bluuebunny/crossref_metadata_2025 huggingface dataset:
Family history of prostate cancer and obesity in relation to high‐grade disease and extraprostatic extension in young men with prostate cancer
Authors: Rohrmann Sabine , Roberts William W. , Walsh Patrick C. , Platz Elizabeth A.
Published: March 2003

Background

Little is known about predictors of prostate cancer severity in young men. Therefore, we examined whether family history and obesity influence risk of high‐grade disease and extraprostatic extension in men < 55‐years old.

Methods

Four hundred ninety‐eight men aged < 55 years who had had a radical prostatectomy (1992–1999) by one surgeon were mailed a survey in 2000 to assess family history of PCa and anthropometrics. Body mass index (BMI = kg/m2) was calculated as an indicator of obesity. Logistic regression was used to compute odds ratios (OR) for high‐grade disease (Gleason score ≥ 7) and extraprostatic extension.

Results

Of the 363 respondents, 35.8% had at least one first‐degree relative with PCa. Men with a family history were younger at surgery than those without a family history (48.8 vs. 50.1 years, P < 0.001). After controlling for age, cigarette smoking, and race/ethnicity, men with an affected father had a lower risk of high‐grade disease compared to those without an affected father (OR = 0.42, 95% CI 0.23–0.76). Risk of high‐grade disease increased with increasing BMI, especially in men < 50‐years old (P‐trend = 0.02). Family history and BMI were not clearly associated with extraprostatic extension.

Conclusions

After taking into account a younger age at presentation among men with a family history, young men with a family history of PCa were less likely to have high‐grade disease. Obesity may be associated with a poorer histology in young men with PCa, especially in men younger than 50 years of age. Prostate 55: 140–146, 2003. © 2003 Wiley‐Liss, Inc.
Differential expression and/or activation of P38MAPK, erk1/2, and jnk during the initiation and progression of prostate cancer
Authors: Uzgare Aarti R. , Kaplan Paula J. , Greenberg Norman M.
Published: March 2003

Background

Members of the mitogen‐activated protein kinase (MAPK) family are capable of transducing signals from a wide variety of stimuli, including growth factors, G‐protein coupled receptors, and cytokines that are likely to play a role in the initiation and/or progression of prostate cancer.

Methods

The expression and activation of three members of the MAPK family, namely, erk, jnk, and p38MAPK was examined using Western blotting and immunohistochemistry during tumor progression in a transgenic mouse model for prostate cancer.

Results

Activation of p38MAPK was significantly elevated (2.3‐fold) in well‐differentiated prostatic tumors compared to normal controls. Furthermore, prostatic intraepithelial neoplastic (PIN) lesions expressing activated p38MAPK were observed to be proliferative rather than apoptotic. Expression of activated erk1/2 also preferentially co‐located to a sub‐population of epithelial cells within PIN lesions that correlated with Ki67 expression. In dramatic contrast, activated forms of erk1/2, jnk, and p38MAPK were reduced or absent in late stage adenocarcinomas and metastatic deposits.

Conclusions

Erk1/2, jnk, and p38MAPKs are differentially expressed and/or activated during prostate cancer progression. Activation of both erk1/2 and p38MAPK occurs concomitant with prostatic epithelial cell proliferation and the initiation of prostate cancer while inactivation is contemporaneous with the emergence of the poorly differentiated metastatic and androgen‐independent phenotype. Prostate 55: 128–139, 2003. © 2003 Wiley‐Liss, Inc.
Ca2+‐activated Cl− channel currents in rat ventral prostate epithelial cells
Authors: Kim Sung Joon , Shin Sun Young , Lee Ji Eun , Kim Jun Hee , Uhm Dae‐Yong
Published: March 2003

Background

In many epithelial tissues, the Cl− efflux via Ca2+‐activated Cl− channels (ClCa) play a key role for the fluid secretion. To elucidate the mechanism of prostatic fluid secretion, the properties of whole‐cell chloride conductance were investigated.

Materials and Methods

Rat prostate secretory epithelial cells (RPSECs) were isolated by collagenase treatment, and were used for the whole‐cell voltage clamp. Both extra‐ and intracellular monovalent cations were replaced by N‐methyl‐D‐glucamate to record the Cl− current selectively.

Results

A bath application of Ca2+‐ionophore, ionomycin (0.2 μM), increased the membrane conductance with outwardly rectifying voltage‐dependence. On step‐like depolarization from −60 to +80 mV (500 msec), the ionomycin‐induced current showed slowly activating kinetics, a known property of ClCa current (ICl(Ca)) of other tissues. The relative permeability of ClCa to various anions was calculated from the reversal potentials measured under a total replacement of extracellular Cl− with various anions, and the relative order of permeability was SCN−>I−>Br−>Cl−>>gluconate. The amplitude of ICl(Ca) was decreased by various anion channel blockers: niflumic acid (100 μM), DPC (100 μM), DIDS (1 mM), and NPPB (200 μM).

Conclusions

RPSECs have ClCa that may provide Cl− efflux pathways for the exocrine secretions of the prostate. Prostate 55: 118–127, 2003. © 2003 Wiley‐Liss, Inc.
Negative bacterial polymerase chain reaction (PCR) findings in prostate tissue from patients with symptoms of chronic pelvic pain syndrome (CPPS) and localized prostate cancer
Authors: Leskinen Markku J. , Rantakokko‐Jalava Kaisu , Manninen Raija , Leppilahti Mikael , Marttila Timo , Kylmälä Timo , Tammela Teuvo L. J.
Published: March 2003

Background

The etiology of chronic pelvic pain syndrome (CPPS) remains obscure. Although, bacterial etiology has frequently been suggested, evidence of both bacterial involvement in CPPS and the presence of normal bacterial flora in the prostate remain uncertain.

Materials and Methods

We investigated the presence of bacterial DNA using polymerase chain reaction (PCR) techniques on prostatic tissue samples obtained in radical prostatectomy from 10 patients with moderate to severe symptoms of CPPS and 10 nonsymptomatic patients with localized prostate cancer. For symptom evaluation we used the National Institutes of Health‐Chronic Prostatitis Symptom Index (NIH‐CPSI).

Results

All but one sample were negative for bacterial DNA. The PCR from a symptomatic patient was reproducibly positive in 16S rDNA PCR but negative in 23S rDNA PCR. Bacterial DNA was found in only one out of two sample aliquots and cloning yielded different sequences in two PCR products.

Conclusions

A bacterial etiology for CPPS symptoms could not be demonstrated in patients with prostate cancer. The results also suggest that the prostate is unlikely to harbor bacterial normal flora. Prostate 55: 105–110, 2003. © 2003 Wiley‐Liss, Inc.
Registering α‐helices and β‐strands using backbone CH…O interactions
Authors: Singh S. Kumar , Babu M. Madan , Balaram P.
Published: March 2003

The possible occurrence of a novel helix terminating structural motif in proteins involving a stabilizing short CH…O interaction has been examined using a dataset of 634 non‐homologous protein structures (≤2.0 Å). The search for this motif was prompted by the crystallographic characterization of a novel structural feature in crystals of a synthetic decapeptide in which extension of a Schellman motif led to the formation of a CH…O hydrogen bond between the T‐4 CαH and the T+1 CO groups, where T is the helix terminator adopting a left handed (αL) conformation. More than 100 such motifs with backbone conformation superposing well with the peptide examples were identified. In several examples, formation of this motif led to an approximately antiparallel arrangement of a helical segment with an extended β‐strand. Careful examination of these examples suggested the possibility of registering antiparallel arrangement of helices and strands by means of backbone CH…O interactions with a regular periodicity. Model building resulted in the generation of idealized αβ and βα motifs, which can then be generalized to higher‐order repetitive structures. Inspection of the antiparallel αβ motif revealed a significant propensity for Ser, Glu, and Gln residues at the T‐4 position resulting in further stabilization using an O…HN side‐chain–backbone hydrogen bond. Modeling studies revealed ready accommodation of serine residues along the helix face that contacts the strand. The theoretically generated folds correspond to “open” polypeptide structures. Proteins 2003;51:167–171. © 2003 Wiley‐Liss, Inc.
Pharmacophore‐based molecular docking to account for ligand flexibility
Authors: Joseph‐McCarthy Diane , Thomas Bert E. , Belmarsh Michael , Moustakas Demetri , Alvarez Juan C.
Published: March 2003

Rapid computational mining of large 3D molecular databases is central to generating new drug leads. Accurate virtual screening of large 3D molecular databases requires consideration of the conformational flexibility of the ligand molecules. Ligand flexibility can be included without prohibitively increasing the search time by docking ensembles of precomputed conformers from a conformationally expanded database. A pharmacophore‐based docking method whereby conformers of the same or different molecules are overlaid by their largest 3D pharmacophore and simultaneously docked by partial matches to that pharmacophore is presented. The method is implemented in DOCK 4.0. Proteins 2003;51:172–188. © 2003 Wiley‐Liss, Inc.
Molecular dynamics simulations of a protein model in uniform and elongational flows
Authors: Lemak Alexandre S. , Lepock James R. , Chen Jeff Z. Y.
Published: March 2003

We present a molecular dynamics study of the conformational deformation of a minimalist β‐barrel protein model in two different types of hydrodynamic flows: uniform and elongational. We investigate the characteristics of protein stretching, paying special attention to the unfolding intermediate states and their relationship to the protein folding/unfolding problem. In the uniform flow simulations, one end of the modeled protein was tethered to a fixed point in space and the forced unfolding process was observed. The unfolding takes place via a few stages involving one or two intermediate states, depending on which end is tethered. The calculated force‐extension curves show plateau regimes and hysteresis as the protein is stretched and refolded, in qualitative agreement with the experimental measurements. The physical behavior observed in our numerical simulations of the forced unfolding in an elongational flow is very different from that in uniform flow. The protein unfolds abruptly from the globular state to a fully stretched state without going through any observable intermediate states. From these observation, we stress that protein unfolding pathways under the influence of an external force are highly dependent on the mechanism of the exerted force. Proteins 2003;51:224–235. © 2003 Wiley‐Liss, Inc.
Hierarchical protein folding pathways: A computational study of protein fragments
Authors: Haspel Nurit , Tsai Chung‐Jung , Wolfson Haim , Nussinov Ruth
Published: March 2003

We have previously presented a building block folding model. The model postulates that protein folding is a hierarchical top‐down process. The basic unit from which a fold is constructed, referred to as a hydrophobic folding unit, is the outcome of combinatorial assembly of a set of “building blocks.” Results obtained by the computational cutting procedure yield fragments that are in agreement with those obtained experimentally by limited proteolysis. Here we show that as expected, proteins from the same family give very similar building blocks. However, different proteins can also give building blocks that are similar in structure. In such cases the building blocks differ in sequence, stability, contacts with other building blocks, and in their 3D locations in the protein structure. This result, which we have repeatedly observed in many cases, leads us to conclude that while a building block is influenced by its environment, nevertheless, it can be viewed as a stand‐alone unit. For small‐sized building blocks existing in multiple conformations, interactions with sister building blocks in the protein will increase the population time of the native conformer. With this conclusion in hand, it is possible to develop an algorithm that predicts the building block assignment of a protein sequence whose structure is unknown. Toward this goal, we have created sequentially nonredundant databases of building block sequences. A protein sequence can be aligned against these, in order to be matched to a set of potential building blocks. Proteins 2003;51:203–215. © 2003 Wiley‐Liss, Inc.
Automated generation of MCSS‐derived pharmacophoric DOCK site points for searching multiconformation databases
Authors: Joseph‐McCarthy Diane , Alvarez Juan C.
Published: March 2003

All docking methods employ some sort of heuristic to orient the ligand molecules into the binding site of the target structure. An automated method, MCSS2SPTS, for generating chemically labeled site points for docking is presented. MCSS2SPTS employs the program Multiple Copy Simultaneous Search (MCSS) to determine target‐based theoretical pharmacophores. More specifically, chemically labeled site points are automatically extracted from selected low‐energy functional‐group minima and clustered together. These pharmacophoric site points can then be directly matched to the pharmacophoric features of database molecules with the use of either DOCK or PhDOCK to place the small molecules into the binding site. Several examples of the ability of MCSS2SPTS to reproduce the three‐dimensional pharmacophoric features of ligands from known ligand–protein complex structures are discussed. In addition, a site‐point set calculated for one human immunodeficiency virus 1 (HIV1) protease structure is used with PhDOCK to dock a set of HIV1 protease ligands; the docked poses are compared to the corresponding complex structures of the ligands. Finally, the use of an MCSS2SPTS‐derived site‐point set for acyl carrier protein synthase is compared to the use of atomic positions from a bound ligand as site points for a large‐scale DOCK search. In general, MCSS2SPTS‐generated site points focus the search on the more relevant areas and thereby allow for more effective sampling of the target site. Proteins 2003;51:189–202. © 2003 Wiley‐Liss, Inc.
Subunit E of mitochondrial ATP synthase: A bioinformatic analysis reveals a phosphopeptide binding motif supporting a multifunctional regulatory role and identifies a related human brain protein with the same motif
Authors: Hong Sangjin , Pedersen Peter L.
Published: March 2003

The mitochondrial adenosine triphosphate (ATP) synthase is located in the inner membrane and consists of at least 16 subunit types in animals, one of which is subunit e, the function of which is not clearly defined. A highly homologous protein is located in the nucleus and named progesterone receptor binding protein (RBF), to designate its role in this organelle. In addition, the expression level of subunit e in mammalian cells fluctuates greatly and is induced by certain carcinogens and elevated in liver cancers. Because these previous observations suggested to us that subunit e may play multifunctional regulatory roles, we employed a bioinformatic approach to test this view. First, from sequence alignment studies, secondary structure analyses, and basic local alignment search tool (BLAST) searches, we concluded that mitochondrial subunit e and the homologous nuclear protein RBF are most likely the same protein. Second, we examined the known sequence and structure of one of the most common multifunctional cell regulatory proteins, the 14‐3‐3 protein, involved in phosphopeptide binding, and deduced that it has an apparent binding motif (—KX6R––—RY—). Third, from careful examination of the conserved residues within all subunit e sequences in the database, we discovered that this protein has a comparable binding motif (—RY––—KX6R—). Finally, in a BLAST search for additional homologs of subunit e, we found a human brain protein, KIAA1578, the C‐terminal 30 amino acids of which are identical to those of human subunit e. This protein also contains a potential phosphopeptide binding motif. In summary, these studies provide support for the view that subunit e is a multifunctional cell regulator involved in cell signaling, and implicate the involvement of the KIAA1578 protein in cell signaling as well. These studies suggest also that, while functioning as a subunit of mitochondrial ATP synthases, subunit e may help regulate these complexes by binding to phosphopeptides within one or more of the other subunit types. Proteins 2003;51:155–161. © 2003 Wiley‐Liss, Inc.
Minimal model for studying prion‐like folding pathways
Authors: Chen Jeff Z. Y. , Lemak Alexander S. , Lepock James R. , Kemp Josh P.
Published: March 2003

The Monte Carlo technique is used to simulate the energy landscape and the folding kinetics of a minimal prion‐like protein model. We show that the competition between hydrogen‐bonding and hydrophobic interactions yields two energetically favored secondary structures, an α‐helix and a β‐hairpin. Folding simulations indicate that the probability of reaching the α‐helix form from a denatured random conformation is much higher than the probability of reaching the β‐sheet form, even though the β‐sheet has a lower energy. The existence of a lower energy β‐sheet state gives the possibility for the normal α‐helix structure to take a structural transformation into the β‐sheet structure under external influences. Proteins 2003;51:283–288. © 2003 Wiley‐Liss, Inc.
Chain length is the main determinant of the folding rate for proteins with three‐state folding kinetics
Authors: Galzitskaya Oxana V. , Garbuzynskiy Sergiy O. , Ivankov Dmitry N. , Finkelstein Alexei V.
Published: March 2003

We demonstrate that chain length is the main determinant of the folding rate for proteins with the three‐state folding kinetics. The logarithm of their folding rate in water (kf) strongly anticorrelates with their chain length L (the correlation coefficient being −0.80). At the same time, the chain length has no correlation with the folding rate for two‐state folding proteins (the correlation coefficient is −0.07). Another significant difference of these two groups of proteins is a strong anticorrelation between the folding rate and Baker's “relative contact order” for the two‐state folders and the complete absence of such correlation for the three‐state folders. Proteins 2003;51:162–166. © 2003 Wiley‐Liss, Inc.
Impact of the tail and mutations G131V and M129V on prion protein flexibility
Authors: Santini Sébastien , Claude Jean‐Baptiste , Audic Stéphane , Derreumaux Philippe
Published: March 2003

Within the “protein‐only” hypothesis, a detailed mechanism for the conversion of a α‐helix to β‐sheet structure is unclear. We have investigated the effects of the tail 90–123 and the point mutations G131V and M129V on prion protein conformational plasticity at neutral pH. Molecular dynamics simulations show that the dynamics of the core 124–226 is essentially independent of the tail and that the point mutation G131V does not affect PrP thermodynamic stability. Both mutations, however, enhance the flexibility of residues that participate in the two‐step process for prion propagation. They also extend the short β‐sheet in the normal protein into a larger sheet at neutral pH. This finding suggests a critical role of the tail for triggering the topological change. Proteins 2003;51:258–265. © 2003 Wiley‐Liss, Inc.
Kinetics of cytochrome C folding: Atomically detailed simulations
Authors: Cárdenas Alfredo E. , Elber Ron
Published: March 2003

The vast range of time scales (from nanoseconds to seconds) during protein folding is a challenge for experiments and computations. To make concrete predictions on folding mechanisms, atomically detailed simulations of protein folding, using potentials derived from chemical physics principles, are desired. However, due to their computational complexity, straightforward molecular dynamics simulations of protein folding are impossible today. An alternative algorithm is used that makes it possible to compute approximate atomically detailed long time trajectories (the Stochastic Difference Equation in Length). This algorithm is used to compute 26 atomically detailed folding trajectories of cytochrome c (a millisecond process). The early collapse of the protein chain (with marginal formation of secondary structure), and the earlier formation of the N and C helices (compare to the 60's helix) are consistent with the experiment. The existence of an energy barrier upon entry to the molten globule is examined as well. In addition to (favorable) comparison to experiments, we show that non‐native contacts drive the formation of the molten globule. In contrast to popular folding models, the non‐native contacts do not form off‐pathway kinetic traps in cytochrome c. Proteins 2003;51:245–257. © 2003 Wiley‐Liss, Inc.
The catalytic mechanism of Drosophila alcohol dehydrogenase: Evidence for a proton relay modulated by the coupled ionization of the active site Lysine/Tyrosine pair and a NAD+ ribose OH switch
Authors: Koumanov Assen , Benach Jordi , Atrian Silvia , Gonzàlez‐Duarte Roser , Karshikoff Andrey , Ladenstein Rudolf
Published: March 2003

The ionization properties of the active site residues in Drosophila lebanonensis alcohol dehydrogenase (DADH) were investigated theoretically by using an approach developed to account for multiple locations of the hydrogen atoms of the titratable and polar groups. The electrostatic calculations show that (a) the protonation/deprotonation transition of the binary complex of DADH is related to the coupled ionization of Tyr151 and Lys155 in the active site and (b) the pH dependence of the proton abstraction is correlated with a reorganization of the hydrogen bond network in the active site. On this basis, a proton relay mechanism for substrate dehydrogenation is proposed in which the O2′ ribose hydroxyl group from the coenzyme has a key role and acts as a switch. The proton relay chain includes the active site catalytic residues, as well as a chain of eight water molecules that connects the active site with the bulk solvent. Proteins 2003;51:289–298. © 2003 Wiley‐Liss, Inc.
Non‐intertwined binary patterns of hydrophobic/nonhydrophobic amino acids are considerably better markers of regular secondary structures than nonconstrained patterns
Authors: Hennetin Jérôme , Le Tuan Khanh , Canard Luc , Colloc'h Nathalie , Mornon Jean‐Paul , Callebaut Isabelle
Published: March 2003

Patterns of hydrophobic and hydrophilic residues (binary patterns) play an important role in protein architecture and can be roughly categorized into two classes regarding their preferential participation in α‐helices or β‐strands. However, a single binary pattern can be embedded into different longer patterns carrying opposite structural information and thus cannot be as much informative as expected. Here, we consider conditional binary patterns, or hydrophobic clusters, whose existence is conditioned by the presence of a minimum number of nonhydrophobic residues, called the connectivity distance, that separate two hydrophobic amino acids assumed to belong to two distinct patterns. Conditional binary patterns are distinct from simple ones in that they are not intertwined, i.e., they can not include or be included in other conditional patterns and therefore carry a much more differentiated information, in particular being dramatically better correlated with regular secondary structures (especially β ones). The distribution of these nonintertwined binary patterns in natural proteins was assessed relative to randomness, evidencing the structural bricks that are favored and disfavored by evolutionary selection. Several connectivity distances as well as several hydrophobic alphabets were tested, evidencing the clear superiority of a connectivity distance of 4, which mimics the minimum current length of loops in globular domains, and of the VILFMYW alphabet, selected from structural data (secondary structure propension and Voronoï tesselation), in highlighting fundamental properties of protein folds. Proteins 2003;51:236–244. © 2003 Wiley‐Liss, Inc.
Conservation and amyloid formation: A study of the gelsolin‐like family
Authors: Benyamini Hadar , Gunasekaran K. , Wolfson Haim , Nussinov Ruth
Published: March 2003

The mechanism through which globular proteins transform into amyloid fibrils is still not understood. Here we analyze the structure and sequence conservation to assess the differential stability of segments from two structurally related protein families: the amyloidogenic gelsolin‐like and its structurally related cofilin‐like. The two families belong to the actin depolymerizing proteins, with a central β‐sheet stacked between 2 and 4 α‐helices. Although sequentially remote, the two families share regions of high and low conservation and stability. Our results show a highly conserved hydrophobic and aromatic cluster, located at a central buried β‐hairpin. The geometry of the aromatic residues with respect to each other is strictly conserved, suggesting involvement in strand registering and β‐sheet stabilization. Consistent with experiment, we find a region of weak conservation and stability at one of the exposed β‐strands (strand B in the gelsolin‐like family). This region was recently found to be affected by a point mutation‐mediated destabilization of the human gelsolin domain 2, which facilitates the first proteolytic event in the formation of the amyloidogenic fragment. Thus, both experimental and computational conservation analyses suggest that this unstable region may constitute a first step in amyloid formation. Our analysis uses a recently developed multiple‐structure comparison algorithm in which molecules are aligned simultaneously. Proteins 2003;51:266–282. © 2003 Wiley‐Liss, Inc.
Large contact surface interactions between proteins detected by time series analysis methods: Case study on C‐phycocyanins
Authors: Giuliani Alessandro , Benigni Romualdo , Colafranceschi Mauro , Chandrashekar Indu , Cowsik Sudha M.
Published: March 2003

A purely sequence‐dependent approach to the modeling of protein–protein interaction was applied to the study of C‐phycocyanin αβ dimers. The interacting pairs (α and β subunits) share an almost complete structural homology, together with a general lack of sequence superposition; thus, they constitute a particularly relevant example for protein–protein interaction prediction. The present analysis is based on a description posited at an intermediate level between sequence and structure, that is, the hydrophobicity patterning along the chains. Based on the description of the sequence hydrophobicity patterns through a battery of nonlinear tools (recurrence quantification analysis and other sequence complexity descriptors), we were able to generate an explicit equation modeling α and β monomers interaction; the model consisted of canonical correlation between the hydrophobicity autocorrelation structures of the interacting pairs. The general implications of this holistic approach to the modeling of protein–protein interactions, which considers the protein primary structures as a whole, are discussed. Proteins 2003;51:299–310. © 2003 Wiley‐Liss, Inc.
Functional role for Tyr 31 in the catalytic cycle of chicken dihydrofolate reductase
Authors: Shrimpton Paul , Mullaney Alex , Allemann Rudolf K.
Published: March 2003

Despite much work, many key aspects of the mechanism of the dihydrofolate reductase (DHFR) catalyzed reduction of dihydrofolate remain unresolved. In bacterial forms of DHFR both substrate and water access to the active site are controlled by the conformation of the mobile M20 loop. In vertebrate DHFRs only one conformation of the residues corresponding to the M20 loop has been observed. Access to the active site was proposed to be controlled by residue 31. MD simulations of chicken DHFR complexed with substrates and cofactor revealed a closing of the side chain of Tyr 31 over the active site on binding of dihydrofolate. This conformational change was dependent on the presence of glutamate on the para‐aminobenzoylamide moiety of dihydrofolate. In its absence, the conformation remained open. Although water could enter the active site and hydrogen bond to N5 of dihydrofolate, indicating the feasibility of water as the proton donor, this was not controlled by the conformation of Tyr 31. The water accessibility of the active site was low for both conformations of Tyr 31. However, when hydride was transferred from NADPH to C6 of dihydrofolate before protonation, the average time during which water was found in hydrogen bonding distance to N5 of dihydrofolate in the active site increased almost fivefold. These results indicated that water can serve as the Broensted acid for the protonation of N5 of dihydrofolate during the DHFR catalyzed reduction. Proteins 2003;51:216–223. © 2003 Wiley‐Liss, Inc.
Disordering effect on optical absorption processes in CuInP2S6 layered ferrielectrics
Authors: Studenyak I. P. , Mitrovcij V. V. , Kovacs Gy. S. , Gurzan M. I. , Mykajlo O. A. , Vysochanskii Yu. M. , Cajipe V. B.
Published: March 2003

The optical absorption edge of CuInP2S6 crystals is studied between 77 and 573 K. The nature of optical transitions, resulting in absorption edge formation in ferrielectric and paraelectric phases, is elucidated. The temperature variation of the energy gap in the ferrielectric phase transition range and the temperature behavior of the Urbach absorption edge in the paraelectric phase are studied. The effect of temperature and structural disordering on the absorption edge energy position and shape is analyzed.
Structural modulation induced by the incommensurate antiferromagnetic phase transitionin ZnCr2Se4
Authors: Hidaka M. , Yoshimura M. , Tokiwa N. , Akimitsu J. , Park Yong Jun , Park Jae Hyun , Ji Sung Dae , Lee Ki Bong
Published: March 2003

The structural properties of normal‐type spinel ZnCr2Se4 have been studied as a function of temperature by means of X‐ray diffraction using synchrotron radiation. It is found that a structural phase transition from cubic to orthorhombic symmetry occurs at 22.5 K (Tc). It is also found that, below Tc, Se ions are cooperatively displaced in a pseudo‐tetragonal (001) plane. Since the Cr3+ ion has no orbital angular momentum, a CrSe6 octahedron is not distorted by a crystal field produced by surrounding Se2– anions. It is interpreted that the pseudo‐tetragonal displacements of Se ions are induced by magnetostriction among Cr3+ ions in CrSe2 chains, in which Cr ions share two Se2– with each other along 〈110〉.
ESR studies on Er3+‐doped YBiPt compound
Authors: Güner S. , Rameev B. , Aktaş B.
Published: March 2003

The semi‐metallic cubic compound YBiPt doped by Er3+ (4f11) has been studied by ESR technique between 4 and 300 K. X‐band and Q‐band measurements have been performed. The angular dependence of the ESR spectra on the crystal orientation with respect to the static magnetic field has been measured. Two anisotropic lines with hyperfine peaks coming from the interaction between electronic and nuclear spins of 167Er3+ (I = 7/2) isotopes have been observed below 30 K in the spectra. Computer modeling showed that these lines are the ESR signals from the quadruplet ground state of Er3+ ions in the cubic crystal field. The values of crystal field parameters B4 = –5.68 × 10–4 cm–1 and B6 = –6.64 × 10–6 cm–1 have been extracted. Also an isotropic line near g = 2 have been observed in both frequency bands. Dysonian lineshape of the spectra components due to the skin‐depth effect shows the conducting property of the sample under study. The temperature dependence of the spectra intensity obeys the well‐known Curie law for paramagnetism arising from the unpaired electrons of Er3+ ion.
Semi‐empirical descriptions of temperature dependences of band gaps in semiconductors
Authors: Pässler Roland
Published: March 2003

Starting from general foundations of the semi‐empirical theory of monotonic temperature dependences of band gaps in semiconductors, we devote ourselves in this article to further analytical development and applications of the power function model. On the basis of a detailed analytical study of asymptotic low and high temperature behaviors, including numerical comparisons for intermediate temperatures, we devise a novel analytical (higher order root) expression. Applications to least‐mean‐square fittings of fundamental band gap data available for a variety of group IV, III–V, and II–VI materials are shown to provide, both for regimes of moderate and large phonon dispersion, self‐consistent values for basic dispersion‐related parameters. This is essential for detailed comparisons of the power function model with other elaborate semi‐empirical models developed in last years, which differ above all by qualitatively different types of low temperature asymptotes. An exemplification for bulk samples of Si and GaAs shows that it is rather difficult to distinguish clearly between T → 0 asymptotes, [E(0) – E(T)] ∝ T p, that are controlled by system‐specific fractional exponents (2 < p < 3) and other dispersion‐related descriptions that admit exclusively quadratic asymptotes (p = 2). Novel high‐precision data for single quantum dot luminescence peak positions are found to give us better chances for distinguishing between qualitatively different types of low temperature asymptotes.
Ordering in undoped hexagonal AlxGa1–xN grown on sapphire (0001) with 0.09 < x < 0.247
Authors: Laügt M. , Bellet‐Amalric E. , Ruterana P. , Omnès F.
Published: March 2003

Multiple ordering has been observed both by high resolution X‐ray diffraction (HRXRD) and transmission electron microscopy (TEM) in AlxGa1–xN grown by low pressure metal‐organic vapor phase epitaxy (LP‐MOVPE) on sapphire (0001) with x varying from 9 to 25 percent. This is shown to take place even simultaneously in the same sample; beside the disordered alloy, AlGaN2 (1:1), and Al0.25Ga0.75N (3:1), there is an additional type which a quite large unit cell. In the latter, the c parameter is six times larger than that of the disordered alloy. Through the analysis of X‐ray diffraction data and comparison with TEM observations, a structure model is proposed. Taking into account the super‐lattice reflections intensity and symmetry, we conclude that this ordered phase contains two consecutive AlN monolayers in the 3.1 nm unit cell that corresponds to Al0.16Ga0.84N (10:2).
Morbidity measures in the presence of recurrent composite endpoints
Authors: Scott Martin , Möcks Joachim , Givens Sam , Köhler Walter , Maurer Jörg , Budde Michael
Published: March 2003

The analysis of recurrent event data in clinical trials presents a number of difficulties. The statistician is faced with issues of event dependency, composite endpoints, unbalanced follow‐up times and informative dropout. It is not unusual, therefore, for statisticians charged with responsibility for providing reliable and valid analyses to need to derive new methods specific to the clinical indication under investigation. One method is proposed that appears to have possible advantages over those that are often used in the analysis of recurrent event data in clinical trials. Based on an approach that counts periods of time with events instead of single event counts, the proposed method makes an adjustment for patient time on study and incorporates heterogeneity by estimating an individual per‐patient risk of experiencing a morbid event. Monte Carlo simulations demonstrate that, with use of a real clinical study data, the proposed method consistently outperforms other measures of morbidity. Copyright © 2003 John Wiley & Sons, Ltd.
Software for non‐linear mixed effects modelling: a review of several packages
Authors: Smith Michael K.
Published: March 2003

This paper gives some background information on what non‐linear mixed effects models are, why they can be useful in analysing repeated measures and what makes analysing such data challenging. Various software packages and routines are available to perform this kind of analysis, and this paper will compare and contrast these. Copyright © 2003 John Wiley & Sons, Ltd.
Case study in the Bayesian analysis of a cost‐effectiveness trial in the evaluation of health care technologies: Depression
Authors: Stevens John W. , O'Hagan Anthony , Miller Paul
Published: March 2003

We present a case study based on a depression study that will illustrate the use of Bayesian statistics in the economic evaluation of cost‐effectiveness data, demonstrate the benefits of the Bayesian approach (whilst honestly recognizing any deficiencies) with respect to frequentist methods, and provide details of using the methods, including computer code where appropriate. Copyright © 2003 John Wiley & Sons, Ltd.
Numerical methods for multicenter integrals for numerically defined basis functions applied in molecular calculations
Authors: Talman James D.
Published: March 2003

An alternative approach to using functions defined analytically as basis functions for molecular orbital calculations is to use functions defined numerically on some mesh. It is then necessary to evaluate various integrals involving products of such functions that are centered at different points in space, usually the nuclei. This article discusses in detail the problem of evaluating overlap and kinetic energy integrals, nuclear attraction three‐center integrals, and electron–electron repulsion four‐center integrals for such functions. The problem of evaluating these functions in translated coordinate systems, which arises in density functional theory applications, and the associated convergence problems are also discussed. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
First‐principles molecular dynamics simulations in a continuum solvent
Authors: Fattebert Jean‐Luc , Gygi François
Published: March 2003

A new continuum solvation model for density functional theory first‐principles simulations is presented in the context of plane wave Car–Parrinello molecular dynamics. The Poisson problem—with dielectric function representing the solvent effects—is solved by a compact finite difference method on a regular grid. The smoothness of the solute–solvent transition, and the density‐based solute cavity, provide good numerical properties to the model and allow for total energy calculations, reaction barriers calculations, and energy‐conserving molecular dynamics. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
High‐resolution detection of adulteration of maize oil using multi‐component compound‐specificδ13C values of major and minor components and discriminant analysis
Authors: Mottram Hazel R. , Woodbury Simon E. , Rossell J. Barry , Evershed Richard P.
Published: March 2003

Maize oil commands a premium price and is thus a target for adulteration with cheaper vegetable oils. Detection of this activity presents a particular challenge to the analyst because of the natural variability in the fatty acid composition of maize oils and because of their high sterol and tocopherol contents. This paper describes a method that allows detection of adulteration at concentrations of just 5% (m/m), based on the Mahalanobis distances of the principal component scores of theδ13C values of major and minor vegetable oil components. The method makes use of a database consisting ofδ13C values and relative abundances of the major fatty acyl components of over 150 vegetable oils. The sterols and tocopherols of 16 maize oils and 6 potential adulterant oils were found to be depleted in13C by a constant amount relative to the bulk oil. Moreover, since maize oil contains particularly high levels of sterols and tocopherols, theirδ13C values were not significantly altered when groundnut oil was added up to 20% (m/m) and it is possible to use the values for the minor components to predict the values that would be expected in a pure oil; therefore, comparison of the predicted values with those obtained experimentally allows adulteration to be detected. A refinement involved performing a discriminant analysis on theδ13C values of the bulk oil and the major fatty acids (16:0, 18:1 and 18:2) and using the Mahalanobis distances to determine the percentage of adulterant oil present. This approach may be refined further by including theδ13C values of the minor components in the discriminant analysis thereby increasing the sensitivity of the approach to concentrations at which adulteration would not be attractive economically. Copyright © 2003 John Wiley & Sons, Ltd.
Initial implementation of external accumulation liquid chromatography/electrospray ionization Fourier transform ion cyclotron resonance with automated gain control
Authors: Belov Mikhail E. , Rakov Vsevolod S. , Nikolaev Eugene N. , Goshe Michael B. , Anderson Gordon A. , Smith Richard D.
Published: March 2003

Capillary liquid chromatography (LC) separation coupled with external accumulation Fourier transform ion cyclotron resonance (FTICR) mass spectrometry has recently been demonstrated to have significant potential for proteomics research. Accumulation of an excessive space charge external to the FTICR cell ion trap has been shown to result in increased mass measurement error, undesirable ion discrimination and/or fragmentation, potentially causing misrepresentation or incorrect assignments of lower abundance peptides in the acquired mass spectra. In this work we report on the capability of data‐dependent adjustment of ion accumulation times in the course of LC separations, further referred to as automated gain control (AGC). Three different AGC approaches were evaluated based on the number of putative peptides from a tryptic digest of four casein proteins detected in the course of LC/FTICR separations. When compared with the conventional technique, AGC was found to increase, up to a factor of 3, the total number of peptides identified. Copyright © 2003 John Wiley & Sons, Ltd.
The shielding effect of glycerol against protein ionization in electrospray mass spectrometry
Authors: Mendes Maria Anita , Chies Jocelei Maria , Dias Ana Christina de Oliveira , Filho Spartacos Astofi , Palma Mario Sergio
Published: March 2003

Most commercial recombinant proteins used as molecular biology tools, as well as many academically made preparations, are generally maintained in the presence of high glycerol concentrations after purification to maintain their biological activity. The present study shows that larger proteins containing high concentrations of glycerol are not amenable to analysis using conventional electrospray ionization mass spectrometry (ESI‐MS) interfaces. In this investigation the presence of 25% (v/v) glycerol suppressed the signals of Taq DNA polymerase molecules, while 1% (v/v) glycerol suppressed the signal of horse heart myoglobin. The signal suppression was probably caused by the interaction of glycerol molecules with the proteins to create a shielding effect that prevents the ionization of the basic and/or acidic groups in the amino acid side chains. To overcome this difficulty the glycerol concentration was decreased to 5% (v/v) by dialyzing the Taq polymerase solution against water, and the cone voltage in the ESI triple‐quadrupole mass spectrometer was set at 80–130 V. This permitted observation of a mass spectrum that contained ions corresponding to protonation of up to 50% of the ionizable basic groups. In the absence of glycerol up to 85% of the basic groups of Taq polymerase became ionized, as observed in the mass spectrum at relatively low cone voltages. An explanation of these and other observations is proposed, based on strong interactions between the protein molecules and glycerol. For purposes of comparison similar experiments were performed on myoglobin, a small protein with 21 basic groups, whose ionization was apparently suppressed in the presence of 1% (v/v) glycerol, since no mass spectrum could be obtained even at high cone voltages. Copyright © 2003 John Wiley & Sons, Ltd.
Analysis of native and chemically modified oligonucleotides by tandem ion‐pair reversed‐phase high‐performance liquid chromatography/electrospray ionization mass spectrometry
Authors: Fountain Kenneth J. , Gilar Martin , Gebler John C.
Published: March 2003

Ion‐pair reversed‐phase high‐performance liquid chromatography (IP‐RP‐HPLC) was utilized in tandem with negative‐ion electrospray ionization time‐of‐flight mass spectrometry (ESI‐TOFMS) for the analysis of native and chemically modified oligonucleotides. Separation was performed on a 1.0 × 50 mm column packed with porous C18 sorbent with a particle size of 2.5 μm and an average pore diameter of 140 Å. A method was developed which maximizes both chromatographic separation and mass spectrometric sensitivity using an optimized buffer system containing triethylamine and 1,1,1,3,3,3‐hexafluoro‐2‐propanol with a methanol gradient. The ESI‐TOFMS tuning parameters were also optimized in order to minimize in‐source fragmentation and achieve the best sensitivity. Analyses of native, phosphorothioate, and guanine‐rich oligonucleotides were performed by LC/MS. Detection limits were at sub‐picomole levels with an average mass accuracy of 125 ppm. The described method allowed for the LC/MS analysis of oligonucleotides up to 110mer in length with little alkali cation adduction. Since sensitive detection of oligonucleotides was achieved with ultraviolet (UV) detection, we utilized a combination of UV‐MS for quantitation (UV) and characterization (MS) of oligonucleotides and their failure sequence fragments/metabolites. Copyright © 2003 John Wiley & Sons, Ltd.
Determination of patterns of biologically relevant aldehydes in exhaled breath condensate of healthy subjects by liquid chromatography/atmospheric chemical ionization tandem mass spectrometry
Authors: Andreoli Roberta , Manini Paola , Corradi Massimo , Mutti Antonio , Niessen Wilfried M. A.
Published: March 2003

A method for the simultaneous determination of several classes of aldehydes in exhaled breath condensate (EBC) was developed using liquid chromatography/atmospheric pressure chemical ionization tandem mass spectrometry (LC/APCI‐MS/MS). EBC is a biological matrix obtained by a relatively new, simple and noninvasive technique and provides an indirect assessment of pulmonary status. The measurement of aldehydes in EBC represents a biomarker of the effect of oxidative stress caused by smoke, disease, or strong oxidants like ozone. Malondialdehyde (MDA), acrolein, α,β‐unsaturated hydroxylated aldehydes [namely 4‐hydroxyhexenal (4‐HHE) and 4‐hydroxynonenal (4‐HNE)], and saturated aldehydes (n‐hexanal, n‐heptanal and n‐nonanal) were measured in EBC after derivatization with 2,4‐dinitrophenylhydrazine (DNPH). Atmospheric pressure chemical ionization of the analytes was obtained in positive‐ion mode for MDA, and in negative‐ion mode for acrolein, 4‐HHE, 4‐HNE, and saturated aldehydes. DNPH derivatives were separated on a C18 column using variable proportions of 20 mM aqueous acetic acid and methanol. Linearity was established over 4–5 orders of magnitude and limits of detection were in the 0.3–1.0 nM range. Intra‐day and inter‐day precision were in the 1.3–9.9% range for all the compounds. MDA, acrolein and n‐alkanals were detectable in all EBC samples, whereas the highly reactive 4‐HHE and 4‐HNE were found in only a few samples. Statistically significant higher concentrations of MDA, acrolein and n‐hexanal were found in EBC from smokers. Copyright © 2003 John Wiley & Sons, Ltd.