bluuebunny/crossref_metadata_2025 huggingface dataset:
Fractional populations in multiple gene inheritance
Authors: Chung Myung-Hoon , Kim Chul Koo , Nahm Kyun
Published: January 2003

Motivation: With complete knowledge of the human genome sequence, one of the most interesting tasks remaining is to understand the functions of individual genes and how they communicate. Using the information about genes (locus, allele, mutation rate, fitness, etc.), we attempt to explain population demographic data. This population evolution study could complement and enhance biologists’ understanding about genes.

Results: We present a general approach to study population genetics in complex situations. In the present approach, multiple allele inheritance, multiple loci inheritance, natural selection and mutations are allowed simultaneously in order to consider a more realistic situation. A simulation program is presented so that readers can readily carry out studies with their own parameters. It is shown that the multiplicity of the loci greatly affects the demographic results of fractional population ratios. Furthermore, the study indicates that some high infant mortality rates due to congenital anomalies can be attributed to multiple loci inheritance.

Availability: The simulation program can be downloaded from http://won.hongik.ac.kr/~mhchung/index_files/yapop.htm. In order to run this program, one needs Visual Studio .NET platform, which can be downloaded from http://msdn.microsoft.com/netframework/downloads/default.asp.

Contact: mhchung@hongik.ac.kr

* To whom correspondence should be addressed.
FluxAnalyzer: exploring structure, pathways, and
flux distributions in metabolic networks on interactive flux maps
Authors: Klamt Steffen , Stelling Jörg , Ginkel Martin , Gilles Ernst Dieter
Published: January 2003

Motivation: The analysis of structure, pathways and flux distributions in metabolic networks has become an important approach for understanding the functionality of metabolic systems. The need of a user-friendly platform for stoichiometric modeling of metabolic networks in silico is evident.

Results: The FluxAnalyzer is a package for MATLAB® and facilitates integrated pathway and flux analysis for metabolic networks within a graphical user interface. Arbitrary metabolic network models can be composed by instances of four types of network elements. The abstract network model is linked with network graphics leading to interactive flux maps which allow for user input and display of calculation results within a network visualization. Therein, a large and powerful collection of tools and algorithms can be applied interactively including metabolic flux analysis, flux optimization, detection of topological features and pathway analysis by elementary flux modes or extreme pathways. The FluxAnalyzer has been applied and tested for complex networks with more than 500 000 elementary modes. Some aspects of the combinatorial complexity of pathway analysis in metabolic networks are discussed.

Availability: Upon request from the corresponding author. Free for academic users (license agreement). Special contracts are available for industrial corporations.

Supplementary information: http://www.mpi-magdeburg.mpg.de/projects/fluxanalyzer.

Contact: klamt@mpi-magdeburg.mpg.de

* To whom correspondence should be addressed.
Reconstruction of metabolic networks from genome data and analysis
of their global structure for various organisms
Authors: Ma Hongwu , Zeng An-Ping
Published: January 2003

Motivation: Information from fully sequenced genomes makes it possible to reconstruct strain-specific global metabolic network for structural and functional studies. These networks are often very large and complex. To properly understand and analyze the global properties of metabolic networks, methods for rationally representing and quantitatively analyzing their structure are needed.

Results: In this work, the metabolic networks of 80 fully sequenced organisms are in silico reconstructed from genome data and an extensively revised bioreaction database. The networks are represented as directed graphs and analyzed by using the‘ breadth first searching algorithm to identify the shortest pathway (path length) between any pair of the metabolites. The average path length of the networks are then calculated and compared for all the organisms. Different from previous studies the connections through current metabolites and cofactors are deleted to make the path length analysis physiologically more meaningful. The distribution of the connection degree of these networks is shown to follow the power law, indicating that the overall structure of all the metabolic networks has the characteristics of a small world network. However, clear differences exist in the network structure of the three domains of organisms. Eukaryotes and archaea have a longer average path length than bacteria.

Availability: The reaction database in excel format and the programs in VBA (Visual Basic for Applications) are available upon request.

Supplementary Material: Bioinformatics Online.

Contact: aze@gbf.de; hwm@gbf.de

* To whom correspondence should be addressed.
A task framework for the web interface W2H
Authors: Ernst Peter , Glatting Karl-Heinz , Suhai Sándor
Published: January 2003

Summary: The W3H task framework allows the execution of compound jobs utilizing the description of work and data flows in a heterogeneous bioinformatics environment using meta-data information. By means of these descriptions, the task system can schedule the necessary execution of applications available in the environment, depending on rules specified in the meta-data. By integrating this task framework into the publicly available web interface W2H, similarly based on meta-data, web access and data management are immediately available for each task description. Authors of task descriptions can base their work on the underlying classes and objects to be able to describe dependency rules between previously independent applications. The result of a compound task is given as XML data that is translated according to XSLT data into web pages or plain text to report the result of the task to the user.

Availability: Within the HUSAR environment at DKFZ http://genome.dkfz-heidelberg.de/

Contact: P.Ernst@dkfz.de

* To whom correspondence should be addressed.
QuickLIMS: facilitating the data management for DNA-microarray fabrication
Authors: Kokocinski Felix , Wrobel Gunnar , Hahn Meinhard , Lichter Peter
Published: January 2003

Summary: QuickLIMS is a Microsoft Access-based laboratory information and management system, capable of processing all information for microarray production. The program’s operational flow is protocol-based, dynamically adapting to changes of the process. It interacts with the laboratory robot and with other database systems over the network, and it represents a complete solution for the management of the entire manufacturing process.

Availability and supplementary information: http://www.dkfz-heidelberg.de/kompl_genome/Other/QuickLims/index.html

Contact: f.kokocinski@dkfz.def.kokocinski@dkfz.de

* To whom correspondence should be addressed.
An efficient algorithm for minimal primer set selection
Authors: Hsieh Ming-Hua , Hsu Wei-Che , Chiu Sung-Kay , Tzeng Chi-Meng
Published: January 2003

Summary: We have developed U-PRIMER, a primer design program, to compute a minimal primer set (MPS) for any given set of DNA sequences. The U-PRIMER algorithm, which uses automatic variable fixing and automatic redundant constraint elimination to tackle the binary integer programming problem associated with the MPS selection problem. The program has been tested successfully with 32 adipocyte development-related genes and 9 TB-specific genes to obtain their respective MPSs.

Availability: A free copy of U-PRIMER implemented in C++ programming language is available from http://www.u-vision-biotech.com

Contact: cmtzeng@u-vision-biotech.com

* To whom correspondence should be addressed.
Efficient selective screening of haplotype tag SNPs
Authors: Ke Xiayi , Cardon Lon R.
Published: January 2003

Abstract: Haplotypes defined by common single nucleotide polymorphisms (SNPs) have important implications for mapping of disease genes and human traits. Often only a small subset of the SNPs is sufficient to capture the full haplotype information. Such subsets of markers are called haplotype tagging SNPs (htSNPs). Although htSNPs can be identified by eye, efficient computer algorithms and flexible interactive software tools are required for large datasets such as the human genome haplotype map. We describe a java-based program, SNPtagger, which screens for minimal sets of SNP markers to represent given haplotypes according to various user requirements. The program offers several options for inclusion/exclusion of specific markers and presents alternative panels for final selection.

Availability: The www-based program is available at http://www.well.ox.ac.uk/~xiayi/haplotype/index.html.

Contact: xiayi@well.ox.ac.uk

* To whom correspondence should be addressed.
Simulating haplotype blocks in the human genome
Authors: Posada David , Wiuf Carsten
Published: January 2003

Summary: A bioinformatic tool was written to simulate haplotypes and SNPs under a modified coalescent with recombination. The most important feature of this program is that it allows for the specification of non-homogeneous recombination rates, which results in the formation of the so-called ‘haplotype blocks’ of the human genome. The program also implements different mutation models and flexible demographic histories. The samples generated can be very useful to better understand the architecture of the human genome and to investigate its impact in association studies searching for disease genes.

Availability: The SNPsim package is available at http://www.evolgenics.com/software

Contact: dposada@evolgenics.com

* To whom correspondence should be addressed.
Pedstrip: extracting a maximal subset of available,
unrelated individuals from a pedigree
Authors: Martin Jeremy M.R. , Mackay lan J. , Rawlings Christopher J.
Published: January 2003

Summary: Certain types of genetic analysis are simplified by assembling a collection of unrelated individuals, e.g. case-control experiments. If a family study is being performed then it will be necessary to extract subsets of unrelated, available individuals from pedigress. Our program provides an optimal method for performing this task.

Availability: The software is available, free of charge, on request from Oxagen Ltd.

Contact: SD@oxagen.co.uk

Supplementary information: http://www.oxagen.co.uk

* To whom correspondence should be addressed.
AVA: visual analysis of gene expression microarray data
Authors: Zhou Yihua , Liu Jingdong
Published: January 2003

Summary: AVA (Array Visual Analyzer) is a Java program that provides a graphical environment for visualization and analysis of gene expression microarray data. Together with its interactive visualization tools and a variety of built-in data analysis and filtration methods, AVA effectively integrates microarray data normalization, quality assessment, and data mining into one application.

Availability: The software is freely available for academic users on request from the authors.

Contact: yihua-zhou2@monsanto.com

* To whom correspondence should be addressed.
Matrix2png: a utility for visualizing matrix data
Authors: Pavlidis Paul , Noble William Stafford
Published: January 2003

We describe a simple software tool, ‘matrix2png’, for creating color images of matrix data. Originally designed with the display of microarray data sets in mind, it is a general tool that can be used to make simple visualizations of matrices for use in figures, web pages, slide presentations and the like. It can also be used to generate images ‘on the fly’ in web applications. Both continuous-valued and discrete-valued (categorical) data sets can be displayed. Many options are available to the user, including the colors used, the display of row and column labels, and scale bars. In this note we describe some of matrix2png’s features and describe some places it has been useful in the authors’ work.

Availability: A simple web interface is available, and Unix binaries are available from http://microarray.cpmc.columbia.edu/matrix2png. Source code is available on request.

Contact: pp175@columbia.edu

* To whom correspondence should be addressed at Russ Berrie Pavilion Room 121, 1150 St. Nicholas Ave, New York, NY 10025, USA.
RnaViz 2: an improved representation of RNA secondary structure
Authors: De Rijk Peter , Wuyts Jan , De Wachter Rupert
Published: January 2003

Summary: RnaViz has been developed to easily create nice, publication quality drawings of RNA secondary structure. RnaViz 2 supports CT, DCSE, and RNAML input formats and improves on many aspects of the first version, notably portability and structure annotation. RnaViz is written using a hybrid programming approach combining pieces written in C and in the scripting language Tcl/Tk, making the program very portable and extensible.

Availability: Source code, binaries for Linux and MS Windows, and additional documentation are available athttp://rrna.uia.ac.be/rnaviz/

Contact: derijkp@uia.ua.ac.be

* To whom correspondence should be addressed.
TopDraw: a sketchpad for protein structure topology cartoons
Authors: Bond Charles S.
Published: January 2003

Summary: Protein topology cartoons are a representation of structural data commonly used by structural biologists to illustrate the relationship between one-dimensional sequence and three-dimensional structural data in a convenient two-dimensional format. TopDraw is a simple, freely available TCL/Tk based drawing program designed specifically for the production of publication quality topology cartoons in a style commonly presented by structural biologists.

Availability: TopDraw is freely available under the terms of the GNU General Public License. It can be downloaded from http://stein.bioch.dundee.ac.uk/~charlie/scripts/topdraw.html.

Contact: C.S.Bond@dundee.ac.uk
ARIA: automated NOE assignment and NMR structure
calculation
Authors: Linge Jens P. , Habeck Michael , Rieping Wolfgang , Nilges Michael
Published: January 2003

Motivation: In the light of several ongoing structural genomics projects, faster and more reliable methods for structure calculation from NMR data are in great demand. The major bottleneck in the determination of solution NMR structures is the assignment of NOE peaks (nuclear Overhauser effect). Due to the high complexity of the assignment problem, most NOEs cannot be directly converted into unambiguous inter-proton distance restraints.

Results: We present version 1.2 of our program ARIA (Ambiguous Restraints for Iterative Assignment) for automated assignment of NOE data and NMR structure calculation. We summarize recent progress in correcting for spin diffusion with a relaxation matrix approach, representing non-bonded interactions in the force field and refining final structures in explicit solvent. We also discuss book-keeping, data exchange with spectra assignment programs and deposition of the analysed experimental data to the databases.

Availability: ARIA 1.2 is available from: http://www.pasteur.fr/recherche/unites/Binfs/aria/.

Supplementary information: XML DTDs (for chemical shifts and NOE crosspeaks), Python scripts for the conversion of various NMR data formats and the results of example calculations using data from the S. cerevisiae HRDC domain are available from: http://www.pasteur.fr/recherche/unites/Binfs/aria/.

Contact: linge@pasteur.fr
Visualization and analysis of protein interactions
Authors: Ju Byong-Hyon , Park Byungkyu , Park Jong H. , Han Kyungsook
Published: January 2003

Summary: We have developed a new program called InterViewer for drawing large-scale protein interaction networks in three-dimensional space. Unique features of InterViewer include (1) it is much faster than other recent implementations of drawing algorithms; (2) it can be used not only for visualizing protein interactions but also for analyzing them interactively; and (3) it provides an integrated framework for querying protein interaction databases and directly visualizes the query results.

Availability: http://wilab.inha.ac.kr/protein/

Contact: khan@inha.ac.kr

* To whom correspondence should be addressed.
Analyzing Second-Stage Ecological Regressions: Comment on Herron and Shotts
Authors: Adolph Christopher , King Gary
Published: January 2003

We take this opportunity to comment on Herron and Shotts (2003; hereinafter HS) because of its interesting and productive ideas and because of the potential to affect the way a considerable body of practical research is conducted. This article, and the literature referenced therein, is based on the suggestions in three paragraphs in King (1997, pp. 289–290). Because these paragraphs were not summarized in HS, we thought they might be a useful place to start.
Singapore Airlines: what it takes to sustain service excellence – a senior management perspective
Authors: Wirtz Jochen , Johnston Robert
Published: January 2003

Singapore Airlines (SIA) is internationally recognized as one of the world’s leading carriers. This article details the results of a series of in‐depth interviews with SIA’s senior management on their views on what made SIA a service champion, and what it will take to maintain its lead in the industry. Excerpts from there interviews were broadly organized into four sections. They are: “SIA’s perspective of service excellence and key challenges”; “Understanding customers and anticipating their needs”; “Training and motivating the front line”; and “Managing with an eye for detail and profits”. The interviews show what SIA’s senior management sees as their key drivers of service excellence. The drivers are then related to key frameworks and models from the services marketing/management literature. Implications for current and aspiring service champions are derived.
A content analysis of complaints and compliments
Authors: Friman Margareta , Edvardsson Bo
Published: January 2003

The research question focused on in this study is whether complaint and compliment contain different service quality attributes. A sample of 236 complaints and 69 compliments collected by a public transport company were analyzed by means of the critical incident technique. The results of previous research were confirmed and showed that perceived service quality attributes in public transport involve employee behavior, reliability, simplicity and design. It was further concluded that reliability of service causes frequently more complaints than compliments. How customers are treated by the employees was found to be more frequent in compliments.
Culture, the built environment and healthcare organizational performance
Authors: Mallak Larry A. , Lyth David M. , Olson Suzan D. , Ulshafer Susan M. , Ulshafer Susan M. , Sardone Frank J.
Published: January 2003

Healthcare organization performance is a function of many variables. This study measured relationships among culture, the built environment, and outcome variables in a healthcare provider organization. A culture survey composed of existing scales and custom scales was used as the principal measurement instrument. Results supported culture strength’s links with higher performance levels and identified the built environment’s role as a moderating variable that can lead to improved processes and outcomes. Job satisfaction and patient satisfaction were found to be significantly and positively correlated with culture strength and with ratings of the built environment.
The antecedents of service quality and product quality and their influences on bank reputation: evidence from the banking industry in China
Authors: Wang Yonggui , Lo Hing‐P. , Hui Yer V.
Published: January 2003

Although an increasing number of studies is being performed in the field of service management, less work is being done on an integrated framework of service quality and product quality, especially that supported with evidence from developing countries. As a result, little is known about the distinction between service quality and product quality, their respective antecedents, and their distinctive contributions to performance in service industries in the developing world. Generalization of related findings from developed countries is not necessarily appropriate. Unlike most related studies that are based on evidence from developed countries, focuses attention on the distinction between, and respective antecedents of, service quality and product quality in the Chinese context. Gives much emphasis to the importance of a positive bank reputation. The findings are based on structural equation models developed by AMOS.
Measurements and simulation of SMT components
Authors: Pryputniewicz Ryszard J. , Rosato David , Furlong Cosme
Published: January 2003

Integrity of surface mount technology (SMT) components depends on their response to temperature changes caused by operating conditions. Temperature induced differential thermal expansions lead to strains in the interconnection structures of active devices. To evaluate these strains, temperature profiles of the interconnected components must be known. In this paper, a methodology for developing thermal models of SMT components is presented using thermal analysis system (TAS) and its application is demonstrated by simulating thermal fields of a representative package. Then, thermomechanical deformations of the package are measured quantitatively using state‐of‐the‐art laser‐based optoelectronic holography (OEH) methodology.
Multi‐layer thick‐film microwave components and measurements
Authors: Tian Zhengrong , Free Charles , Aitchison Colin , Barnwell Peter , Wood James
Published: January 2003

The trend in wireless and mobile communications for broader bandwidth microwave circuitry, coupled with high packaging density and low cost fabrication has triggered investigations of new circuit configurations and technologies that meet these requirements. We have addressed these issues through the study of multilayer microwave structures using advanced thick‐film technology. The techniques described employ several layers of metal sandwiched by thick‐film dielectric. This leads to an efficient solution for system miniaturisation. The significance of this work is that it shows the multilayer approach to microwave structures, coupled with new thick‐film technology, offers a viable and economic solution to achieve high‐density, high‐performance microwave circuits.
High‐Q RF inductors on 20 Ω.cm silicon realized through wafer‐level packaging techniques
Authors: Carchon G.J. , De Raedt W. , Beyne E.
Published: January 2003

High Q on‐chip inductors and low loss on‐chip interconnects and transmission lines are an important roadblock for the further development of Si‐based technologies at RF and microwave frequencies. In this paper, inductors are realized on standard Si wafers (20 Ω.cm) using MCM‐D processing. This consists of realizing two low K dielectric layers (BCB) and a thick Cu interconnect layer. Inductors with 5 μm lines and spaces are demonstrated for a 5 μm thick Cu layer, hereby leading to a very compact and high performance inductors: Q‐factors in the range of 25 to 30 have been obtained for inductances in the range of 1 to 5 nH. It is also shown how the Q‐factor and resonance frequency vary as a function of the inductor layout parameters and the thickness of the BCB and Cu layers. The realized 50 Ω CPW lines (lateral dimension of 40 μm) have a measured loss of only 0.2 dB/mm at 25 GHz.
High‐resolution integration of passives using micro‐contact printing (μCP)
Authors: Lakeman Charles D.E. , Fleig Patrick F.
Published: January 2003

As the number of passive components in electronic circuits increases, new methods for fabricating passives are under development to optimize utilization of board space. In this paper, we will describe the performance capabilities of TPL's micro‐contact printing (μCP) process to fabricate near‐net‐shape structures with feature sizes ranging from 100 microns to the sub‐micron scale. Like thick film processes, this novel process is compatible with a broad materials base, making a large range of materials properties available. Unlike thick film, however, this novel process employs powder‐free inks that can be patterned with high resolution. It is anticipated that this process will enable integration of passive components that show thin film performance at thick film cost. Emphasis in this paper will be placed on processing conditions, and materials properties to demonstrate the feasibility of this process for passive device fabrication.
Insights into binding cooperativity of MATa1/MATα2 from the crystal structure of a MATa1 homeodomain‐maltose binding protein chimera
Authors: Ke Ailong , Wolberger Cynthia
Published: January 2003

The Yeast MATa1 and MATα2 are homeodomain proteins that bind DNA cooperatively to repress transcription of cell type specific genes. The DNA affinity and specificity of MATa1 in the absence of MATα2, however, is very low. MATa1 is converted to a higher affinity DNA‐binding protein by its interaction with the C‐terminal tail of MATα2. To understand why MATa1 binds DNA weakly by itself, and how the MATα2 tail affects the affinity of MATa1 for DNA, we determined the crystal structure of a maltose‐binding protein (MBP)‐a1 chimera whose DNA binding behavior is similar to MATa1. The overall MATa1 conformation in the MBP‐a1 structure, which was determined in the absence of α2 and DNA, is similar to that in the a1/α2/DNA structure. The sole difference is in the C‐terminal portion of the DNA recognition helix of MATa1, which is flexible in the present structure. However, these residues are not in a location likely to be affected by binding of the MATα2 tail. The results argue against conformational changes in a1 induced by the tail of MATα2, suggesting instead that the MATα2 tail energetically couples the DNA binding of MATα2 and MATa1.
Accurate and automated classification of protein secondary structure with PsiCSI
Authors: Hung Ling‐Hong , Samudrala Ram
Published: January 2003

PsiCSI is a highly accurate and automated method of assigning secondary structure from NMR data, which is a useful intermediate step in the determination of tertiary structures. The method combines information from chemical shifts and protein sequence using three layers of neural networks. Training and testing was performed on a suite of 92 proteins (9437 residues) with known secondary and tertiary structure. Using a stringent cross‐validation procedure in which the target and homologous proteins were removed from the databases used for training the neural networks, an average 89% Q3 accuracy (per residue) was observed. This is an increase of 6.2% and 5.5% (representing 36% and 33% fewer errors) over methods that use chemical shifts (CSI) or sequence information (Psipred) alone. In addition, PsiCSI improves upon the translation of chemical shift information to secondary structure (Q3 = 87.4%) and is able to use sequence information as an effective substitute for sparse NMR data (Q3 = 86.9% without 13C shifts and Q3 = 86.8% with only Hα shifts available). Finally, errors made by PsiCSI almost exclusively involve the interchange of helix or strand with coil and not helix with strand (<2.5 occurrences per 10000 residues). The automation, increased accuracy, absence of gross errors, and robustness with regards to sparse data make PsiCSI ideal for high‐throughput applications, and should improve the effectiveness of hybrid NMR/de novo structure determination methods. A Web server is available for users to submit data and have the assignment returned.
Stabilization of a pH‐sensitive apoptosis‐linked coiled coil through single point mutations
Authors: Dutta Kaushik , Engler Frank A. , Cotton Levaughn , Alexandrov Andrei , Bedi Gurrinder S. , Colquhoun Jennifer , Pascal Steven M.
Published: January 2003

The apoptosis‐associated Par‐4 protein has been implicated in cancers of the prostate, colon, and kidney, and in Alzheimer's and Huntington's diseases, among other neurodegenerative disorders. Previously, we have shown that a peptide from the Par‐4 C‐terminus, which is responsible for Par‐4 self‐association as well as interaction with all currently identified effector molecules, is natively unfolded at neutral pH, but forms a tightly associated coiled coil at acidic pH and low temperature. Here, we have alternately mutated the two acidic residues predicted to participate in repulsive electrostatic interactions at the coiled coil interhelical interface. Analysis of circular dichroism spectra reveals that a dramatic alteration of the folding/unfolding equilibrium of this peptide can be effected through directed‐point mutagenesis, confirming that the two acidic residues are indeed key to the pH‐dependent folding behavior of the Par‐4 coiled coil, and further suggesting that alleviation of charge repulsion through exposure to either a low pH microenvironment or an electrostatically complementary environment may be necessary for efficient folding of the Par‐4 C‐terminus.
Non‐animal origin of animal thioredoxin reductases: Implications for selenocysteine evolution and evolution of protein function through carboxy‐terminal extensions
Authors: Novoselov Sergey V. , Gladyshev Vadim N.
Published: January 2003

Thioredoxin reductase (TR) and thioredoxin constitute a major cellular redox system present in all organisms. In contrast to a single form of thioredoxin, there are two TR types: One (bacterial type or small TR) is present in bacteria, archaea, plants, and most unicellular eukaryotes, whereas the second (animal or large TR) is only found in animals and typically contains a carboxy‐terminal penultimate selenocysteine encoded by TGA. Surprisingly, we detected sequences of large TRs in various unicellular eukaryotes. Moreover, green algae Chlamydomonas reinhardtii had both small and large TRs, with the latter being a selenoprotein, but no examples of horizontal gene transfer from animals to the green algae could be detected. In addition, phylogenetic analyses revealed that large TRs formed a subgroup of lower eukaryotic glutathione reductases (GRs). The data suggest that the large TR evolved in a lower eukaryote capable of selenocysteine insertion rather than in an animal. The enzyme appeared to evolve by a carboxy‐terminal extension of GR such that the resulting carboxy‐terminal glutathionelike peptide became an intramolecular substrate for GR and a reductant for thioredoxin. Subsequently, small TRs were lost in an organism that gave rise to animals, large TRs were lost in plants and fungi, and selenocysteine/cysteine replacements took place in some large TRs. Our data implicate carboxy‐terminal extension of proteins as a general mechanism of evolution of new protein function.
NMR solution structure of the activation domain of human procarboxypeptidase A2
Authors: Jiménez M. Angeles , Villegas Virtudes , Santoro Jorge , Serrano Luis , Vendrell Josep , Avilés Francesc X. , Rico Manuel
Published: January 2003

The activation domain of human procarboxypeptidase A2, ADA2h, is an 81‐residue globular domain released during the proteolytic activation of the proenzyme. The role of this and other similar domains as assistants of the correct folding of the enzyme is not fully understood. The folding pathway of ADA2h was characterized previously, and it was also observed that under certain conditions it may convert into amyloid fibrils in vitro. To gain insight into these processes, a detailed description of its three‐dimensional structure in aqueous solution is required so that eventual changes could be properly monitored. A complete assignment of the 1H and 15N resonances of ADA2h was performed, and the solution structure, as derived from a set of 1688 nonredundant constraints, is very well defined (pairwise backbone RMSD = 0.67 ± 0.17 Å for residues 10–80). The structure is composed of two antiparallel α‐helices comprising residues 19–32 and 58–69 packed on the same side of a three‐stranded β‐sheet spanning residues 10–15, 50–55, and 73–75. The global fold for the isolated human A2 activation domain is very similar to that of porcine carboxypeptidase B, as well as to the structure of the domain in the crystal of the intact human proenzyme. The observed structural differences relative to the intact human proenzyme are located at the interface between the activation domain and the enzyme and can be related with the activation mechanism. The backbone amide proton exchange behavior of ADA2h was also examined. The global free energy of unfolding obtained from exchange data of the most protected amide protons at pH 7.0 and 298K is 4.9 ± 0.3 kcal.mole−1, in good agreement with the values determined by thermal or denaturant unfolding studies.
Motions and structural variability within toxins: Implication for their use as scaffolds for protein engineering
Authors: Gilquin Bernard , Bourgoin Marjorie , Ménez Renée , Le Du Marie‐Hélène , Servent Denis , Zinn‐Justin Sophie , Ménez André
Published: January 2003

Animal toxins are small proteins built on the basis of a few disulfide bonded frameworks. Because of their high variability in sequence and biologic function, these proteins are now used as templates for protein engineering. Here we report the extensive characterization of the structure and dynamics of two toxin folds, the “three‐finger” fold and the short α/β scorpion fold found in snake and scorpion venoms, respectively. These two folds have a very different architecture; the short α/β scorpion fold is highly compact, whereas the “three‐finger” fold is a β structure presenting large flexible loops. First, the crystal structure of the snake toxin α was solved at 1.8‐Å resolution. Then, long molecular dynamics simulations (10 ns) in water boxes of the snake toxin α and the scorpion charybdotoxin were performed, starting either from the crystal or the solution structure. For both proteins, the crystal structure is stabilized by more hydrogen bonds than the solution structure, and the trajectory starting from the X‐ray structure is more stable than the trajectory started from the NMR structure. The trajectories started from the X‐ray structure are in agreement with the experimental NMR and X‐ray data about the protein dynamics. Both proteins exhibit fast motions with an amplitude correlated to their secondary structure. In contrast, slower motions are essentially only observed in toxin α. The regions submitted to rare motions during the simulations are those that exhibit millisecond time‐scale motions. Lastly, the structural variations within each fold family are described. The localization and the amplitude of these variations suggest that the regions presenting large‐scale motions should be those tolerant to large insertions or deletions.
Turn stability in β‐hairpin peptides: Investigation of peptides containing 3:5 type I G1 bulge turns
Authors: Blandl Tamas , Cochran Andrea G. , Skelton Nicholas J.
Published: January 2003

The turn‐forming ability of a series of three‐residue sequences was investigated by substituting them into a well‐characterized β‐hairpin peptide. The starting scaffold, bhpW, is a disulfide‐cyclized 10‐residue peptide that folds into a stable β‐hairpin with two antiparallel strands connected by a two‐residue reverse turn. Substitution of the central two residues with the three‐residue test sequences leads to less stable hairpins, as judged by thiol‐disulfide equilibrium measurements. However, analysis of NMR parameters indicated that each molecule retains a significant folded population, and that the type of turn adopted by the three‐residue sequence is the same in all cases. The solution structure of a selected peptide with a PDG turn contained an antiparallel β‐hairpin with a 3:5 type I + G1 bulge turn. Analysis of the energetic contributions of individual turn residues in the series of peptides indicates that substitution effects have significant context dependence, limiting the predictive power of individual amino acid propensities for turn formation. The most stable and least stable sequences were also substituted into a more stable disulfide‐cyclized scaffold and a linear β‐hairpin scaffold. The relative stabilities remained the same, suggesting that experimental measurements in the bhpW context are a useful way to evaluate turn stability for use in protein design projects. Moreover, these scaffolds are capable of displaying a diverse set of turns, which can be exploited for the mimicry of protein loops or for generating libraries of reverse turns.
On the evaluation and optimization of protein X‐ray structures for pKa calculations
Authors: Nielsen Jens Erik , McCammon J. Andrew
Published: January 2003

The calculation of the physical properties of a protein from its X‐ray structure is of importance in virtually every aspect of modern biology. Although computational algorithms have been developed for calculating everything from the dynamics of a protein to its binding specificity, only limited information is available on the ability of these methods to give accurate results when used with a particular X‐ray structure. We examine the ability of a pKa calculation algorithm to predict the proton‐donating residue in the catalytic mechanism of hen egg white lysozyme. We examine the correlation between the ability of the pKa calculation method to obtain the correct result and the overall characteristics of 41 X‐ray structures such as crystallization conditions, resolution, and the output of structure validation software. We furthermore examine the ability of energy minimizations (EM), molecular dynamics (MD) simulations, and structure‐perturbation methods to optimize the X‐ray structures such that these give correct results with the pKa calculation algorithm. We propose a set of criteria for identifying the proton donor in a catalytic mechanism, and demonstrate that the application of these criteria give highly accurate prediction results when using unmodified X‐ray structures. More specifically, we are able to successfully identify the proton donor in 85% of the X‐ray structures when excluding structures with crystal contacts near the active site. Neither the use of the overall characteristics of the X‐ray structures nor the optimization of the structure by EM, MD, or other methods improves the results of the pKa calculation algorithm. We discuss these results and their implications for the design of structure‐based energy calculation algorithms in general.
Amino acid sequence and homology modeling of obtustatin, a novel non‐RGD‐containing short disintegrin isolated from the venom ofVipera lebetina obtusa
Authors: Moreno‐Murciano M. Paz , Monleón Daniel , Calvete Juan J. , Celda Bernardo , Marcinkiewicz Cezary
Published: January 2003

Disintegrins represent a group of cysteine‐rich peptides occurring inCrotalidaeandViperidaesnake venoms, and are potent antagonists of several integrin receptors. A novel disintegrin, obtustatin, was isolated from the venom of theVipera lebetina obtusaviper, and represents the first potent and selective inhibitor of the binding of integrin α1β1to collagen IV. The primary structure of obtustatin contains 41 amino acids and is the shortest disintegrin described to date. Obtustatin shares the pattern of cysteines of other short disintegrins. However, in contrast to known short disintegrins, the integrin‐binding loop of obtustatin is two residues shorter and does not express the classical RGD sequence. Using synthetic peptides, a KTS motif was identified as the integrin‐binding sequence. A three‐dimensional model of obtustatin, built by homology‐modeling structure calculations using different templates and alignments, strongly indicates that the novel KTS motif may reside at the tip of a flexible loop.
Low free energy cost of very long loop insertions in proteins
Authors: Scalley‐Kim Michelle , Minard Philippe , Baker David
Published: January 2003

Long insertions into a loop of a folded host protein are expected to have destabilizing effects because of the entropic cost associated with loop closure unless the inserted sequence adopts a folded structure with amino‐ and carboxy‐termini in close proximity. A loop entropy reduction screen based on this concept was used in an attempt to retrieve folded sequences from random sequence libraries. A library of long random sequences was inserted into a loop of the SH2 domain, displayed on the surface of M13 phage, and the inserted sequences that did not disrupt SH2 function were retrieved by panning using beads coated with a phosphotyrosine containing SH2 peptide ligand. Two sequences of a library of 2 × 108 sequences were isolated after multiple rounds of panning, and were found to have recovery levels similar to the wild‐type SH2 domain and to be relatively intolerant to further mutation in PCR mutagenesis experiments. Surprisingly, although these inserted sequences exhibited little nonrandom structure, they do not significantly destabilize the host SH2 domain. Additional insertion variants recovered at lower levels in the panning experiments were also found to have a minimal effect on the stability and peptide‐binding function of the SH2 domain. The additional level of selection present in the panning experiments is likely to involve in vivo folding and assembly, as there was a rough correlation between recovery levels in the phage‐panning experiments and protein solubility. The finding that loop insertions of 60–80 amino acids have minimal effects on SH2 domain stability suggests that the free energy cost of inserting long loops may be considerably less than polymer theory estimates based on the entropic cost of loop closure, and, hence, that loop insertion may have provided an evolutionary route to multidomain protein structures.
High‐pressure 1H NMR study of pressure‐induced structural changes in the heme environments of metcyanomyoglobins
Authors: Kitahara Ryo , Kato Minoru , Taniguchi Yoshihiro
Published: January 2003

The effect of pressure on the heme environment structure of sperm whale and horse heart metcyanomyoglobins was investigated up to 300 MPa by high‐pressure 1H NMR spectroscopy. Pressure‐induced changes in the distances between the observed protons and the heme iron atom were estimated from changes in the dipolar shift due to the paramagnetic effect on the protons. The changes showed that the heme peripheral structure as a whole was compressed by pressure; the movements of the protons in the heme peripheral residues were in the range of +0.16 to −0.54 Å/300 MPa. One‐dimensional compressibilities for the protons, excluding the protons of the distal His residue, were in the range of 1.0 × 10−4 to 6.1 × 10−4/MPa. The movements of the protons induced by pressure correlated well with the distance between the protons and cavities in the protein. The distal His residue (His 64) moved toward the outside of the heme pocket, but remained in the pocket even at 300 MPa. This movement was driven dominantly by a change in the dihedral angle around the Cα–Cβ rotational bond of the residue. Comparative work on horse heart metcyanomyoglobin implied that the conformational change of the His 64 imidazole ring was larger in the horse heart metcyanomyoglobin than in the sperm whale metcyanomyoglobin.
Skeletal Muscle Reflex in Heart Failure Patients
Authors: Scott Adam C. , Wensel Roland , Davos Constantinos H. , Georgiadou Panagiota , Kemp Michael , Hooper James , Coats Andrew J.S. , Piepoli Massimo F.
Published: January 2003

Background—

An important role of the increased stimulation of skeletal muscle ergoreceptors (intramuscular afferents sensitive to products of muscle work) in the genesis of symptoms of exertion intolerance in chronic heart failure (CHF) has been proposed. With the use of selective infusions and dietary manipulation methods, we sought to identify the role of H
+
, K
+
, lactate, and peripheral hemodynamics on ergoreflex overactivation.

Methods and Results—

Ten stable CHF patients (aged 67.9±2.5 years, peak oxygen uptake 16.3±1.2 mL · kg
−1
· min
−1
) and 10 age-matched and sex-matched healthy subjects were studied. The ergoreflex contribution to ventilation was assessed by post-handgrip regional circulatory occlusion (PH-RCO) and computed as the difference in ventilation between PH-RCO and a control run without PH-RCO. This test was performed on 6 separate occasions. On each occasion a different chemical was infused (insulin, sodium nitroprusside, sodium bicarbonate, dopamine, or saline) or a 36-hour glucose-free diet was undertaken before the test. During all stages of the protocol, the local muscular blood effluent concentrations of H
+
, K
+
, glucose, and lactate were assessed. An ergoreflex effect on the ventilatory response was seen in patients (versus control subjects) during the saline infusions (6.7±2.3 L/min versus −0.1±0.5 L/min,
P
<0.01). The only intervention to significantly lower the ergoreflex was sodium bicarbonate (0.4±0.3 L/min versus −0.2±0.4 L/min in control subjects,
P
=NS; versus saline
P
<0.05), which also reduced H
+
concentration during exercise (47.4±1.3 versus 50.0±1.4 nmol/L on saline,
P
<0.05).

Conclusion—

A reduction of the H
+
concentration by infusion of sodium bicarbonate abolishes the increased ergoreceptor activity in CHF, suggesting a role of H
+
in ergoreflex activation, either directly or indirectly.
Inhibition of Experimental Intimal Thickening in Mice Lacking a Novel G-Protein–Coupled Receptor
Authors: Tsukada Shuichi , Iwai Masaru , Nishiu Jun , Itoh Makoto , Tomoike Hitonobu , Horiuchi Masatsugu , Nakamura Yusuke , Tanaka Toshihiro
Published: January 2003

Background—

Vascular restenosis attributable to intimal thickening remains a major problem after percutaneous transluminal coronary angioplasty (PTCA).

Methods and Results—

Through differential-display analysis, we have identified a novel gene whose expression was increased after catheter injury of rabbit aorta. The gene that is expressed predominantly in vascular smooth muscle cells encodes a novel protein with 7 transmembrane domains, and we termed it
ITR
(intimal thickness–related receptor). The
ITR
sequence contains a motif common to the Rhodopsin-like GPCR (G-protein-coupled receptor) superfamily. In vivo analyses of this gene revealed that expression of ITR protein increased with intimal thickening induced by cuff placement around murine femoral artery. Furthermore,
ITR
-knockout mice were found to be resistant to this experimental intimal thickening.

Conclusions—

ITR
thus seems to be a novel receptor that may play a role in vascular remodeling and that may represent a good target for development of drugs in the prevention of vascular restenosis.