bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cocrystallization of Lysyl–tRNA synthetase from Thermus thermophilus with its cognate tRNAlys and with Escherichia coli tRNAlys
Authors: Yaremchuk A. D. , Cusack S. , Tukalo M. A. , Krikliviy I. A. 
Published: May 2005

AbstractLysyl‐tRNA synthetase from Thermus thermophilus has been cocrystallized with either its cognate tRNAlYS or Escherichia coli tRNAlys using ammonium sulfate as precipitant. The crystals grow from solutions containing a 1:2.5 stoichiometry of synthetase dimer to tRNA in 18–22% ammonium sulfate in 50 mM Tris‐maleate buffer at pH 7.5. Both complexes form square prismatic, tetragonal crystals with very similar unit cell parameters (a = b = 233 Å, c = 119 Å) and diffract to at least 2.7 Å resolution. However the homocomplex is of space group P4212 and the heterocomplex of space group I422. © 1995 Wiley‐Liss, Inc.
Purification, crystallization, and preliminary X‐ray diffraction analysis of even‐skipped homeodomain complexed to DNA
Authors: Hirsch Joel A. , Aggarwal Aneel K. 
Published: May 2005

AbstractEmbryonic development in metazoa, to a significant extent, is directed by genes which contain a conserved sequence motif named the homeobox. This sequence encodes a polypeptide called the homeodomain which has sequence specific DNA‐binding activity. We report the purification, crystallization, and preliminary diffraction analysis of the Drosophila Even‐skipped homeodomain (Eve HD) bound to two different oligonucleotides. Crystals of Eve HD complexed with an AT‐rich sequence belong to space group P21, a = 34.06, b = 61.61, c = 39.99 Å, b=90.0°. These crystals diffract to at least 2.0 Å and both native and derivative data sets have been collected. Crystals of Eve HD complexed with a GC‐rich sequence belong to space group P63, a = b = 124.52, c = 66.78 Å and diffract to 3.5 Å resolution. A native data set has been collected. © 1995 Wiley‐Liss, Inc.
Investigation of the folding pathway of the TEM‐1 β‐lactamase
Authors: Vanhove Marc , Raquet Xavier , Frère Jean‐Marie 
Published: May 2005

AbstractThe TEM‐1 β‐lactamase is a globular protein containing 12 proline residues. The folding mechanism of this enzyme was investigated by kinetic and equilibrium experiments with the help of fluorescence spectroscopy and circular dichroism. The equilibrium denaturation of the protein induced by guanidine hydrochloride occurs in two discrete steps, indicating the existence of a thermodynamically stable intermediate state. Thisstate is 5.2 ± 0.4 kcal/mol less stable than the native conformation and 5.7 ± 0.2 kcal/mol more stable than the fully denaturedprotein. This intermediate state exhibits a high content of native secondary structure elements but is devoid of specific tertiary organization; its relation to the “molten globule” is discussed. Refolding kinetic experimentsrevealed the existence of a transient intermediate conformation between thethermodynamically stable intermediate and the native protein. This transient intermediate appears rapidly during the folding reaction. It exhibits a secondary structure content very similar to that of the native protein and has also recovered a significant amount of tertiary organisation. The final refolding step of the TEM‐1 β‐lactamase, leading to the native enzyme, is dominated by two major slow kinetic phases which probablyreflect a very complex process kinetically limited by proline cis/transisomerization. © 1995 Wiley‐Liss, Inc.
Insulin and epidermal growth factor receptors contain the cysteine repeat motif found in the tumor necrosis factor receptor
Authors: Ward C. W. , Hoyne P. A. , Flegg R. H. 
Published: May 2005

AbstractThe insulin receptor (INSR) and epidermal growth factor receptor (EGFR) are representatives of two structurally related subfamilies of tyrosine kinase receptors. Using the Wisconsin GCG sequence analysis programs, we have demonstrated that the cysteinerich regions of INSR and EGFR conform to the structural motif found in the tumor necrosis factorreceptor (TNFR) family. The study also revealed that these regions were not composed of simple repeats of eight cysteine residues as previously proposed and that the second Cysrich region of EGFR contained one fewer TNFR repeat than the first. The sequence alignments identified two cysteineresidues in INSR that could be responsible for the additional disulfide bonds known to be involved in dimer formation. The published data on the alignments for the fibronectin type III repeat region of the INSR together with previous cysteine mutagenesis studies indicated that there were two disulfide bonds linking the α and β chains of the INSR, but only one α‐β linkage in the insulin‐like growth factor 1 receptor (IG 1R). Database searches and sequence alignments showed that the TNFR motif is also found in the cysteine‐rich repeats of laminins and the noncatalytic domains of furin‐like proteases. If the starting position of the repeat is altered the characteristic laminin repeat of eight cysteine residues can be shown to consist of a TNFR‐like motif fused to the last half of an EGF‐like repeat. The overlapping regions of these two motifs are known to have identical disulfide bonding patterns and similar protein folds. © 1995 Wiley‐Liss, Inc.
Molecular dynamics simulations of rubredoxin from Clostridium pasteurianum: Changes in structure and electrostatic potential duringredox reactions
Authors: Yelle Robert B. , Park Noh‐Sum , Ichiye Toshiko 
Published: May 2005

AbstractMolecular dynamics simulations of Clostridium pasteurianum rubredoxin in the oxidized and reduced forms have been performed. Good agreement between both forms and crystal data has been obtained (rms deviation of backbone atoms of 1.06 and 1.42 Å, respectively), which was due in part to the use of explicit solvent and counterions. The reduced form exhibits an unexpected structural change: the redox site becomes much more solvent‐accessible, so that water enters a channel between the surface and the site, but with little actual structural rearrangement (the rms deviation of backbone atoms between the oxidized and reduced is 0.77 Å). The increase in solvent accessibility is also seen, although to a much lesser extent, between the oxidized and reduced crystal structures of Pyrococcus furiosus rubredoxin, but no high resolution crystal or nuclear magnetic resonance solution data exist for reduced C. pasteurianum rubredoxin. The electrostatic potential at the iron site and fluctuations in the potential, which contribute to both the redox and electron transfer properties, have also been evaluated for both the oxidized and the reduced simulations. These results show that the backbone plays a significant role (62–70 kcall/mol/e) and the polar sidechains contribute relatively little (0–4 kcal/mol/e) to the absolute electrostatic potential at the iron of rubredoxin for both forms. However, both groups contribute significantly to the change in redox state by becoming more polarized and more densely packed around the redox site upon reduction. Furthermore, these results show that the solvent becomes much more polarized in the reduced form than in the oxidized form, even excluding the penetrating water. Finally, the simulation indicates that the contribution of the charged side chains to the electrostatic potential is largely canceled by that of the counterions. © 1995 Wiley‐Liss, Inc.
The cytidylyltransferase superfamily: Identification of the nucleotide‐binding site and fold prediction
Authors: Bork Peer , Holm Liisa , Koonin Eugene V. , Sander Chris 
Published: May 2005

AbstractThe crystal structure of glycerol‐3‐phosphate cytidylyltransferase from B. subtilis (TagD) is about to be solved. Here, we report a testable structure prediction based on the identification by sequence analysis of a superfamily of functionally diverse but structurally similar nucleotide‐binding enzymes. We predict that TagD is a member of this family. The most conserved region in this superfamily resembles the ATP‐binding HiGH motif of class I aminoacyI‐tRNA synthetases. The predicted secondary structure of cytidylyltransferase and its homologues is compatible with the α/β topography of the class I aminoacyl‐tRNA synthetases. The hypothesis of similarity of fold is strengthened by sequence‐structure alignment and 3D model building using the known structure of tyrosyl tRNA synthetase as template. The proposed 3D model of TagD is plausible both structurally, with a well packed hydrophobic core, and functionally, as the most conserved residues cluster around the putative nucleotide binding site. If correct, the model would imply a very ancient evolutionary link between class I tRNA synthetases and the novel cytidylyltransferase superfamily. © 1995 Wiley‐Liss, Inc.
Size‐independent comparison of protein three‐dimensional structures
Authors: Maiorov Vladimir N. , Crippen Gordon M. 
Published: May 2005

AbstractProtein structures are routinely compared by their root‐mean‐square deviation (RMSD) in atomic coordinates after optimal rigid body superposition. What is not so clear is the significance of different RMSD values, particularly above the customary arbitrary cutoff for obvious similarity of 2–3 Å. Our earlier work argued for an intrinsic cutoff for protein similarity that varied with the number of residues in the polypeptide chains being compared. Here we introduce a new measure, ρ, of structural similarity based on RMSD that is independent of the sizes of the molecules involved, or of any other special properties of molecules. When ρ is less than 0.4–0.5, protein structures are visually recognized to be obviously similar, but the mathematically pleasing intrinsic cutoff of ρ>1.0 corresponds to overall similarity in folding motif at a level not usually recognized until smoothing of the polypeptide chain path makes it striking. When the structures are scaled to unit radius of gyration and equal principle moments of inertia, the comparisons are even more universal, since they are no longer obscured by differences in overall size and ellipticity. With increasing chain length, the distribution of ρ for pairs of random structures is skewed to higher values, but the value for the best 1% of the comparisons rises only slowly with the number of residues. This level is close to an intrinsic cutoff between similar and dissimilar comparisons, namely the maximal scaled ρ possible for the two structures to be more similar to each other than one is to the other's mirror image. The intrinsic cutoff is independent of the number of residues or points being compared. For proteins having fewer than 100 residues, the 1% ρ falls below the intrinsic cutoff, so that for very small proteins, geometrically significant similarity can often occur by chance. We believe these ideas will be helpful in judging success in NMR structure determination and protein folding modeling. © 1995 Wiley‐Liss, Inc.
Crystallization and preliminary crystallographic analysis of a 2,3‐dihydroxybiphenyl dioxygenase from Pseudomonas sp. strain KKS102 having polychlorinated biphenyl (PCB)‐degrading activity
Authors: Sugiyama Kazuyuki , Narita Hiroki , Yamamoto Takeshi , Senda Toshiya , Kimbara Kazuhide , Inokuchi Norio , Iwama Masanori , Irie Masachika , Fukuda Masao , Yano Keiji , Mitsui Yukio 
Published: May 2005

AbstractCrystals have been obtained for a 2,3‐dihydroxybiphenyl dioxygenase (conventionally called BphC) from a polychlorinated biphenyl (PCB)‐degrader, Pseudomonas sp. strain KKS1O2. The crystals were grown using both ammonium sulfate and MPD as the precipitating agents. The crystals belonged to a tetragonal space group (I422) and diffracted to 2.5 Å. © 1995 Wiley‐Liss, Inc.
Crystallization and preliminary X‐ray crystallographic studies of nonhistone region of macroH2A.1
Authors: Senadhi Vijay‐Kumar , Chandra Naveen , Dharia Chhaya , Pehrson John R. 
Published: May 2005

AbstractHistone macroH2A has a novel hybrid structure consisting of a large nonhistone region and a region that closely resembles a full‐length histone H2A. One key to understanding macroH2A function is determining the structure and function of its nonhistone region. The nonhistone region of one of the two known macroH2A subtypes was expressed in Escherichia coli and purified using affinity and molecular sieve chromatography. Crystals of the protein suitable for structural studies were grown from polyethylene glycol solutions by vapor equilibration techniques. The crystals belong to the hexagonal space group P64 (or its enantiomorph P62) with unit cell parameters: a = b = 106.2 Å, c = 125.9 Å, α = β = 90°, and γ = 120°. There are four molecules in the asymmetric unit. Self‐rotation function studies revealed three twofold noncrystallographic rotation axes related approximately by 222 symmetry. These crystals have 47% solvent content and diffract to 3.8 Å resolution. © 1995 Wiley‐Liss, Inc.
Automatic identification of discrete substates in proteins: Singular value decomposition analysis of time‐averaged crystallographic refinements
Authors: Romo T. D. , Clarage J. B. , Sorensen D. C. , Phillips G. N. 
Published: May 2005

AbstractThe singular value decomposition (SVD) provides a method for decomposing a molecular dynamics trajectory into fundamental modes of atomic motion. The right singular vectors are projections of the protein conformations onto these modes showing the protein motion in a generalized low‐dimensional basis. Statistical analysis of the right singular vectors can be used to classify discrete configurational substates in the protein. The configuration space portraits formed from the right singular vectors can also be used to visualize complex high‐dimensional motion and to examine the extent of configuration space sampling by the simulation. © 1995 Wiley‐Liss, Inc.
Phe‐46(CD4) orients the distal histidine for hydrogen bonding to bound ligands in sperm whale myoglobin
Authors: Lai Henry H. , Li Tiansheng , Lyons Daniel S. , Phillips George N. , Olson John S. , Gibson Quentin H. 
Published: May 2005

AbstractThe role of Phe‐46(CD4) in modulating the functional properties of sperm whale myoglobin was investigated by replacing this residue with Leu, Ile, Val, Ala, Trp, Tyr, and Glu. This highly conserved amino acid almost makes direct contact with the distal histidine and has been postulated to affect ligand binding. The overall association rate constants for CO, O2, and NO binding were little affected by decreasing the size of residue 46 step‐wise from Phe to Leu to Val to Ala. In contrast, the rates of CO, O2, and NO dissociation increased 4‐, 10‐, and 25‐fold, respectively, for the same series of mutants, causing large decreases in the affinity of myoglobin for all three diatomic gases. The rates of autooxidation at 37°C, pH 7.0 increased dramatically from ∼0.1–0.3 h−1 for wild‐type, Tyr‐46, and Trp‐46 myoglobins to 1.5, 5.2, 4.9, and 5.0 h−1 for the Leu‐46, Ile‐46, Val‐46, and Ala‐46 mutants, respectively. Rates of NO and O2 geminate recombination were measured using 35 ps and 9 ns laser excitation pulses. Decreasing the size of residue 46 causes significant decreases in the extent of both picosecond and nanosecond rebinding processes. High resolution structures of Leu‐46 and Val‐46 metmyoglobins, Val‐46 CO‐myoglobin, and Val‐46 deoxymyoglobin were determined by X‐ray crystallography. When Phe‐46 is replaced by Val, the loss of internal packing volume is compensated by (1) contraction of the CD corner toward the core of the protein, (2) movement of the E‐helix toward the mutation site, (3) greater exposure of the distal pocket to intruding solvent molecules, and (4) large disorder in the position of the side chain of the distal histidine (His‐64). In wild‐type myoglobin, the van der Waals contact between Cζ of Phe‐46 and Cβ of His‐64 appears to restrict rotation of the imidazole side chain. Insertion of Val at position 46 relieves this steric restriction, allowing the imidazole side chain to rotate about the Cα–Cβ bond toward the surface of the globin and about the Cβ–Cγ bond toward the space previously occupied by the native Phe‐46 side chain. This movement disrupts hydrogen bonding with bound ligands, causing significant decreases in affinity, and opens the distal pocket to solvent water molecules, causing marked increases in the rate of autooxidation. The upward movement of the imidazole side chain also creates new space for photodissociated ligands and for incoming water molecules to approach the iron atom. Both of these phenomena inhibit geminate recombination and can be correlated with molecular dynamics calculations. All of these results show that this mutation in the second shell of amino acids around the distal pocket can influence ligand binding significantly. © 1995 Wiley‐Liss, Inc.
Empirical correlation for the replacement of Ala by Gly: Importance of amino acid secondary intrinsic propensities
Authors: López‐Hernández Eva , Serrano Luis 
Published: May 2005

AbstractA series of Ala vs. Gly mutations at different helical and nonhelical positions of the chemotactic protein CheY, fromE. coli, has been made. We have used this information to fit a general analytical equation that describes the free energy changes of an Ala to Gly mutation within ±0.45 kcal mol−1with 95% confidence. The equation includes three terms: (1) the change in solvent‐accessible hydrophobic surface area, corrected for the possible closure of the cavity left by deleting the Cβof the Ala; (2) the change in hydrophilic area of the nonintramolecularly hydrogen‐bonded groups; and (3) the dihedral angles of the position being mutated. This last term extends the calculation to any conformation, not only α‐helices. The general applicability of the equation for Ala vs. Gly mutations, when Ala or a small solvent‐exposed polar residue is the wild‐type residue, has been tested using data from other proteins: barnase, CI2 trypsin inhibitor, T4 lysozyme, andStaphylococcusnuclease. The predictive power of this simple approach offers the possibility of extending it to more complex mutations. © 1995 Wiley‐Liss, Inc.
Interaction stabilizing tertiary structure of bacteriorhodopsin studied by denaturation experiments
Authors: Mitaku Shigeki , Suzuki Keiko , Odashima Seiji , Ikuta Kazuya , Suwa Makiko , Kukita Fumio , Ishikawa Mitsuru , Itoh Hiroyasu 
Published: May 2005

AbstractThe structural stability of bacteriorhodopsin was studied by denaturation experiments, using aliphatic alcohol as denaturants. The disappearance of a positive peak at 285 nm of the circular dichroism spectra, the change in the intrinsic fluorescence decay time, and the decrease of the regeneration activity bacteriorhodopsin indicated the denaturation of the tertiary structure of this protein at a methanol concentration of about 3 M. The circular dichroism band at 222 nm was unchanged by the denaturation. It was concluded that the alcohol‐denatured state in water was similar to the molten globule state of soluble proteins, in which only the tertiary structure was destroyed. Solvent substitution from water to hexane did not cause denaturation of bacteriorhodopsin. However, further addition of alcohol destroyed the secondary as well as the tertiary structures. Comparing the alcohol effects on bacteriorhodopsin in water to that in hexane, the dominant interactions for the structure formation of this protein could be revealed: the hydrophobic interaction that arose from the structure of water is essential for the stability of membrane spanning helices, while the interaction which binds the helices is polar in nature. © 1995 Wiley‐Liss, Inc.
Multiple modes of ligand recognition: Crystal structures of cyclin‐dependent protein kinase 2 in complex with ATP and two inhibitors, olomoucine and isopentenyladenine
Authors: Schulze‐Gahmen Ursula , Brandsen Jeroen , Jones Heather D. , Morgan David O. , Meijer Laurent , Vesely Jaroslav , Kim Sung‐Hou 
Published: May 2005

AbstractCyclin‐dependent kinases (CDKs) are conserved regulators of the eukaryotic cell cycle with different isoforms controlling specific phases of the cell cycle. Mitogenic or growth inhibitory signals are mediated, respectively, by activation or inhibition of CDKs which phosphorylate proteins associated with the cell cycle. The central role of CDKs in cell cycle regulation makes them a potential new target for inhibitory molecules with anti‐proliferative and/or anti‐neoplastic effects. We describe the crystal structures of the complexes of CDK2 with a weakly specific CDK inhibitor, N6‐(δ2‐isopentenyl)adenine, and a strongly specific inhibitor, olomoucine. Both inhibitors are adenine derivatives and bind in the adenine binding pocket of CDK2, but in an unexpected and different orientation from the adenine of the authentic ligand ATP. The N6‐benzyl substituent in olomoucine binds outside the conserved binding pocket and is most likely responsible for its specificity. The structural information from the CDK2‐olomoucine complex will be useful in directing the search for the next generation inhibitors with improved properties. © 1995 Wiley‐Liss, Inc.
Optimal local propensities for model proteins
Authors: Govindarajan Sridhar , Goldstein Richard A. 
Published: May 2005

AbstractLattice models of proteins were used to examine the role of local propensities in stabilizing the native state of a protein, using techniques drawn from spin‐glass theory to characterize the free‐energy landscapes. In thestrongevolutionary limit, optimal conditions for folding are achieved when the contributions from local interactions to the stability of the native state is small. Further increasing the local interactions rapidly decreases the foldability. © 1995 Wiley‐Liss, Inc.
Stability of TEM β‐lactamase mutants hydrolyzing third generation cephalosporins
Authors: Raquet X. , Vanhove M. , Lamotte‐Brasseur J. , Goussard S. , Courvalin P. , Frère J‐M. 
Published: May 2005

AbstractThe stability properties of six natural mutants of the TEM‐1 β‐lactamase have been studied. The glutamate to lysine substitution at positions 104 and 240 stabilize the enzyme. Conversely, the G238S mutant's decreased stability might reflect an altered conformation of the active site and thus be related to the modified substrate profile. The relative stability of the R164S and R164H mutants is explained by the formation of a hydrogen bond between these residues and Asp‐179 conferring a somewhat different structure to the omega loop and thus also explaining the extended substrate profile of these mutants. The loss of stability of the R164H mutant with increasing pH values can be explained by the titration of a hydrogen bond between the Nδ of His‐164 and the Oδ of Asp‐179. The properties of the G238S+E104K double mutant which is the most active against third‐generation cephalosporins result from a balance of destabilizing and stabilizing substitutions, and their effects seem to be additive. The behavior of the R164S + E240K mutant might be explained on the basis of a similar compensation phenomenon. © 1995 Wiley‐Liss, Inc.