis, A. flos-aquae, A. lemmermannii, Anabaena sp., Aphanizomenonflos-aquae, Gloeotrichia echinulata, G. pisum, Microcystis aeruginosa and Oscillatoria sp. These data suggest that toxic forms of cyanobacteria are widespread in Karelian lakes belonging to the drainage basin of Lake Ladoga.     

Crystal structure of the YjeE protein from Haemophilus influenzae: a putative Atpase involved in cell wall synthesis

A hypothetical protein encoded by the gene YjeE of Haemophilus influenzae was selected as part of a structural genomics project for X-ray analysis to assist with the functional assignment. The protein is considered essential to bacteria because the gene is present in virtually all bacterial genomes but not in those of archaea or eukaryotes. The amino acid sequence shows no homology to other proteins except for the presence of the Walker A motif G-X-X-X-X-G-K-T that indicates the possibility of a nucleotide-binding protein. The YjeE protein was cloned, expressed, and the crystal structure determined by the MAD method at 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. Crystallization of YjeE in the presence of ATP and Mg2+ resulted in the structure with ADP bound in the P-loop. The ATPase activity of YjeE was confirmed by kinetic measurements. The distribution of conserved residues suggests that the protein may work as a "molecular switch" triggered by ATP hydrolysis. The phylogenetic pattern of YjeE suggests its involvement in cell wall biosynthesis.     

On a probabilistic model for the numerical estimation of nocturnal migration of birds

The study of nocturnal bird migration by cone methods of observation has a century-long history but has continued to be used up to the present. To describe the flux and estimate the number of passing birds a probabilistic model is proposed. This model is based on the concept of dynamic Poisson ensemble of points in appropriate phase space and has two parameters. One is scalar and the other one is functional. We constructed consistent estimations of these parameters and discuss their use for the numerical estimation of the flux of birds observed in a narrow light cone generated by the bright lunar disk and formed by an open angle of telescope. Selection on the same type of birds was suggested as the necessary condition for the model application. Ground speed of each bird was introduced into the model as a new but obligatory value determining the quantification of the flux of bird.     

Ceruloplasmin: Macromolecular Assemblies with Iron-Containing Acute Phase Proteins

Copper-containing ferroxidase ceruloplasmin (Cp) forms binary and ternary complexes with cationic proteins lactoferrin (Lf) and myeloperoxidase (Mpo) during inflammation. We present an X-ray crystal structure of a 2Cp-Mpo complex at 4.7 Å resolution. This structure allows one to identify major protein–protein interaction areas and provides an explanation for a competitive inhibition of Mpo by Cp and for the activation of p-phenylenediamine oxidation by Mpo. Small angle X-ray scattering was employed to construct low-resolution models of the Cp-Lf complex and, for the first time, of the ternary 2Cp-2Lf-Mpo complex in solution. The SAXS-based model of Cp-Lf supports the predicted 1∶1 stoichiometry of the complex and demonstrates that both lobes of Lf contact domains 1 and 6 of Cp. The 2Cp-2Lf-Mpo SAXS model reveals the absence of interaction between Mpo and Lf in the ternary complex, so Cp can serve as a mediator of protein interactions in complex architecture. Mpo protects antioxidant properties of Cp by isolating its sensitive loop from proteases. The latter is important for incorporation of Fe³⁺ into Lf, which activates ferroxidase activity of Cp and precludes oxidation of Cp substrates. Our models provide the structural basis for possible regulatory role of these complexes in preventing iron-induced oxidative damage.     

Fused in Sarcoma (FUS) Protein Lacking Nuclear Localization Signal (NLS) and Major RNA Binding Motifs Triggers Proteinopathy and Severe Motor Phenotype in Transgenic Mice

Dysfunction of two structurally and functionally related proteins, FUS and TAR DNA-binding protein of 43 kDa (TDP-43), implicated in crucial steps of cellular RNA metabolism can cause amyotrophic lateral sclerosis (ALS) and certain other neurodegenerative diseases. The proteins are intrinsically aggregate-prone and form non-amyloid inclusions in the affected nervous tissues, but the role of these proteinaceous aggregates in disease onset and progression is still uncertain. To address this question, we designed a variant of FUS, FUS 1–359, which is predominantly cytoplasmic, highly aggregate-prone, and lacks a region responsible for RNA recognition and binding. Expression of FUS 1–359 in neurons of transgenic mice, at a level lower than that of endogenous FUS, triggers FUSopathy associated with severe damage of motor neurons and their axons, neuroinflammatory reaction, and eventual loss of selective motor neuron populations. These pathological changes cause abrupt development of a severe motor phenotype at the age of 2.5–4.5 months and death of affected animals within several days of onset. The pattern of pathology in transgenic FUS 1–359 mice recapitulates several key features of human ALS with the dynamics of the disease progression compressed in line with shorter mouse lifespan. Our data indicate that neuronal FUS aggregation is sufficient to cause ALS-like phenotype in transgenic mice.     

Detoxification of Mercury by Methanobactin from Methylosinus trichosporium OB3b

Many methanotrophs have been shown to synthesize methanobactin, a novel biogenic copper-chelating agent or chalkophore. Methanobactin binds copper via two heterocyclic rings with associated enethiol groups. The structure of methanobactin suggests that it can bind other metals, including mercury. Here we report that methanobactin from Methylosinus trichosporium OB3b does indeed bind mercury when added as HgCl₂ and, in doing so, reduced toxicity associated with Hg(II) for both Alphaproteobacteria methanotrophs, including M. trichosporium OB3b, M. trichosporium OB3b ΔmbnA (a mutant defective in methanobactin production), and Methylocystis sp. strain SB2, and a Gammaproteobacteria methanotroph, Methylomicrobium album BG8. Mercury binding by methanobactin was evident in both the presence and absence of copper, despite the fact that methanobactin had a much higher affinity for copper due to the rapid and irreversible binding of mercury by methanobactin. The formation of a gray precipitate suggested that Hg(II), after being bound by methanobactin, was reduced to Hg(0) but was not volatilized. Rather, mercury remained associated with methanobactin and was also found associated with methanotrophic biomass. It thus appears that although the mercury-methanobactin complex was cell associated, mercury was not removed from methanobactin. The amount of biomass-associated mercury in the presence of methanobactin from M. trichosporium OB3b was greatest for M. trichosporium wild-type strain OB3b and the ΔmbnA mutant and least for M. album BG8, suggesting that methanotrophs may have selective methanobactin uptake systems that may be based on TonB-dependent transporters but that such uptake systems exhibit a degree of infidelity.     

The seashore sedges of the Russian Kola Peninsula: How many species?

A necessary basis for environmental protection is thorough knowledge of the biodiversity to be protected. Setting conservation priorities in taxonomically complex groups is an especially difficult task. The seashore sedges of the Carex salina group (Cyperaceae) of the Russian White and Barents Seas form important parts of the coastal ecosystems and include species listed as rare and endangered. However, their taxonomy is poorly understood and supposed to be blurred by hybridization, also including the closely related C. aquatilis and possibly other species of sect. Phacocystis (C. bigelowii, C. nigra s. lat.). We address the taxonomic situation in the C. salina group in the Kola Peninsula with emphasis on taxa of supposed hybrid origin (C. salina and C. recta coll.). We analyzed 92 plants from 28 sites for 101 amplified fragment length polymorphisms (AFLPs) and 10 morphological characters. The plants referred to three supposedly “pure” species (C. aquatilis, C. paleacea and C. subspathacea) formed different extreme parts of the morphological and molecular variation. These species could be discriminated by a combination of morphological characters. The two taxa of proposed hybrid origin had extremely variable morphology and could not be clearly distinguished from each other or from the supposedly “pure” species. Our results demonstrate extensive gene flow between all taxa, suggesting that the entire C. salina group including C. aquatilis acts as a single large biological species.