bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing strategies for improved superfamily recognition
Authors: Sillitoe Ian , Dibley Mark , Bray James , Addou Sarah , Orengo Christine 
Published: June 2005

AbstractThere are more than 200 completed genomes and over 1 million nonredundant sequences in public repositories. Although the structural data are more sparse (∼13,000 nonredundant structures solved to date), several powerful sequence‐based methodologies now allow these structures to be mapped onto related regions in a significant proportion of genome sequences. We review a number of publicly available strategies for providing structural annotations for genome sequences, and we describe the protocol adopted to provide CATH structural annotations for completed genomes. In particular, we assess the performance of several sequence‐based protocols employing Hidden Markov model (HMM) technologies for superfamily recognition, including a new approach (SAMOSA [sequence augmented models of structure alignments]) that exploits multiple structural alignments from the CATH domain structure database when building the models. Using a data set of remote homologs detected by structure comparison and manually validated in CATH, a single‐seed HMM library was able to recognize 76% of the data set. Including the SAMOSA models in the HMM library showed little gain in homolog recognition, although a slight improvement in alignment quality was observed for very remote homologs. However, using an expanded 1D‐HMM library, CATH‐ISL increased the coverage to 86%. The single‐seed HMM library has been used to annotate the protein sequences of 120 genomes from all three major kingdoms, allowing up to 70% of the genes or partial genes to be assigned to CATH superfamilies. It has also been used to recruit sequences from Swiss‐Prot and TrEMBL into CATH domain superfamilies, expanding the CATH database eightfold.
The aggregation kinetics of Alzheimer's β‐amyloid peptide is controlled by stochastic nucleation
Authors: Hortschansky Peter , Schroeckh Volker , Christopeit Tony , Zandomeneghi Giorgia , Fändrich Marcus 
Published: June 2005

AbstractWe report here a recombinant expression system that allows production of large quantities of Alzheimer's Aβ(1–40) peptide. The material is competent to dissolve in water solutions with “random‐coil properties,” although its conformation and factual oligomerization state are determined by the physico‐chemical solution conditions. When dissolved in 50 mM sodium phosphate buffer (pH 7.4) at 37°C, the peptide is able to undergo a nucleated polymerization reaction. The aggregation profile is characteristically bipartite, consisting of lag and growth phase. From these curves we determined the lag time as well as the rate of aggregation. Both values were found to depend on peptide concentration and addition or formation of seeds. Moreover, they can vary considerably between apparently identical samples. These data imply that the nucleation event is under influence of a stochastic factor that can manifest itself in profound macroscopic differences in the aggregation kinetics of otherwise indistinguishable samples.
Crystal structure of methylenetetrahydromethanopterin reductase (Mer) in complex with coenzyme F420: Architecture of the F420/FMN binding site of enzymes within the nonprolyl cis‐peptide containing bacterial luciferase family
Authors: Aufhammer Stephan W. , Warkentin Eberhard , Ermler Ulrich , Hagemeier Christoph H. , Thauer Rudolf K. , Shima Seigo 
Published: June 2005

AbstractMethylenetetratetrahydromethanopterin reductase (Mer) is involved in CO2 reduction to methane in methanogenic archaea and catalyses the reversible reduction of methylenetetrahydromethanopterin (methylene‐H4MPT) to methyl‐H4MPT with coenzyme F420H2, which is a reduced 5′‐deazaflavin. Mer was recently established as a TIM barrel structure containing a nonprolyl cis‐peptide bond but the binding site of the substrates remained elusive. We report here on the crystal structure of Mer in complex with F420 at 2.6 Å resolution. The isoalloxazine ring is present in a pronounced butterfly conformation, being induced from the Re‐face of F420 by a bulge that contains the non‐prolyl cis‐peptide bond. The bindingmode of F420 is very similar to that in F420‐dependent alcohol dehydrogenase Adf despite the low sequence identity of 21%. Moreover, binding of F420 to the apoenzyme was only associated with minor conformational changes of the polypeptide chain. These findings allowed us to build an improved model of FMN into its binding site in bacterial luciferase, which belongs to the same structural family as Mer and Adf and also contains a nonprolyl cis‐peptide bond in an equivalent position.
Structural analysis of an HIV‐1 protease I47A mutant resistant to the protease inhibitor lopinavir
Authors: Kagan Ron M. , Shenderovich Mark D. , Heseltine Peter N.R. , Ramnarayan Kal 
Published: June 2005

AbstractWe have identified a rare HIV‐1 protease (PR) mutation, I47A, associated with a high level of resistance to the protease inhibitor lopinavir (LPV) and with hypersusceptibility to the protease inhibitor saquinavir (SQV). The I47A mutation was found in 99 of 112,198 clinical specimens genotyped after LPV became available in late 2000, but in none of 24,426 clinical samples genotyped from 1998 to October 2000. Phenotypic data obtained for five I47A mutants showed unexpected resistance to LPV (86‐ to >110‐fold) and hypersusceptibility to SQV (0.1‐ to 0.7‐fold). Molecular modeling and energy calculations for these mutants using our structural phenotyping methodology showed an increase in the binding energy of LPV by 1.9–3.1 kcal/mol with respect to the wild type complex, corresponding to a 20‐ to >100‐fold decrease in binding affinity, consistent with the observed high levels of LPV resistance. In the WT PR–LPV complex, the Ile 47 side chain is positioned close to the phenoxyacetyl moiety of LPV and its van der Waals interactions contribute significantly to the ligand binding. These interactions are lost for the smaller Ala 47 residue. Calculated binding energy changes for SQV ranged from −0.4 to −1.2 kcal/mol. In the mutant I47A PR–SQV complexes, the PR flaps are packed more tightly around SQV than in the WT complex, resulting in the formation of additional hydrogen bonds that increase binding affinity of SQV consistent with phenotypic hypersusceptibility. The emergence of mutations at PR residue 47 strongly correlates with increasing prescriptions of LPV (Spearman correlation rs=0.96, P<.0001).
DOM‐fold: A structure with crossing loops found in DmpA, ornithine acetyltransferase, and molybdenum cofactor‐binding domain
Authors: Cheng Hua , Grishin Nick V. 
Published: June 2005

AbstractUnderstanding relationships between sequence, structure, and evolution is important for functional characterization of proteins. Here, we define a novel DOM‐fold as a consensus structure of the domains inDmpA (L‐aminopeptidase D‐Ala‐esterase/amidase),OAT (ornithine acetyltransferase), andMocoBD (molybdenum cofactor‐binding domain), and discuss possible evolutionary scenarios of its origin. As shown by a comprehensive structure similarity search, DOM‐fold distinguished by a two‐layered β/α architecture of a particular topology with unusual crossing loops is unique to those three protein families. DmpA and OAT are evolutionarily related as indicated by their sequence, structural, and functional similarities. Structural similarity between the DmpA/OAT superfamily and the MocoBD domains has not been reported before. Contrary to previous reports, we conclude that functional similarities between DmpA/OAT proteins and N‐terminal nucleophile (Ntn) hydrolases are convergent and are unlikely to be inherited from a common ancestor.
Characterization of calretinin I–II as an EF‐hand, Ca2+, H+‐sensing domain
Authors: Palczewska Małgorzata , Batta Gyula , Groves Patrick , Linse Sara , Kuźnicki Jacek 
Published: June 2005

AbstractCalretinin, a neuronal protein with well‐defined calcium‐binding properties, has a poorly defined function. The pH dependent properties of calretinin (CR), the N‐terminal (CR I–II), and C‐terminal (CR III–VI) domains were investigated. A drop in pH within the intracellular range (from pH 7.5 to pH 6.5) leads to an increased hydrophobicity of calcium‐bound CR and its domains as reported by fluorescence spectroscopy with the hydrophobic probe 2‐(p‐toluidino)‐6‐naphthalenesulfonic acid (TNS). The TNS data for the N‐ and C‐terminal domains of CR are additive, providing further support for their independence within the full‐length protein. Our work concentrated on CR I–II, which was found to have hydrophobic properties similar to calmodulin at lower pH. The elution of CR I–II from a phenyl‐Sepharose column was consistent with the TNS data. The pH‐dependent structural changes were further localized to residues 13–28 and 44–51 using nuclear magnetic resonance spectroscopy chemical shift analysis, and there appear to be no large changes in secondary structure. Protonation of His 12 and/or His 27 side chains, coupled with calcium chelation, appears to lead to the organization of a hydrophobic pocket in the N‐terminal domain. CR may sense and respond to calcium, proton, and other signals, contributing to conflicting data on the proteins role as a calcium sensor or calcium buffer.
Urea‐induced denaturation of apolipoprotein serum amyloid A reveals marginal stability of hexamer
Authors: Wang Limin , Colón Wilfredo 
Published: June 2005

AbstractSerum Amyloid A (SAA) is an acute phase reactant protein that is predominantly found bound to high‐density lipoprotein in plasma. Upon inflammation, the plasma concentration of SAA can increase dramatically, occasionally leading to the development of amyloid A (AA) amyloidosis, which involves the deposition of SAA amyloid fibrils in major organs. We previously found that the murine isoform SAA2.2 exists in aqueous solution as a hexamer containing a central channel. Here we show using various biophysical and biochemical techniques that the SAA2.2 hexamer can be totally dissociated into monomer by ∼2 M urea, with the concerted loss of its α‐helical structure. However, limited trypsin proteolysis experiments in urea showed a conserved digestion profile, suggesting the preservation of major backbone topological features in the urea‐denatured state of SAA2.2. The marginal stability of hexameric SAA2.2 and the presence of residual structure in the denatured monomeric protein suggest that both forms may interconvert in vivo to exert different functions to meet the various needs during normal physiological conditions and in response to inflammatory stimuli.
Protein dynamics control proton transfer from bulk solvent to protein interior: A case study with a green fluorescent protein
Authors: Saxena Anoop M. , Udgaonkar Jayant B. , Krishnamoorthy Guruswamy 
Published: June 2005

AbstractThe kinetics of proton transfer in Green Fluorescent Protein (GFP) have been studied as a model system for characterizing the correlation between dynamics and function of proteins in general. The kinetics in EGFP (a variant of GFP) were monitored by using a laser‐induced pH jump method. The pH was jumped from 8 to 5 by nanosecond flash photolysis of the “caged proton,” o‐nitrobenzaldehyde, and subsequent proton transfer was monitored by following the decrease in fluorescence intensity. The modulation of proton transfer kinetics by external perturbants such as viscosity, pH, and subdenaturing concentrations of GdnHCl as well as of salts was studied. The rate of proton transfer was inversely proportional to solvent viscosity, suggesting that the rate‐limiting step is the transfer of protons through the protein matrix. The rate is accelerated at lower pH values, and measurements of the fluorescence properties of tryptophan 57 suggest that the enhancement in rate is associated with an enhancement in protein dynamics. The rate of proton transfer is nearly independent of temperature, unlike the rate of the reverse process. When the stability of the protein was either decreased or increased by the addition of co‐solutes, including the salts KCl, KNO3, and K2SO4, a significant decrease in the rate of proton transfer was observed in all cases. The lack of correlation between the rate of proton transfer and the stability of the protein suggests that the structure is tuned to ensure maximum efficiency of the dynamics that control the proton transfer function of the protein.
Charge–charge interactions in the denatured state influence the folding kinetics of ribonuclease Sa
Authors: Trefethen Jared M. , Pace C. Nick , Scholtz J. Martin , Brems David N. 
Published: June 2005

AbstractGaining a better understanding of the denatured state ensemble of proteins is important for understanding protein stability and the mechanism of protein folding. We studied the folding kinetics of ribonuclease Sa (RNase Sa) and a charge‐reversal variant (D17R). The refolding kinetics are similar, but the unfolding rate constant is 10‐fold greater for the variant. This suggests that charge–charge interactions in the denatured state and the transition state ensembles are more favorable in the variant than in RNase Sa, and shows that charge–charge interactions can influence the kinetics and mechanism of protein folding.
Solution structure and backbone dynamics of Calsensin, an invertebrate neuronal calcium‐binding protein
Authors: Venkitaramani Deepa V. , Fulton D. Bruce , Andreotti Amy H. , Johansen Kristen M. , Johansen Jørgen 
Published: June 2005

AbstractCalsensin is an EF‐hand calcium‐binding protein expressed by a subset of peripheral sensory neurons that fasciculate into a single tract in the leech central nervous system. Calsensin is a 9‐kD protein with two EF‐hand calcium‐binding motifs. Using multidimensional NMR spectroscopy we have determined the solution structure and backbone dynamics of calcium‐bound Calsensin. Calsensin consists of four helices forming a unicornate‐type four‐helix bundle. The residues in the third helix undergo slow conformational exchange indicating that the motion of this helix is associated with calciumbinding. The backbone dynamics of the protein as measured by15N relaxation rates and heteronuclear NOEs correlate well with the three‐dimensional structure. Furthermore, comparison of the structure of Calsensin with other members of the EF‐hand calcium‐binding protein family provides insight into plausible mechanisms of calcium and target protein binding.
Investigation of protein refolding using a fractional factorial screen: A study of reagent effects and interactions
Authors: Willis Melissa Swope , Hogan James K. , Prabhakar Prakash , Liu Xun , Tsai Kuenhi , Wei Yunyi , Fox Ted 
Published: June 2005

AbstractA recurring obstacle for structural genomics is the expression of insoluble, aggregated proteins. In these cases, the use of alternative salvage strategies, like in vitro refolding, is hindered by the lack of a universal refolding method. To overcome this obstacle, fractional factorial screens have been introduced as a systematic and rapid method to identify refolding conditions. However, methodical analyses of the effectiveness of refolding reagents on large sets of proteins remain limited. In this study, we address this void by designing a fractional factorial screen to rapidly explore the effect of 14 different reagents on the refolding of 33 structurally and functionally diverse proteins. The refolding data was analyzed using statistical methods to determine the effect of each refolding additive. The screen has been miniaturized for automation resulting in reduced protein requirements and increased throughput. Our results show that the choice of pH and reducing agent had the largest impact on protein refolding. Bis‐mercaptoacetamide cyclohexane (BMC) and tris (2‐carboxyethylphosphine) (TCEP) were superior reductants when compared to others in the screen. BMC was particularly effective in refolding disulfide‐containing proteins, while TCEP was better for nondisulfide‐containing proteins. From the screen, we successfully identified a positive synergistic interaction between nondetergent sulfobetaine 201 (NDSB 201) and BMC on Cdc25A refolding. The soluble protein resulting from this interaction crystallized and yielded a 2.2 Å structure. Our method, which combines a fractional factorial screen with statistical analysis of the data, provides a powerful approach for the identification of optimal refolding reagents in a general refolding screen.
Stereo‐selectivity of HIV‐1 reverse transcriptase toward isomers of thymidine‐5′‐O‐1‐thiotriphosphate
Authors: Radzio Jessica , Sluis‐Cremer Nicolas 
Published: June 2005

AbstractThe first pre‐steady‐state kinetic analysis of the stereo‐selective incorporation of Rp‐ and Sp‐isomers of thymidine‐5′‐O‐1‐thiotriphosphate (TTPαS) by HIV‐1 reverse transcriptase (RT) is reported. Rates of polymerization (kpol), apparent dissociation constants (Kd), and substrate specificities (kpol/Kd) were measured for TTP, Rp‐TTPαS, and Sp‐TTPαS in the presence of Mg2+, Mn2+, and Co2+. HIV‐1 RT exhibits a strong preference to incorporate Sp‐TTPαS over Rp‐TTPαS in the presence of Mg2+; however, this stereo‐selective preference was decreased when Mg2+ was replaced with Mn2+ and Co2+. Furthermore, HIV‐1 RT exhibited no phosphorothioate elemental effects for the incorporation of Sp‐TTPαS, but large elemental effects were calculated for Rp‐TTPαS for each of the metals tested. These results are discussed in relation to our current understanding of the RT active‐site structure and the mechanism of DNA synthesis.
Do all backbone polar groups in proteins form hydrogen bonds?
Authors: Fleming Patrick J. , Rose George D. 
Published: June 2005

AbstractEvidence from proteins and peptides supports the conclusion that intrapeptide hydrogen bonds stabilize the folded form of proteins. Paradoxically, evidence from small molecules supports the opposite conclusion, that intrapeptide hydrogen bonds are less favorable than peptide–water hydrogen bonds. A related issue—often lost in this debate about comparing peptide–peptide to peptide– water hydrogen bonds—involves the energetic cost of an unsatisfied hydrogen bond. Here, experiment and theory agree that breaking a hydrogen bond costs between 5 and 6 kcal/mol. Accordingly, the likelihood of finding an unsatisfied hydrogen bond in a protein is insignificant. This realization establishes a powerful rule for evaluating protein conformations.
Crystal structure of an enhancer of rudimentary homolog (ERH) at 2.1 Å resolution
Authors: Arai Ryoichi , Kukimoto‐Niino Mutsuko , Uda‐Tochio Hiroko , Morita Satoshi , Uchikubo‐Kamo Tomomi , Akasaka Ryogo , Etou Yuuka , Hayashizaki Yoshihide , Kigawa Takanori , Terada Takaho , Shirouzu Mikako , Yokoyama Shigeyuki 
Published: June 2005

AbstractThe enhancer of rudimentary gene, e(r), of Drosophila melanogaster encodes an enhancer of rudimentary (ER) protein with functions implicated in pyrimidine biosynthesis and the cell cycle. The ER homolog (ERH) is highly conserved among vertebrates, invertebrates, and plants. Xenopus laevis ERH was reported to be a transcriptional repressor. Here we report the 2.1 Å crystal structure of murine ERH (Protein Data Bank ID 1WZ7), determined by the multiwavelength anomalous dispersion (MAD) method. The monomeric structure of ERH comprises a single domain consisting of three α‐helices and four β‐strands, which is a novel fold. In the crystal structure, ERH assumes a dimeric structure, through interactions between the β‐sheet regions. The formation of an ERH dimer is consistent with the results of analytical ultracentrifugation. The residues at the core region and at the dimer interface are highly conserved, suggesting the conservation of the dimer formation as well as the monomer fold. The long flexible loop (44∼53) is also significantly conserved, suggesting that this loop region may be important for the functions of ERH. In addition, the putative phosphorylation sites are located at the start of the β2‐strand (Thr18) and at the start of the α1‐helix (Ser24), implying that the phosphorylation might cause some structural changes.
Mold Accessibility via Gauss Map Analysis
Authors: Elber Gershon , Chen Xianming , Cohen Elaine 
Published: June 2005

Abstract
In manufacturing processes like injection molding or die casting, a two-piece mold is required to be separable, that is, be able to have both pieces of the mold removed in opposite directions while interfering neither with the mold nor with each other. The fundamental problem is to find a viewing (i.e., separating) direction, from which a valid partition line (i.e., the contact curves of the two mold pieces) exists. While previous research work on this problem exists for polyhedral models, verifying and finding such a partition line for general freeform shapes, represented by NURBS surfaces, is still an open question. This paper shows that such a valid partition exists for a compact surface of genus g, if and only if there is a viewing direction from which the silhouette consists of exactly g+1 nonsingular disjoint loops. Hence, the two-piece mold separability problem is essentially reduced to the topological analysis of silhouettes. In addition, we deal with removing almost vertical surface regions from the mold so that the form can more easily be extracted from the mold. It follows that the aspect graph, which gives all topologically distinct silhouettes, allows one to determine the existence of a valid partition as well as to find such a partition when it exists. In this paper, we present an aspect graph computation technique for compact free-form objects represented as NURBS surfaces. All the vision event curves (parabolic curves, flecnodal curves, and bitangency curves) relevant to mold separability are computed by symbolic techniques based on the NURBS representation, combined with numerical processing. An image dilation technique is then used for robust aspect graph cell decomposition on the sphere of viewing directions. Thus, an exact solution to the two-piece mold separability problem is given for such models.
Liquid-Crystal Thermography: Illumination Spectral Effects. Part
1—Experiments
Authors: Anderson M. R. , Baughn J. W. 
Published: June 2005

Abstract
Experiments have been performed to examine the spectral effects of the illumination source on the hue-temperature characteristics of thermochromic liquid crystals (TLCs) used in a liquid-crystal thermography system. Five illumination sources were compared in this study. It was found that “full spectrum” sources, which have a relatively uniform radiant intensity across the visible spectrum, tend to have the lowest temperature uncertainties and the broadest useful ranges, which are desirable calibration attributes. Radiation in the infrared, which leads to (usually undesirable) heating of a test surface, and in the ultraviolet, which can damage TLCs, are discussed for the various light sources. Experimental observations of the effect that UV damage has on liquid crystal calibrations are also provided. The use of a new method called background subtraction and the use of white balancing are investigated as methods of improving the calibration characteristics of TLCs. The uncertainty in temperature associated with different illumination sources and both background subtraction and white balancing is determined and discussed. It is shown that these methods can reduce the uncertainty in some cases.