bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single crystals of bacteriophage T7 RNA polymerase
Authors: Sousa Rui , Rose John P. , Je Chung Yong , Lafer Eileen M. , Wang Bi‐Cheng 
Published: May 2005

AbstractSingle crystals of T7 RNA polymerase have been grown to a maximum size of 1.8 × 0.3 × 0.3 mm. The crystals are composed of fully intact T7 RNA polymerase which in enzymatically active upon dissolution. These crystals belong to the monoclinic space group P21 and have unit cell parameters a =114.5 Å, b=139.6 Å, c=125.7 Å, β=98.1° Self‐rotation function studies indicate that there are three molecules per asymmetricunit. The crystals diffract to at least 3.0 Å resolution. These are the first crystals of a DNA‐dependent RNA polymerase suitable for high‐resolution X‐ray structure determination.
Three‐dimensional structure of a fluorescein–Fab complex crystallized in 2‐methyl‐2,4‐pentanediol
Authors: Herron James N. , He Xiao‐min , Mason Martha L. , Voss Edward W. , Edmundson Allen B. 
Published: May 2005

AbstractThe crystal structure of a fluorescein–Fab (4‐4‐20) complex was determined at 2.7 Å resolution by molecularreplacement methods. The starting model was the refined 2.7 Å structure of unliganded Fab from an autoantibody (BV04‐01) with specificity for single‐stranded DNA. In the 4‐4‐20 complex fluorescein fits tightly into a relatively deep slot formed by a network of tryptophan and tyrosine side chains. The planar xanthonyl ring of the hapten is accommodated at the bottom of the slot while the phenylcarboxyl group interfaces with solvent. Tyrosine 37 (light chain) and tryptophan 33 (heavy chain) flank the xanthonyl group and tryptophan 101 (light chain) provides the floor of the combining site. Tyrosine 103 (heavy chain) is situated near the phenyl ring of the hapten and tyrosine 102 (heavy chain) forms part of the boundary of the slot. Histidine 31 and arginine 39 of the light chain are located in positions adjacent to the two enolic groups at opposite ends of the xanthonyl ring, and thus account for neutralization of one of two negative charges in the haptenic dianion. Formation of an enol‐arginine ion pair in a region of low dielectric constant may account for an incremental increase in affinity of 2‐3 orders of magnitude in the 4‐4‐20 molecules relative to other members of an idiotypic family of monoclonalantifluorescyl antibodies. The phenyl carboxyl group of fluorescein appearsto be hydrogen bonded to the phenolic hydroxyl group of tyrosine 37 of the light chain. A molecule of 2‐methyl‐2,4‐pentanediol (MPD), trapped in the interface of the variable domainsjust below the fluorescein binding site, may be partly responsible for the decrease in affinity for the hapten in MPD.
Molecular dynamics effects on protein electrostatics
Authors: Wendoloski John J. , Matthew James B. 
Published: May 2005

AbstractElectrostatic calculations have been carried out on a number of structural conformers of tuna cytochrome c Conformers were generated using molecular dynamics simulations with a range of solvent simulating, macroscopic dielectric formalisms, and one solvent model that explicitly included solvent water molecules. Structures generated using the lowest dielectric models were relatively tight, with‐side chains collapsed on the surface, while those from the higher dielectric modelshad more internal and external fluidity, with surface side chains exploring a fuller range of conformational space. The average structure generated with the explicitly solvated model corresponded most closely with the crystal structure. Individual pK values, overall titration curves, and electrostatic potential surfaces were calculated for average structures and along each simulation. Differences between structural conformers within each simulation give rise to substantial changes in calculated local electrostatic interactions, resulting in pK value fluctuations for individual sites in the protein that very by 0.3–2.0 pK units from the calculated time average. These variations are due to the thermal side chain reorientations that produce fluctuations in charge site separations. Properties like overall titration curves and pH dependent stability are not as sensitive to side chain fluctuations within a simulation, but there are substantial effects between simulation due to markeddifferences in average side chain behavior. These findings underscore the importance of proper dielectric formalism in molecular dynamics simulations when used to generate alternate solution structures from a crystal structure, and suggest that conformers significantly removed from the averagestructure have altered electrostatic properties that may prove important inepisodic protein properties such as catalysis.
A 3D building blocks approach to analyzing and predicting structure of proteins
Authors: Unger Ron , Harel David , Wherland Scot , Sussman Joel L. 
Published: May 2005

AbstractA new approach is introduced for analyzing and ultimately predicting protein structures, defined at the level of Cα coordinates. We analyze hexamers (oligopeptides of six amino acid residues) and show that their structure tends to concentrate in specific clusters rather than vary continuously. Thus, we can use a limited set ofstandard structural building blocks taken from these clusters as representatives of the repertoire of observed hexamers. We demonstrate that protein structures can be approximated by concatenating such building blocks. We have identified about 100 building blocks by applying clustering algorithms, and have shown that they can “replace” about 76% ofall hexamers in well‐refined known proteins with an error of less than 1 Å, and can be joined together to cover 99% of the residues. After replacing each hexamer by a standard building block with similar conformation, we can approximately reconstruct the actual structure by smoothly joining the overlapping building blocks into a full protein. The reconstructed structures show, in most cases, high resemblance to the original structure, although using a limited number of building blocks and local criteria of concatenating them is not likely to produce a very precise global match. Since these building blocks reflect, in many cases, some sequence dependency, it may be possible to use the results of this study as a basis for a protein structure prediction procedure.
Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses
Authors: Badger John , Minor Iwona , Oliveira Macros A. , Smith Thomas J. , Rossmann Michael G. 
Published: May 2005

AbstractX‐Ray diffraction data have been obtained for nine related antiviral agents (“WIN compounds”) while bound to human rhinovirus 14 (HRV14).These compounds can inhibit both viral attachment to host cells and uncoating. To calculate interpretable electron density maps it was necessary to account for (1) the low (∼60percnt;) occupancies of these compounds in the crystal, (2) the large (up to 7.9 Å) conformational changes induced at the attachment site, and (3) the incomplete diffraction data. Application of a density difference map technique, which exploits the 20‐fold noncrystallographic redundancy in HRV14, resulted in clear images of the HRV14:WIN complexes. A real‐space refinement procedure was used to fit atomic models to these maps.The binding site of WIN compounds in HRV14 is a hydrophobic pocket composed mainly from residues that form the β‐barrel of VP1. Among rhinoviruses, the residues associated with the binding pocket are far more conserved than external residues and are mostly contained within regular secondary structural elements. Molecular dynamics simulations of three HRV14:WIN complexes suggest that portions of the WIN compounds and viral protein near the entrance of the binding pocket are more flexible than portions deeper within the β‐barrel.
An NMR‐based molecular dynamics simulation of the interaction of the lac repressor headpiece and its operator in aqueous solution
Authors: de Vlieg J. , Berendsen H. J. C , van Gunsteren W. F. 
Published: May 2005

AbstractThe results of a 125 psec molecular dynamics simulation of a lac headpiece–operator complex in aqueous solution are reported. The complexsatisfies essentially all experimental distance information derived from two‐dimensional nuclear magnetic resonance (2‐D‐NMR) studies. The interaction between lac repressor headpiece and its operator based on many direct‐ and water‐mediated hydrogenbonds and nonpolar contacts which allow the formation of a tight complex. Nostable hydrogen bonds between side chains and bases and found, while specific contacts occur between both nonpolar groups and, to a lesserextent, through water‐mediated hydrogen bonds. The simulated complex structure in water is intrinsically stable without application of nuclear Overhauser effect (NOE) distance restraints, while being compatible with most of the available biochemical, genetic, andchemically induced dynamic nuclear polarization (CIDNP) data.
Comparing short protein substructures by a method based on backbone torsion angles
Authors: Karpen Mary E. , de Haseth Pieter L. , Neet Kenneth E. 
Published: May 2005

AbstractAn efficient algorithm was characterized that determines the similarity in main chain conformation between short protein substructures. The algorithm computes Δt, the root mean square difference in ϕ and ψ torsion angles over a small number of amino acids (typically 3–5). Using this algorithm, large number of protein substrates comparisons were feasible. The parameter Δt was sensitive to variations in local protein conformation, and it correlates with Δr, the root mean square deviation in atomic coordinates. Values for Δt were obtained that define similarity thresholds, which determine whether two substructure are considered structurally similar. To set a lower bound on the similarity threshold, we estimated the component of Δt due to measurement noise fromcomparisons of independently refined coordinates of the same protein. A sample distribution of Δt from nonhomologous protein comparisons identified an upper bound on the similarity threshold, one that refrains from incorporating large numbers of nonmatching comparisons large numbers of nonmatching comparisons. Unlike methods based on Cα atoms alone, Δt was sensitive to rotations in the peptide plane, shown to occur in several proteins. Comparisons of homologus proteins by Δt showed that the active site torsion angles are highly conserved. The Δt method was applied to the α‐chain of human hemoglobin, where it readily demonstrated the local differences in the structures of different ligation states.
A computer model to dynamically simulate protein folding: Studies with crambin
Authors: Wilson Charles , Doniach Sebastian 
Published: May 2005

AbstractThe current work describes a simplified representation of protein structure with uses in the simulation of protein folding. The model assumes that a protein can be represented by a freely rotating rigid chain with a single atom approximately the effect of each side chains. Potentials describing the attraction or repulsion between different types of amino acids are determined directly from the distribution of amino acids in the database of known protein structures. The optimization technique of simulated annealinghas been used to dynamically sample the conformations available to this sample model, allowing the protein to evolve from an extended, random coil into a compact globular structure. Many characteristics expected of true proteins, such as the sequence‐dependent formation of secondary structure, the partitioning of hydrophobic residues, and specific disulfide, suggestion the model may accurately simulate the folding process.
Ras interaction with the GTPase‐activating protein (GAP)
Authors: Schaber Michael D. , Garsky Victor M. , Boylan Douglas , Hill Wendy S. , Scolnick Edward M. , Marshall Mark S. , Sigal Irving S. , Gibbs Jackson B. 
Published: May 2005

AbstractBiologically active forms of Ras complexed to GTP can bind to the GTP ase‐activating protein (GAP), which has been implicated as a possible target of Ras in mammalian cells. In order to study the structural features of Ras required for this interaction, we have evaluated a series of mutant ras proteins for the ability to bind GAP and a series of Ras peptides for the ability to interfere with this interaction. Point mutations in the putative effector region of Ras (residues 32–40) that inhibit biological activity also impair Ras binding to GAP. An apparent exception is the Thr to Ser substitution at residue 35; [Ser‐35]Ras binds to GAP as effectively as wild‐type Ras even though this mutant is biologically weak in both mammalian and S. cerevisiae cells. In vitro, [Ser‐35]Ras can also efficiently stimulate the S. cerevisiae target of Ras adenylyl cyclase, indicating that other factors may influence Ras/protein interactions in vivo. Peptides having Ras residues 17–44 and 17–32 competed with the binding of RAS to E. coli‐expressed GAP with IC50 values of 2.4 and 0.9 μM, respectively, whereas Ras peptide 17–26 was without effect up to 400 μM. A related peptide from the yeast GTP‐binding protein YPT1 analogous to Ras peptide 17–32 competed with an IC50 value of 19 μM even though the YPT1 protein itself is unable to bind to GAP. These results suggest that determinants within Ras peptide 17–32 may be important for Ras binding to GAP.
Recombinant HIV1 protease secreted by Saccharomyces cerevisiae correctly processes myristylated gag polyprotein
Authors: Pichuantes Sergio , Babé Lilia M. , Barr Philip J. , Craik Charles S. 
Published: May 2005

AbstractThe protease of the human immunodeficiency virus type I (HIV1) was expressed both intracellularly and extracellularly in Saccharomyces cerevisiae. Intracellular expression of the protease was achieved by fusing a 179 amino acid precursor form of the protease to human superoxide dismutase (hSOD). Self‐processing of the viral enzyme from the hybrid precursor was demonstrated to ocur within the yeast host. Secretion of the protease was achieved by fusing the leader sequence of yeast α‐factor to the precursor form of the protrease or to the 99 amino acid mature form of the protease. Authentic and active forms of the retroviral enzyme were detected in yeast supernatants of cells expressing the precursor or the mature form of the protease. A D25E active site variant of the retroviral enzyme exhibited diminished autocatalytic activity when expressed intracellularly or secreted from yeast. The wild‐type protease was active in an in vitro assay on the natural substrate, myristylated gag precursor, Pr53gag. Correct processing of Pr53gag at the Tyr 138–Pro 139 junction was confirmed by amino terminal sequence analysis of the resulting capsid protein (CA, p24). The secreted protease was purified to homogeneity from yeast media using preparative isoelectric focusing and reverse‐phase HPLC. Amino terminal sequence analysis showed a sequence beginning at amino acid 1 of the mature enzyme (Pro) and another sequence beginning at amino acid 6 (Trp). This shorter sequence may represent a natural autolytic product of the proteaseaspartyl protease.
Axial ligand replacement in horse heart cytochrome c by semisynthesis
Authors: Raphael Adrienne L. , Gray Harry B. 
Published: May 2005

AbstractSemisynthesis has been employed to replace the axial methionine in horse heart cytochrome c with histidine. The reduction potential of the His‐80 protein (cyt c‐His‐80) is 41 mV vs NHE (0.1 M phosphate; pH 7.0; 25°C). The absorption spectra of oxidized and reduced cyt c‐His‐80 are very similar to those of the native protein in the porphyrin region, but the 695 nm band is absent in the oxidized His‐80 protein.
Alternate succession of steps can lead to the folding of a multidomain oligomeric protein
Authors: Murry‐Brelier Anne , Goldberg Michel E. 
Published: May 2005

AbstractThe β2 subunit of Escherichia coli tryptophan synthase can be either unfolded in 6 M guanidine, or extensively denatured at acidic pH. These two denatured form of β2 have different circular dichroism spectra and thus correspond to distinct physical states. Here we compare the folding pathways of these two different denatured forms of β chains. We describe the kinetics of regain of a variety of physical, functional, ad immunochemical signals characteristic of six successive steps previously identified on the folding pathway of guanidine unfolded β2. It is shown that whereas identical molecular events over with the same kinetics, the two folding pathways are different, and involve different structural intermediates.
The surface area of monomeric proteins: Significance of power law behavior
Authors: Bryant Stephen H. , Islam Suhail A. , Weaver David L. 
Published: May 2005

AbstractThe coefficients in a power low fit of accessible area versus molecular weight for high‐reslution monomeric protein structures are assessed with respect to statistical accuracy using bootstrap analyses, and with respect to physical significance using model systems and the concept of roughness or fractal structure of the protein surface.
On the nature of antibody combining sites: Unusual structural features that may confer on these sites an enhanced capacity for binding ligands
Authors: Padlan Eduardo A. 
Published: May 2005

AbstractA detailed analysis of the structural aspects of antibody–antigen interactions has been made possible by the availability of X‐ray structures for three complexes of antilysozyme Fabs to lysozyme (reviewed by Davies et al: J. Biol. Chem. 263:10541–10544, 1988.) Examination of the antigen‐contacting residues in the three antilysozyme Fabs reveals the occurrence of a large number of aromatics, particularly tyrosines, and the absence of apolar, aliphatic residues. Calculation of the frequency of occurrence of the various amino acids types reveals that tyrosines are three times, and histidines and asparagines eight times, more likely to be found in the complementarity‐determinig regions that in the framework of the variability of the residue in FVs (the modules containing variable domains of the light and heavy chains) of known three‐dimensional structure indicates that tryosines and tryptophans are more exposed when they occur in the complementarity‐determining regions that when in the framework. Furthermore, many more of the asparagines in the complementarity‐determining regions than in the framework are buried. These aspararagines appear to have a structural role in that they hydrogen bond through their side chains to other side chains and, Even more so, to the protein backbone. The stabilizing effect of the asparragines, plus the rigidity of the framework, may serve to allow the greater exposure of the aromatic residues to solvent. In view of the greater potential contribution of aromatic side chains to the total binding energy, these results suggest that antibody‐combining sites have structural features that make them especially studied for interacting with lagands.
β‐Lactamase of Bacillus licheniformis 749/C at 2 Å resolution
Authors: Moews Paul C. , Knox James R. , Dideberg Otto , Charlier Paulette , Frère Jean‐Marie 
Published: May 2005

AbstractTwo crystal (A and B) of the 29,500 Da Class A β‐lactamase (penicillinase) from Bacillus licheniformis 749/C have been examined crystallographically. The structure of B‐form crystals has been solved to 2 Å resolution, the starting model for which was a 3.5 Å structure obtained from A‐form crystals. The β‐lactamase has an α + β structure with 11 helices and 5 β‐strands seen also in a peinicilin target DD‐peptidase of Streptomyces R61.1 Atomic parameters of the two molecules in the asymmetric unit were refined by simulated annealing at 2.0 Å resolution. The R factor is 0.208 for the 27,330 data greater than 3 (F), with water molecules excluded from the model. The catalytic Ser‐70 is at the N‐terminus of a helix and is within hydrogen bonding distance of conversed Lys‐73. Also interacting with the Lys‐73 are Asn‐132 and the conserved Glu‐166, which is on a potentially flexible helix‐containing loop. The structure suggests the binding of β‐lactam substrates is facilitated by interactions with Lys‐234, Tyhr‐235, and Ala‐237 in a conserved β‐strand peptide, which is antiparallel to the β‐lactam's acylamido linkage; an exposed cavity near Asn‐170 exits for acylamido Substituent. The reactive double bond of clavulanate‐type inhibitors may interact with Arg‐244 on the fourth β‐strand. A very similar binding site architecture is seen in the DD‐peptidase.
Molecular dynamics study of secondary structure motion in proteins: Application to myohemerythrin
Authors: Rojewska Danuta , Elber Ron 
Published: May 2005

AbstractThe concept of secondary structure motions is examined in a molecular dynamics simulation of the protein myohemerythrin. We extracted from the simulation a corresponding trajectory of helices and demonstrated that the fluctuations of the protein are dominated by a rigid shift of these secondary structure elements. The relative motions of the helices are regular, with no clear periodicity. They are bounded by ∼2 for the center of mass motions and by 20° for the relative orientations. The potential of mean force for the interactions of the helices was calculated, and the correlations between the different extended motions were investigated. It shown that the one‐dimensional mean force potentials are close to quadratic for most of the helices coordinates. The anharmonicity is reflected by changes in the direction of the normal modes as a function of the energy and by the existence of multiple free energy minima for the helices packing. The multiple conformations are associated with a single type of secondary structure coordinate: the angle that describes the relative orientation of the helices in a plane perpendicular to the line connecting their center of mass.
Bundles of amphipathic transmembrane α‐helices as a structural motif for ion‐conducting channel proteins: Studies on sodium channels and acetylcholine receptors
Authors: Oiki Shigetoshi , Madison Vincent , Montal Mauricio 
Published: May 2005

AbstractChannel proteins are transmembrane symmetric (or pseudosymmetric) oligomers organized around a central ionic pore. We present here a molecular model of the pore forming structures of two channel proteins with different primary structures and oligomeric size: the voltage‐sensitive sodium channel and the nicotinic cholinergic receptor. We report low‐energy arrangements of α‐helical bundles calculated by semiempiricial potential energy functions and optimization routines and further refined using molecular dynamics. The ion‐conducting pore is considered to be a symmetric or pseudosymmetric homooligomer of 3–5 amphipathic α‐helices arranged such that the polar residues line a central hydrophilic pathway and the apolar residues face the hydrophobic bilayer interior. The channel lining exposes either charged (Asp, Glu, Arg, Lys) or polar‐neutral (Ser, Thr) residues. A bundle of four parallel helices constrained to C4 symmetry, the helix axis aligned with the symmetry axis, and the helices constrained to idealized dihedral angles, produces a structure with a pore of the size inferred for the sodium channel protein (area ∼ 16 Å2). Similarly, a pentameric array optimized with constraints to maintain C5 symmetry and backbone torsions characteristic of α‐helices adopts a structure that appears well suited to form the lining of the nicotinic cholinergic receptor (pore area ∼ 46 Å2). Thus, bundles of amphipathic α‐helices satisfy the structural, energetic, and dynamic requirements to be the molecular structural motif underlying the function of ionic channels.