bluuebunny/crossref_metadata_2025_split huggingface dataset:
The NMR solution structure of the pheromone Er‐2 from the ciliated protozoan Euplotes raikovi
Authors: Ottiger M. , Szyperski T. , Luginbühl P. , Ortenzi C. , Luporini P. , Bradshaw R. A. , WÜthrich K. 
Published: February 2009

AbstractThe NMR structure of the pheromone Er‐2 from the ciliated protozoan Euplotes raikovi has been determined in aqueous solution. The structure of this 40‐residue protein was calculated with the distance geometry program DIANA from 621 distance constraints and 89 dihedral angle constraints; the program OPAL was employed for the energy minimization. For a group of 20 conformers used to characterize the solution structure, the average pairwise RMS deviation from the mean structure calculated for the backbone heavy atoms N, Cα, and C′ of residues 3–37 was 0.31 Å. The molecular architecture is dominated by an up‐down‐up bundle of 3 short helices of residues 5–11, 14–20, and 23–33, which is similar to the structures of the homologous pheromones Er‐1 and Er‐10. Novel structural features include a well‐defined N‐cap on the first helix, a 1‐residue deletion in the second helix resulting in the formation of a 310‐helix rather than an α‐helix as found in Er‐1 and Er‐10, and the simultaneous presence of 2 different conformations for the C‐terminal tetrapeptide segment, i.e., a major conformation with the Leu 39‐Pro 40 peptide bond in the trans form and a minor conformation with this peptide bond in the cis form.
Derivation of rules for comparative protein modeling from a database of protein structure alignments
Authors: ŠAli Andrej , Overington John P. 
Published: February 2009

AbstractWe describe a database of protein structure alignments as well as methods and tools that use this database to improve comparative protein modeling. The current version of the database contains 105 alignments of similar proteins or protein segments. The database comprises 416 entries, 78,495 residues, 1,233 equivalent entry pairs, and 230,396 pairs of equivalent alignment positions. At present, the main application of the database is to improve comparative modeling by satisfaction of spatial restraints implemented in the program MODELLER (Šali A, Blundell TL, 1993, J Mol Biol 234:779–815). To illustrate the usefulness of the database, the restraints on the conformation of a disulfide bridge provided by an equivalent disulfide bridge in a related structure are derived from the alignments; the prediction success of the disulfide dihedral angle classes is increased to approximately 80%, compared to approximately 55% for modeling that relies on the stereochemistry of disulfide bridges alone. The second example of the use of the database is the derivation of the probability density function for comparative modeling of the cis/trans isomerism of the proline residues; the prediction success is increased from 0% to 82.9% for cis‐proline and from 93.3% to 96.2% for trans‐proline. The database is available via electronic mail.
A neural network model for the prediction of membrane‐spanning amino acid sequences
Authors: Lohmann Reinhard , Schneider Gisbert , Behrens Dirk , Wrede Paul 
Published: February 2009

AbstractThe architecture and weights of an artificial neural network model that predicts putative transmembrane sequences have been developed and optimized by the algorithm of structure evolution. The resulting filter is able to classify membrane/nonmembrane transition regions in sequences of integral human membrane proteins with high accuracy. Similar results have been obtained for both training and test set data, indicating that the network has focused on general features of transmembrane sequences rather than specializing on the training data. Seven physicochemical amino acid properties have been used for sequence encoding. The predictions are compared to hydrophobicity plots.
Viral cell recognition and entry
Authors: Rossmann Michael G. 
Published: February 2009

AbstractRhinovirus infection is initiated by the recognition of a specific cell‐surface receptor. The major group of rhino‐virus serotypes attach to intercellular adhesion molecule‐1 (ICAM‐1). The attachment process initiates a series of conformational changes resulting in the loss of genomic RNA from the virion. X‐ray crystallography and sequence comparisons suggested that a deep crevice or canyon is the site on the virus recognized by the cellular receptor molecule. This has now been verified by electron microscopy of human rhinovirus 14 (HRV14) and HRV16 complexed with a soluble component of ICAM‐1.A hydrophobic pocket underneath the canyon is the site of binding of various hydrophobic drug compounds that can inhibit attachment and uncoating. This pocket is also associated with an unidentified, possibly cellular in origin, “pocket factor.” The pocket factor binding site overlaps the binding site of the receptor. It is suggested that competition between the pocket factor and receptor regulates the conformational changes required for the initiation of the entry of the genomic RNA into the cell.
Sequence determinants of the capping box, a stabilizing motif at the N‐termini of α‐helices
Authors: Seale Jeffrey W. , Srinivasan Rajgopal , Rose George D. 
Published: February 2009

AbstractThe capping box, a recurrent hydrogen bonded motif at the N‐termini of α‐helices, caps 2 of the initial 4 backbone amide hydrogen donors of the helix (Harper ET, Rose GD, 1993, Biochemistry 32:7605–7609). In detail, the side chain of the first helical residue forms a hydrogen bond with the backbone of the fourth helical residue and, reciprocally, the side chain of the fourth residue forms a hydrogen bond with the backbone of the first residue. We now enlarge the earlier definition of this motif to include an accompanying hydrophobic interaction between residues that bracket the capping box sequence on either side. The expanded box motif—in which 2 hydrogen bonds and a hydrophobic interaction are localized within 6 consecutive residues — resembles a glycine‐based capping motif found at helix C‐termini.
Template‐assembled melittin: Structural and functional characterization of a designed, synthetic channel‐forming protein
Authors: Pawlak Michael , Meseth Ulrich , Vogel Horst , Dhanapal Boopathy , Mutter Manfred 
Published: February 2009

AbstractTemplate‐assembled proteins (TASPs) comprising 4 peptide blocks, each of either the natural melittin sequence (melittin‐TASP) or of a truncated melittin sequence (amino acids 6–26, melittin6–26‐TASP), C‐terminally linked to a (linear or cyclic) 10‐amino acid template were synthesized and characterized, structurally by CD, by fluorescence spectroscopy, and by monolayer experiments, and functionally, by electrical conductance measurements on planar bilayers and release experiments on dye‐loaded vesicles. Melittin‐TASP and the truncated analogue preferentially adopt α‐helical structures in methanol (56% and 52%, respectively) as in lipid membranes. Unlike in methanol, the melittin‐TASP self‐aggregates in water. On an air‐water interface, the differently sized molecules can be self‐assembled and compressed to a compact structure with a molecular area of around 600 Å2, compatible with a 4‐helix bundle preferentially oriented perpendicular to the interface. The proteins reveal a strong affinity for lipid membranes. A partition coefficient of 1.5 × 109 M−1 was evaluated from changes of the Trp fluorescence spectra of the TASP in water and in the lipid bilayer. In planar lipid bilayers, TASP molecules are able to form defined ion channels, exhibiting a small single‐channel conductance of 7 pS (in 1 M NaCl). With increasing protein concentration in the lipid bilayer, additional, larger conductance states of up to 1 nS were observed. These states are likely to be formed by aggregated TASP structures as inferred from a strongly voltage‐dependent channel activity on membranes of large area. In this respect, melittin‐TASP reveals channel features of the native peptide, but with a considerably lower variation in the size of the channel states. Compared to the free peptide, template‐assembled melittin has a much higher membrane activity: it is about 100 times more effective in channel formation and 20 times more effective in releasing dye molecules from lipid vesicles. This demonstrates that the lytic properties are not solely related to channel formation.
On the evolution of alternate core packing in eightfold β/α‐barrels
Authors: Raine Andrew R.C. , Scrutton Nigel S. , Mathews F. Scott 
Published: February 2009

AbstractTwo sequence‐related subfamilies of flavin‐binding β/α‐barrels have been identified (the type I and type II proteins) that differ in the nature of residue packing in the core of the barrel domain. Similar observed differences in the packing of internal amino acid side chains in β/α‐barrels have previously been used to argue that these domains have evolved convergently toward a stable structural framework. Using structural alignments of flavin‐binding barrel proteins, we demonstrate that simple genetic alterations may be responsible for switching the nature of side‐chain packing observed in β/α‐barrels. The implication is that the 2 structural classes of β/α‐barrel cores can arise divergently from an ancestral barrel framework and that convergent evolution to a stable fold need not be invoked to account for the emergence of 2 classes of β/α‐barrel core.
The tyrosine corner: A feature of most greek key β‐barrel proteins
Authors: Hemmingsen Jens M. , Gernert Kim M. , Richardson Jane S. , Richardson David C. 
Published: February 2009

AbstractThe Tyr corner is a conformation in which a tyrosine (residue “Y”) near the beginning or end of an antiparallel β‐strand makes an H bond from its side‐chain OH group to the backbone NH and/or CO of residue Y – 3, Y – 4, or Y – 5 in the nearby connection. The most common “classic” case is a Δ4 Tyr corner (more than 40 examples listed), in which the H bond is to residue Y – 4 and the Tyr x1 is near −60°. Y – 2 is almost always a glycine, whose left‐handed β or very extended β conformation helps the backbone curve around the Tyr ring. Residue Y – 3 is in polyproline II conformation (often Pro), and residue Y – 5 is usually a hydrophobic (often Leu) that packs next to the Tyr ring. The consensus sequence, then, is LxPGxY, where the first x (the H‐bonding position) is hydrophilic. Residues Y and Y – 2 both form narrow pairs of β‐sheet H‐bonds with the neighboring strand, Δ5 Tyr corners have a 1‐residue insertion between the Gly and the Tyr, forming a β‐bulge. One protein family has a Δ4 corner formed by a His rather than a Tyr, and several examples use Trp in place of Tyr. For almost all these cases, the protein or domain is a Greek key β‐barrel structure, the Tyr corner ends a Greek key connection, and it is well‐conserved in related proteins. Most low‐twist Greek key β‐barrels have 1 Tyr corner. “Reverse” Δ4 Tyr corners (H bonded to Y + 4) and other variants are described, all less common and less conserved. It seems likely that the more classic Tyr corners (Δ4, Δ5, and Δ3 Tyr, Trp, or His) contribute to the stability of a Greek key connection over a hairpin connection, and also that they may aid in the process of folding up Greek key structures.
Engineering the quaternary structure of an enzyme: Construction and analysis of a monomeric form of malate dehydrogenase from Escherichia coli
Authors: Breiter Deborah R. , Resnik Ernesto , Banaszak Leonard J. 
Published: February 2009

AbstractThe citric acid cycle enzyme, malate dehydrogenase (MDH), is a dimer of identical subunits. In the crystal structures of 2 prokaryotic and 2 eukaryotic forms, the subunit interface is conformationally homologous. To determine whether or not the quaternary structure of MDH is linked to the catalytic activity, mutant forms of the enzyme from Escherichia coli have been constructed. Utilizing the high‐resolution structure of E. coli MDH, the dimer interface was analyzed critically for side chains that were spatially constricted and needed for electrostatic interactions. Two such residues were found, D45 and S226. At their nearest point in the homodimer, they are in different subunits, hydrogen bond across the interface, and do not interact with any catalytic residues. Each residue was mutated to a tyrosine, which should disrupt the interface because of its large size. All mutants were cloned and purified to homogeneity from an mdh− E. coli strain (BHB111). Gel filtration of the mutants show that D45Y and D45Y/S226Y are both monomers, whereas the S226Y mutant remains a dimer. The monomeric D45Y and D45Y/S226Y mutants have 14,000‐ and 17,500‐fold less specific activity, respectively, than the native enzyme. The dimeric S226Y has only 1.4‐fold less specific activity. All forms crystallized, indicating they were not random coils. Data have been collected to 2.8 Å resolution for the D45Y mutant. The mutant is not isomorphous with the native protein and work is underway to solve the structure by molecular replacement.
A structural model for the prostate disease marker, human prostate‐specific antigen
Authors: Villoutreix Bruno O. , Griffin John H. , Getzoff Elizabeth D. 
Published: February 2009

AbstractProstate‐specific antigen (PSA) provides an excellent serum marker for prostate cancer, the most frequent form of cancer in American males. PSA is a 237‐residue protease based on sequence homology to kallikrein‐like enzymes. To predict the 3‐dimensional structure of PSA, homology modeling studies were performed based on sequence and structural alignments with tonin, pancreatic kallikrein, chymotrypsin, and trypsin. The structurally conserved regions of the 4 reference X‐ray proteins provided the core structure of PSA, whereas the loop structures were modeled on the loops of tonin and kallikrein. The unique “kallikrein loop” insert, between Ser 95b and Pro 95k of kallikrein, was constructed using molecular mechanics, dynamics, and electrostatics calculations. In the resulting PSA structure, the catalytic triad, involving residues His 57, Asp 102, and Ser 195, and hydrophobic and electrostatic interactions typical of serine proteases were extremely well conserved. Similarly, the 5 disulfide bonds of kallikrein were also conserved in PSA. These results, together with the fact that no major steric clashes arose during the modeling process, provide strong evidence for the validity of the PSA model. Calculation of the electrostatic potential contours of kallikrein and PSA was carried out using the finite difference Poisson‐Boltzmann method. The calculations revealed matching areas of negative potential near the catalytic triad, but differences in the positive potential surrounding the active site. The PSA glycosylation site, Asn 61, is fully accessible to the solvent and is enclosed in a positive region of the isopotential map. The bottom of the substrate specificity pocket, residue SI, is a serine (Ser 189) as in chymotrypsin, rather than aspartate (Asp 189) as in tonin, kallikrein, and trypsin. This fact, plus other features of the SI binding‐pocket region, suggest that PSA would prefer substrates with hydrophobic residues at the PI position. The location of a potential zinc ion binding site involving the side chain of histidines 91, 101, and 233 is also suggested. This PSA model should facilitate the understanding and prediction of structural and functional properties of this important cancer marker.
Eukaryotic translation elongation factor 1γ contains a glutathione transferase domain—Study of a diverse, ancient protein super family using motif search and structural modeling
Authors: Koonin Eugene V. , Tatusov Roman L. , Altschul Stephen F. , Bryant Stephen H. , Mushegian Arcady R. , Bork Peer , Valencia Alfonso 
Published: February 2009

AbstractUsing computer methods for multiple alignment, sequence motif search, and tertiary structure modeling, we show that eukaryotic translation elongation factor 1γ (EF1γ) contains an N‐terminal domain related to class θ glutathione S‐transferases (GST). GST‐like proteins related to class θ comprise a large group including, in addition to typical GSTs and EF1γ, stress‐induced proteins from bacteria and plants, bacterial reductive dehalogenases and β‐etherases, and several uncharacterized proteins. These proteins share 2 conserved sequence motifs with GSTs of other classes (α, μ, and π). Tertiary structure modeling showed that in spite of the relatively low sequence similarity, the GST‐related domain of EF1γ is likely to form a fold very similar to that in the known structures of class α, μ, and π GSTs. One of the conserved motifs is implicated in glutathione binding, whereas the other motif probably is involved in maintaining the proper conformation of the GST domain. We predict that the GST‐like domain in EF1γ is enzymatically active and that to exhibit GST activity, EF1γ has to form homodimers. The GST activity may be involved in the regulation of the assembly of multisubunit complexes containing EF1 and aminoacyl‐tRNA synthetases by shifting the balance between glutathione, disulfide glutathione, thiol groups of cysteines, and protein disulfide bonds. The GST domain is a widespread, conserved enzymatic module that may be covalently or noncovalently complexed with other proteins. Regulation of protein assembly and folding may be 1 of the functions of GST.
Unique dicistronic operon (ptsI‐crr) in Mycoplasma capricolum encoding Enzyme I and the glucose‐specific Enzyme IIA of the phosphoenolpyruvate: Sugar phosphotransferase system: Cloning, sequencing, promoter analysis, and protein characterization
Authors: Zhu Peng‐Peng , Peterkofsky Alan , Reizer Jonathan 
Published: February 2009

AbstractThe region of the genome of Mycoplasma capricolum encompassing the genes for Enzymes I and IIAglc of the phosphoenolpyruvate:sugar phosphotransferase system (PTS) was cloned and sequenced. Examination of the sequence revealed a unique arrangement of the pts operon. In all other bacterial species characterized thus far, the gene encoding Enzyme I (ptsI) in the pts operon is located immediately downstream of the gene (ptsH) encoding HPr, a general energy coupling protein of the PTS. In M. capricolum, ptsH and ptsI reside on 2 distinct operons at separate loci on the chromosome (Zhu PP, Reizer J, Reizer A, Peterkofsky A, 1993, J Biol Chem 268:26531–26540). In the present work, it is shown that the Mycoplasma Enzyme I gene is preceded by an open reading frame homologous to the product of the Escherichia coli kdtB gene and is followed by the gene (crr) encoding Enzyme IIAglc. Northern blot analysis indicated that ptsI and crr constitute a dicistronic operon that includes an independent promoter for the crr gene. Primer extension studies established the transcription start sites for the ptsI and crr genes. The products of the ptsI and crr genes are homologous to previously sequenced Enzymes I and IIAglc proteins but are more similar to the counterpart proteins from gram‐positive than to those from gram‐negative organisms. The deduced amino acid sequence of the Mycoplasma Enzyme I shows that it differs from other Enzymes I by having fewer acidic amino acids and more basic, amidated, and aromatic amino acids. The deduced amino acid sequence of the Mycoplasma Enzyme IIAglc indicates that it is the shortest (154 residues) of the proteins in this class and it is the only Enzyme IIAglc with a tryptophan and a cysteine residue. In vitro sugar phosphorylation studies with extracts from E. coli and Bacillus subtilis and purified proteins indicated that the Mycoplasma HPr is not a phosphoacceptor from the E. coli Enzyme I, whereas the Mycoplasma Enzyme IIAglc accepts and transfers phosphate from both E. coli and B. subtilis PTS components.
A structural comparison of 21 inhibitor complexes of the aspartic proteinase from Endothia parasitica
Authors: Bailey David , Cooper Jonathan B. 
Published: February 2009

AbstractThe aspartic proteinases are an important family of enzymes associated with several pathological conditions such as hypertension (renin), gastric ulcers (pepsin), neoplastic disease (cathepsins D and E), and AIDS (HIV proteinase). Studies of inhibitor binding are therefore of great importance for design of novel inhibitors for potential therapeutic applications. Numerous X‐ray analyses have shown that transition‐state isostere inhibitors of aspartic proteinases bind in similar extended conformations in the active‐site cleft of the target enzyme. Upon comparison of 21 endothiapepsin inhibitor complexes, the hydrogen bond lengths were found to be shortest where the isostere (P1–P'1) interacts with the enzyme's catalytic aspartate pair. Hydrogen bonds with good geometry also occur at P'2, and more so at P3, where a conserved water molecule is involved in the interactions. Weaker interactions also occur at P2, where the side‐chain conformations of the inhibitors appear to be more variable than at the more tightly held positions. At P2 and, to a lesser extent, P3, the side‐chain conformations depend intriguingly on interactions with spatially adjacent inhibitor side chains, namely P'1 and P1, respectively. The tight binding at P1–P'1, P3, and P'2 is also reflected in the larger number of van der Waals contacts and the large decreases in solvent‐accessible area at these positions, as well as their low temperature factors. Our analysis substantiates earlier proposals for the locations of protons in the transition‐state complex. Aspartate 32 is probably ionized in the complexes, its charge being stabilized by 1, or sometimes 2, hydrogen bonds from the transition‐state analogues at P1. The detailed comparison also indicates that the P1 and P2 residues of substrate in the ES complex may be strained by the extensive binding interactions at P3, P'1, and P'2 in a manner that would facilitate hydrolysis of the scissile peptide bond.
Immunoglobulin fold characteristics of B7–1 (CD80) and B7–2 (CD86)
Authors: Bajorath Jürgen , Peach Robert J. , Linsley Peter S. 
Published: February 2009

AbstractB7–1 and B7–2 are expressed on antigen‐presenting cells and bind to the CD28 and CTLA‐4 receptors on T cells. These interactions trigger a costimulatory pathway that is essential for T‐cell activation. B7–1 and B7–2 are members of the immunoglobulin superfamily (IgSF) and, despite sharing common function, have only limited sequence similarity. The B7–1 extracellular region was previously subdivided into 2 IgSF domains, an N‐terminal V(ariable)‐like domain, followed by a C(onstant)‐like domain. We recently reported that the V‐like domains of B7–1 and B7–2 share some significant sequence similarities with 3 major histocompatibility complex (MHC)‐encoded members of the IgSF. We have now applied inverse folding methodology to assess the compatibility of the B7–1 and B7–2 extracellular region sequences with currently available 3‐dimensional structures. In these calculations, the sequences of the N‐terminal (V‐like) domains in B7–1 and B7–2 were not compatible with known structures, including the IgSF V‐set. In contrast, the sequences of the C‐like domains were compatible with IgSF C‐set structures and were best recognized by the β2‐microglobulin (β2m) domain of MHC Class I. A sequence comparison of the C‐like domains in the B7 molecules showed that 11 of 17 rigorously conserved residues in B7–1 and B7–2 are not IgSF C‐1 set consensus residues. When mapped onto the corresponding positions of the β2m structure, the conserved residues in B7 cluster on the surface, where they may interact with the B7 V‐like domain or other molecules.