bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid protein domain assignment from amino acid sequence using predicted secondary structure
Authors: Marsden Russell L. , McGuffin Liam J. , Jones David T. 
Published: November 2002

AbstractThe elucidation of the domain content of a given protein sequence in the absence of determined structure or significant sequence homology to known domains is an important problem in structural biology. Here we address how successfully the delineation of continuous domains can be accomplished in the absence of sequence homology using simple baseline methods, an existing prediction algorithm (Domain Guess by Size), and a newly developed method (DomSSEA). The study was undertaken with a view to measuring the usefulness of these prediction methods in terms of their application to fully automatic domain assignment. Thus, the sensitivity of each domain assignment method was measured by calculating the number of correctly assigned top scoring predictions. We have implemented a new continuous domain identification method using the alignment of predicted secondary structures of target sequences against observed secondary structures of chains with known domain boundaries as assigned by Class Architecture Topology Homology (CATH). Taking top predictions only, the success rate of the method in correctly assigning domain number to the representative chain set is 73.3%. The top prediction for domain number and location of domain boundaries was correct for 24% of the multidomain set (±20 residues). These results have been put into context in relation to the results obtained from the other prediction methods assessed.
Regulatory implications of a novel mode of interaction of calmodulin with a double IQ‐motif target sequence from murine dilute myosin V
Authors: Martin Stephen R. , Bayley Peter M. 
Published: November 2002

AbstractApo‐Calmodulin acts as the light chain for unconventional myosin V, and treatment with Ca2+ can cause dissociation of calmodulin from the 6IQ region of the myosin heavy chain. The effects of Ca2+ on the stoichiometry and affinity of interactions of calmodulin and its two domains with two myosin‐V peptides (IQ3 and IQ4) have therefore been quantified in vitro, using fluorescence and near‐ and far‐UV CD. The results with separate domains show their differential affinity in interactions with the IQ motif, with the apo‐N domain interacting surprisingly weakly. Contrary to expectations, the effect of Ca2+ on the interactions of either peptide with either isolated domain is to increase affinity, reducing the Kd at physiological ionic strengths by >200‐fold to ∼75 nM for the N domain, and ∼10‐fold to ∼15 nM for the C domain. Under suitable conditions, intact (holo‐ or apo‐) calmodulin can bind up to two IQ‐target sequences. Interactions of apo‐ and holo‐calmodulin with the double‐length, concatenated sequence (IQ34) can result in complex stoichiometries. Strikingly, holo‐calmodulin forms a high‐affinity 1:1 complex with IQ34 in a novel mode of interaction, as a “bridged” structure wherein two calmodulin domains interact with adjacent IQ motifs. This apparently imposes a steric requirement for the α‐helical target sequence to be discontinuous, possibly in the central region, and a model structure is illustrated. Such a mode of interaction could account for the Ca2+‐dependent regulation of myosin V in vitro motility, by changing the structure of the regulatory complex, and paradoxically causing calmodulin dissociation through a change in stoichiometry, rather than a Ca2+‐dependent reduction in affinity.
Definition of the tempo of sequence diversity across an alignment and automatic identification of sequence motifs: Application to protein homologous families and superfamilies
Authors: May Alex C.W. 
Published: November 2002

AbstractIt is often possible to identify sequence motifs that characterize a protein family in terms of its fold and/or function from aligned protein sequences. Such motifs can be used to search for new family members. Partitioning of sequence alignments into regions of similar amino acid variability is usually done by hand. Here, I present a completely automatic method for this purpose: one that is guaranteed to produce globally optimal solutions at all levels of partition granularity. The method is used to compare the tempo of sequence diversity across reliable three‐dimensional (3D) structure‐based alignments of 209 protein families (HOMSTRAD) and that for 69 superfamilies (CAMPASS). (The mean alignment length for HOMSTRAD and CAMPASS are very similar.) Surprisingly, the optimal segmentation distributions for the closely related proteins and distantly related ones are found to be very similar. Also, optimal segmentation identifies an unusual protein superfamily. Finally, protein 3D structure clues from the tempo of sequence diversity across alignments are examined. The method is general, and could be applied to any area of comparative biological sequence and 3D structure analysis where the constraint of the inherent linear organization of the data imposes an ordering on the set of objects to be clustered.
Transmembrane helix predictions revisited
Authors: Chen Chien Peter , Kernytsky Andrew , Rost Burkhard 
Published: November 2002

AbstractMethods that predict membrane helices have become increasingly useful in the context of analyzing entire proteomes, as well as in everyday sequence analysis. Here, we analyzed 27 advanced and simple methods in detail. To resolve contradictions in previous works and to reevaluate transmembrane helix prediction algorithms, we introduced an analysis that distinguished between performance on redundancy‐reduced high‐ and low‐resolution data sets, established thresholds for significant differences in performance, and implemented both per‐segment and per‐residue analysis of membrane helix predictions. Although some of the advanced methods performed better than others, we showed in a thorough bootstrapping experiment based on various measures of accuracy that no method performed consistently best. In contrast, most simple hydrophobicity scale‐based methods were significantly less accurate than any advanced method as they overpredicted membrane helices and confused membrane helices with hydrophobic regions outside of membranes. In contrast, the advanced methods usually distinguished correctly between membrane‐helical and other proteins. Nonetheless, few methods reliably distinguished between signal peptides and membrane helices. We could not verify a significant difference in performance between eukaryotic and prokaryotic proteins. Surprisingly, we found that proteins with more than five helices were predicted at a significantly lower accuracy than proteins with five or fewer. The important implication is that structurally unsolved multispanning membrane proteins, which are often important drug targets, will remain problematic for transmembrane helix prediction algorithms. Overall, by establishing a standardized methodology for transmembrane helix prediction evaluation, we have resolved differences among previous works and presented novel trends that may impact the analysis of entire proteomes.
Long membrane helices and short loops predicted less accurately
Authors: Chen Chien Peter , Rost Burkhard 
Published: November 2002

AbstractLow‐resolution experiments suggest that most membrane helices span over 17–25 residues and that most loops between two helices are longer than 15 residues. Both constraints have been used explicitly in the development of prediction methods. Here, we compared the largest possible sequence—unique data sets from high‐ and low‐resolution experiments. For the high‐resolution data, we found that only half of the helices fall into the expected length interval and that half of the loops were shorter than 10 residues. We compared the accuracy of detecting short loops and long helices for 28 advanced and simple prediction methods: All methods predicted short loops less accurately than longer ones. In particular, loops shorter than 7 residues appeared to be very difficult to detect by current methods. Similarly, all methods tended to be more accurate for longer than for shorter helices. However, helices with more than 32 residues were predicted less accurately than all other helices. Our findings may suggest particular strategies for improving predictions of membrane helices.
Crystal structure of a major secreted protein of Mycobacterium tuberculosis—MPT63 at 1.5‐Å resolution
Authors: Goulding Celia W. , Parseghian Angineh , Sawaya Michael R. , Cascio Duilio , Apostol Marcin I. , Gennaro Maria Laura , Eisenberg David 
Published: November 2002

AbstractMPT63 is a small, major secreted protein of unknown function from Mycobacterium tuberculosis that has been shown to have immunogenic properties and has been implicated in virulence. A BLAST search identified that MPT63 has homologs only in other mycobacteria, and is therefore mycobacteria specific. As MPT63 is a secreted protein, mycobacteria specific, and implicated in virulence, MPT63 is an attractive drug target against the deadliest infectious disease, tuberculosis (TB). As part of the TB Structural Genomics Consortium, the X‐ray crystal structure of MPT63 was determined to 1.5‐Ångstrom resolution with the hope of yielding functional information about MPT63. The structure of MPT63 is an antiparallel β‐sandwich immunoglobulin‐like fold, with the unusual feature of the first β‐strand of the protein forming a parallel addition to the small antiparallel β‐sheet. MPT63 has weak structural similarity to many proteins with immunoglobulin folds, in particular, Homo sapiens β2‐adaptin, bovine arrestin, and Yersinia pseudotuberculosis invasin. Although the structure of MPT63 gives no conclusive evidence to its function, structural similarity suggests that MPT63 could be involved in cell‐host interactions to facilitate endocytosis/phagocytosis.
Extension of a local backbone description using a structural alphabet: A new approach to the sequence‐structure relationship
Authors: de Brevern Alexandre G. , Valadié Hélène , Hazout Serge , Etchebest Catherine 
Published: November 2002

AbstractProtein Blocks (PBs) comprise a structural alphabet of 16 protein fragments, each 5 Cα long. They make it possible to approximate and correctly predict local protein three‐dimensional (3D) structures. We have selected the 72 most frequent sequences of five PBs, which we call Structural Words (SWs). Analysis of four different protein data banks shows that SWs cover 92% of the amino acids in them and provide a good structural approximation for residues (i.e., sequences) 9 Cα long. We present most of them in a simple network that describes 90% of the overall residues and, interestingly, includes more than 80% of the amino acids present in coils. Analysis of the network shows the specificity and quality of the 3D descriptions as well as a new type of relation between local folds and amino acid distribution. The results show that the 3D structure of these protein data banks can be easily described by a combination of subgraphs included in the network. Finally, a Bayesian probabilistic approach improved the prediction rate by 4%.
Redox‐dependent structural changes in archaeal and bacterial Rieske‐type [2Fe‐2S] clusters
Authors: Cosper Nathaniel J. , Eby D. Matthew , Kounosu Asako , Kurosawa Norio , Neidle Ellen L. , Kurtz Donald M. , Iwasaki Toshio , Scott Robert A. 
Published: November 2002

AbstractProteins containing Rieske‐type [2Fe‐2S] clusters play important roles in many biological electron transfer reactions. Typically, [2Fe‐2S] clusters are not directly involved in the catalytic transformation of substrate, but rather supply electrons to the active site. We report herein X‐ray absorption spectroscopic (XAS) data that directly demonstrate an average increase in the iron–histidine bond length of at least 0.1 Å upon reduction of two distantly related Rieske‐type clusters in archaeal Rieske ferredoxin from Sulfolobus solfataricus strain P‐1 and bacterial anthranilate dioxygenases from Acinetobacter sp. strain ADP1. This localized redox‐dependent structural change may fine tune the protein–protein interaction (in the case of ARF) or the interdomain interaction (in AntDO) to facilitate rapid electron transfer between a lower potential Rieske‐type cluster and its redox partners, thereby regulating overall oxygenase reactions in the cells.
Modifying specificity of antidigoxin antibodies using insertional mutagenesis
Authors: Krykbaev Rustem A. , Tsantili Panayota , Jeffrey Philip D. , Margolies Michael N. 
Published: November 2002

AbstractCertain antibodies (Abs) elicited using the cardiac glycoside digoxin (digoxigenin tridigitoxoside) bind preferentially to analogs that differ from digoxin by substitutions on the cardenolide rings, the lactone, or by the presence or absence of attached sugars. Antibody 26–10 binds equally well to digoxin and digitoxin, which differ only by the presence in the former and the absence in the latter of an hydroxyl group at C12. Other antidigoxin Abs, however, can distinguish between these ligands by three orders of magnitude in binding. Inspection of the structure of Fab 26–10 complexed with digoxin shows a gap in complementarity in the region between the digoxin O12 and LCDR3. We proposed that insertions in LCDR3 might result in Abs that bind digitoxin preferentially. We produced libraries of mutants displayed on bacteriophage which were randomized at LCDR3 and contained LCDR3 insertions. Mutants were selected by panning against digoxin and analogs. The mutants bound digitoxin preferentially up to 47‐fold greater than digoxin. The mutants that bound well to digitoxin demonstrated a consensus sequence including the substitution of Trp at position L:94. Using site‐directed mutagenesis, the binding to digitoxin was shown to be maximized by the combination of an insertion and L:Trp94 mutation, moving the L 94 side chain closer to digoxin. We also selected mutants that bound preferentially to gitoxin, which, like digitoxin, lacks the 12‐hydroxyl, increasing relative binding to gitoxin up to 600‐fold compared to the unmutated Ab 26–10.
Cloning, overexpression, and characterization of a bacterial Ca2+‐dependent phospholipase D
Authors: Yang Hongying , Roberts Mary F. 
Published: November 2002

AbstractPhospholipase D (PLD), an important enzyme involved in signal transduction in mammals, is also secreted by many microorganisms. A highly conserved HKD motif has been identified in most PLD homologs in the PLD superfamily. However, the Ca2+‐dependent PLD from Streptomyces chromofuscus exhibits little homology to other PLDs. We have cloned (using DNA isolated from the ATCC type strain), overexpressed in Escherichia coli (two expression systems, pET‐23a(+) and pTYB11), and purified the S. chromofuscus PLD. Based on attempts at sequence alignment with other known Ca2+‐independent PLD enzymes from Streptomyces species, we mutated five histidine residues (His72, His171, His187, His200, His226) that could be part of variants of an HKD motif. Only H187A and H200A showed dramatically reduced activity. However, mutation of these histidine residues to alanine also significantly altered the secondary structure of PLD. Asparagine replacements at these positions yielded enzymes with structure and activity similar to the recombinant wild‐type PLD. The extent of phosphatidic acid (PA) activation of PC hydrolysis by the recombinant PLD enzymes differed in magnitude from PLD purified from S. chromofuscus culture medium (a 2‐fold activation rather than 4–5‐fold). One of the His mutants, H226A, showed a 12‐fold enhancement by PA, suggesting this residue is involved in the kinetic activation. Another notable difference of this bacterial PLD from others is that it has a single cysteine (Cys123); other Streptomyces Ca2+‐independent PLDs have eight Cys involved in intramolecular disulfide bonds. Both C123A and C123S, with secondary structure and stability similar to recombinant wild‐type PLD, exhibited specific activity reduced by 10−5 and 10−4. The Cys mutants still bound Ca2+, so that it is likely that this residue is part of the active site of the Ca2+‐dependent PLD. This would suggest that S. chromofuscus PLD is a member of a new class of PLD enzymes.
Prediction of partial membrane protein topologies using a consensus approach
Authors: Nilsson Johan , Persson Bengt , von Heijne Gunnar 
Published: November 2002

AbstractWe have developed a method to reliably identify partial membrane protein topologies using the consensus of five topology prediction methods. When evaluated on a test set of experimentally characterized proteins, we find that approximately 90% of the partial consensus topologies are correctly predicted in membrane proteins from prokaryotic as well as eukaryotic organisms. Whole‐genome analysis reveals that a reliable partial consensus topology can be predicted for ∼70% of all membrane proteins in a typical bacterial genome and for ∼55% of all membrane proteins in a typical eukaryotic genome. The average fraction of sequence length covered by a partial consensus topology is 44% for the prokaryotic proteins and 17% for the eukaryotic proteins in our test set, and similar numbers are found when the algorithm is applied to whole genomes. Reliably predicted partial topologies may simplify experimental determinations of membrane protein topology.
WHAT DO TOPOLOGISTS WANT FROM SEIBERG–WITTEN THEORY?
Authors: IGA KEVIN 
Published: November 2002

In 1983, Donaldson shocked the topology world by using instantons from physics to prove new theorems about four-dimensional manifolds, and he developed new topological invariants. In 1988, Witten showed how these invariants could be obtained by correlation functions for a twisted N = 2 SUSY gauge theory. In 1994, Seiberg and Witten discovered dualities for such theories, and in particular, developed a new way of looking at four-dimensional manifolds that turns out to be easier, and is conjectured to be equivalent to, Donaldson theory. This review describes the development of this mathematical subject, and shows how the physics played a pivotal role in the current understanding of this area of topology.
Intramucosal–arterial PCO
2 gap fails to reflect intestinal dysoxia in hypoxic hypoxia
Authors: Dubin Arnaldo , Murias Gastón , Estenssoro Elisa , Canales Héctor , Badie Julio , Pozo Mario , Sottile Juan P , Barán Marcelo , Pálizas Fernando , Laporte Mercedes 
Published: November 2002

Abstract
Introduction
An elevation in intramucosal–arterial PCO2 gradient (ΔPCO2) could be determined either by tissue hypoxia or by reduced blood flow. Our hypothesis was that in hypoxic hypoxia with preserved blood flow, ΔPCO2 should not be altered.

Methods
In 17 anesthetized and mechanically ventilated sheep, oxygen delivery was reduced by decreasing flow (ischemic hypoxia, IH) or arterial oxygen saturation (hypoxic hypoxia, HH), or no intervention was made (sham). In the IH group (n = 6), blood flow was lowered by stepwise hemorrhage; in the HH group (n = 6), hydrochloric acid was instilled intratracheally. We measured cardiac output, superior mesenteric blood flow, gases, hemoglobin, and oxygen saturations in arterial blood, mixed venous blood, and mesenteric venous blood, and ileal intramucosal PCO2 by tonometry. Systemic and intestinal oxygen transport and consumption were calculated, as was ΔPCO2. After basal measurements, measurements were repeated at 30, 60, and 90 minutes.

Results
Both progressive bleeding and hydrochloric acid aspiration provoked critical reductions in systemic and intestinal oxygen delivery and consumption. No changes occurred in the sham group. ΔPCO2 increased in the IH group (12 ± 10 [mean ± SD] versus 40 ± 13 mmHg; P < 0.001), but remained unchanged in HH and in the sham group (13 ± 6 versus 10 ± 13 mmHg and 8 ± 5 versus 9 ± 6 mmHg; not significant).

Discussion
In this experimental model of hypoxic hypoxia with preserved blood flow, ΔPCO2 was not modified during dependence of oxygen uptake on oxygen transport. These results suggest that ΔPCO2 might be determined primarily by blood flow.
Cricothyroidotomy for elective airway management in critically ill trauma patients with technically challenging neck anatomy
Authors: Rehm Christina G , Wanek Sandra M , Gagnon Eliot B , Pearson Slone K , Mullins Richard J 
Published: November 2002

Abstract
Introduction
To assess the value of elective cricothyroidotomy for airway management in critically ill trauma patients with technically challenging neck anatomy.

Materials and methods
A retrospective chart review of patients admitted to the Trauma Service at a Level I Trauma Center who underwent cricothyroidotomy for elective airway management over a 40-month period from January 1997 to April 2000. Comparison was made with a cohort of Trauma Service patients who received a tracheostomy.

Results
Eighteen patients met study criteria, and an unpaired t test revealed significance (P < 0.05) for age only. There was no difference with Injury Severity Score, number of days in the intensive care unit, number of days requiring ventilation post procedure or number of days intubated prior to procedure. The major difference was the more technically challenging neck anatomy in the patients undergoing cricothyroidotomy. Five out of 18 patients undergoing cricothyroidotomy died prior to discharge and two out of 18 died after discharge from complications unrelated to their airway. Two out of 18 patients undergoing tracheostomy died prior to discharge from complications unrelated to their airway. For a period of 1 week–15 months (average, 5.5 months), notes in subsequent clinic appointments were reviewed for subjective assessment of wound healing, breathing and swallowing difficulties, and voice changes. One patient with a cricothyroidotomy required silver nitrate to treat some granulation tissue. Otherwise, no complications were identified. Telephone interviews were conducted with eight of the 11 surviving cricothyroidotomy patients and nine of the 16 surviving tracheostomy patients. One tracheostomy patient required surgical closure 3 months after discharge; otherwise, the only noted change was minor voice changes in three patients in each group. All six of these patients denied that this compromised them in any way.

Conclusion
Elective cricothyroidotomy has a low complication rate and is a reasonable, technically less demanding option in critically ill patients with challenging neck anatomy requiring a surgical airway.
Fast principal component analysis of large data sets based on information extraction
Authors: Vogt F. , Tacke M. 
Published: November 2002

AbstractPrincipal component analysis (PCA) and principal component regression (PCR) are routinely used for calibration of measurement devices and for data evaluation. However, their use is hindered in some applications, e.g. hyperspectral imaging, by excessive data sets that imply unacceptable calculation time. This paper discusses a fast PCA achieved by a combination of data compression based on a wavelet transformation and a spectrum selection method prior to the PCA itself. The spectrum selection step can also be applied without previous data compression. The calculation speed increase is investigated based on original and compressed data sets, both simulated and measured. Two different data sets are used for assessment of the new approach. One set contains 65 536 synthetically generated spectra at four different noise levels with 256 measurement points each. Compared with the conventional PCA approach, these examples can be accelerated 20 times. Evaluation errors of the fast method were calculated and found to be comparable with those of the conventional approach. Four experimental spectra sets of similar size are also investigated. The novel method outperforms PCA in speed by factors of up to 12, depending on the data set. The principal components obtained by the novel algorithm show the same ability to model the measured spectra as the conventional time‐consuming method. The acceleration factors also depend on the possible compression; in particular, if only a small compression is feasible, the acceleration lies purely with the novel spectrum selection step proposed in this paper. Copyright © 2002 John Wiley & Sons, Ltd.