bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatial optimization of electrostatic interactions between the ionized groups in globular proteins
Authors: Spassov Velin Z. , Atanasov Boris P.
Published: May 2005

A model approach is suggested to estimate the degree of spatial optimization of the electrostatic interactions in protein molecules. The method is tested on a set of 44 globular proteins, representative of the available crystallographic data. The theoretical model is based on macroscopic computation of the contribution of charge–charge interactions to the electrostatic term of the free energy for the native proteins and for a big number of virtual structures with randomly distributed on protein surface charge consetellations (generated by a Monte‐Carlo technique). The statistical probability of occurrence of random structures with electrostatic energies lower than the energy of the native protein is suggested as a criterion for spatial optimization of the electrostatic interactions. The results support the hypothesis that the folding process optimizes the stabilizing effect of electrostatic interactions, but to very different degree for different proteins. A parallel analysis of ion pairs shows that the optimization of the electrostatic term in globular proteins has increasingly gone in the direction of rejecting the repulsive short contacts between charges of equal sign than of creating of more salt bridges (in comparison with the statistically expected number of shortrange ion pairs in the simulated random structures). It is observed that the decrease in the spatial optimization of the electrostatic interactions is usually compensated for by an appearance of disulfide bridges in the covalent structure of the examined proteins. © 1994 Wiley‐Liss, Inc.
Crystallization and preliminary X‐ray diffraction study of the green flavoenzyme 5‐Hydroxyvaleryl‐CoA dehydratase/dehydrogenase from Clostridium aminovalericum
Authors: Eikmanns Ulrich , Buta Christiane , Buckel Wolfgang , Pai Emil F.
Published: May 2005

The bifunctional flavoenzyme 5‐hydroxyvaleryl‐CoA dehydratase/ dehydrogenase has been crystallized from solutions containing ammonium sulfate (form I) or polyethylene glycol (form II) as precipitant. In both cases, the crystals grew in the monoclinic space group C2. The unit cell dimensions for form I crystals were determined as a = 162.8 Å, b = 71.8 Å, c = 83.5 Å, β = 109.1°. Corresponding values for form II crystals were a = 161.2 Å, b = 71.6 Å, c = 82.2 Å, β = 109.3°. In both cases most probably there are two monomers per asymmetric unit. The crystals diffract to about 2 Å resolution and are rather stable in the X‐ray beam. © 1994 Wiley‐Liss, Inc.
Multiple copy sampling: Rigid versus flexible protein
Authors: Zheng Qiang , Kyle Donald J.
Published: May 2005

Effects of protein flexibility on multiple copy conformational sampling were systematically evaluated by studying the side‐chain placement of Phe‐14 in protein Zif268. The multiple copy sampling is shown to be significantly more efficient when a flexible but harmonically constrained protein is used instead of a rigid protein. A range of constraint force from 1 to 25 kcal/mol. Å per atom is determined to be sufficient to prevent the protein from distortion while allowing the protein to fluctuate for enhanced sampling. The protein fluctuations are essential in smoothing the effective energy surface as shown by the opening‐closing of a protein hydrophobic pocket during a multiple copy energy minimization, a phenomenon that has been previously observed only in molecular dynamics. These results provide a practical guidance for applying the multiple copy techniques to molecular modeling and computer‐aided drug design. © 1994 Wiley‐Liss, Inc.
Crystallization and preliminary X‐ray diffraction studies of mandelonitrile lyase from almonds
Authors: Lauble Hanspeter , Müller Kirsten , Schindelin Hermann , Förster Siegfried , Effenberger Franz
Published: May 2005

Single crystals of three different isoenzymes of (R)−(+) mandelonitrile lyase (hydroxynitrile lyase) from almonds (Prunus amygdalus) have been obtained by hanging drop vapor diffusion using polyethylene glycol 4000 and isopropanol as co‐precipitants. The crystals belong to the monoclinic space group P2l with unit cell parameters a = 69.9, b = 95.1, c = 95.6 Å, and β = 118.5°. A complete set of diffraction data has been collected to 2.6 Å resolution on native crystals of isoenzyme III. © 1994 Wiley‐Liss, Inc.
Pyrrolidone carboxyl peptidase (Pcp): An enzyme that removes pyroglutamic acid (pGlu) from pGlu‐peptides and pGlu‐proteins
Authors: Awadé A. C. , Cleuziat Ph. , GonzalèS Th. , Robert‐Baudouy J.
Published: May 2005

Pyrrolidone carboxyl peptidase (EC 3.4.11.8) is an exopeptidase commonly called PYRase, which hydrolytically removes the pGlu from pGlu‐peptides or pGlu‐proteins.

pGlu also known as pyrrolidone carboxylic acid may occur naturally by an enzymatic procedure or may occur as an artifact in proteins or peptides. The enzymatic synthesis of pGlu suggests that this residue may have important biological and physiological functions. Several studies are consistent with this supposition.

PYRase has been found in a variety of bacteria, and in plant, animal, and human tissues For over two decades, biochemical and enzymatic properties of PYRase have been investigated. At least two classes of PYRase have been characterized. The first one includes the bacterial and animal type I PYRases and the second one the animal type II and serum PYRases. Enzymes from these two classes present differences in their molecular weight and in their enzymatic properties.

Recently, the genes of PYRases from four bacteria, have been cloned and characterized, allowing the study of the primary structure of these enzymes, and their over‐expression in heterelogous organisms. Comparison of the primary structure of these enzymes revealed striking homologies.

Type I PYRases and bacterial PYRases are generally soluble enzymes, whereas type II PYRases are membrane‐bound enzymes. PYRase II appears to play as important a physiological role as other neuropeptide degrading enzymes. However, the role of type I and bacterial PYRases remains unclear.

The primary application of PYRase has been its utilization for some protein or peptide sequencing. Development of chromogenic substrates for this enzyme has allowed its use in bacterial diagnosis. © 1994 Wiley‐Liss, Inc.
Solvent‐induced organization: A physical model of folding myoglobin
Authors: Callaway David J. E.
Published: May 2005

The essential features of the in vitro refolding of myoglobin are expressed in a solvable physical model. Alpha helices are taken as the fundamental collective coordinates of the system, while the refolding is assumed to be mainly driven by solvent‐induced hydrophobic forces. A quantitative model of these forces is developed and compared with experimental and theoretical results. The model is then tested by being employed in a simulation scheme designed to mimic solvent effects. Realistic dynamic trajectories of myoglobin are shown as it folds from an extended conformation to a close approximation of the native state. Various suggestive features of the process are discussed. The tenets of the model are further tested by folding the single‐chain plant protein leghemoglobin. © 1994 Wiley‐Liss, Inc.
Preliminary crystallographic analysis of an enzyme involved in erythromycin biosynthesis: Cytochrome P450eryF
Authors: Cupp‐Vickery Jill R. , Li Huiying , Poulos Thomas L.
Published: May 2005

Cytochrome P450eryF was overexpressed in Escherichia coli and purified in high yield. Crystals of the protein in the presence of the substrate, 6‐deoxyerythronolide B, have been obtained by the hanging drop vapor diffusion method, using polyethylene glycol 4000 as a precipitant. The crystals belong to the orthorhombic space group P212121 with unit cell dimensions of a = 54.16 Å, b = 79.67 Å, and c = 99.48 Å and one molecule per asymmetric unit. A complete native data set has been collected to a resolution of 2.1 Å, and anomalous dispersion difference Patterson maps have revealed the location of the single heme iron atom. © 1994 Wiley‐Liss, Inc.
Molecular dynamics simulations of trp apo‐and holorepressors: Domain structure and ligand–protein interaction
Authors: Komeiji Yuto , Uebayasi Masami , Yamato Ichiro
Published: May 2005

Molecular dynamics simulations of the apo‐ and holo‐forms of thetrp‐repressor protein were performed under extensively solvated conditions in order to elucidate their dynamic structures and ligand–protein interactions. The root mean square fluctuations calculated from the trajectories agreed with those calculated from X‐ray temperature factors. Distance, distance fluctuation, and dynamic cross‐correlation maps were drawn to provide information on the dynamic structures and communications among the domains. A three‐domain format has been proposed for the crystal structure (Zhang et at., Nature 327:591–597, 1987) namely, helices A–C and F of both subunits make up a central core, and D and E of each subunit forms a DNA binding head. The results of the simulations were mostly consistent with the three‐domain format. However, helix F was more flexible and freer than other parts of the central core. The turn DE, the helix‐turn‐helix DNA binding motif, was free from interactions and correlations with other domains in both forms of the repressor. A comparison of the simulations of the aporepressor and holorepressor showed that tryptophan binding made the DNA‐binding helix D more flexible but helix F less flexible. Several amino acid residues in contact with the bound tryptophan were identified as making concerted motions with it. Interaction energies between the corepressor and the amino acid residues of the protein were analyzed; the results were mostly consistent with the mutational experiments. © 1994 Wiley‐Liss, Inc.
A surface mutant (G82R) of a human α‐glutathione S‐transferase shows decreased thermal stability and a new mode of molecular association in the crystal
Authors: Zeng Ke , Rose John P. , Chen Hong‐Chi , Strickland Corey L. , Tu Chen‐Pei D. , Wang Bi‐Cheng
Published: May 2005

A chimeric enzyme (GST121) of the human α‐glutathione S‐transferases GST1‐1 and GST2‐2, which has improved catalytic efficiency and thermostability from its wild‐type parent proteins, has been crystallized in a space group that is isomorphous with that reported for crystals of GST1‐1. However, a single‐site (G82R) mutant of GST121, which exhibits a significant reduction both in vitro and in vivo in protein thermostability, forms crystals that are not isomorphous with GST1‐1. The mutant protein crystallizes in space group P212121, with cell dimensions a = 49.5, b = 92.9, c = 115.9 Å, and one dimer per asymmetric unit. Preliminary crystallographic results show that a mutation of the surface residue Gly 82 from a neutral to a charged residue causes new salt bridges to be formed among the GST dimers, suggesting that the G82R mutant might aggregate more readily than does GST121 in solution resulting in a change of its solution properties. © 1994 Wiley‐Liss, Inc.
Crystallization and preliminary crystallographic study of human CksHs1: A cell cycle regulatory protein
Authors: Arvai Andrew S. , Bourne Yves , Williams DeWight , Reed Steve I. , Tainer John A.
Published: May 2005

The cell cycle regulatory protein CksHs1 has been crystallized in a form suitable for X‐ray studies. CksHsl crystals were grown in the presence of vanadate, a phos‐phatase inhibitor, but were also obtained with phosphate or tungstate as a cofactor. They belong to the hexagonal space group P6122 with unit cell dimensions: a=b=94 Å, c=131.6 Å, and γ =120. The crystals grown in the presence of vanadate diffract X‐rays to at least 2.8 Å. Molecular replacement results from the homologous human CksHs2 structure reveal that a dimer forms the crystal habit, giving the unusual Vm value of 4.4 Å3/Da or a solvent content of 72%. © 1995 Wiley‐Liss, Inc.
Crystals of an antibody FV fragment against an integral membrane protein diffracting to 1.28 Å resolution
Authors: Ostermeier Christian , Essen Lars‐Oliver , Michel Hartmut
Published: May 2005

The Fv fragment of a monoclonal antibody, 7E2 (IgG1, κ, murine), which is directed against the integral membrane protein cytochrome c oxidase (EC 1.9.3.1) from Paracoccus denitrificans, was cloned and produced in Escherichia coli. Crystals suitable for highresolution X‐ray analysis were obtained by microdialysis under low salt conditions. The crystals belong to the orthorhombic space group P212121 with unit cell dimensions of a = 51.51 Å, b = 56.15 Å, c = 99.86 Å (1 Å = 0.1 nm) and contain one F v fragment per asymmetric unit. Using synchrotron radiation diffraction data were collected up to 1.28 Å resolution. This high resolution is very unusual for a heterodimeric protein. The crystals should open the way for refining not only the atomic positions, but also for obtaining information about internal dynamics. © 1995 Wiley‐Liss, Inc.
Packing constraints of hydrophobic side chains in (α/β)8 barrels
Authors: Vtyurin Nickolie , Panov Victor
Published: May 2005

An analysis of possible tight packing of hydrophobic groups simultaneously at the both surfaces of β‐hyperboloid‐8 was conducted. This analysis shows that the disposition of amino acid side chains at the real β‐structure's surface is unique. If we sign the mean distance between adjacent β‐strands as “a,” and the mean distance along β‐strand between Cα atoms, whose side chains are directed to one side of the β‐sheet, as “b,” the ratio b/a = √2 very precisely. This ratio ensures the most efficient packing of side hydrophobic groups at the outer surface of β‐hyperboloid‐8, forming, at the same time, the second by efficiency packing at its inner surface. © 1995 Wiley‐Liss, Inc.
Preliminary X‐ray diffraction analysis of crystals of tomato aspermy virus (TAV)
Authors: Canady Mary A. , Leja Catherine A. , Day John , McPherson Alexander
Published: May 2005

Tomato aspermy virus (TAV) is a member of the T = 3 cucumovirus group, and the chrysanthemum strain (C‐TAV) has been crystallized in a form suitable for X‐ray structural analysis. The crystals, which grow in 14–17% ethanol at pH 8.5, are of orthorhombic space group I222 with unit cell dimensions of a = 295.1 Å, b = 320.5 Å, and c = 383.6 Å. There are two T = 3 virus particles in the unit cell, which means that they must be centered at 0,0,0 and 1/2, 1/2, 1/2 with icosahedral 222 symmetry elements coincident with crystallographic symmetry operators. The asymmetric unit of the crystals, therefore, contains one quarter of a virus particle, or 45 capsid subunits. Native diffraction data to 4 Å resolution have been collected using synchrotron radiation, though data appear to be present beyond that resolution. © 1995 Wiley‐Liss, Inc.
An analysis of side chain interactions and pair correlations within antiparallel β‐sheets: The differences between backbone hydrogen‐bonded and non‐hydrogen‐bonded residue pairs
Authors: Wouters Merridee A. , Curmi Paul M. G.
Published: May 2005

Cross‐strand pair correlations are calculated for residue pairs in antiparallel β‐sheet for two cases: pairs whose backbone atoms are hydrogen bonded together (H‐bonded site) and pairs which are not (non‐H‐bonded site). The statistics show that this distinction is important. When glycine is located on the edge of a sheet, it shows a 3:1 preference for the H‐bonded site. Thestrongest observed correlations are for pairs of disulfide‐bonded cystines, many of which adopt a close‐packed conformation with each cystine in a spiral conformation of opposite chirality to its partner. It is likely that these pairs are a signature for the family of small, cystine‐rich proteins. Most other strong positive and negative correlations involve charged and polar residues. It appears that electrostatic compatibility is the strongest factor affecting pair correlation. Significant correlations are observed for β‐ and γ‐branched residues inthe non‐H‐bonded site. An examination of the structures showsa directionality in side chain packing. There is a correlation between (1) the directionality in the packing interactions of non‐H‐bonded β‐ and γ‐branched residue pairs, (2) the handedness of the observed enantiomers of chiral β‐branched side chains, and (3) the handedness of the twist of β‐sheet. These findings have implications for the formation of β‐sheets during protein folding and the mechanism by which the sheet becomes twisted. © 1995 Wiley‐Liss, Inc.
Structural basis for serpin inhibitor activity
Authors: Wright H. Tonie , Scarsdale J. Neel
Published: May 2005

The mechanism of formation and the structures of serpin–inhibitor complexes are not completely understood, despite detailed knowledge of the structures of a number of cleaved and uncleaved inhibitor, noninhibitor, and latent serpins. It has been proposed from comparison of inhibitor and noninhibitor serpins in the cleaved and uncleaved forms that insertion of strand s4A into preexisting β‐sheet A is a requirement for serpin inhibitor activity. We have investigated the role of this strand in formation of serpin–proteinase complexes and in serpin inhibitor activity through homology modeling of wild type inhibitor, mutant substrate, and latent serpins, and of putative serpin–proteinase complexes. These models explain the high stability of the complexes and provide an understanding of substrate behavior in serpins with point mutations in s4A and of latency in plasmingoen activator inhibitor I. © 1995 Wiley‐Liss, Inc.
A Continuum theory for the prediction of lateral and rotational positioning of α‐helices in membrane proteins: Bacteriorhodopsin
Authors: Suwa Makiko , Hirokawa Takatsugu , Mitaku Shigeki
Published: May 2005

We have developed a new method for the prediction of the lateral and the rotational positioning of transmembrane helices, based upon the present status of knowledge about the dominant interaction of the tertiary structure formation. The basic assumption about the interaction is that the interhelix binding is due to the polar interactions and that very short extramembrane loop segments restrict the relative position of the helices. Another assumption is made for the simplification of the prediction that a helix may be regarded as a continuum rod having polar interaction fields around it. The polar interaction field is calculated by a probe helix method, using a copolymer of serine and alanine as probe helices. The lateral position of helices is determined by the strength of the interhelix binding estimated from the polar interaction field together with the length of linking loop segments. The rotational positioning is determined by the polar interaction field, assuming the optimum lateral configuration. The structural change due to the binding of a prosthetic group is calculated, fixing the rotational freedom of a helix that is connected to the prosthetic group. Applying this method to bacteriorhodopsin, the optimum lateral and rotational positioning of transmembrane helices that are very similar to the experimental configuration was obtained. This method was implemented by a software system, which was developed for this work, and automatic calculation became possible for membrane proteins comprised of several transmembrane helices. © 1995 Wiley‐Liss, Inc.
The heat capacity of proteins
Authors: Gómez Javier , Hilser Vincent J. , Xie Dong , Freire Ernesto
Published: May 2005

The heat capacity plays a major role in the determination of the energetics of protein folding and molecular recognition. As such, a better understanding of this thermodynamic parameter and its structural origin will provide new insights for the development of better molecular design strategies. In this paper we have analyzed the absolute heat capacity of proteins in different conformations. The results of these studies indicate that three major terms account for the absolute heat capacity of a protein: (1) one term that depends only on the primary or covalent structure of a protein and contains contributions from vibrational frequencies arising from the stretching and bending modes of each valence bond and internal rotations; (2) a term that contains the contributions of noncovalent interactions arising from secondary and tertiary structure; and (3) a term that contains the contributions of hydration. For a typical globular protein in solution the bulk of the heat capacity at 25°C is given by the covalent structure term (close to 85% of the total). The hydration term contributes about 15 and 40% to the total heat capacity of the native and unfolded states, respectively. The contribution of non‐covalent structure to the total heat capacity of the native state is positive but very small and does not amount to more than 3% at 25°C. The change in heat capacity upon unfolding is primarily given by the increase in the hydration term (about 95%) and to a much lesser extent by the loss of noncovalent interactions (up to ∼5%). It is demonstrated that a single universal mathematical function can be used to represent the partial molar heat capacity of the native and unfolded states of proteins in solution. This function can be experimentally written in terms of the molecular weight, the polar and apolar solvent accessible surface areas, and the total area buried from the solvent. This unique function accurately predicts the different magnitude and temperature dependences of the heat capacity of both the native and unfolded states, and therefore of the heat capacity changes associated with folding/unfolding transitions. © 1995 Wiley‐Liss, Inc.
Effects of cavity‐creating mutations on conformational stability and structure of the dimeric 4‐α‐helical protein ROP: Thermal unfolding studies
Authors: Steif Christian , Hinz Hans‐Jürgen , Cesareni Giovanni
Published: May 2005

The structural and energetic perturbations caused by cavity‐creating mutations (Leu‐41 → Val and Leu‐41 → Ala) in the dimeric 4‐α‐helical‐bundle protein ROP have been characterized by CD spectroscopy and differential scanning calorimetry (DSC). Deconvolution of the CD spectra showed a decrease in α ‐helicity as a result of the amino acid exchanges that follows qualitatively the overall decrease in conformational stability. Transition enthalpies are sensitive probes of the energetic change associated with point mutations. ΔH0 values at the respective transition temperatures, T1/2 (71.0, 65.3, and 52.9°C at 0.5 mg/ml) decrease from 580 ± 20 to 461 ± 20 kJ/(mol of dimmer) and 335 ± 20 kJ/(mol of dimmer) for wildtype ROP (Steif, C., Weber, P., Hinz, H.‐J., Flossdorf, J., Cesareni, G., Kokkinidis, M. Biochemistry 32:3867‐3876, 1993), L41V, and L41A, respectively. The conformational stabilities at 25°C expressed by the standard Gibbs energies of denaturation, ΔG, are 71.7, 61.1, and 46.1 kJ/(mol of dimmer). The corresponding transition enthalpies have been obtained from extrapolation using the c(T)and c(T) functions. Their values at 25°C are 176.3, 101.9, and 141.7 kJ/(mol of dimmer) for wild‐type ROP, L41V, and L41A, respectively. When the stability perturbation resulting from the cavity creating mutations is referred to the exchange of 1 mol of CH2 group, the average ΔΔG value is −5.0 ± 1 kJ/(mol of CH2 group). This decrease in conformation stability suggests that dimeric ROP exhibits the same susceptibility to Leu → Yal and Leu → Ala exchanges as small monomeric proteins. Careful determinations of the partial specific heat capacities of wild‐type and mutated protein solutions suggest that the mutational effects are predominantly manifested in the native rather than the unfolded state. © 1995 Wiley‐Liss, Inc.
Molecular modeling indicates that homodimers form the basis for intermediate filament assembly from human and mouse epidermal keratins
Authors: Downing Donald T.
Published: May 2005

Mammalian epidermal keratin molecules adopt rod‐shaped conformations that aggregate to form cytoplasmic intermediate filaments. To investigate these keratin conformations and the basis for their patterns of molecular association, graphical methods were developed to relate known amino acid sequences to probable spacial configurations. The results support the predominantly α‐helical conformation of keratin chains, interrupted by short non‐α‐helical linkages. However, it was found that many of the linkages have amino acid sequences typical of β‐strand conformations. Space‐filling atomic models revealed that the β‐strand sequences would permit the formation of 2‐chain and 4‐chain cylindrical β‐helices, fully shielding the hydrophobic amino acid chains that alternate with hydrophilic residues in these sequences. Because of the locations of the β‐helical regions in human and mouse stratum corneum keratin chains, only homodimers of the keratins could interact efficiently to form 2‐chain and 4‐chain β‐helices. Tetramers having the directions and degrees of overlap of constituent dimers that have been identified by previous investigators are also predicted from the interactions of β‐helical motifs. Heterotetramers formed from dissimilar homodimers could combine, through additional β‐helical structures, to form higher oligomers having the dimensions seen in electron microscopic studies. Previous results from chemical crosslinking studies can be interpreted to support the concept of homodimers rather than heterodimers as the basis for keratin filament assembly. © 1995 Wiley‐Liss, Inc.
Dynamic structure of human serum transferrin from transient electric birefringence experiments
Authors: van Haeringen Bart , de Lange Frank , van Stokkum Ivo. H. M. , Srai S. Kaila S. , Evans Robert W. , van Grondelle Rienk , Bloemendal Michael
Published: May 2005

In order to investigate the secondary, tertiary, and dynamic structure of the iron‐free (apo) and iron‐saturated (holo) forms of human serum transferrin and its amino (N)‐terminal lobe at the physiologically relevant pHs 7.4 and 5.0, we have combined ultraviolet circular dichroism (CD) spectroscopy with transient‐electric birefringence (TEB) measurements. No significant changes are found in the protein's secondary structure under the different conditions studied. The tertiary structure as monitored by near‐UV CD is affected by iron binding, but does not change upon decrease in pH. In contrast, TEB results indicate dramatic changes in the dynamic structure of transferrin both upon binding of iron and decrease of pH. In apotransferrin freedom of movement is found for the lobes with respect to each other, and for the domains within the lobes. The interlobal flexibility is considerably enhanced at the lower pH. Holotransferrin is found to behave as a rigid molecule. © 1995 Wiley‐Liss, Inc.
Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing
Authors: Jones David T. , Miller Robert T. , Thornton Janet M.
Published: May 2005

Analysis of the results of the recent protein structure prediction experiment for our method shows that we achieved a high level of success, Of the 18 available prediction targets of known structure, the assessors have identified 11 chains which either entirely match a previously known fold, or which partially match a substantial region of a known fold. Of these 11 chains, we made predictions for 9, and correctly assigned the folds in 5 cases. We have also identified a further 2 chains which also partially match known folds, and both of these were correctly predicted. The success rate for our method under blind testing is therefore 7 out of 11 chains. A further 2 folds could have easily been recognized but failed due to either overzealous filtering of potential matches, or to simple human error on our part. One of the two targets for which we did not submit a prediction, prosubtilisin, would not have been recognized by our usual criteria, but even in this case, it is possible that a correct prediction could have been made by considerin a combination of pairwise energy and solvation energy Z‐scores. Inspection of the threading alignments for the (αβ)8 barrels provides clues as to how fold recognition by threading works, in that these folds are recognized by parts rather than as a whole. The prospects for developing sequence threading technology further is discussed. © 1995 Wiley‐Liss, Inc.
The phospho‐β‐galactosidase and synaptotagmin predictions
Authors: Benner Steven A. , Gerloff Dietlind , Chelvanayagam Gareth
Published: May 2005

Two bona fide consensus predictions of secondary and tertiary structure in a protein family, made and announced before experimental structures were known, are evaluated in light of the subsequently determined experimental structures. The first, for phospho‐β‐galactosidase, identified the core strands of an 8‐fold α–β barrel, and identified the 8‐fold α–β barrel itself, which was found in the subsequently determined experimental structure to be the core folding domain. The second, for synaptotagmin, identified seven out of eight β‐strands in the structure correctly, missing only a noncore strand. Three preferred “topologies” were selected from several hundred thousand possible topologies of these seven predicted strands using a rule‐based analysis. The subsequently determined experimental structure showed that these seven strands in synaptotagmin adopt one of the three preferred topologies. We were unable, however, to identify the correct topology from among these three topologies. © 1995 Wiley‐Liss, Inc.
An automated method for dynamic ligand design
Authors: Miranker Andrew , Karplus Martin
Published: May 2005

An automated method for the dynamic ligand design (DLD) for a binding site of known structure is described. The method can be used for the creation of de novo ligands and for the modification of existing ligands. The binding site is saturated with atoms (sp3 carbon atoms in the present implementation) that form molecules under the influence of a potential function that joins atoms to each other with the correct stereochemistry. The resulting molecules are linked to precomputed functional group minimum energy positions in the binding site. The generalized potential function allows atoms to sample a continuous parameter space that includes the Cartesian coordinates and their occupancy and type, e.g., the method allows change of an sp3 carbon into an sp2 carbon or oxygen. A parameter space formulated in this way can then be sampled and optimized by a variety of methods. In this work, molecules are generated by use of a Monte Carlo simulated annealing algorithm. The DLD method is illustrated by its application to the binding site of FK506 binding protein (FKBP), an immunophilin. De novo ligands are designed and modification of the immunosuppressant drug FK506 are suggested. The results demonstrate that the dynamic ligand design approach can automatically construct ligands which complement both the shape and charge distribution of the binding site. © 1995 Wiley‐Liss, Inc.
Hinge‐bending motion in citrate synthase arising from normal mode calculations
Authors: Marques Osni , Sanejouand Yves‐Henri
Published: May 2005

A normal mode analysis of the closed form of dimeric citrate synthase has been performed. The largest‐amplitude collective motion predicted by this method compares well with the crystallographically observed hinge‐bending motion. Such a result supports those obtained previously in the case of hinge‐bending motions of smaller systems, such as lysozyme or hexokinase. Taken together, all these results suggest that low‐frequency normal modes may become useful for determining a first approximation of the conformational path between the closed and open forms of these proteins. © 1995 Wiley‐Liss, Inc.
Preliminary X‐ray crystallographic analysis of Tritrichomonas foetus inosine‐5′‐monophosphate dehydrogenase
Authors: Whitby Frank G. , Huete‐Perez Jorge , Luecke Hartmut , Wang C. C.
Published: May 2005

Inosine‐5′‐monophosphate dehydrogenase (IMPDH) from the protozoan parasite Tritrichomonas foetus has been expressed in E. coli and crystallized. Crystals were grown to 0.1 mm in each dimension in 18 to 72 h using ammonium sulfate and low‐molecular‐weight polyethylene glycols. The crystals belong to the cubic space group P432 with unit cell edge = 157.25 Å. The enzyme is a homotetramer with each monomer having a molecular weight of 55,534 Da. There is one monomer per asymmetric unit, based on a volume/mass ratio of 2.7 Å3/Da and self‐rotation analysis. The crystals are adequately stable to allow a complete data set to be collected from a single crystal. Complete native data sets have been collected to 2.3 Å resolution at 4°C using synchrotron radiation. High‐quality complete data extending to 3.0 Å resolution have been collected from crystals of four putative derivatives, and the data appear to be isomorphous with that of the native crystals in each case. Efforts to solve the derivatives for use in MIR phasing are underway. © 1995 Wiley‐Liss, Inc.
Purification, crystallization, and preliminary X‐ray analysis of Bacillus subtilis ferrochelatase
Authors: Hansson Mats , Al‐Karadaghi Salam
Published: May 2005

Bacillus subtilis ferrochelatase (EC 4.99.1.1), the final enzyme in protoheme IX biosynthesis, was produced with an inducible T7 RNA polymerase expression system in Escherichia coli and purified from the soluble cell fraction. It was crystallized from polyethylene glycol solution using the microseeding technique. The crystals diffract to a minimum Bragg spacing of 2.1 Å. The space group is P42 with unit cell dimensions a = b = 50.2 Å, c = 120.1 Å. © 1995 Wiley‐Liss, Inc.
Relativistic atomic structure theory: Some recent work
Authors: Grant I. P.
Published: May 2005

Recent developments in relativistic atomic structure have been more in terms of program improvement than in fundamental theory. Some comments on both aspects of this work are illustrated by a description of two different recent applications. In the first, we study the contribution of the interaction of relativity and correlation to the 2 3S−2 3P0,1,2 intervals in heliumlike ions, whose theoretical estimation is important for testing QED. The study of satellite structure in the Kβ x‐ray emission spectrum of Ar illustrates a quite different use of the program packages developed at Oxford for investigating configuration interaction. The use of shake theory to predict the initial states, populated along with the primary vacancy giving rise to the diagram line, gives a satellite line intensity distribution which agrees very well with recent experimental spectra.
Isospin basis for atoms in relativistic approximation
Authors: Šimonis V. Č. , Kaniauskas J. M. , Rudzikas Z. B.
Published: May 2005

The isospin basis is put into operation for investigation of atomic configurations, having two shells of equivalent electrons, characterized by the same orbital (LS coupling) or total (jj coupling) angular momenta of each electron. Tensorial properties of both the operators and the wave functions are studied in this basis. The two‐particle operator is expressed in terms of the tensors irreducible in the isospin space. The problem of the additional classification of the levels is considered. The accuracy of the quantum numbers of the isospin basis in jj coupling scheme is discussed.
1/Z perturbation theory for calculation of line strengths in the neon isoelectronic sequence
Authors: Pokleba A. K. , Safronova U. I.
Published: May 2005

The line strengths of 2–2 and 3–3 transitions (2s22p53s–2s22p53p–2s22p53d, 2s2s2p63s–2s2p63p‐2s2p63d, 2s22p53l‐2s2p63l) have been calculated for the Ne isoelectronic sequence (Z = 14 ÷ 100). The calculation has been carried out in intermediate coupling. Relativistic corrections have been included through the Breit operator. Perturbation theory in 1/Z has been used to account for electronic interactions.
Core polarization and relativistic effects competition in the first ionization potentials for some systems in the Cu, Ag, and Au isoelectronic sequences
Authors: Migdalek J. , Baylis W. E.
Published: May 2005

Single‐configuration relativistic Hartree–Fock values of the first ionization potentials for Cu through Kr7+, Ag through I6+, and Au through Pb3+ are computed in “frozen” and “relaxed core” approximations with and without allowance for core polarization. Effects of polarization of the atomic core by the valence electron are included by introducing a polarization potential in the one‐electron Hamiltonian of the valence electron. The core polarization potential depends on two parameters, the static dipole polarizability of the core α and the cut‐off radius r0, which are chosen independently of the ionization potential data. It is demonstrated that by including the core polarization potential with α and r0 parameters, which are simply chosen instead of being empirically fitted, it is still possible to account, on the average, for at least 70% of the discrepancy between the single‐configuration relativistic Hartree–Fock ionization potentials and the experiment, a discrepancy usually ascribed to the contribution of valence‐core electron correlations, and to bring the theoretical ionization potentials to an average agreement with experiment of around 1%. It can be concluded from this study that for low and medium Z elements the core polarization dominates for neutral systems or systems in low ionization stages, whereas for highly ionized systems the relativistic effects prevail. For heavy elements, however, the core polarization influence is comparable to the relativistic one only for neutral systems, whereas for ions the relativistic effects are overwhelmingly predominant.
Collision systems
Authors: Fricke B. , Rosén A.
Published: May 2005

Various approximations which are possible for the theoretical description of colliding ion–atom systems are reviewed. With the emphasis on relativistic influences, a few comparisons of experimental results with relativistic calculations are made.
Basis set expansion of the dirac operator without variational collapse
Authors: Kutzelnigg Werner
Published: May 2005

The eigenstates of the matrix representation of the Dirac operator for c → ∞ do not approach their nonrelativistic counterparts in the same basis. This wrong “Schrödinger limit” is shown to be the main reason for the phenomenon known as “variational collapse.” After a short review of existing proposals to overcome the “variational collapse,” a systematic study of the possible ways to avoid it is given. All discussed approaches are analyzed in terms of various criteria that one wants to fulfill. The most promising approach consists of a free‐particle Foldy–Wouthuysen (FW) transformation on operator level and a back transformation on matrix level (approaches C2 and C3). This implies a modification of the free‐electron part of the matrix representation of the Dirac operator and leads to the correct Schrödinger limit (and if one wishes even the correct Pauli limit) in the same basis (and to the exact results for a complete basis). The potential energy is unchanged, which makes the application to n ‐electron systems straightforward. Projection of the Dirac operator to positive energy states does not remove the variational collapse unless this is done in a very special way.
Relativistic calculations of dissociation energies and related properties
Authors: Pitzer Kenneth S.
Published: May 2005

Methods of calculation of potential energy curves or surfaces, including dissociation energies, bond distances, and vibration frequencies, are discussed as well as recently obtained results for several molecules. The ab initio relativistic methods involve the derivation of “shape‐consistent” effective potentials from Dirac–Fock atomic calculations. These effective potentials are averaged and differenced with respect to spin with the differences, p3/2 – p1/2, etc., yielding spin‐orbit operators. The molecular calculations are then set up in a familiar manner through the SCF stage using spin‐averaged effective potentials. The final stage is a configuration‐interaction calculation including the spin‐orbit terms as well as the electron repulsion terms. Calculations that have been made for several low‐lying excited states as well as the ground state for Au2, TlH, Tl2, Sn2, and Pb2 are reviewed. Good agreement is obtained with spectroscopic data and a number of interesting predictions are made.
Electronic structure of molecules using one‐component wave functions and relativistic effective core potentials
Authors: Kahn Luis R.
Published: May 2005

A one‐component approach to molecular electronic structure is discussed that includes the dominant relativistic effects on valence electrons and yet allows the use of the traditional quantum‐chemistry techniques. The approach starts with one‐component Cowan–Griffin relativistic orbitals that successfully incorporate the effects of the mass‐velocity and Darwin terms present in more complicated wave functions such as the Dirac–Hartree–Fock. The approach then constructs “relativistic” effective core potentials (RECPS) from these orbitals, and uses these to bring the relativistic effects into the molecular electronic calculations. The use of effective one‐electron spin‐orbit operators in conjunction with these one‐component wave functions to include the effects of spin‐orbit coupling is discussed. Applications to molecular systems involving heavy atoms and comparisons with available spectroscopic data on molecular geometries and excitation energies are presented. Finally, a new approach to the construction of RECPS encompassing the Hamiltonian and shapeconsistent approach is presented together with a novel analysis of the long‐range behavior of the RECPS.
Electronic structure of the PdCl42− and PtCl42−ions
Authors: Larsson Sven , Olsson Lars‐Fride , Rosén Arne
Published: May 2005

The electronic spectra of PdCl42− and PtCl42− are studied by quantum‐chemical methods with the ultimate object being to understand the differences in reactivity for Pt(II) and Pd(II) complexes. Nonrelativistic ab initio UHF, DV ‐ Xα, and MSXα methods give very similar assignments of the spectra for PdCl42−. The d–d spectrum for PtCl42−, which is very different from the d–d spectrum of PdCl42−, agrees qualitatively with the spectra obtained using the relativistic extended‐Hückel (REX) and Dirac–Slater (DS) methods. Although the latter two methods disagree somewhat in the interpretation of the high intensity bands in PtCl42−, it appears reasonable to interpret at least one of the lines as a 5d → 6p transition.
Electronegativity equalization and the electronic structure of polyhedral clusters of main‐group atoms
Authors: Lohr Lawrence L.
Published: May 2005

The concept of the equalization of atomic electronegativities accompanving molecule formation is applied to a study of the electronic structure of polyhedral clusters of main‐group atoms such as Ge, Sn, Pb, Tl, and Bi. Emphasis is placed upon charged clusters such as Sn9−x Pb(x = 0 → 9), Sn9‐xGe, Sn8−xPbx Tl5−, Sn2Bi, SnTe, etc. The role of the relativistic spin‐orbit splitting of an np shell into np1/2 and np3/2 subshells in modifying atomic and hence molecular electronegativities is discussed. Correlations are made between calculated charge distributions and observed199 Sn NMR chemical shifts for clusters of a given size and charge. It is concluded that a useful picture of charge distributions in these clusters may be obtained from electronegativity equalization considerations.
Butyl nitrite: A novel chemical ionization reagent compound
Authors: Moncur J. H. , Brown R. S. , Ibrahim S. , Wilson J. M. , Jennings Keith R.
Published: May 2005

A Kratos MS‐25RFA medium resolution mass spectrometer and a Concept IS high resolution mass spectrometer were used to analyse a range of highly substituted aromatic alcohols for kinetic studies.
Fast atom bombardment/collisional activation mass spectrometry of β‐D‐mannosyl‐(1→4)‐β‐D‐N‐acetylglucosaminyl (1→N) urea and related compounds
Authors: Heerma W. , Dallinga J. W. , Dorland L. , van Rhee A. M. , van Pelt J. , Duran M. , de Jong E. G.
Published: May 2005

A new compound, obtained during the isolation of oligosaccharides from the urine of two brothers affected with inherited β‐mannosidase deficiency, has been investigated using fast atom bombardment ionization and MS/MS techniques. The compound could be characterized as an N‐acetylglucosamine molecule linked to a hexose and a urea molecule.
How are S ions formed in electron collisions with linear SCS?
Authors: Mazumdar S. , Kumar S. V. K. , Marathe V. R. , Mathur D.
Published: May 2005

The energetics of S ion formation in electron dissociative ionization of linear CS2 are investigated experimentally with a crossed‐beam apparatus. Ab initio self‐consistent‐field molecular orbital (SCF MO) calculations of potential energy curves for low‐lying electronic states of this ion have been made in order to explain how stable S ions are formed, initially at the very large internuclear separation of 3.2 Å.
Structural „memory effects”︁ influencing decompositions of glucose alkoxide anions produced from monoterpene glycoside isomers in tandem mass spectrometry
Authors: Cole R. B. , Tabet J. C. , Salles C. , Jallageas J. C. , Crouzet J.
Published: May 2005

Isomeric glycoconjugates have been distinguished using desorption negative‐ion chemical ionization/tandem mass spectrometry (DNCI–MS/MS). The structure of the leaving terpene influences the orientation of consecutive decompositions during collisionally activated decomposition (CAD) of [M–H]− ions which pass through a glucose alkoxide intermediate ion. This apparent „memory effect”︁ can be rationalized by considering the production of anion‐induced dipole complexes.
Can aluminium‐clad capillary columns be used for gas chromatography/mass spectrometry on a sector mass spectrometer?
Authors: Bowen David V. , Pullen Francis S.
Published: May 2005

Aluminium‐clad fused silica capillary columns can be used with magnetic sector mass spectrometers. The column end needs to be pulled back a millimetre or so from the ion source to avoid electrical arcing. The chromatographic integrity is maintained. This brings the benefits of robust construction and high temperature gas chromatography/mass spectrometry to sector mass spectrometers.
Screening by tandem mass spectrometry for trace levels of alkylbenzenes
Authors: Cairns Thomas , Siegmund Emil G.
Published: May 2005

Product ion spectra derived from molecule ions as the precursor ions for 14 alkylbenzenes have been studied under electron ionization and methane chemical ionization. The data have provided a satisfactory screening method for both detection and confirmation of such compounds at low parts per million levels.
High resolution chromatography/tandem mass spectrometry. Analysis of polychlorinated dibenzo‐p‐dioxins and furans
Authors: Fraisse D. , Gonnord M. F. , Becchi M.
Published: May 2005

Capabilities of high resolution chromatography/tandem mass spectrometry for quantitation of polychlorinated dibenzo‐p‐dioxins and polychlorinated dibenzo furans have been investigated with a hybrid instrument. Selected‐transition monitoring procedures, collision energy and collision gases have been optimized for maximum sensitivity. The results are compared with those obtained by high resolution chromatography/high resolution mass spectrometry.
Computer‐controlled sequencing of peptides by tandem mass spectrometry
Authors: Herrmann Jörg , Schlunegger Urs Peter
Published: May 2005

A fully automated computer‐controlled system was used to generate series of different linked scans at constant B2E and constant neutral loss in the second field‐free region. This system has been shown to be suitable for deriving the amino acid sequence of oligopeptides.
Tandem mass spectrometry of fatty acid methyl esters. Evidence for bicyclic product ions
Authors: Cairns Thomas , Siegmund Emil G.
Published: May 2005

Product‐ion spectra derived from both protonated and hydride‐abstracted molecules of long chain esters have revealed an unusual homologous series of ions which suggest a cyclization mechanism to form stabilized bicyclodecenes or bicyclononenes.