bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crystallization and preliminary X‐ray diffraction studies of peroxidase from a fungus Arthromyces ramosus
Authors: Kunishima Naoki , Fukuyama Keiichi , Wakabayashi Sadao , Sumida Motoo , Takaya Masamitsu , Shibano Yuji , Amachi Teruo , Matsubara Hiroshi 
Published: May 2005

AbstractPeroxidase (donor: H2O2 oxi‐doreductase [EC 1.11.1.7]) was purified from the culture broth of the hyphomycete Arthromyces ramosus in the early log phase to show a single band on SDS‐PAGE. The crystals of A. ramosus peroxidase (ARP) were formed by salting out with ammonium sulfate at room temperature and pH 7.5. The repeated seeding technique was employed to grow the crystals to the size large enough for X‐ray diffraction study. The crystals were characterized as tetragonal, space group P42212, with unit cell dimensions of a = b = 74.5 Å, c = 117.6 Å. The asymmetric unit contains one molecule of peroxidase. They diffract X‐rays to at least 2.0 Å resolution and are stable to X‐rays. © 1993 Wiley‐Liss, Inc.
“Ensemble” iterative relaxation matrix approach: A new NMR refinement protocol applied to the solution structure of crambin
Authors: Bonvin Alexandre M. J. J. , Rullmann J. Antoon C. , Lamerichs Rolf M. J. N. , Boelens Rolf , Kaptein Robert 
Published: May 2005

AbstractThe structure in solution of crambin, a small protein of 46 residues, has been determined from 2D NMR data using an iterative relaxation matrix approach (IRMA) together with distance geometry, distance bound driven dynamics, molecular dynamics, and energy minimization. A new protocol based on an “ensemble” approach is proposed and compared to the more standard initial rate analysis approach and a “single structure” relaxation matrix approach. The effects of fast local motions are included and R‐factor calculations are performed on NOE build‐ups to describe the quality of agreement between theory and experiment. A new method for stereospecific assignment of prochiral groups, based on a comparison of theoretical and experimental NOE intensities, has been applied. The solution structure of crambin could be determined with a precision (rmsd from the average structure) of 0.7 Å on backbone atoms and 1.1 Å on all heavy atoms and is largely similar to the crystal structure with a small difference observed in the position of the side chain of Tyr‐29 which is determined in solution by both J‐coupling and NOE data. Regions of higher structural variability (suggesting higher mobility) are found hi the solution structure, in particular for the loop between the two helices (Gly‐20 to Pro‐22). © 1993 Wiley‐Liss, Inc.
Perturbation of Trp 138 in T4 lysozyme by mutations at Gln 105 used to correlate changes in structure, stability, solvation, and spectroscopic properties
Authors: Pjura Philip , McIntosh Lawrence P. , Wozniak Joan A. , Matthews Brian W. 
Published: May 2005

AbstractIn order to correlate between spectroscopic and structural changes in a protein, the environment of Trp 135 in T4 lysozyme was deliberately perturbed by the replacement of Gln 105 with alanine (Q105A), glycine (Q105G), and glutamic acid (Q105E). In wild‐type lysozyme, Trp 135 is buried, but the indole nitrogen is hydrogen‐bonded to the side‐chain of Gln 105. In the Q105G and Q105A mutant structures, the indole nitrogen becomes accessible to solvent. Crystallographic analysis shows that the structures of all of the mutants are similar to wild‐type. There are, however, distinct rearrangements of the local solvent structure in response to the new side‐chains. There are also small but significant changes in the relative orientations of the two domains of the protein that appear to result from a series of small, concerted movements of side‐chains adjacent to residue 105. Evaluation of the fluorescence and phosphorescence of the mutant proteins in terms of their observed three‐dimensional structures shows that large spectral changes do not necessarily imply large changes in structure or in static solvent accessibility. Increases in polar relaxation about the excited state of tryptophan may be the result of only small increases in local dynamics or solvent exposure. 1H‐NMR was also used to monitor the effects of the substitutions on Trp 138. In Q105E, but not in Q105G, Q105A and WT, the Hε1 chemical shift of Trp 138 is very pH‐dependent, apparently reflecting the titration of Glu 105 which has a spectroscopically determined pKa of 6.0. The elevation of the pKa of Glu 105 in Q105E is also reflected in the pH dependence of the stability of this mutant. © 1993 Wiley‐Liss, Inc.
Novel mechanism‐based substrates of dihydrofolate reductase and the thermodynamics of ligand binding: A comparison of theory and experiment for 8‐methylpterin and 6,8‐dimethylpterin
Authors: Cummins Peter L. , Gready Jill E. 
Published: May 2005

AbstractMolecular dynamics simulation and free energy perturbation techniques have been used to study the relative binding free energies of the designed mechanism‐based pterins, 8‐methylpterin and 6,8‐dimethylpterin, to dihydrofolate reductase (DHFR), with co‐factor nicotinamide adenine dinucleotide phosphate (NADPH). The calculated free energy differences suggest that DHFR.NADPH.6,8‐dimethylpterin is thermodynamically more stable than DHFR.NADPH.8‐methylpterin by 2.4 kcal/mol when the substrates are protonated and by 1.3 kcal/mol when neutral. The greater binding strength of 6,8‐dimethylpterin may be attributed largely to hydration effects. In terms of an appropriate model for the pH‐dependent kinetic mechanism, these differences can be interpreted consistently with experimental data obtained from previous kinetic studies, i.e., 6,8‐dimethylpterin is a more efficient substrate of vertebrate DHFRs than 8‐methylpterin. The kinetic data suggest a value of 6.6 ± 0.2 for the pKa of the active site Glu‐30 in DHFR.NADPH. We have also used experimental data to estimate absolute values for thermodynamic dissociation constants of the active (i.e., protonated) forms of the substrates: these are of the same order as for the binding of folate (0.1–10 μM). The relative binding free energy calculated from the empirically derived dissociation constants for the protonated forms of 8‐methylpterin and 6,8‐dimethylpterin is 1.4 kcal/mol, a value which compares reasonably well with the theoretical value of 2.4 kcal/mol. © 1993 Wiley‐Liss, Inc.
Crystallization and preliminary X‐ray diffraction data of two heparin‐binding fragments of human fibronectin
Authors: Pechik Lgor , Nachman Joseph , Ingham Kenneth , Gilliland Gary L. 
Published: May 2005

AbstractTwo different heparin‐binding fragments of human fibronectin have been crystallized in forms which are suitable for crystal structure analyses. The 30 kDa hep‐2A fragment, consisting of type III domains 12–14, was crystallized from solutions containing ammonium sulfate or polyethylene glycol 6000. The crystals grown in ammonium sulfate solutions were orthorhombic with space group I222 or I212121 with a = 68.1 Å, b = 88.6 Å, and c = 144.9 Å. The crystals grown in polyethylene glycol solutions are hexagonal with space group P6122 or P6522 witha a = b = 66.7 Å and c = 245.7 Å. The 40 kDa hep‐2B fragment, consisting of type III domains 12–15, was also crystallized from solutions containing ammonium sulfate with the addition of glycerol. Glycerol proved an effective agent for reducing the number of crystals in the crystallization experiments, and thus, increasing the size of the crystals in these experiments. This crystal form is nearly isomorphous to the orthorhombic form of the hep‐2A fragment with space group I222 or I212121 and a = 67.5 Å, b = 87.0 Å, and c = 144.3 Å. All crystal forms diffract to at least 3.5 Å resolution and contain a single molecule in the asymmetric unit. © 1993 Wiley‐Liss, Inc.
Picosecond timescale rigid‐helix and side‐chain motions in deoxymyoglobin
Authors: Furois‐Corbin Sylvie , Smith Jeremy C. , Kneller Gerald R. 
Published: May 2005

AbstractThe contribution of rigidbody motions to the atomic trajectories in a 100 ps molecular dynamics simulation of deoxymyoglobin is examined. Two typesof rigid‐body motions are considered: one in which the helices are rigid units and one in which the side‐chains are rigid units. Using a quaternionbased algorithm, fits of the rigid reference structures are made to each time frame of the simulation to derive trajectories of the rigid‐body motions. The fitted trajectories are analysed in terms of atomic position fluctuations, mean‐square displacements as a function of time, velocity autocorrelation functions and densities of states. The results are compared with the corresponding quantities calculated from the full trajectory. The relative contribution of the rigid helix motions to the helix atom dynamics depends on which quantity is examined and on which subset of atoms is chosen: rigid‐helix motions contribute 86% of the rms helix backbone atomic position fluctuations, but 30% of the helix,: atom (backbone and side‐chain) mean square displacements and only 1.1% of total kinetic energy. Only very low‐frequency motions contribute to the rigid‐helix dynamics; the rigid‐body analysis allows characteristic rigid‐helix vibrations to be identified and described. Treating the side‐chains as rigid bodies is foundto be an excellent approximation to both their diffusive and vibrationalmean‐square displacements: 96% of side‐chain atom mean‐square displacements originate from rigid side‐Chain motions. However, the errors in theside‐chain atomic positional fits are not always small. An analysis is madeof factors contributing to the positional error for different types of side‐chain. © Wiley‐Liss, Inc.
Calcium‐independent subtilisin by design
Authors: Gallagher Travis , Bryan Philip , Gilliland Gary L. 
Published: May 2005

AbstractA version of subtilisin BPN′ lacking the high affinity calcium site (site A) has been produced through genetic engineering methods, and its crystal structure refined at 1.8 Å resolution. This protein and the corresponding version containing the calcium A site are describedand compared. The deletion of residues 75–83 was made in the context of four site‐specific replacements previously shown to stabilize subtilisin. The helix that in wild type is interrupted by the calcium binding loop, is continuous in the deletion mutant, with normal geometry. A few residues adjacent to the loop, principally those that were involved in calcium coordination, are repositioned and/or destabilized by the deletion. Because refolding is greatly facilitated by the absence of the Caloop, this proteinoffers a new vehicle for analysis and dissection of the folding reaction. This is among the largest internal changes to a protein to be described at atomic resolution. © Wiley‐Liss, Inc.
Improved calculations of compactness and a reevaluation of continuous compact units
Authors: Zehfus Micheal H. 
Published: May 2005

AbstractA new method for calculating compactness (Z) that uses look‐up table‐based algorithms for area and volume computations is introduced. These algorithms can be used in any iterative area orvolume calculation, are more than 1000 times faster than the originalalgorithms, and have equal or better precision. With the faster algorithms it is now possible to calculate the compactness of all continuous units in a protein, and to precisely locate the optimal compact units without the screening functions and limited resolution used previously. These methods have been incorporated into a fully automatic domain finding algorithm, and this method has been applied to the 21 proteins originally analyzed as well as 12 additional proteins. This method is robust, and yields similar units even when applied to coordinates of protein crystals grown under different experimental conditions. © 1993 Wiley‐Liss, Inc.
The structure of a centrosymmetric protein crystal
Authors: Zawadzke Laura E. , Berg Jeremy M. 
Published: May 2005

AbstractCrystals of racemic rubredoxin, prepared by independent chemical synthesis of the two enantiomers, have been grown and characterized. The unit cell contains two molecules, one of each enantiomer. Examination of the intensity distribution in the diffraction pattern revealed that the crystals are centrosymmetric. This was confirmed by solution of thestructure to 2 Å resolution via molecular replacement methods. The electron density maps are of very high quality due to the fact that the phaseof each reflection must be exactly 0° or exactly 180°. These results demonstrate the feasibility of using synthetic racemic proteins to yield centrosymmetric protein crystals with electron density maps that have very low phase error and model bias. © 1993 Wiley‐Liss, Inc.
Mutational tests of the NMR‐docked structure of the staphylococcal nuclease–metal–3′,5′‐pdTp complex
Authors: Chuang Woei‐Jer , Weber David J. , Gittis Apostolos G. , Mildvan Albert S. 
Published: May 2005

AbstractIn the X‐ray structure of the staphylococcal nuclease–Ca2+ −3′,5′‐pdTp complex, the conformation of the inhibitor 3′,5′‐pdTp is distroteed Lys‐70* and Lys‐71* from an adjacent molecule of staphylococcal nuclease (Loll, P.J., Lattman, E.E. Proteins 5 : 183‐201, 1989). In order to correct this crystal packing problem, the solution conformation of enzyme‐bound 3′,5′‐pdTp in the staphylococcal nuclease–metal–pdTp Complex determined by NMR methods was docked into the X‐ray structure of the enzyme [Weber, D. J., Serpersu, E. H., Gittis, A. G., Lattman, E. E., Mildvan, A. S. (preceding paper)]. In the NMR‐docked structure, the 5′‐phophate of 3′,5′‐pdTp overlaps with that in the X‐ray Structure. However the 3′‐phosphate accepts a hydrogen bond from Lys‐49 (2.89Å) rather than from Lys‐84 (8.63 Å), and N3 of thymine donates a hydrogen bond to the OH of Tyr‐115 (3.16 Å) which does not occur in the X‐ray structure (5.28 Å). These interactions have been tested by binding studies of 3′,5′‐pdTp, Ca2+, and Mn2+ to the K49A, K84A, and Y115A mutants of staphylococcal nuclease using water proton relaxation rate and EPR methods. Each mutant was fully active and structurally intact, as found by CD and two‐dimensional NMR spectroscopy, but bound Ca2+ 9.1‐ to 9.9‐fold more weakly than the wild‐type enzyme. While thye K84A mutation did not significantly weaken 3′,5′‐pdTp binding to the enzyme (1.5 ± 0.7 fold), the K49A mutation weakened 3′,5′‐pdTp binding to the enzyme by the factor of 4.4 ± 1.8‐fold. Similarly, the Y115A mutation weakened 3′,5′‐pdTp binding to the enzyme 3.6 ± 1.6‐fold. Comparable weakening effects of these mutations were found on the binding of Ca2+‐3′,5′‐pdTp. These results are more readily explained by the NMR‐docked structure of staphylococcal nuclease‐metal‐3′,5′‐pdTp than by the X‐ray structure. © 1993 Wiley‐Liss, Inc.
Structural relationships of homologous proteins as a fundamental principle in homology modeling
Authors: Hilbert Martina , Böhm Gerald , Jaenicke Rainer 
Published: May 2005

AbstractProtein structure prediction is based mainly on the modeling of proteins by homology to known structures; this knowledgebased approach is the most promising method to date. Although it is used in the whole area of protein research, no general rules concerning the quality and applicability of concepts and procedures used in homology modeling have been put forward yet. Therefore, the main goal of the present work is to provide tools for the assessment of accuracy of modeling at a given level of sequence homology. A large set of known structures from different conformational and functional classes, but various degrees of homology was selected. Pairwise structure superpositions were performed. Starting with the definition of the structurally conserved regions and determination of topologically correct sequence alignments, we correlated geometrical properties with sequence homology (defined by the 250 PAM Dayhoff Matrix) and identity. It is shown that both the topological differences of the protein backbones and the relative positions of corresponding side chains diverge with decreasing sequence identity. Below 50% identity, the deviation in regions that are structurally not conserved continually increases, thus implying that with decreasing sequence identity modeling has to take into account more and more structurally diverging loop regions that are difficult to predict. © 1993 Wiley‐Liss, Inc.
Influence of protein flexibility on the redox potential of rubredoxin: Energy minimization studies
Authors: Shenoy Vaishali S. , Ichiye Toshiko 
Published: May 2005

AbstractA theoretical investigation of the protein contribution to the redox potential of the iron–sulfur protein rubredoxin is presented. Structures of the oxidized and reduced forms of the protein were obtained by energy minimizing the oxidized crystal structure of Clostridium pasteurianum rubredoxin with appropriate charges and parameters. By including 102 crystal waters, structures close to the original crystal structure were obtained (rms difference of 1.16 Å), even with extensive minimization, thus allowing accurate calculations of comparative energies. Our calculations indicate an energy change of about –60 kcal/mol (2.58 eV) in the protein alone upon reduction. This energy change was due to both the change in charge of the redox site and the subsequent relaxation of the protein. An energy minimization procedure for the relaxation gives rms differences between the oxidized and reduced states of about 0.2 Å. The changes were small and occurred in both the backbone and sidechain mainly near the Fe–S center but contributed about – 16 kcal/mol (0.69 eV) to the total protein contribution. Although the neglect of certain effects such as electronic polarization may make the relaxation energies calculated an upper limit, the results indicate that protein relaxation contributes substantially to the redox potential. © 1993 Wiley‐Liss, Inc.
Molecular skins: A new concept for quantitative shape matching of a protein with its small molecule mimics
Authors: Masek Brian B. , Merchant Arshad , Matthew James B. 
Published: May 2005

AbstractA novel analytical method for comparing molecular shapes by optimizing the intersection of molecular “SKINS” has been developed. This method provides a quantitative measure of the shape similarity by maximizing the intersection volume of molecular surfaces with a finite thickness; a molecular skin. We report shape matching of a small tripeptide inhibitor (DFKi) of elastase class proteins with the 56 residue turkey ovomucoid inhibitor (TOMI). To match a large elastase inhibitor such as TOMI with a small inhibitor or drug, we found that it is necessary to use a skin match rather than molecular volume. Skin based comparisons of TOMI protein with DFKi successfully found the alignment expected from comparison of their respective crystallographic complexes with elastase (i.e. HLE/TOMI complex and PPE/tripeptide complex). In the skin comparison of the tripeptide with the TOMI protein, blind searching for skin matches involved optimization of the skin intersection from 172 starting positions randomly selected from a set of 500 points on the TOMI van der Waals surface [within 9.5 Å of the Leu‐18 on the TOMI binding loop (1 point/Å2)]. The tripeptide center of mass was placed at these points and its orientation was randomized before optimization was initiated. The best skin intersection, 86.4 Å3, was found thre times and corresponds to the experimental alignment. The next best skin intersection was 78.1 Å3 giving a discrimination factor in this case of 10%. Searches over the entire surface of the TOMI protein did not identify any new matches with skin intersection greater than 78.1 Å3. Matching the DFKi with a TOMI structure relaxed from its crystal conformation by molecular dynamics gives similar results. © 1993 Wiley‐Liss, Inc.
A reduced representation of proteins for use in restraint satisfaction calculations
Authors: Herzyk Pawel , Hubbard Rodrick E. 
Published: May 2005

AbstractA reduced representation of paroteins has been developed for use in restraint satisfaction calculations with dynamic simulated annealing. Each amino acid residue is represented by up to four spherical virtual atoms. The virtual bonds and excluded volume of these atoms has ben parameterized by analysis of 83 protein structures determined at high resolution by X‐ray crystallography. The use of the new representation in NOE distance restraint satisfaction has been compared with the standard all‐atom represntation for the determination of the structures of crambin, eshistatin, and protein G. Using the reduced representation, there is a 30‐fold decrease in the computer time needed for generatin a single structure, and up to a 20‐fold decrease in the time taken to produce an acceptable structure compared to using the all‐atom representation. The root mean square deviation between the mean structure obtain with all‐atom and reduced representation si between 1.5 and 1.7 Å for Cα atoms. The new representation is adequate for describing the “low‐resolution” features of protein structure such as the general fold and the positions of the secondary structure for more detailed refinement with the full all‐atom representation. © 1993 Wiley‐Liss, Inc.
Growth and analysis of crystal forms of toxic shock syndrome toxin 1
Authors: Earhart Cathleen A. , Prasad G. Sridhar , Murray Debra L. , Novick Richard P. , Schlievert Patrick M. , Ohlendorf Douglas H. 
Published: May 2005

AbstractNative toxic shock syndrom toxin 1 (TSST‐1) purified from Staphylococcus aurius has been crystallized in four different forms. The highest resolution data (2.05 Å) was collected from orthorhombic crystals belonging to the space group C2221. The unit cell dimension are a = 108.7 Å, b = 177.5 Å, c = 97.6 Å. Rotation function analysis of this from indicates that there is trimer of toxin molecules in the asymmetric unit with a local 3‐fold axis parallel to the crystallographic c axis. Crystals of a double mutant of TSST‐1 have been grown which has a single molecule in the asymmetric unit and diffract to 1.9 Å. The space group is P21 with unit cell parameters of a = 44.4 Å, b = 34.0 Å, c = 55.2 Å, β = 93.0°. © 1993 Wiley‐Liss, Inc.
Orientation and rotational dynamics of spin‐labeled phalloidin bound to actin in muscle fibers
Authors: Naber Nariman , Ostap E. Michael , Thomas David D. , Cooke Roger 
Published: May 2005

AbstractWe have used electron paramagnetic resonance spectroscopy (EPR) to investigate the orientational distribution of actin in thin filaments of glycerinated muscle fibers in rigor, relaxation, and contraction. A spin‐labeled derivative of a mushroom toxin, phalloidin (PHSL), was bound to actin in the muscle fibers (PHSL–fibers). The EPR spectrum of unoriented PHSL–labeled myofibrils consisted of three sharp lines with a splitting between the outer extrema (2T) of 42.8 ± 0.1 G, indicating that the spin labels undergo restricted nanosecond rotational motion within an estimated halfcone angle of 76°. When the PHSL–fiber bundle was oriented parallel to the magnetic field, the splitting between the zero‐crossing points (2T′) was 42.7 ± 0.1 G. When the fiber bundle was perpendicular to the magnetic field, 2T′ decreased to 34.5 ± 0.2 G. This anisotropy shows that the motion of the probe is restricted in orientation by its binding site on actin, so that the EPR spectrum of PHSL–fiber bundles would be sensitive to small changes in the mean axial orientation of the PHSL–actin interface. No differences in the EPR spectra were observed in fibers during rigor, relaxation, or contraction, indicating that the mean axial orientation of the PHSL binding site changes by less than 5°, and that the amplitude of nanosecond probe rotational motion, which should be quite sensitive to the local environment of the phalloidin, changes by no more than 1°. These results rule out large changes in the overall geometry of the actin filament and in the local conformation of actin near the phalloidin binding site during the generation of isometric tension in muscle fibers. © 1993 Wiley‐Liss, Inc.