Structure of L-tyrosyl-L-leucine monohydrate

C15H22N204.H20 , Mr= 312.37, monoclinic,P21, a=5.577(2), b=8.686(2), c= 16.228 (2) A,fl=92.63(2) ° , V=785(1)A 3, Z=2, O =1.34,Dx= 1.32Mgm -3, CuKa, 2= 1.54184'~, /2=0.78 mm -I, F(000) = 320, T= 293 K. The final R value for 1607 observed reflections ll,,>_3tr(l,,)l is 0.039. The terminal N 1 is protonated and the dipeptide exists as a zwitterion. The crystal structure is stabilized by extensive hydrogen-bonding interactions involving N and O atoms, with N...O in the range 2.65 (1)-2.95 (1) ,/~ and O...O in the range 2.60 (1)-2.78 (1) A.

Structure of L-Arginyl-L-aspartie Acid Dihydrate

C~0H~gN5Os.2H20, Mr=325.32, monoclinic,P2~, a = 12.029 (2), b=4.904 (2), c=13.215 (2) A, fl= 107.68 (2) ° , F= 743 (1) A 3, Z= 2,D m = 1-45, D x = 1.45 Mg m -3, Cu Ka, 2 = 1.54184 A,fl= 1.01mm -1, F(000)=348, T=293K. The final R value for 1277 observed reflections 110 >_ 3tr(Io)l is 0.031. The dipeptide exists as a zwitterion. The arginyl side-chain conformation is similar to that found in arginyl-glutamic acid [Pandit, Seshadri & Viswamitra (1983). Acta Cryst. C39, 1669-16721. The guanidyl group forms a pair of hydrogen bonds with oxygen atoms of the backbone carboxyl group. The crystal structure is also stabilized by -bonding interactions involving both water molecules.

Structure of N2-carbamoyl-L-asparagine

CsH9N304, M r= 175.1, orthorhombic,P212~2 ~, a = 7.486 (1), b = 9.919 (2), c =20.279 (2) A, V= 1505.8 A 3, z = 8, D x = 1.54, D m = 1.60 Mg m -3, ~,(Cu Ka) = 1.5418 A, g = 1. I I mm -~, F(000) = 736, T = 300 K, final R = 0.032 for 1345 observed reflections. The two independent molecules in the asymmetric unit are related by a pseudo twofold axis, with the asparagine side chains having different conformations [X 2 being -132.1 (3) and 139.6 (2)°]. The crystal structure is stabilized by extensive hydrogen bonding, with a specific interaction between the carboxyl group of one molecule and the carbamoyl group of another forming hydrogen-bonded chains.

Studies on the metabolism of l-menthol in rats

Metabolism of l-menthol in rats was investigated both in vivo and in vitro. Metabolites isolated and characterized from the urine of rats after oral administration (800 mg/kg of body weight/day) of l-menthol were the following: p-menthane-3,8-diol (II), p-menthane-3,9-diol (III), 3,8-oxy-p-menthane-7-carboxylic acid (IV), and 3,8-dihyroxy-p-menthane-7-carboxylic acid (V). In vivo, the major urinary metabolites were compounds II and V. Repeated oral administration (800 mg/kg of body weight/day) of l-menthol to rats for 3 days resulted in the increase of both liver microsomal cytochrome P-450 content and NADPH-cytochrome c reductase activity by nearly 80%. Further treatment (for 7 days total) reduced their levels considerably, although the levels were still higher than the control values. Both cytochrome b5 and NADH-cytochrome c reductase levels were not changed during the 7 days of treatment. Rat liver microsomes readily converted l-menthol to p-menthane-3,8-diol (II) in the presence of NADPH and O2. This activity was significantly higher in microsomes obtained from phenobarbital (PB)-induced rats than from control microsomal preparations, whereas 3-methylcholanthrene (3-MC)-induced microsomes failed to convert l-menthol to compound II in the presence of NADPH and O2. l-Menthol elicited a type I spectrum with control (Ks = 60.6 microM) and PB-induced (Ks = 32.3 microM) microsomes whereas with 3MC-induced microsomes it produced a reverse type I spectrum.

An algorithm to find distant repeats in a pair of protein sequences

Distant repeats between a pair of protein sequences can be exploited to study the various aspects of proteins such as structure-function relationship, disorders due to protein malfunction, evolutionary analysis, etc. An in-depth analysis of the distant repeats would facilitate to establish a stable evolutionary relation of the repeats with respect to their three-dimensional structure. To this effect, an algorithm has been devised to identify the distant repeats in a pair of protein sequences by essentially using the scores of PAM (Percent Accepted Mutation) matrices. The proposed algorithm will be of much use to researchers involved in the comparative study of various organisms based on the amino-acid repeats in protein sequences. (C) 2010 Elsevier B.V. All rights reserved.

Enantiodivergent Formal Total Synthesis of Aspercyclide C from L-(+)-Tartaric Acid

The enantiodivergent formal syntheses of both enantiomers of aspercyclide C is accomplished. Starting from L-(+)-tartaric acid, the key protected allylic alcohol, (3R,4R)-4-(methoxy-methoxy) non-1-en-3-ol is prepared, and is then elaborated into both enantiomers of 3-(4-methoxybenzyl)oxy]non-1-en-4-ol via Mitsunobu inversion. Esterification with a known biaryl acid, followed by ring-closing metathesis and deprotection completes the syntheses.

Performance comparison of dynamical decoupling sequences for a qubit in a rapidly fluctuating spin bath

Avoiding the loss of coherence of quantum mechanical states is an important prerequisite for quantum information processing. Dynamical decoupling (DD) is one of the most effective experimental methods for maintaining coherence, especially when one can access only the qubit system and not its environment (bath). It involves the application of pulses to the system whose net effect is a reversal of the system-environment interaction. In any real system, however, the environment is not static, and therefore the reversal of the system-environment interaction becomes imperfect if the spacing between refocusing pulses becomes comparable to or longer than the correlation time of the environment. The efficiency of the refocusing improves therefore if the spacing between the pulses is reduced. Here, we quantify the efficiency of different DD sequences in preserving different quantum states. We use C-13 nuclear spins as qubits and an environment of H-1 nuclear spins as the environment, which couples to the qubit via magnetic dipole-dipole couplings. Strong dipole-dipole couplings between the proton spins result in a rapidly fluctuating environment with a correlation time of the order of 100 mu s. Our experimental results show that short delays between the pulses yield better performance if they are compared with the bath correlation time. However, as the pulse spacing becomes shorter than the bath correlation time, an optimum is reached. For even shorter delays, the pulse imperfections dominate over the decoherence losses and cause the quantum state to decay.

Spectral Invariance of SG Pseudo-Differential Operators on L-P(R-n)

We prove the spectral invariance of SG pseudo-differential operators on L-P(R-n), 1 < p < infinity, by using the equivalence of ellipticity and Fredholmness of SG pseudo-differential operators on L-p(R-n), 1 < p < infinity. A key ingredient in the proof is the spectral invariance of SC pseudo-differential operators on L-2(R-n).

A helical peptide containing a majority of valyl residues. The crystal structure of t-butyloxy- carbonyl-(L-valyl-_-aminoisobutyryl)3-L-valyl methyl ester onohydrate

The monohydrate of the heptapeptide t-butyloxycarbonyl-(L-valyl-α-aminoiso-butyryl)3-L-valyl methyl ester crystallizes in the orthorhombic space group P212121 with four molecules in a unit cell with the dimensions α= 9.375, b = 19.413 and c = 25.878 ÅA. The structure has been solved by direct methods and refined to an R value of 0.059 for 3633 observed reflections. The molecule in the structure exists as a slightly distorted 310-helix stabilized by five 4 -> 1 intramolecular hydrogen bonds, indicating the overwhelming influence of α-aminoisobutyryl (Aib) residues in dictating helical fold even when a majority of residues in the peptide have a low intrinsic propensity to be in helices. Contrary to what is expected in helical structures, the valyl side chains, two of which are disordered, exhibit all three possible conformations. The molecules arrange themselves in a head-to-tail fashion along the c-axis. The columns thus generated pack nearly hexagonally in the crystal.

Climatic adaptation of Norway spruce (Picea abies (L.) Karsten) in Finland based on male flowering phenology.

Anthesis was studied at the canopy level in 10 Norway spruce stands from 9 localities in Finland from 1963 to 1974. Distributions of pollen catches were compared to the normal Gaussian distribution. The basis for the timing studies was the 50 per cent point of the anthesis-fitted normal distribution. Development up to this point was given in calendar days, in degree days (>5 °C) and in period units. The count of each parameter began on March 19 (included). Male flowering in Norway spruce stands was found to have more annual variation in quantity than in Scots pine stands studied earlier. Anthesis in spruce in northern Finland occurred at a later date than in the south. The heat sums needed for anthesis varied latitudinally less in spruce than in pine. The variation of pollen catches in spruce increased towards north-west as in the case of Scots pine. In the unprocessed data, calendar days were found to be the most accurate forecast of anthesis in Norway spruce both for a single year and for the majority of cases of stand averages over several years. Locally, the period unit could be a more accurate parameter for the stand average. However, on a calendar day basis, when annual deviations between expected and measured heat sums were converted to days, period units were narrowly superior to days. The geographical correlations respect to timing of flowering, calculated against distances measured along simulated post-glacial migration routes, were stronger than purely latitudinal correlations. Effects of the reinvasion of Norway spruce into Finland are thus still visible in spruce populations just as they were in Scots pine populations. The proportion of the average annual heat sum needed for spruce anthesis grew rapidly north of a latitude of ca. 63° and the heat sum needed for anthesis decreased only slighty towards the timberline. In light of flowering phenology, it seems probable that the northwesterly third of Finnish Norway spruce populations are incompletely adapted to the prevailing cold climate. A moderate warming of the climate would therefore be beneficial for Norway spruce. This accords roughly with the adaptive situation in Scots pine.

PeptideMine - A webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes

Background: Signal transduction events often involve transient, yet specific, interactions between structurally conserved protein domains and polypeptide sequences in target proteins. The identification and validation of these associating domains is crucial to understand signal transduction pathways that modulate different cellular or developmental processes. Bioinformatics strategies to extract and integrate information from diverse sources have been shown to facilitate the experimental design to understand complex biological events. These methods, primarily based on information from high-throughput experiments, have also led to the identification of new connections thus providing hypothetical models for cellular events. Such models, in turn, provide a framework for directing experimental efforts for validating the predicted molecular rationale for complex cellular processes. In this context, it is envisaged that the rational design of peptides for protein-peptide binding studies could substantially facilitate the experimental strategies to evaluate a predicted interaction. This rational design procedure involves the integration of protein-protein interaction data, gene ontology, physico-chemical calculations, domain-domain interaction data and information on functional sites or critical residues. Results: Here we describe an integrated approach called ``PeptideMine'' for the identification of peptides based on specific functional patterns present in the sequence of an interacting protein. This approach based on sequence searches in the interacting sequence space has been developed into a webserver, which can be used for the identification and analysis of peptides, peptide homologues or functional patterns from the interacting sequence space of a protein. To further facilitate experimental validation, the PeptideMine webserver also provides a list of physico-chemical parameters corresponding to the peptide to determine the feasibility of using the peptide for in vitro biochemical or biophysical studies. Conclusions: The strategy described here involves the integration of data and tools to identify potential interacting partners for a protein and design criteria for peptides based on desired biochemical properties. Alongside the search for interacting protein sequences using three different search programs, the server also provides the biochemical characteristics of candidate peptides to prune peptide sequences based on features that are most suited for a given experiment. The PeptideMine server is available at the URL: http://caps.ncbs.res.in/peptidemine

Therapeutic change in interaction

A process of change within a single case of cognitive-constructivist therapy is analyzed by means of conversation analysis (CA). The focus is on a process of change in the sequences of interaction, which consist of the therapist’s conclusion and the patient’s response to it. In the conclusions, the therapist investigates and challenges the patient’s tendency to transform her feelings of disappointment and anger into self-blame. Over the course of the therapy, the patient’s responses to these conclusions are recast: from the patient first rejecting the conclusion, to then being ambivalent, and finally to agreeing with the therapist. On the basis of this case study, we suggest that an analysis that focuses on sequences of talk that are interactionally similar offers a sensitive method to investigate the manifestation of therapeutic change. It is suggested that this line of research can complement assimilation analysis and other methods of analyzing changes in a client’s talk.