Establishment of the functional importance of thiamin carrier protein in pregnant rats by using monoclonal antibodies

Monoclonal antibodies (mAbs) to chicken thiamin carrier protein (TCP) have been produced by hybridoma technology to identify the crucial epitopes involved in bioneutralization of the vitamin carrier. The monoclonality of these mAbs (A4C4, F3H6, H8H3, C8C1 and G7H10) was sought to be confirmed by sub-class isotyping; they all belong to IgG1, k type. The epitopes recognized by all the five mAbs are conserved in TCP from the chicken to the rat as assessed by liquid phase RIA and immunoprecipitation of I-125-labelled proteins from pregnant rat serum. Among these mAbs, passive immunization of pregnant rats with the mAb C8C1 only on three consecutive days (day 10, 11 and 12) resulted in embryonic resorption. These results demonstrate the importance of epitopic structure specified by the mAb C8C1 on TCP during pregnancy in rats.

Functional analysis of conserved motifs in EcoP15I DNA methyltransferase

EcoP15I DNA methyltransferase recognizes the sequence 5'-CAGCAG-3' and transfers a methyl group to N-6 of the second adenine residue in the recognition sequence. All N-6 adenine methyltransferases contain two highly conserved sequences, FxGxG (motif I), postulated to form part of the S-adenosyl-L-methionine binding site and (D/N/S)PP(Y/F) (motif IV) involved in catalysis. We have altered the second glycine residue in motif I to arginine and serine, and substituted tyrosine in motif IV with tryptophan in EcoP15I DNA methyltransferase, using site-directed mutagenesis. The mutant enzymes were overexpressed, purified and characterized by biochemical methods. The mutations in motif I completely abolished AdoMet binding but left target DNA recognition unaltered. Although the mutation in motif IV resulted in loss of enzyme activity, we observed enhanced crosslinking of S-adenosyl-L-methionine and DNA. This implies that DNA and AdoMet binding sites are close to motif IV. Taken together, these results reinforce the importance of motif I in AdoMet binding and motif IV in catalysis. Additionally, limited proteolysis and UV crosslinking experiments with EcoP15I DNA methyltransferase imply that DNA binds in a cleft formed by two domains in the protein. Methylation protection analysis provides evidence for the fact that EcoP15I DNA MTase makes contacts in the major groove of its substrate DNA. Interestingly, hypermethylation of the guanine residue next to the target adenine residue indicates that the protein probably flips out the target adenine residue. (C) 1996 Academic Press Limited

Crystal structures, dynamics and functional implications of molybdenum-cofactor biosynthesis protein MogA from two thermophilic organisms

Molybdenum-cofactor (Moco) biosynthesis is an evolutionarily conserved pathway in almost all kingdoms of life, including humans. Two proteins, MogA and MoeA, catalyze the last step of this pathway in bacteria, whereas a single two-domain protein carries out catalysis in eukaryotes. Here, three crystal structures of the Moco-biosynthesis protein MogA from the two thermophilic organisms Thermus thermophilus (TtMogA; 1.64 angstrom resolution, space group P2(1)) and Aquifex aeolicus (AaMogA; 1.70 angstrom resolution, space group P2(1) and 1.90 angstrom resolution, space group P1) have been determined. The functional roles and the residues involved in oligomerization of the protein molecules have been identified based on a comparative analysis of these structures with those of homologous proteins. Furthermore, functional roles have been proposed for the N- and C-terminal residues. In addition, a possible protein-protein complex of MogA and MoeA has been proposed and the residues involved in protein-protein interactions are discussed. Several invariant water molecules and those present at the subunit interfaces have been identified and their possible structural and/or functional roles are described in brief. In addition, molecular-dynamics and docking studies with several small molecules (including the substrate and the product) have been carried out in order to estimate their binding affinities towards AaMogA and TtMogA. The results obtained are further compared with those obtained for homologous eukaryotic proteins.

Critical earthquake input power spectral density function models for engineering structures

The problem of determining optimal power spectral density models for earthquake excitation which satisfy constraints on total average power, zero crossing rate and which produce the highest response variance in a given linear system is considered. The solution to this problem is obtained using linear programming methods. The resulting solutions are shown to display a highly deterministic structure and, therefore, fail to capture the stochastic nature of the input. A modification to the definition of critical excitation is proposed which takes into account the entropy rate as a measure of uncertainty in the earthquake loads. The resulting problem is solved using calculus of variations and also within linear programming framework. Illustrative examples on specifying seismic inputs for a nuclear power plant and a tall earth dam are considered and the resulting solutions are shown to be realistic.

Reaction of diisopropoxytitanium(III) tetrahydroborate with selected organic compounds containing representative functional groups

Diisopropoxytitanium(III) tetrahydroborate, ((PrO)-Pr-1)(2)TiBH4), generated in situ in dichloromethane from diisopropoxytitanium dichloride and benzyltriethylammonium borohydride in a 1:2 ratio selectively reduces aldehydes, ketones, acid chlorides, carboxylic acids, and N-Boc-protected amino acids to the corresponding alcohols in excellent yield under very mild reaction conditions (-78 to 25 degrees C).

Saturation throughput analysis of an input queueing ATM switch with multiclass bursty traffic

In this paper we consider an N x N non-blocking, space division ATM switch with input cell queueing. At each input, the cell arrival process comprises geometrically distributed bursts of consecutive cells for the various outputs. Motivated by the fact that some input links may be connected to metropolitan area networks, and others directly to B-ISDN terminals, we study the situation where there are two classes of inputs with different values of mean burst length. We show that when inputs contend for an output, giving priority to an input with smaller expected burst length yields a saturation throughput larger than if the reverse priority is given. Further, giving priority to less bursty traffic can give better throughput than if all the inputs were occupied by this less bursty traffic. We derive the asymptotic (as N --> infinity) saturation throughputs for each priority class.

Primary Sequence That Determines the Functional Overlap between Mitochondrial Heat Shock Protein 70 Ssc1 and Ssc3 of Saccharomyces cerevisiae

The evolutionary diversity of the HSP70 gene family at the genetic level has generated complex structural variations leading to altered functional specificity and mode of regulation in different cellular compartments. By utilizing Saccharomyces cerevisiae as a model system for better understanding the global functional cooperativity between Hsp70 paralogs, we have dissected the differences in functional properties at the biochemical level between mitochondrial heat shock protein 70 (mtHsp70) Ssc1 and an uncharacterized Ssc3 paralog. Based on the evolutionary origin of Ssc3 and a high degree of sequence homology with Ssc1, it has been proposed that both have a close functional overlap in the mitochondrial matrix. Surprisingly, our results demonstrate that there is no functional cross-talk between Ssc1 and Ssc3 paralogs. The lack of in vivo functional overlap is due to altered conformation and significant lower stability associated with Ssc3. The substrate-binding domain of Ssc3 showed poor affinity toward mitochondrial client proteins and Tim44 due to the open conformation in ADP-bound state. In addition to that, the nucleotide-binding domain of Ssc3 showed an altered regulation by the Mge1 co-chaperone due to a high degree of conformational plasticity, which strongly promotes aggregation. Besides, Ssc3 possesses a dysfunctional inter-domain interface thus rendering it unable to perform functions similar to generic Hsp70s. Moreover, we have identified the critical amino acid sequence of Ssc1 and Ssc3 that can ``make or break'' mtHsp70 chaperone function. Together, our analysis provides the first evidence to show that the nucleotide-binding domain of mtHsp70s plays a critical role in determining the functional specificity among paralogs and orthologs across kingdoms.

Mutations in beta ` subunit of Escherichia coli RNA polymerase perturb the activator polymerase functional interaction required for promoter clearance

P>Transcription activator C employs a unique mechanism to activate mom gene of bacteriophage Mu. The activation process involves, facilitating the recruitment of RNA polymerase (RNAP) by altering the topology of the promoter and enhancing the promoter clearance by reducing the abortive transcription. To understand the basis of this multi-step activation mechanism, we investigated the nature of the physical interaction between C and RNAP during the process. A variety of assays revealed that only DNA-bound C contacts the beta' subunit of RNAP. Consistent to these results, we have also isolated RNAP mutants having mutations in the beta' subunit which were compromised in C-mediated activation. Mutant RNAPs show reduced productive transcription and increased abortive initiation specifically at the C-dependent mom promoter. Positive control (pc) mutants of C, defective in interaction with RNAP, retained the property of recruiting RNAP to the promoter but were unable to enhance promoter clearance. These results strongly suggest that the recruitment of RNAP to the mom promoter does not require physical interaction with C, whereas a contact between the beta' subunit and the activator, and the subsequent allosteric changes in the active site of the enzyme are essential for the enhancement of promoter clearance.

Role of feedback in mammalian vision: a new hypothesis and a computational model

This paper presents a novel hypothesis on the function of massive feedback pathways in mammalian visual systems. We propose that the cortical feature detectors compete not for the right to represent the output at a point, but for exclusive rights to abstract and represent part of the underlying input. Feedback can do this very naturally. A computational model that implements the above idea for the problem of line detection is presented and based on that we suggest a functional role for the thalamo-cortical loop during perception of lines. We show that the model successfully tackles the so called Cross problem. Based on some recent experimental results, we discuss the biological plausibility of our model. We also comment on the relevance of our hypothesis (on the role of feedback) to general sensory information processing and recognition. (C) 1998 Published by Elsevier Science Ltd. All rights reserved.

Precoding with X-codes to increase capacity with discrete input alphabets

We consider Gaussian multiple-input multiple-output (MIMO) channels with discrete input alphabets. We propose a non-diagonal precoder based on X-Codes in to increase the mutual information. The MIMO channel is transformed into a set of parallel subchannels using Singular Value Decomposition (SVD) and X-codes are then used to pair the subchannels. X-Codes are fully characterized by the pairings and the 2 × 2 real rotation matrices for each pair (parameterized with a single angle). This precoding structure enables to express the total mutual information as a sum of the mutual information of all the pairs. The problem of finding the optimal precoder with the above structure, which maximizes the total mutual information, is equivalent to i) optimizing the rotation angle and the power allocation within each pair and ii) finding the optimal pairing and power allocation among the pairs. It is shown that the mutual information achieved with the proposed pairing scheme is very close to that achieved with the optimal precoder by Cruz et al., and significantly better than mercury/waterfilling strategy by Lozano et al.. Our approach greatly simplifies both the precoder optimization and the detection complexity, making it suitable for practical applications.

Functional Significance of an Evolutionarily Conserved Alanine (GCA) Resume Codon in tmRNA in Escherichia coli

Occasionally, ribosomes stall on mRNAs prior to the completion of the polypeptide chain. In Escherichia coli and other eubacteria, tmRNA-mediated trans-translation is a major mechanism that recycles the stalled ribosomes. The tmRNA possesses a tRNA-like domain and a short mRNA region encoding a short peptide (ANDENYALAA in E. coli) followed by a termination codon. The first amino acid (Ala) of this peptide encoded by the resume codon (GCN) is highly conserved in tmRNAs in different species. However, reasons for the high evolutionary conservation of the resume codon identity have remained unclear. In this study, we show that changing the E. coli tmRNA resume codon to other efficiently translatable codons retains efficient functioning of the tmRNA. However, when the resume codon was replaced with the low-usage codons, its function was adversely affected. Interestingly, expression of tRNAs decoding the low-usage codon from plasmid-borne gene copies restored efficient utilization of tmRNA. We discuss why in E. coli, the GCA (Ala) is one of the best codons and why all codons in the short mRNA of the tmRNA are decoded by the abundant tRNAs.

Precoding by Pairing Subchannels to Increase MIMO Capacity With Discrete Input Alphabets

We consider Gaussian multiple-input multiple-output (MIMO) channels with discrete input alphabets. We propose a non-diagonal precoder based on the X-Codes in 1] to increase the mutual information. The MIMO channel is transformed into a set of parallel subchannels using singular value decomposition (SVD) and X-Codes are then used to pair the subchannels. X-Codes are fully characterized by the pairings and a 2 x 2 real rotation matrix for each pair (parameterized with a single angle). This precoding structure enables us to express the total mutual information as a sum of the mutual information of all the pairs. The problem of finding the optimal precoder with the above structure, which maximizes the total mutual information, is solved by: i) optimizing the rotation angle and the power allocation within each pair and ii) finding the optimal pairing and power allocation among the pairs. It is shown that the mutual information achieved with the proposed pairing scheme is very close to that achieved with the optimal precoder by Cruz et al., and is significantly better than Mercury/waterfilling strategy by Lozano et al. Our approach greatly simplifies both the precoder optimization and the detection complexity, making it suitable for practical applications.

DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins

Depth measures the extent of atom/residue burial within a protein. It correlates with properties such as protein stability, hydrogen exchange rate, protein-protein interaction hot spots, post-translational modification sites and sequence variability. Our server, DEPTH, accurately computes depth and solvent-accessible surface area (SASA) values. We show that depth can be used to predict small molecule ligand binding cavities in proteins. Often, some of the residues lining a ligand binding cavity are both deep and solvent exposed. Using the depth-SASA pair values for a residue, its likelihood to form part of a small molecule binding cavity is estimated. The parameters of the method were calibrated over a training set of 900 high-resolution X-ray crystal structures of single-domain proteins bound to small molecules (molecular weight < 1.5 KDa). The prediction accuracy of DEPTH is comparable to that of other geometry-based prediction methods including LIGSITE, SURFNET and Pocket-Finder (all with Matthew's correlation coefficient of similar to 0.4) over a testing set of 225 single and multi-chain protein structures. Users have the option of tuning several parameters to detect cavities of different sizes, for example, geometrically flat binding sites. The input to the server is a protein 3D structure in PDB format. The users have the option of tuning the values of four parameters associated with the computation of residue depth and the prediction of binding cavities. The computed depths, SASA and binding cavity predictions are displayed in 2D plots and mapped onto 3D representations of the protein structure using Jmol. Links are provided to download the outputs. Our server is useful for all structural analysis based on residue depth and SASA, such as guiding site-directed mutagenesis experiments and small molecule docking exercises, in the context of protein functional annotation and drug discovery.

Manipulation of the Hydration Levels in Minerals of Sodium Cadmium Bisulfate toward the Design of Functional Materials

Several variants of hydrated sodium cadmium bisulfate, Na(2)Cd(2)(SO(4))(3) center dot 3H(2)O, Na(2)Cd(SO(4))(2) center dot 2H(2)O, and Na(2)Cd(SO(4))(2) center dot 4H(2)O have been synthesized, and their thermal properties followed by phase transitions have been invesigated. The formation of these phases depends on the stochiometry and the time taken for crystallization from water. Na(2)Cd(2)(SO(4))(3)center dot 3H(2)O, which crystallizes in the trigonal system, space group P3c, is grown from the aqueous solution in about four weeks. The krohnkite type mineral Na(2)Cd(SO(4))(2) center dot 2H(2)O and the mineral astrakhanite, also known as blodite, Na(2)Cd (SO(4))(2)center dot 4H(2)O, crystallize concomittantly in about 24 weeks. Both these minerals belong to the monoclinic system(space group P2(1)/c). Na(2)Cd(2)(SO(4))(3)center dot 3H(2)O loses water completely when heated to 250 degrees C and transforms to a dehydrated phase (cubic system, space group I (4) over bar 3d) whose structure has been established using ab initio powder diffration techniques. Na(2)Cd(SO(4))(2)center dot 2H(2)O transforms to alpha-Na(2)Cd(SO(4))(2) (space group C2/c) on heating to 150 degrees C which is a known high ionic conductor and remains intact over prolonged periods of exposure to moisture (over six months). However, when alpha-Na(2)Cd(SO(4))(2) is heated to 570 degrees C followed by sudden quenching in liquid nitrogen beta-Na(2)Cd(SO(4))(2) (P2(1)/c) is formed. beta-Na(2)Cd(SO(4))(2) takes up water from the atmosphere and gets converted completely to the krohnkite type mineral in about four weeks. Further, beta-Na(2)Cd(SO(4))(2) has a conductivity behavior comparable to the a-form up to 280 degrees C, the temperature required for the transformation of the beta- to alpha-form. These experiments demonstrate the possibility of utilizing the abundantly available mineral sources as precursors to design materials with special properties.

Temperature and density dependent solute vibrational relaxation in supercritical fluoroform

Temperature- and density-dependent vibrational relaxation data for the v6 asymmetric stretch of W(CO)6 in supercritical fluoroform (trifluoromethane, CHF3) are presented and compared to a recent theory of solute vibrational relaxation. The theory, which uses thermodynamic and hydrodynamic conditions of the solvent as input parameters, shows very good agreement in reproducing the temperature- and density-dependent trends of the experimental data with a minimum of adjustable parameters. Once a small number of parameters are fixed by fitting the functional form of the density dependence, there are no adjustable parameters in the calculations of the temperature dependence. © 2001 American Institute of Physics.