bluuebunny/crossref_metadata_2025_split huggingface dataset:
Can transcriptome size be estimated from SAGE catalogs?
Authors: Stern Michael D. , Anisimov Sergey V. , Boheler Kenneth R. 
Published: February 2003

Abstract
Motivation: SAGE (Serial Analysis of Gene Expression) can be used to estimate the number of unique transcripts in a transcriptome. A simple estimator that corrects for sequencing and sampling errors was applied to a SAGE library (137 832 tags) obtained from mouse embryonic stem cells, and also to Monte Carlo simulated libraries generated using assumed distributions of‘ true’ expression levels consistent with the data.
Results: When the corrected data themselves were taken as the underlying model of ‘ground truth’, the estimator converged to the ‘ true’ value (53 535) only after counting 300 000 simulated tags, more than twice the number in the experiment. The SAGE data could also be well fit by a Monte Carlo model based on a truncated inverse-square distribution of expression levels, with 130 000 ‘true’ transcripts and 106 samples needed for convergence. We conclude that the size of a transcriptome is ill-determined from SAGE libraries of even moderately large size. In order to obtain a valid estimate, one must sample a number of tags inversely proportional to the lowest abundance level, which is not known a priori. This constrains the design of SAGE experiments intended to determine biological complexity.
Availability: The ‘homemade’ software used for this analysis was not designed for general or ‘production’ use, but the authors will be happy to share Fortran sourcecode with interested parties.
Contact: sternm@grc.nia.nih.gov
* To whom correspondence should be addressed.
Protein family annotation in a multiple alignment viewer
Authors: Johnson Jason M. , Mason Keith , Moallemi Ciamac , Xi Hualin , Somaroo Shyamal , Huang Enoch S. 
Published: February 2003

Abstract
Summary: The Pfaat protein family alignment annotation tool is a Java-based multiple sequence alignment editor and viewer designed for protein family analysis. The application merges display features such as dendrograms, secondary and tertiary protein structure with SRS retrieval, subgroup comparison, and extensive user-annotation capabilities.
Availability: The program and source code are freely available from the authors under the GNU General Public License at http://www.pfizerdtc.com
Contact: jason_johnson@merck.comenoch_huang@cambridge.pfizer.com
* To whom correspondence should be addressed.
† Present address: Rosetta Inpharmatics, 12040 115th Avenue NE, Kirkland, WA 98034, USA.
MaxSubSeq: an algorithm for segment-length
optimization. The case study of the transmembrane
spanning segments
Authors: Fariselli Piero , Finelli Michele , Marchignoli Davide , Martelli Pier Luigi , Rossi Ivan , Casadio Rita 
Published: February 2003

Abstract
Motivation: A problem in predicting the topography of transmembrane proteins is the optimal localization of the transmembrane segments along the protein sequences, provided that each residue is associated with a propensity of being or not being included in the transmembrane protein region. From previous work it is known that post-processing of propensity signals with suited algorithms can greatly improve the quality and the accuracy of the predictions. In this paper we describe a general dynamic programming-like algorithm (MaxSubSeq, Maximal SubSequence) specifically designed to optimize the number and length of segments with constrained length in a given protein sequence. Previous application of our algorithm, has proved its effectiveness in the optimization task of both neural network and hidden Markov models output, and in this paper we present the detailed description of MaxSubSeq.
Results: We describe the application of MaxSubSeq to the location of both helical and beta strand transmembrane segments, optimizing the outputs derived with different predictive algorithms. For all-alpha transmembrane proteins we use both the standard Kyte–Doolittle (KD) hydropathy scale and the TMHMM predictor (http://www.cbs.dtu.dk/). Using a set of 188 well characterized membrane proteins, MaxSubSeq nearly doubles the correct location of transmembrane segments as compared to the standard KD hydrophobicity plot, reaching 51% accuracy. If MaxSubSeq is used to optimize the TMHMM method the accuracy increases from 68 to 72%. When used to regularize the prediction of beta transmembrane strands, obtained using both a neural network and a HMM based predictors, MaxSubSeq increases the accuracy per protein up to 72 and 73% respectively.
Availability: The program is available upon request to the authors, or it is accessible through our web server (http://gpcr.biocomp.unibo.it/predictors/)
Contact: piero@biocomp.unibo.itcasadio@alma.unibo.it
* To whom correspondence should be addressed.
PopHist: inferring population history from the spectrum of allele frequencies
Authors: Wooding Stephen 
Published: February 2003

Abstract
Summary: PopHist is a computer program that uses the frequency spectrum of alleles to: (a) estimate maximum likelihood parameters describing a population’s history; and (b) compare alternative hypotheses about population history using likelihood ratio tests. The program uses the matrix coalescent, a method for calculating theoretical frequency spectra that can be applied to sets of unlinked sites.
Availability: Source code and documentation are available at http://mombasa.anthro.utah.edu/wooding/PopHist
Contact: swooding@genetics.utah.edu
Simultaneous assignment and structure determination of a membrane protein from NMR orientational restraints
Authors: Marassi Francesca M. , Opella Stanley J. 
Published: February 2003

AbstractA solid‐state NMR approach for simultaneous resonance assignment and three‐dimensional structure determination of a membrane protein in lipid bilayers is described. The approach is based on the scattering, hence the descriptor “shotgun,” of 15N‐labeled amino acids throughout the protein sequence (and the resulting NMR spectra). The samples are obtained by protein expression in bacteria grown on media in which one type of amino acid is labeled and the others are not. Shotgun NMR short‐circuits the laborious and time‐consuming process of obtaining complete sequential assignments prior to the calculation of a protein structure from the NMR data by taking advantage of the orientational information inherent to the spectra of aligned proteins. As a result, it is possible to simultaneously assign resonances and measure orientational restraints for structure determination. A total of five two‐dimensional 1H/15N PISEMA (polarization inversion spin exchange at the magic angle) spectra, from one uniformly and four selectively 15N‐labeled samples, were sufficient to determine the structure of the membrane‐bound form of the 50‐residue major pVIII coat protein of fd filamentous bacteriophage. Pisa (polarity index slat angle) wheels are an essential element in the process, which starts with the simultaneous assignment of resonances and the assembly of isolated polypeptide segments, and culminates in the complete three‐dimensional structure of the protein with atomic resolution. The principles are also applicable to weakly aligned proteins studied by solution NMR spectroscopy.[The structure we determined for the membrane‐bound form of the Fd bacteriophage pVIII coat protein has been deposited in the Protein Data Bank as PDB file 1MZT.]
Hydrophobicity of transmembrane proteins: Spatially profiling the distribution
Authors: Silverman B. David 
Published: February 2003

AbstractA hallmark of soluble globular protein tertiary structure is a hydrophobic core and a protein exterior populated predominantly by hydrophilic residues. Recent hydrophobic moment profiling of the spatial distribution of 30 globular proteins of diverse size and structure had revealed features of this distribution that were comparable. Analogous profiling of the hydrophobicity distribution of the α‐helical buried bundles of several transmembrane proteins, as the lipid/protein interface is approached from within the bilayer, reveals spatial hydrophobicity profiles that contrast with those obtained for the soluble proteins. The calculations, which enable relative changes of hydrophobicity to be simply identified over the entire spatial extent of the multimer within the lipid bilayer, show the accumulated zero‐order moments of the bundles to be mainly inverted with respect to that found for the soluble proteins. This indicates a statistical increase in the average residue hydrophobic content as the lipid bilayer is approached. This result differs from that of a relatively recent calculation and qualitatively agrees with earlier calculations involving lipid exposed and buried residues of the α‐helices of transmembrane proteins. Spatial profiling, over the entire spatial extent of the multimer with scaled values of residue hydrophobicity, provides information that is not available from calculations using lipid exposure alone.
Backbone dynamics of the human MIA protein studied by 15N NMR relaxation: Implications for extended interactions of SH3 domains
Authors: Stoll Raphael , Renner Christian , Buettner Reinhard , Voelter Wolfgang , Bosserhoff Anja‐Katrin , Holak Tad A. 
Published: February 2003

AbstractThe melanoma inhibitory activity (MIA) protein is a clinically valuable marker in patients with malignant melanoma as enhanced values diagnose metastatic melanoma stages III and IV. Here, we report the backbone dynamics of human MIA studied by 15N NMR relaxation experiments. The folded core of human MIA is found to be rigid, but several loops connecting β‐sheets, such as the RT‐loop for example, display increased mobility on picosecond to nanosecond time scales. One of the most important dynamic features is the pronounced flexibility of the distal loop, comprising residues Asp 68 to Ala 75, where motions on time scales up to milliseconds occur. Further, significant exchange contributions are observed for residues of the canonical binding site of SH3 domains including the RT‐loop, the n‐Src loop, for the loop comprising residues 13 to 19, which we refer to as the“disulfide loop”, in part for the distal loop, and the carboxyl terminus of human MIA. The functional importance of this dynamic behavior is discussed with respect to the biological activity of several point mutations of human MIA. The results of this study suggest that the MIA protein and the recently identified highly homologous fibrocyte‐derived protein (FDP)/MIA‐like (MIAL) constitute a new family of secreted proteins that adopt an SH3 domain‐like fold in solution with expanded ligand interactions.
The hydration of amides in helices; a comprehensive picture from molecular dynamics, IR, and NMR
Authors: Walsh Scott T.R. , Cheng Richard P. , Wright Wayne W. , Alonso Darwin O.V. , Daggett Valerie , Vanderkooi Jane M. , DeGrado William F. 
Published: February 2003

AbstractWe examined the hydration of amides of α3D, a simple, designed three‐helix bundle protein. Molecular dynamics calculations show that the amide carbonyls on the surface of the protein tilt away from the helical axis to interact with solvent water, resulting in a lengthening of the hydrogen bonds on this face of the helix. Water molecules are bonded to these carbonyl groups with partial occupancy (∼50%–70%), and their interaction geometries show a large variation in their hydrogen bond lengths and angles on the nsec time scale. This heterogeneity is reflected in the carbonyl stretching vibration (amide I′ band) of a group of surface Ala residues. The surface‐exposed amides are broad, and shift to lower frequency (reflecting strengthening of the hydrogen bonds) as the temperature is decreased. By contrast, the amide I′ bands of the buried 13C‐labeled Leu residues are significantly sharper and their frequencies are consistent with the formation of strong hydrogen bonds, independent of temperature. The rates of hydrogen‐deuterium exchange and the proton NMR chemical shifts of the helical amide groups also depend on environment. The partial occupancy of the hydration sites on the surface of helices suggests that the interaction is relatively weak, on the order of thermal energy at room temperature. One unexpected feature that emerged from the dynamics calculations was that a Thr side chain subtly disrupted the helical geometry 4–7 residues N‐terminal in sequence, which was reflected in the proton chemical shifts and the rates of amide proton exchange for several amides that engage in a mixed 310/α/π‐helical conformation.
In vitro unfolding, refolding, and polymerization of human γD crystallin, a protein involved in cataract formation
Authors: Kosinski‐Collins Melissa S. , King Jonathan 
Published: February 2003

AbstractHuman γD crystallin (HγD‐Crys), a major protein of the human eye lens, is a primary component of cataracts. This 174‐residue primarily β‐sheet protein is made up of four Greek keys separated into two domains. Mutations in the human gene sequence encoding HγD‐Crys are implicated in early‐onset cataracts in children, and the mutant protein expressed in Escherichia coli exhibits properties that reflect the in vivo pathology. We have characterized the unfolding, refolding, and competing aggregation of human wild‐type HγD‐Crys as a function of guanidinium hydrochloride (GuHCl) concentration at neutral pH and 37°C, using intrinsic tryptophan fluorescence to monitor in vitro folding. Wild‐type HγD‐Crys exhibited reversible refolding above 1.0 M GuHCl. The GuHCl unfolded protein was more fluorescent than its native counterpart despite the absence of metal or ion‐tryptophan interactions. Aggregation of refolding intermediates of HγD‐Crys was observed in both equilibrium and kinetic refolding processes. The aggregation pathway competed with productive refolding at denaturant concentrations below 1.0 M GuHCl, beyond the major conformational transition region. Atomic force microscopy of samples under aggregating conditions revealed the sequential appearance of small nuclei, thin protofibrils, and fiber bundles. The HγD‐Crys fibrous aggregate species bound bisANS appreciably, indicating the presence of exposed hydrophobic pockets. The mechanism of HγD‐Crys aggregation may provide clues to understanding age‐onset cataract formation in vivo.
Enhanced correction methods for hydrogen exchange‐mass spectrometric studies of amyloid fibrils
Authors: Kheterpal Indu , Wetzel Ronald , Cook Kelsey D. 
Published: February 2003

AbstractWe describe methods for minimization of and correction for artifactual forward and backward exchange occurring during hydrogen exchange–mass spectrometric (HX–MS) studies of amyloid fibrils of the Aβ(1–40) peptide. The quality of the corrected data obtained using published and new correction algorithms is evaluated quantitatively. Using the new correction methods, we have determined that 20.1 ± 1.4 of the 39 backbone amide hydrogens in Aβ(1–40) exchange with deuteriums in 100 h when amyloid fibrils of this peptide are suspended in D2O. These data reinforce our previous conclusions based on uncorrected data that amyloid fibrils contain a rigid protective core structure that involves only about half of the Aβ backbone amides. The methods developed here should be of general value for HX–MS studies of amyloid fibrils and other protein aggregates.
Mutations in the B1 domain of protein G that delay the onset of amyloid fibril formation in vitro
Authors: Ramírez‐Alvarado Marina , Cocco Melanie J. , Regan Lynne 
Published: February 2003

AbstractWe previously reported that under certain experimental conditions, many variants of the B1 domain of IgG‐binding protein G from Streptococcus form fibrils reproducibly. The variant I6T53 was the focus of the present study because the lag phase in the kinetics of fibril formation by this variant is significantly longer than that of other variants. This lag phase is distinguished by changes in both intrinsic fluorescence intensity and in light scattering of the protein. NMR diffusion measurements suggest that the soluble protein during the lag phase is monomeric. The kinetic profiles of fibril formation are found to depend on experimental conditions. The first kinetic phase diminishes almost completely when the reaction is seeded with preformed amyloid fibrils.
Solution structure of termicin, an antimicrobial peptide from the termite Pseudacanthotermes spiniger
Authors: Da Silva Pedro , Jouvensal Laurence , Lamberty Mireille , Bulet Philippe , Caille Anita , Vovelle Françoise 
Published: February 2003

AbstractThe solution structure of termicin from hemocytes of the termite Pseudacanthotermes spiniger was determined by proton two‐dimensional nuclear magnetic resonance spectroscopy and molecular modeling techniques. Termicin is a cysteine‐rich antifungal peptide also exhibiting a weak antibacterial activity. The global fold of termicin consists of an α‐helical segment (Phe4–Gln14) and a two‐stranded (Phe19–Asp25 and Gln28–Phe33) antiparallel β‐sheet forming a “cysteine stabilized αβ motif” (CSαβ) also found in antibacterial and antifungal defensins from insects and from plants. Interestingly, termicin shares more structural similarities with the antibacterial insect defensins and with MGD‐1, a mussel defensin, than with the insect antifungal defensins such as drosomycin and heliomicin. These structural comparisons suggest that global fold alone does not explain the difference between antifungals and antibacterials. The antifungal properties of termicin may be related to its marked hydrophobicity and its amphipatic structure as compared to the antibacterial defensins. [SWISS‐PROT accession number: Termicin (P82321); PDB accession number: 1MM0.]
Prediction of β‐turns in proteins from multiple alignment using neural network
Authors: Kaur Harpreet , Raghava Gajendra Pal Singh 
Published: February 2003

AbstractA neural network‐based method has been developed for the prediction of β‐turns in proteins by using multiple sequence alignment. Two feed‐forward back‐propagation networks with a single hidden layer are used where the first‐sequence structure network is trained with the multiple sequence alignment in the form of PSI‐BLAST–generated position‐specific scoring matrices. The initial predictions from the first network and PSIPRED‐predicted secondary structure are used as input to the second structure‐structure network to refine the predictions obtained from the first net. A significant improvement in prediction accuracy has been achieved by using evolutionary information contained in the multiple sequence alignment. The final network yields an overall prediction accuracy of 75.5% when tested by sevenfold cross‐validation on a set of 426 nonhomologous protein chains. The corresponding Qpred, Qobs, and Matthews correlation coefficient values are 49.8%, 72.3%, and 0.43, respectively, and are the best among all the previously published β‐turn prediction methods. The Web server BetaTPred2 (http://www.imtech.res.in/raghava/betatpred2/) has been developed based on this approach.
Reinvestigation of the proposed folding and self‐association of the Neuropeptide Head Activator
Authors: Lai Jonathan R. , Gellman Samuel H. 
Published: February 2003

AbstractThe Neuropeptide Head Activator (HA), pGlu‐Pro‐Pro‐Gly‐Gly‐Ser‐Lys‐Val‐Ile‐Leu‐Phe (pGlu is pyroglutamic acid), is involved in head‐specific growth and differentiation processes in the freshwater coelenterate Hydra attenuata. Peptides of identical sequence have also been isolated from higher‐organism tissues such as human and bovine hypothalamus. Early studies by molecular sieve chromatography suggested that HA dimerizes with high affinity (Kd ≈ 1 nM). This dimerization was proposed to occur via antiparallel β‐sheet formation between the Lys7‐Phe11 segments in each HA molecule. We conducted biophysical studies on synthetic HA in order to gain insight into its structure and aggregation tendencies. We found by analytical ultracentrifugation that HA is monomeric at low millimolar concentrations. Studies by 1H‐NMR revealed that HA did not adopt any significant secondary structure in solution. We found no NOEs that would support the proposed dimer structure. We probed the propensity of the Lys7‐Phe11 fragment to form antiparallel β‐sheet by designing peptides in which two such fragments are joined by a two‐residue linker. These peptides were intended to form stable β‐hairpin structures with cross‐strand interactions that mimic those of the proposed HA dimer interface. We found that the HA‐derived fragments may be induced to form intramolecular β‐sheet, albeit only weakly, when linked by the highly β‐hairpin‐promoting d‐Pro‐Gly turn, but not when linked by the more flexible Gly‐Gly unit. These findings suggest that the postulated mode of HA dimerization and the proposed propensity of the molecule to form discrete aggregates with high affinity are incorrect.
Purification of correctly oxidized MHC class I heavy‐chain molecules under denaturing conditions: A novel strategy exploiting disulfide assisted protein folding
Authors: Ferré Henrik , Ruffet Emmanuel , Blicher Thomas , Sylvester‐Hvid Christina , Nielsen Lise Lotte B. , Hobley Timothy J. , Thomas Owen R.T. , Buus Søren 
Published: February 2003

AbstractThe aim of this study has been to develop a strategy for purifying correctly oxidized denatured major histocompability complex class I (MHC‐I) heavy‐chain molecules, which on dilution, fold efficiently and become functional. Expression of heavy‐chain molecules in bacteria results in the formation of insoluble cellular inclusion bodies, which must be solubilized under denaturing conditions. Their subsequent purification and refolding is complicated by the fact that (1) correct folding can only take place in combined presence of β2‐microglobulin and a binding peptide; and (2) optimal in vitro conditions for disulfide bond formation (∼pH 8) and peptide binding (∼pH 6.6) are far from complementary. Here we present a two‐step strategy, which relies on uncoupling the events of disulfide bond formation and peptide binding. In the first phase, heavy‐chain molecules with correct disulfide bonding are formed under non‐reducing denaturing conditions and separated from scrambled disulfide bond forms by hydrophobic interaction chromatography. In the second step, rapid refolding of the oxidized heavy chains is afforded by disulfide bond–assisted folding in the presence of β2‐microglobulin and a specific peptide. Under conditions optimized for peptide binding, refolding and simultaneous peptide binding of the correctly oxidized heavy chain was much more efficient than that of the fully reduced molecule.
WW domain sequence activity relationships identified using ligand recognition propensities of 42 WW domains
Authors: Otte Livia , Wiedemann Urs , Schlegel Brigitte , Pires José Ricardo , Beyermann Michael , Schmieder Peter , Krause Gerd , Volkmer‐Engert Rudolf , Schneider‐Mergener Jens , Oschkinat Hartmut 
Published: February 2003

AbstractWW domains mediate protein–protein interactions in a number of different cellular functions by recognizing proline‐containing peptide sequences. We determined peptide recognition propensities for 42 WW domains using NMR spectroscopy and peptide library screens. As potential ligands, we studied both model peptides and peptides based on naturally occurring sequences, including phosphorylated residues. Thirty‐two WW domains were classified into six groups according to detected ligand recognition preferences for binding the motifs PPx(Y/poY), (p/ϕ)P(p,g)PPpR, (p/ϕ)PPRgpPp, PPLPp, (p/ξ)PPPPP, and (poS/poT)P (motifs according to modified Seefeld Convention 2001). In addition to these distinct binding motifs, group‐specific WW domain consensus sequences were identified. For PPxY‐recognizing domains, phospho‐tyrosine binding was also observed. Based on the sequences of the PPx(Y/poY)‐specific group, a profile hidden Markov model was calculated and used to predict PPx(Y/poY)‐recognition activity for WW domains, which were not assayed. PPx(Y/poY)‐binding was found to be a common property of NEDD4‐like ubiquitin ligases.