bluuebunny/crossref_metadata_2025 huggingface dataset:
Two‐dimensional gel electrophoresis
Authors: Görg Angelika , Weiss Walter , Dunn Michael J.
Published: January 2005

Two‐dimensional gel electrophoresis (2DE) with immobilized pH gradients (IPGs) combined with protein identification by mass spectrometry (MS) is currently the workhorse for proteomics. In spite of new promising technologies that have emerged (MudPIT, stable isotope labeling, arrays), 2DE is currently the only technique that can be routinely applied for parallel quantitative expression profiling of large sets of complex protein mixtures such as whole cell lysates. 2DE couples isoelectric focusing (IEF) and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS‐PAGE) to resolve proteins according to two independent parameters, that is, isoelectric point (pI) in the first dimension and molecular mass (M
r
) in the second. 2DE can resolve more than 5000 proteins simultaneously (∼2000 proteins routinely), and can detect <1 ng of protein per spot. Furthermore, it delivers a map of intact proteins, which reflects changes in protein expression level, isoforms or posttranslational modifications. This is in contrast to LC‐MS/MS‐based methods, which perform analysis on peptides, where M
r
and pI information is lost. Whatever technology is used, proteome analysis is technically challenging, because the number of different proteins expressed at a given time under defined biological conditions is likely to be in the range of at least several thousand in total cell lysates. In this article, we describe the 2DE‐MS workflow including the following topics: Sample preparation/solubilization, protein separation by 2DE with IPGs, protein detection and quantitation, computer‐assisted analysis of 2DE patterns, protein identification and characterization, and 2D protein databases.
Two‐dimensional gel electrophoresis (2‐DE)
Authors: McGregor Emma , Dunn Michael J.
Published: January 2005

Two‐dimensional gel electrophoresis (2‐DE) with immobilized pH gradients (IPGs) combined with protein identification by mass spectrometry (MS) is currently the method of choice in the majority of proteomic projects. In spite of the development of novel gel‐free technologies, 2‐DE remains the only technique that can be routinely applied to parallel quantitative expression profiling of large sets of complex protein mixtures such as whole‐cell lysates. 2‐DE involves the separation of solubilized proteins in the first dimension according to their charge properties (isoelectric point, pI) by isoelectric focusing (IEF) under denaturing conditions, followed by their separation in the second dimension by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS‐PAGE), according to their relative molecular mass (Mr). As the charge and mass properties of proteins are essentially independent parameters, this orthogonal combination of charge (pI) and size (Mr) separations results in the sample proteins being distributed across the two‐dimensional gel profile. 2‐DE can resolve more than 5000 proteins simultaneously (∼2000 proteins routinely), and can detect <1 ng of protein per spot. Furthermore, it delivers a map of intact proteins, which reflects changes in protein expression level, isoforms, or posttranslational modifications. In this article, we outline the various steps in the 2‐DE proteomics workflow, namely, sample preparation, solubilization, first‐dimension IEF with IPGs, second‐dimension SDS‐PAGE, protein detection and visualization, and protein identification by mass spectrometry. The various parameters that must be considered and optimized for successful 2‐DE separations of various types of sample are discussed.
Human signaling pathways analyzed by protein interaction mapping
Authors: Colland Frédéric , Legrain Pierre
Published: January 2005

Combining protein–protein interaction mapping with cellular assays performed for functional validation provides biological support to large‐scale protein interaction datasets. This strategy was recently developed for specific signal transduction pathways and generates useful biological knowledge.
Membrane‐anchored protein complexes
Authors: Stagljar Igor
Published: January 2005

Proteins associated with membranes total approximately one‐third of all proteins in a typical eukaryotic cell. Owing to their pivotal role in many cellular processes, their direct link to human disease, and their often extracellular accessibility toward drugs, an understanding of membrane protein function is desirable. However, the hydrophobic nature of membrane proteins often results in insoluble proteins, which makes protein isolation difficult and therefore hinders the determination of protein complex composition and protein function. This article provides a brief overview of the available yeast‐based interactive proteomic technologies for detecting protein interactions among membrane proteins.
Structure/function ofO‐glycans
Authors: Corfield Anthony P.
Published: January 2005

O‐glycans linked to protein through anO‐glycosidic linkage betweenN‐acetylgalactosamine and serine or threonine form a large group of oligosaccharides present in a variety of proteins. This article describes the structural characteristics ofO‐glycans, prediction of their occurrence, and location in proteins. The biosynthetic pathways leading to their formation are presented, with examples for selected structures. Examples of the variety of biological functions associated withO‐glycans cover several major areas. These include their influence on protein conformation and stability; their roles in recognition phenomena, including cell proliferation and growth, glycoprotein trafficking and clearance, immunological recognition, selectin ligands, multivalent binding patterns in signal transduction, fertilization; and finally, their roles in the activity of signaling molecules.
O

‐Mannosylation
Authors: Endo Tamao
Published: January 2005

Mammalian cells produce many glycoproteins, that is, proteins with covalently attached sugar chains. The major glycans of glycoproteins can be classified into two groups,
N
‐glycan and
O
‐glycan, according to their glycan‐peptide linkage regions. Developments in glycobiology have revealed a new type of glycosidic linkage to the peptide portion, the
O
‐mannosyl linkage. This linkage used to be considered specific to yeast but has recently been found in mammals. Recently,
O
‐mannosylation has been shown to be important in muscle and brain development. This chapter describes the structure, biosynthesis, and biology of
O
‐mannosylation.
Target selection for structural genomics
Authors: Frishman Dmitrij
Published: January 2005

Bioinformatics analyses provide invaluable guidance in finding the shortest path to the ultimate goal of structural genomics – full understanding of structure–function relationships in proteins and exhaustive exploration of the sequence‐structure space. Advanced computational tools allow for predicting currently intractable target proteins and those that already have a known fold, grouping sequences into families, and propagating available structural information to a large number of protein sequences by means of homology modeling. Rational target selection is also a major cost‐saving factor because it prevents the international structural genomics consortia from duplicating effort and helps to identify the most economical set of target proteins. The main strategies in target selection include the systematic determination of protein structures from completely sequenced genomes of selected model organisms, elucidation of all fold types existing in nature, and exhaustive covering of the entire sequence space with structural information.
Integrative approaches to biology in the twenty‐first century
Authors: Cassman Marvin
Published: January 2005

Systems or integrative biology has become wildly popular in just the past few years. (The two terms will be used interchangeably to refer to the quantitative analysis of biological networks, at whatever level of organization.) The reason is clear – the volume of experimental data generated by genomics and other high‐throughput techniques pose both a problem and an opportunity. The problem is that the mass of data overwhelms the ability to intuitively understand it. The opportunity is that the data may be able to be manipulated in a manner that allows for an unprecedented understanding of the integrated behavior of biological systems. The mechanistic studies that have generated an amazing ability to decipher the molecular workings of individual biological molecules can now be linked to computational approaches, which will illuminate the functions of tightly coupled and highly regulated biological systems. At the end, the processes underlying health and disease will be understood in greater depth than has previously been possible. This article will discuss some of the questions currently facing investigators attempting to move this discipline forward, with a particular emphasis on the concepts of modularity and robustness.
Functional networks in mammalian cells
Authors: Xiong Yuguang , Iyengar Ravi
Published: January 2005

The basic functional unit of multicellular organism is the cell. Cells are complex systems that perform many required fundamental functions such as environmental adaptation, energy utilization, proliferation, and differentiation in a regulated manner. Even cell death is often a controlled process. Cellular functions involve numerous components participating in a variety of processes. A critical aspect for normal cell functionality is the rigorous control of all cellular processes that may take place at different cellular locations at different rates and at different times. Such regulation is achieved by a central intracellular signaling network that receives and processes signals from both extracellular and intracellular sources. The processed signals are then used to regulate the different cellular machines such that they can function co‐operatively to evoke complex physiological responses. In order to achieve reliable functionality, the cell has developed multiple redundant systems that can regulate the cellular machines. Additionally, the systems are arranged in a modular fashion such that disturbances do not substantially propagate between modules. This architecture leads to a complex system where both robustness and fragility are dynamically balanced.
Algorithmic challenges in mammalian whole‐genome assembly
Authors: Batzoglou Serafim
Published: January 2005

Sequencing of the human, mouse, and rat genomes was accomplished more quickly than had seemed feasible a mere eight years ago. The accelerating pace of sequencing has been made possible by the development of large‐scale laboratory operations, assembly algorithms, and less so by changes in the underlying sequencing technologies. This short review summarizes the computational challenges of whole‐genome assembly and the algorithms and software systems that enabled the recent advances in sequencing of mammalian genomes.
Genome signals and assembly
Authors: Kimmel Marek
Published: January 2005

Quality of genome assembly depends to a large extent on the structure of genomic sequences, notably signals such as repeats, polymorphisms, and nucleotide asymmetry as well as structural motifs (seeStatistical signals) such as protein motifs (seeComputational motif discovery), gene promoters, enhancers and suppressors (seePromoter predictionandExon splicing enhancers), transcription factor binding sites, exon/intron splice junctions, regions of homology between sequences (seeIMPALA/RPS‐BLAST/PSI‐BLAST in protein sequence analysis), and protein docking sites. We address probabilistic and statistical issues, departing from modeling the genome assembly as a binomial/Poisson process and considerations of contig size. We then consider estimation of genome size, when repeats are involved, and estimation of the total gap length and of the stringency ratio. Then we consider bubble smoothing in the context of polymorphisms and empirical estimates of the impact of low GC contents on stringency. Finally, we refer to some special issues and examples.
Promoter prediction
Authors: Bajic Vladimir B. , Werner Thomas
Published: January 2005

We review current solutions for computer‐based prediction of promoters. We comment on useful biological signals, implemented technology, end‐user information, and achieved performances. Finally, we present a forecast of future trends in this field.
Operon finding in bacteria
Authors: Ermolaeva Maria D.
Published: January 2005

A number of different strategies can be used to find operons and transcriptional units in bacterial and archaeal genomes. Some of these methods are purely computational: they rely only on the whole‐genome sequence and gene predictions and do not require additional experimental data. Two such methods are discussed in this article: one relies on the fact that the distances between genes are shorter within transcriptional units than between them, while the second one takes advantage of the observation that operons tend to be conserved between genomes. Before discussing these operon‐finding algorithms, we first present a purely computational approach for estimating the number of transcriptional units in the genome.
Computational motif discovery
Authors: Tompa Martin
Published: January 2005

The goal of computational motif discovery is to predict short subsequences of biological sequences that are good candidates to serve some biological function. This article focuses on the computational prediction of protein binding sites in nucleotide sequences. Three types of motif model are described: consensus, IUPAC, and weight matrix. Two types of application are described, statistical overrepresentation (in which the input sequences come from a single genome and are believed to contain instances of a single motif) and phylogenetic footprinting (in which the input sequences are homologous, typically one from each of multiple related genomes). Programs of each of these types are briefly described, with references to fuller descriptions and web sites where the programs are available.
DNA
/protein modeling
Authors: Lavery Richard
Published: January 2005

Considerable progress has been made in modeling both DNA and protein‐DNA complexes. The results help explain how specific base sequences can modify the properties of the double helix, influencing its structure and mechanical properties. These changes are important for the understanding of DNA recognition and packing. In the case of protein‐DNA complexes, modeling can help in identifying protein‐binding sites and in understanding the consequences of mutations in either of the interacting partners. Modeling can also be used to obtain structural and dynamic information from a variety of experimental data and will also contribute to extending the nanotechnological applications of the double helix.
Merging and comparing ontologies
Authors: Noy Natalya F.
Published: January 2005

The use of formal systems to define biomedical concepts and to represent and store biomedical knowledge has never been more important to the informatics community. In the past few years, ontologies have become the cornerstone of the information‐systems research. With the wider use of ontologies, the problem of
ontology management
began to arise: ontology developers and users must be able to find and compare existing ontologies or their parts, merge and align ontologies, compare different versions, and translate ontologies from one formalism to another. We describe various approaches to the ontology‐management tasks and the recent developments in defining a general ontology‐management framework.
Description logics:
OWL
and
DAML
+
OIL
Authors: Lord Phillip , Stevens Robert D. , Goble Carole A. , Horrocks Ian
Published: January 2005

In this chapter, we introduce Description Logics. These logics have achieved mainstream credibility as ontology languages by forming the basis of the W3C Web Ontology Language OWL, and its predecessor,
DAML
 + 
OIL
. From a case study, we explain how the rich expressivity of OWL can be used to model the complexities of biology and bioinformatics. We discuss automated reasoning technologies and the roles that they can play in supporting the process of building ontologies.
Support vector machine software
Authors: Noble William Stafford
Published: January 2005

The support vector machine has been used successfully to perform pattern recognition on many different types of biological data. However, applying the algorithm to a new problem domain is often nontrivial, because the algorithm offers many tunable parameters. Most important among these are the choice of the kernel function and the strength of the soft margin. This chapter describes the SVM algorithm and gives some practical advice for applying the algorithm to real biological data.
Cover Picture: Photolithographic Route to the Fabrication of Micro/Nanowires of III–V Semiconductors (Adv. Funct. Mater. 1/2005)
Authors: Sun Y. , Khang D.‐Y. , Hua F. , Hurley K. , Nuzzo R. G. , Rogers J. A.
Published: January 2005

The cover shows a patterned assembly of GaAs nanowires with their ends tethered to a bulk single‐crystal wafer as described on p. 30 by Rogers and co‐workers. These wires, which have triangular cross‐sections, were fabricated via a top–down process that combines photolithography and anisotropic chemical etching.

Nano/microwires of semiconducting materials (e.g., GaAs and InP) with triangular cross‐sections can be fabricated by “top–down” approaches that combine lithography of high‐quality bulk wafers (using either traditional photolithography or phase‐shift optical lithography) with anisotropic chemical etching. This method gives good control over the lateral dimensions, lengths, and morphologies of free‐standing wires. The behaviors of many different resist layers and etching chemistries are presented. It is shown how wire arrays with highly ordered alignments can be transfer printed onto plastic substrates. This “top–down” approach provides a simple, effective, and versatile way of generating high‐quality single‐crystalline wires of various compound semiconductors. The resultant wires and wire arrays have potential applications in electronics, optics, optoelectronics, and sensing.
Cover Picture: Nanostructured Electrodes and the Low‐Temperature Performance of Li‐Ion Batteries (Adv. Mater. 1/2005)
Authors: Sides C. R. , Martin C. R.
Published: January 2005

The cover image shows a scanning electron micrograph of a commercially available track‐etch polycarbonate filter. This porous membrane serves as the host for the template‐synthesis of V2O5 nanowires of various diameters. Nanowires that are 70 nm in diameter are shown in the inset. Because V2O5 reversibly intercalates Li‐ions, it has potential for use as a cathode material in Li‐ion batteries. On p. 125, Sides and Martin report the use of these V2O5 nanowires as tools to investigate the poor low‐temperature performance of Li‐ion batteries.
Effect of thermohydraulic conditions on fouling of calcium oxalate and silica
Authors: Yu Hong , Sheikholeslami Roya , Doherty William O. S.
Published: January 2005

Calcium oxalate (CaOx) and amorphous silica (SiO2) have been identified as the most intractable components of scale formed in sugar mill evaporators. Effects of thermohydraulic conditions such as surface superheat (5–15 K), fluid velocity (0.8–1.8 m/s), and bulk subcooling (20–30 K) on the composite fouling process of CaOx and SiO2 and deposit characteristics were investigated in a dynamic system that contained a fouling loop under subcooled nucleate flow boiling. The rate of composite fouling was found to increase with increasing superheat as a result of enhanced bubble activities at the boiling surface and increase in deposit strength. For a constant surface superheat, the fouling rate reached a maximum value at a subcooling of 25 K, but remained constant over a range of fluid velocity (≥1.1 m/s). This was attributed to the counterbalancing effects of deposit consolidation and hydrodynamic lift forces at the fouled tube wall. Scanning electron microscopy (SEM) analysis of composite deposits demonstrated the presence of two layers arising from deposit consolidation by CaOx in SiO2 matrix through microlayer evaporation during nucleate boiling. Chemical microanalysis by energy dispersive X‐ray spectroscopy (EDS) also indicated that the degree of deposit consolidation increased with surface superheat, fluid velocity, and bulk subcooling because of an increase in heat flux. © 2005 American Institute of Chemical Engineers AIChE J, 51: 641–648, 2005
Katalysatoren machen's möglich: Selektive C‐C‐Kupplungen mit nichtaktivierten Alkylhalogeniden
Authors: Frisch Anja C. , Beller Matthias
Published: January 2005

In den vergangenen Jahren hat das Interesse an metallkatalysierten Kreuzkupplungen mit Alkylhalogeniden stetig zugenommen, obwohl diese Reaktionen inhärent problematisch sind. Detaillierte mechanistische Untersuchungen brachten eine Reihe neuer Protokolle für die selektive Verknüpfung nichtaktivierter Alkylhalogenide mit β‐Wasserstoffatomen hervor. Unter milden Reaktionsbedingungen gelingen Kupplungen mit verschiedenen Organometallnucleophilen. In diesem Kurzaufsatz werden ausgewählte Beispiele vorgestellt, die dazu anregen sollen, das Potenzial dieser wichtigen metallkatalysierten Kupplungsmethoden in der organischen Synthese zu nutzen.
Modellierung der Lebensdauer und Abbaubarkeit organischer Verbindungen in Luft, Boden und Wasser
Authors: Schüürmann Gerrit
Published: January 2005

Die Abbaubarkeit organischer Verbindungen in Luft, Boden und Wasser ist der wichtigste Faktor zur Beurteilung des Umweltschicksals chemischer Verbindungen und ihrer möglichen Schadenswirkung auf Mensch und Umwelt.

Neben dieser Priorisierung der Exposition und der für das Umweltschicksal wesentlichen Abbauparameter im Rahmen der Risikobewertung bei Chemikalien sind als alternative Sichtweisen die Betonung des Schadwirkungspotenzials der Verbindungen sowie die Betrachtung von Exposition und Wirkung als gleichrangige Komponenten für die Risikobewertung bei Umweltchemikalien vorhanden. Das Risiko ist hierbei durch eine (mathematische) Verknüpfung von Schadensausmaß (Schadwirkungspotenzial oder Gefahrenpotenzial) und zugehöriger Eintrittswahrscheinlichkeit (Exposition) definiert.

In der Troposphäre erfolgt der Abbau chemischer Verbindungen vor allen durch Reaktion mit OH‐Radikalen, in den Kompartimenten Boden und Wasser hingegen durch Bioabbau. Die Ziele dieses Berichts sind: 1) eine Übersicht über publizierte Modelle und ihre Evaluierung zu geben, 2) eine eigene Bewertung der allgemeinen Modelle zur Abschätzung des Abbaus organischer Chemikalien in der Troposphäre und ihres Bioabbaus durchzuführen und 3) Empfehlungen für zuverlässige Verfahren zur Abschätzung des Abbaubarkeit chemischer Verbindungen in der Umwelt zu geben. Ergebnis der umfangreichen Evaluierung ist, dass die Gruppenbeitragsmethode von Atkinson das genaueste Verfahren zur Abschätzung des Abbaus organischer Verbindungen in der Troposphäre ist. Obwohl dieses Verfahren einigen Beschränkungen unterliegt, scheint es die Methode der Wahl zu sein. Eine zukunftsträchtige Alternative ist die direkte Berechnung der Geschwindigkeitskonstanten der Reaktionen mit OH‐Radikalen, was heute schon beinahe routinemäßig möglich ist, und zwar mit einem Verfahren, das mithilfe semiempirischer Energiehyperflächen die Geschwindigkeitskonstanten mit einer maximalen Abweichung von ihren experimentellen Werten um den Faktor 2 liefert. Für die Abschätzung des vollständigen Bioabbaus organischer Verbindungen haben sich als beste Verfahren ein PLS‐Modell (PLS=partial least squares, partielle Regression) und ein Satz von sieben Bioabbau‐Regeln erwiesen. Allerdings wird empfohlen, zur Abschätzung des Bioabbaus alle vier untersuchten Modelle parallel einzusetzen. Sofern deren Vorhersagen übereinstimmen, kann die entsprechende Prognose als recht zuverlässig angesehen werden.

Im englischen Original wird die Prognose bei Übereinstimmung aller vier Modelle als “very reliable” beschrieben.
Dithiol Proteins as Guardians of the Intracellular Redox Milieu in Parasites: Old and New Drug Targets in Trypanosomes and Malaria‐Causing Plasmodia
Authors: Krauth‐Siegel R. Luise , Bauer Holger , Schirmer R. Heiner
Published: January 2005

Parasitic diseases such as sleeping sickness, Chagas' heart disease, and malaria are major health problems in poverty‐stricken areas. Antiparasitic drugs that are not only active but also affordable and readily available are urgently required. One approach to finding new drugs and rediscovering old ones is based on enzyme inhibitors that paralyze antioxidant systems in the pathogens. These antioxidant ensembles are essential to the parasites as they are attacked in the human host by strong oxidants such as peroxynitrite, hypochlorite, and H2O2. The pathogen‐protecting system consists of some 20 thiol and dithiol proteins, which buffer the intraparasitic redox milieu at a potential of −250 mV. In trypanosomes and leishmania the network is centered around the unique dithiol trypanothione (N1,N8‐bis(glutathionyl)spermidine). In contrast, malaria parasites have a more conservative dual antioxidative system based on glutathione and thioredoxin. Inhibitors of antioxidant enzymes such as trypanothione reductase are, indeed, parasiticidal but they can also delay or prevent resistance against a number of other antiparasitic drugs.
Catalysts for Cross‐Coupling Reactions with Non‐activated Alkyl Halides
Authors: Frisch Anja C. , Beller Matthias
Published: January 2005

Despite the problems inherent to metal‐catalyzed cross‐coupling reactions with alkyl halides, these reactions have become increasingly important during the last few years. Detailed mechanistic investigations have led to a variety of novel procedures for the selective cross‐coupling of non‐activated alkyl halides bearing β hydrogen atoms with a variety of organometallic nucleophiles under mild reaction conditions. This Minireview highlights selected examples of metal‐catalyzed coupling methods and is intended to encourage chemists to exploit the potential of these approaches in organic synthesis.
Occurrence and present status of coastal dolphins (Delphinus delphis and Tursiops truncatus) in the eastern Ionian Sea
Authors: Bearzi Giovanni , Politi Elena , Agazzi Stefano , Bruno Sebastiano , Costa Marina , Bonizzoni Silvia
Published: January 2005

Boat surveys aimed at studying short‐beaked common dolphins and common bottlenose dolphins in eastern Ionian Sea coastal waters were conducted between 1993 and 2003. During 835 survey days, 24 771 km of total effort was distributed within an area of 480 km2, resulting in 428 common dolphin and 235 bottlenose dolphin sightings.

Individual photo‐identification was performed extensively throughout this study, making it possible to monitor the number of animals seen in the study area each year and their long‐term residency patterns.

Common dolphins declined across the study period, from 2.18 encounters/100 km in 1997 to 0.40 encounters/100 km in 2003. In contrast, there was a relatively stable presence of bottlenose dolphins, some individuals showing high levels of site fidelity and others using the area only occasionally.

The local decline of common dolphins and the low density of bottlenose dolphins appeared to reflect the general status of these cetacean species in the wider Mediterranean region, where common dolphins were classified as endangered in the IUCN Red List in 2003.

Based on the available evidence, we infer that the present unfavourable status of common dolphins in eastern Ionian Sea coastal waters is largely a consequence of prey depletion.

Copyright © 2005 John Wiley & Sons, Ltd.
The structure of antimicrobial pexiganan peptide in solution probed by Fourier transform infrared absorption, vibrational circular dichroism, and electronic circular dichroism spectroscopy
Authors: Shanmugam Ganesh , Polavarapu Prasad L. , Gopinath D. , Jayakumar R.
Published: January 2005

Pexiganan (Gly–Ile–Gly–Lys–Phe–Leu–Lys–Lys–Ala–Lys–Lys–Phe–Gly–Lys–Ala–Phe–Val–Lys–Ile–Leu–Lys–Lys), a 22 amino acid peptide, is an analogue of the magainin family of antimicrobial peptides present in the skin of the African clawed frog. Conformational analysis of pexiganan was carried out in different solvent environments for the first time. Organic solvents, trifluoroethanol (TFE) and methanol, were used to study the secondary structural preferences of this peptide in the membrane‐mimicking environments. In addition, aqueous (D2O) and dimethyl sulfoxide (DMSO) solutions were also investigated to study the role of hydrogen bonding involved in the secondary structure formation. Fourier transform infrared absorption, vibrational circular dichroism (VCD), and electronic circular dichroism (ECD) measurements were carried out under the same conditions to ascertain the conformational assignments in different solvents. All these spectroscopic measurements suggest that the pexiganan peptide has the tendency to adopt different structures in different environments. Pexiganan appears to adopt an α‐helical conformation in TFE, a sheet‐stabilized β‐turn structure in methanol, a random coil with β‐turn structure in D2O, and a solvated β‐turn structure in DMSO. © 2005 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2005
CD spectral study of Dnp derivatives of amino acids and peptides for their configurational and conformational analysis
Authors: Kawai Masao , Nagai Ukon , Inai Yoshihito , Yamamura Hatsuo , Akasaka Ryougo , Takagi Shigeru , Miwa Yoshihisa , Taga Tooru
Published: January 2005

Rules relating the stereochemistry of N‐Dnp (Dnp: 2,4‐dinitrophenyl) derivatives of α‐amino acids and peptides and the sign of the Cotton effects at the longest wavelength band (ca. 400 nm) are surveyed. Some new data and insights concerning the CD spectra of Dnp–α‐amino acids are included: i.e., the spectra of Dnp derivatives as the composite of the corresponding o‐nitrophenyl and p‐nitrophenyl derivatives; the crystal structure of Dnp–I‐phenylalanine and its solid‐state CD spectra; the CD spectra of Dnp–α‐amino acids containing sulfur atom on their side chains; and the theoretical approach to the CD spectra using molecular orbital method‐based calculation. Conformational analyses of cyclic and linear peptides by the CD spectra of their Dnp derivatives are also discussed. © 2005 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2005
Screw‐sense inversion characteristic of α‐helical poly(β‐p‐chlorobenzyl L‐aspartate) and comparison with other related polyaspartates
Authors: Abe Akihiro , Hiraga Kentaro , Imada Yousuke , Hiejima Toshihiro , Furuya Hidemine
Published: January 2005

This is one of a series of studies on the reversal of the helix sense of polyaspartates originated from the pioneering work of Goodman and his associates in 1960s. Poly(β‐p‐chlorobenzyl L‐aspartate) (PClBLA) is one of the well‐studied polyaspartate derivatives in both solution and the solid state. The chemical structure of PClBLA differs from those of poly(β‐benzyl L‐aspartate) (PBLA) and poly(β‐phenethyl L‐aspartate) (PPLA) only at the terminal of the relatively long side chain. PBLA takes a left‐handed form (L) in conventional helicoidal solvents and does not exhibit any screw‐sense inversion. In contrast to PBLA, both PClBLA and PPLA form a right‐handed helix (R) in chlorinated alkane solvents and exhibits a reversal of α‐helix sense at higher temperatures. Yet the transition behaviors in the presence of denaturant acid are quite different between these two polymers. While PPLA exhibits transitions such as R → L → coil by lowering temperature, PClBLA directly goes into the coil state without showing the reentrant L form. The cause of these phenomenological differences among these polymers has been investigated by constructing the phase diagram. © 2005 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2005
Acid–base titration of melanocortin peptides: Evidence of Trp rotational conformers interconversion
Authors: Fernandez Roberto M. , Vieira Renata F. F. , Nakaie Clóvis R. , Lamy M. Teresa , Ito Amando S.
Published: January 2005

Tryptophantime‐resolved fluorescence was used to monitor acid–base titration properties of α‐melanocyte stimulating hormone (α‐MSH) and the biologically more potent analog [Nle4, D‐Phe7]α ‐MSH (NDP‐MSH), labeled or not with the paramagnetic amino acid probe 2,2,6,6‐tetramthylpiperidine‐N‐oxyl‐4‐amino‐4‐carboxylic acid (Toac). Global analysis of fluorescence decay profiles measured in the pH range between 2.0 and 11.0 showed that, for each peptide, the data could be well fitted to three lifetimes whose values remained constant. The less populated short lifetime component changed little with pH and was ascribed to Trp g+ χ1 rotamer, in which electron transfer deactivation predominates over fluorescence. The long and intermediate lifetime preexponential factors interconverted along that pH interval and the result was interpreted as due to interconversion between Trp g‐ and trans χ1 rotamers, driven by conformational changes promoted by modifications in the ionization state of side‐chain residues. The differences in the extent of interconversion in α‐MSH and NDP‐MSH are indicative of structural differences between the peptides, while titration curves suggest structural similarities between each peptide and its Toac‐labeled species, in aqueous solution. Though less sensitive than fluorescence, the Toac electron spin resonance (ESR) isotropic hyperfine splitting parameter can also monitor the titration of side‐chain residues located relatively far from the probe. © 2005 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2005
Direct observation of spectral differences between normal and basal cell carcinoma (BCC) tissues using confocal Raman microscopy
Authors: Choi Junghyun , Choo Jaebum , Chung Hoeil , Gweon Dae‐Gab , Park Jeunghee , Kim Hyo Jin , Park Sangyong , Oh Chil‐Hwan
Published: January 2005

Raman spectroscopy has strong potential for providing noninvasive dermatological diagnosis of skin cancer. In this study, confocal Raman microscopy was applied to the dermatological diagnosis for one of the most common skin cancers, basal cell carcinoma (BCC). BCC tissues were obtained from 10 BCC patients using a routine biopsy and used for confocal Raman measurements. Autofluorescence signals from tissues, which interfere with the Raman signals, were greatly reduced using a confocal slit adjustment. Distinct Raman band differences between normal and BCC tissues for the amide I mode and the PO symmetric stretching mode showed that this technique has strong potential for use as a dermatological diagnostic tool without the need for statistical treatment of spectral data. It was also possible to precisely differentiate BCC tissue from surrounding noncancerous tissue using the confocal Raman depth profiling technique. We propose that confocal Raman microscopy provides a novel method for dermatological diagnosis since direct observations of spectral differences between normal and BCC tissues are possible. © 2005 Wiley Periodicals, Inc. Biopolymers 77: 264–272, 2005
Cover Picture: Self‐Assembly of the Octanuclear Cluster [Cu8(OH)10(NH2(CH2)2CH3)12]6+ and the One‐Dimensional N‐Propylcarbamate‐Linked Coordination Polymer {[Cu(O2CNH(CH2)2CH3)(NH2(CH2)2CH3)3](ClO4)}n (Chem. Eur. J. 3/2005)
Authors: Bramsen Fabienne , Bond Andrew D. , McKenzie Christine J. , Hazell Rita G. , Moubaraki Boujemaa , Murray Keith S.
Published: January 2005

An octanuclear cluster cation assembled from eight Cu2+ ions, ten OH− ions and twelve neutral monodentate n‐propylamine moieties is depicted on the cover. Remarkably, this discrete cluster does not contain multidentate ligands to limit its further aggregation. Instead, its controllable formation appears to be attributable to the influence of the n‐propyl chains, which pack efficiently in hydrophobic channels running through the crystal lattice. More details are given by C. J. McKenzie et al. on p. 825ff.
A Theoretical Study on the Gas Phase Reactions of the Anions NbO3‐, NbO5‐, and NbO2(OH)2‐ with H2O and O2
Authors: Sambrano J. R. , Gracia L. , Andres J. , Berski S. , Beltran A.
Published: January 2005

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Cage Isomers of N14 and N16: Nitrogen Molecules that Are Not a Multipe of Six
Authors: Strout Douglas L.
Published: January 2005

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Predicting the Energetics, Phase Stability, and Morphology Evolution of Faceted and Spherical Anatase Nanocrystals
Authors: Barnard A. S. , Zapol P.
Published: January 2005

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Single Crystal Investigation of CePd2In4 and CePt2In4 Compounds.
Authors: Nesterenko S. N. , Tursina A. I. , Gribanov A. V. , Seropegin Y. D. , Kurenbaeva J. M.
Published: January 2005

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Synthesis, Crystal Structure Determination and Vibrational Spectra of Indium(II) Indium(III) Oxidephosphate, (In2)4+(In3+)2O2 (PO4)2.
Authors: Thauern H. , Glaum R.
Published: January 2005

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Search for Perovskite‐Type New Borides in the Sc—TM—B (TM: Ti, V, Cr, Mn, Fe, Co, and Ni) Systems.
Authors: Shishido T. , et al. et al.
Published: January 2005

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Preparation and Crystal Structure of Sc3(Sc0.32Al0.68)O6 — A New Derivative of the Mg3TeO6 Type of Structure.
Authors: Mueller Daniel , Assenmacher Wilfried , Mader Werner
Published: January 2005

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Molten Metal Flux Growth and Properties of CrSi2.
Authors: Shishido T. , et al. et al.
Published: January 2005

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Crystal Growth, Microhardness and Oxidation Behavior or LnMn2Si2 Compounds (Ln: La, Ce, Pr, Nd, Sm, Gd).
Authors: Okada Shigeru , Iizumi Kiyokata , Mori Takao , Shishido Toetsu , Kudou Kunio , Tanaka Takaho , Rogl Peter , Lundstroem Torsten
Published: January 2005

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Novel Combination of Coordination Polyhedra in Mg2Co3Sn10+x — The First Phase in the Mg/Co/Sn System.
Authors: Schreyer Martin , Kraus Guenther , Faessler Thomas F.
Published: January 2005

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The First Palladium Tin Selenide: Pd7Sn2Se9.85.
Authors: Pocha R. , Johrendt D.
Published: January 2005

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Preparation and Characterization of OsO2.
Authors: Yen P. C. , Chen R. S. , Chen C. C. , Huang Y. S. , Tiong K. K. , Liao P. C.
Published: January 2005

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Asymmetric Hydrogenation of Ketones Using a Ruthenium(II) Catalyst Containing BINOL‐Derived Monodonor Phosphorus‐Donor Ligands.
Authors: Xu Yingjian , Alcock Nat W. , Clarkson Guy J. , Docherty Gordon , Woodward Gary , Wills Martin
Published: January 2005

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Diastereoselective Synthesis of Thieno[3′,2′:4,5]cyclopenta[1,2‐d][1,3]oxazolines — New Ligands for the Copper‐Catalyzed Asymmetric Conjugate Addition of Diethylzinc to Enones.
Authors: Bonini Bianca Flavia , Capito Elena , Comes‐Franchini Mauro , Ricci Alfredo , Bottoni Andrea , Bernardi Fernando , Miscione Gian Pietro , Giordano Laurent , Cowley Andrew R.
Published: January 2005

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Amino Acids in Heterocyclic Synthesis: Novel Synthesis of Pyrano[2,3‐c]pyrazoles, Pyrazolo[3,4‐b]pyridine, and Pyrido[1,2‐a]benzimidazoles.
Authors: Elgemeie Galal H. , Elghandour Ahmed H. , Hussein Ahmed M.
Published: January 2005

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Synthesis of Fused Imidazoles Based on γ‐Bromodypnone.
Authors: Kovtunenko Volodimir , Potikha Lyudmila , Turov Aleksandr
Published: January 2005

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Enaminones as Building Blocks in Heterocyclic Synthesis. Synthesis of Polyfunctionally Substituted 3‐Azolylpyridines and Azolylazoloazines by Thermal and Microwave Heating.
Authors: Al‐Saleh Balkis , Behbehani Haider , El‐Apasery Morsy Ahmed , Elnagdi Mohamed Hilmy
Published: January 2005

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Scandium—Bipyridine‐Catalyzed Enantioselective Addition of Alcohols and Amines to meso‐Epoxides.
Authors: Schneider Christoph , Sreekanth Anakallil R. , Mai Enzo
Published: January 2005

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Ruthenium Porphyrin Catalyzed Tandem Sulfonium/Ammonium Ylide Formation and [2,3]‐Sigmatropic Rearrangement. A Concise Synthesis of (.+‐.)‐Platynecine.
Authors: Zhou Cong‐Ying , Yu Wing‐Yiu , Chan Philip Wai Hong , Che Chi‐Ming
Published: January 2005

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Pyridinium Sulfonate Chlorochromate (VI), C5H5NSO3H [CrO3Cl] (PSCC): A New Reagent for Oxidation of Organic Substrates.
Authors: Kassaee M. Z. , Bekhradnia A. R.
Published: January 2005

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Silica Sulfuric Acid Catalysis the Oxidation of Organic Compounds with Sodium Bromate.
Authors: Shaabani Ahmad , Soleimani Kamal , Bazgir Ayoob
Published: January 2005

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Development of an Efficient Method for Preparation of 1,3,5‐Trihydroxyisocyanuric Acid (THICA) and Its Use as Aerobic Oxidation Catalyst.
Authors: Hirai Naruhisa , Kagayama Takashi , Tatsukawa Yoshinobu , Sakaguchi Satoshi , Ishii Yasutaka
Published: January 2005

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Oxidation of Organic Compounds by Potassium Permanganate Supported on Montmorillonite K10.
Authors: Shaabani Ahmad , Bazgir Ayoob , Lee Donald G.
Published: January 2005

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Fluorination of Carbinols with 2,2‐Difluoro‐1,3‐dimethylimidazolidine in Ionic Liquid.
Authors: Kitazume Tomoya , Ebata Takuma
Published: January 2005

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Electrophilic Alkylations in Neutral Aqueous or Alcoholic Solutions.
Authors: Hofmann Matthias , Hampel Nathalie , Kanzian Tanja , Mayr Herbert
Published: January 2005

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Low‐Temperature Deacylation of N‐Monosubstituted Amides.
Authors: Spaggiari Alberto , Blaszczak Larry C. , Prati Fabio
Published: January 2005

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Caro′s Acid Supported on Silica Gel. Part 8. An Efficient and Selective Reagent for Conversion of Phenylhydrazones and Semicarbazones to the Corresponding Carbonyl Compounds.
Authors: Tajbakhsh Mahmood , Lakouraj Moslem‐Mansor , Gholami Mohammad‐Hosein , Ramzanian‐Lehmali Farhad
Published: January 2005

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Facile and Efficient Method for Deprotection of 1,3‐Oxathiolanes with N,N′‐Dibromo‐N,N′‐1,2‐ethanediylbis(p‐toluenesulfonamide).
Authors: Ghorbani‐Vaghei Ramin , Khazaei Ardeshir
Published: January 2005

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Phosphorus Pentoxide as an Efficient Catalyst for the Tetrahydropyranylation of Alcohols under Solvent‐Free Conditions.
Authors: Eshghi Hossein , Shafieyoon Parvaneh
Published: January 2005

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Activation of Iron(III) and Bismuth(III) Nitrates by Tungstophosphoric Acid: Solvent‐Free Oxidative Deprotection of Oximes to Carbonyl Compounds.
Authors: Firouzabadi Habib , Iranpoor Nasser , Amani Kamal
Published: January 2005

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Fluorinated Ketene Dithioacetals. Part 11. Reaction of Lithium Enediolates with Perfluoroketene Dithioacetals. Synthesis of α‐Trifluoromethyl γ‐Dicarboxylic Acid Derivatives.
Authors: Sotoca Enrique , Bouillon Jean‐Philippe , Gil Salvador , Parra Margarita , Portella Charles
Published: January 2005

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Synthesis of 3‐Bromo‐3‐nitroacrylates.
Authors: Sarkisyan Z. M. , Sadikov K. D. , Smirnov A. S. , Kuzhaeva A. A. , Makarenko S. V. , Anisimova N. A. , Deiko L. I. , Berestovitskaya V. M.
Published: January 2005

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Synthesis of Fluoroalkyl Vinyl Sulfoxides and Their Use in Diels—Alder Reactions.
Authors: Moise Joelle , Goumont Regis , Magnier Emmanuel , Wakselman Claude
Published: January 2005

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Diels—Alder Reactions in Pyridinium Based‐Ionic Liquids.
Authors: Xiao Ying , Malhotra Sanjay V.
Published: January 2005

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Interaction of α,β‐Unsaturated Ketones of the Adamantane Series with N,N′‐Binucleophiles.
Authors: Pimenov A. A. , Makarova N. V. , Moiseev I. K. , Zemtsova M. N.
Published: January 2005

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Hydrodediazoniation of Dry Arenediazonium o‐Benzenedisulfonimides with Hydrogen Peroxide.
Authors: Barbero Margherita , Degani Iacopo , Dughera Stefano , Fochi Rita
Published: January 2005

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4,4′‐Bis(dichloroiodo)biphenyl and 3‐(Dichloroiodo)benzoic Acid: New Recyclable Hypervalent Iodine Reagents for Vicinal Halomethoxylation of Unsaturated Compounds.
Authors: Yusubov Mehman S. , Drygunova Larisa A. , Zhdankin Viktor V.
Published: January 2005

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Mild and Efficient Synthesis of Propargylamines by Copper‐Catalyzed Mannich Reaction.
Authors: Bieber Lothar W. , da Silva Margarete F.
Published: January 2005

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Zirconium‐Mediated Conversion of Amides to Nitriles: A Surprising Additive Effect.
Authors: Ruck Rebecca T. , Bergman Robert G.
Published: January 2005

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Palladium‐Catalyzed Arylation of Sulfones.
Authors: Mitin A. V. , Kashin A. N. , Beletskaya I. P.
Published: January 2005

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Practical Synthesis of Fenbufen Ethanolamide.
Authors: Zohrabi‐Kalantari Vida , Link Andreas
Published: January 2005

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Palladium‐Catalyzed Suzuki Reaction Using 1,3‐Dialkylbenzimidazol‐2‐ylidene Ligands in Aqueous Media.
Authors: Oezdemir Ismail , Goek Yetkin , Guerbuez Nevin , Cetinkaya Engin , Cetinkaya Bekir
Published: January 2005

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Synthesis of Oxazolidinones and 1,2‐Diamines from N‐Alkyl Aziridines.
Authors: Hancock Matthew T. , Pinhas Allan R.
Published: January 2005

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Reductive Dehalogenation of 4‐Halogenomethyl Azetidin‐2‐one Derivatives. Synthesis of (4‐Oxo‐azetidin‐2‐yl)acetonitriles.
Authors: Boros Eva , Bertha Ferenc , Fetter Jozsef , Vida Laszlo , Kajtar‐Peredy Maria , Czira Gabor
Published: January 2005

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Synthesis of an Isophorone‐Based Nonlinear Optical Chromophore.
Authors: Davis Matthew C. , Chafin Andrew P. , Hollins Richard A. , Baldwin Lawrence C. , Erickson Eric D. , Zarras Peter , Drury Elliott C.
Published: January 2005

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Stereoselective Synthesis of Highly Substituted Bicyclic γ‐Lactones Using Homoaldol Addition of 1‐(1‐Cycloalkenyl)methyl Carbamates.
Authors: Oezluegedik Mustafa , Kristensen Jesper , Reuber Jenny , Froehlich Roland , Hoppe Dieter
Published: January 2005

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C1—C2 Cleavage of C1‐Functionalized 8‐Oxabicyclo‐[3.2.1]‐oct‐6‐en‐3‐one. Stereoselective Preparation of 4‐Substituted Butenolides.
Authors: Montana Angel M. , Garcia Francisca , Batalla Consuelo
Published: January 2005

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Synthetic Studies Towards the Preparation of 2‐Benzyl‐2‐hydroxybenzofuran‐3(2H)‐one, the Prototype of Naturally Occurring Hydrated Auronols.
Authors: Loeser Reik , Chlupacova Marta , Marecek Ales , Opletalova Veronika , Guetschow Michael
Published: January 2005

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Hydroamination/Cyclization of Aminoalkenes Using Cationic Zirconocene and Titanocene Catalysts.
Authors: Gribkov Denis V. , Hultzsch Kai C.
Published: January 2005

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A Novel Pseudo Four‐Component Reaction: Unexpected Formation of Densely Functionalized Pyrroles.
Authors: Shaabani Ahmad , Teimouri Mohammad Bagher , Arab‐Ameri Sakineh
Published: January 2005

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