bluuebunny/crossref_metadata_2025_split huggingface dataset:
Weak correlation between predictive power of individual sequence patterns and overall prediction accuracy in proteins
Authors: Rooman Marianne J. , Wodak Shoshana J. 
Published: May 2005

AbstractPatterns in amino acid properties (polar, hydrophobic, etc.) that characterize secondary structure motifs are derived from a database containing 75 protein structures, with the aim of circumventing the limitations due to data base size so as to increase structure prediction score. Many such sequence–structure associations with high intrinsic predictive power are found, which turn out to be correct 78% of the time when applied individually to proteins outside the learning set. Based on these associations, a prediction method is developed, which reaches the socre of 62% on the 3 states α‐helix, β‐strand, and loop, without using additional constraints. Though this score is quite good compared to that of other available prediction methods, it is much lower than could be expected from the high intrinsic predictive power of the associations used. The reasons underlying this surprising result, which indicate that prediction score and intrinsic predictive power are only weakly coupled, are discussed. It is also shown that the size of the present database still seriously limits prediction scores, even when property patterns are used, and that higher scores are expected in large databases. Clues are provided on the relative influence of neglecting spatial interactions on prediction efficiency, suggesting that, in sufficiently large databases, predicted secondary structures would correspond to those formed early in the folding process. This hypothesis is tested by confronting present predictions with available experimental data on early protein folding intermediates and on small peptides that adopt a relatively stable conformation in water. Although admittedly there are still too few such data, results suggest that the hypothesis might be well founded.
Crystallization of yeast orotidine 5′‐monophosphate decarboxylase complexed with 1‐(5′‐phospho‐β‐D‐ribofuranosyl) barbituric acid
Authors: Bell Juliette B. , Jones Mary Ellen , Carter Charles W. 
Published: May 2005

AbstractUsing an incomplete factorial experimental design, we have identified conditions for crystallization of yeast orotidine 5′‐monophosphate decarboxylase (ODCase) in an unliganded state and complexed separately to two inhibitors: 6‐azauridine 5′‐monophosphate (aza‐UMP) and 1‐(5′‐phospho‐β‐D‐ribofuranosyl) barbituric acid (BMP). Crystals of X‐ray diffraction quality have been obtained of yeast ODCase complexed with BMP, a putative transition state analog inhibitor (Ki = 8.8 × 10−12 M). ODCase:BMP complex crystals with a hexagonal rod habit were grown from a solution initially containing 12 mg/ml ODCase (205 μM dimer) plus 450 μM BMP by microdialysis at 4°C against a mother liquor which consisted of 0.1 M Na‐PIPES‐acetate (pH 6.4), 37.5 μM BMP, 5 mM mercaptoethanol, 1% polyethylene glycol 400, and 2.3 M ammonium sulfate. Crystals were analyzed using precession photography and were assigned to trigonal space group R32 with unit cell dimensions a = b = 115 Å, c = 385 Å. The crystal density is 1.245 g/cm3 indicating the presence of two ODCase:BMP complex dimers (118 kDa each) per asymmetric unit with a packing density of 2.08 Å3/Da and 41% solvent content. The morphological habit of crystals of the ODCase:BMP complex changed when the initial ammonium sulfate concentration was increased in 0.05 M steps from 2.3 to 2.45 M. All of these crystals diffracted to at least 3.0 Å resolution over a period of several weeks at room temperature and are isomorphous.
A metal‐mediated hydride shift mechanism for xylose isomerase based on the 1.6 Å Streptomycs rubiginosus structure with xylitol and D‐xylose
Authors: Whitlow Marc , Howard Andrew J. , Finzel Barry C. , Poulos Thomas L. , Winborne Evon , Gilliland Gary L. 
Published: May 2005

AbstractThe crystal structure of recombinant Streptomyces rubiginous D‐xylose isomerase (D‐xylose keto‐isomerase, EC 5.3.1.5) solved by the multiple isomorphous replacement technique has been refined to R = 0.16 at 1.64 Å resolution. As observed in an earlier study at 4.0 Å (Carrell et al., J. Biol. Chem. 259: 3230–3236, 1984), xylose isomerase is a tetramer composed of four identical subunits. The monomer consists of an eight‐stranded parallel β‐barrel surrounded by eight helices with an extended C‐terminal tail that provides extensive contacts with a neighboring monomer. The active site pocket is defined by an opening in the barrel whose entrance is lined with hydrophobic residues while the bottom of the pocket consists mainly of glutamate, aspartate, and histidine residues coordinated to two manganese ions.The structures of the enzyme in the presence of MnCl2, the inhibitor xylitol, and the substrate D‐xylose in the presence and absence of MnCl2 have also been refined to R = 0.14 at 1.60 Å, R = 0.15 at 1.71 Å, R = 0.15 at 1.60 Å, and R = 0.14 at 1.60 Å, respectively. Both the ring oxygen of the cyclic α‐D‐xylose and its C1 hydroxyl are within hydrogen bonding distance of NE2 of His‐54 in the structure crystallized in the presence of D‐xylose. Both the inhibitor, xylitol, and the extended form of the substrate, D‐xylose, bind such that the C2 and C4 OH groups interact with one of the two divalent cations found in the active site and the C1 OH with the other cation. The remainder of the OH groups hydrogen bond with neighboring amino acid side chains.A detailed mechanism for D‐xylose isomerase is proposed. Upon binding of cyclic α‐D‐xylose to xylose isomerase, His‐54 acts as the catalytic base in a ring opening reaction. The ring opening step is followed by binding of D‐xylose, in volving two divalent cations, in an extended conformation. The isomerization of D‐xylose to D‐xylulose involves a metal‐mediated 1,2‐hydride shift. The final step in the mechanism is a ring closure to produce α‐D‐xylulose. The ring closing is the reverse of the ring opening step.This mechanism accounts for the majority of xylose iomerase's biochemical properties, in cluding (1) the lack of solvent exchange between the 2‐position of D‐xylose and the 1‐pro‐R position of D‐xylulose, (2) the chemical modification of histidine and lysine, (3) the pH vs. activity profile, and (4) the requirement for two divalent cations in the mechanism.
Electron redistribution on binding of a substrate to an enzyme: Folate and dihydrofolate reductase
Authors: Bajorath Jürgen , Kitson David H. , Fitzgerald George , Andzelm Jan , Kraut Joseph , Hagler Arnold T. 
Published: May 2005

AbstractThe migration of electron density of a substrate (folate) on binding to an enzyme (dihydrofolate reductase) is studied by a quantum‐mechanical method originally developed in solid state physics. A significant polarization of the substrate is induced by the enzyme, toward the transition state of the enzymatic reaction, at the same time giving rise to “electronic strain energy” in the substrate and enhanced protein–ligand interactions. The spatial arrangement of protein charges that induces the polarization is identified and found to be structurally conserved for bacterial and vertebrate dihydrofolate reductases.
Topological mirror images in protein structure computation: An underestimated problem
Authors: Pastore Annalisa , Atkinson R. Andrew , Saudek Vladimir , Williams Robert J. P. 
Published: May 2005

AbstractWhen calculating three‐dimensional structures from NMR data, alternative solutions with very large RMS deviation can be obtained. Sometimes local or global inversions of the protein folding can be observed. We call these different solutions topological mirror images, as they keep the correct amino acid chirality. They are observed when the number of restraints is insufficient and represent different solutions from the same scalar information. Therefore they are common in small peptides where the NMR data are often limited and the secondary structure is not very well defined. They can also be observed in large molecules in regions of higher flexibility. In our experience the observation of topological mirror images is independent of the efficiency of sampling of the algorithm used. We present four examples of proteins with different size and folding. We also discuss ways to distinguish among the different solutions.
The crystal structure of the “open” and the “closed” conformation of the flexible loop of trypanosomal triosephosphate isomerase
Authors: Wierenga Rik K. , Noble Martin E. M. , Postma Johan P. M. , Groendijk Hillie , Kalk Kor H. , Hol Wim G. J. , Opperdoes Fred R. 
Published: May 2005

AbstractTriosephosphate isomerase has an important loop near the active site which can exist in a “closed” and in an “open” conformation. Here we describe the structural properties of this “flexible” loop observed in two different structures of trypanosomal triosephosphate isomerase. Trypanosomal triosephosphate isomerase, crystallized in the presence of 2.4 M ammonium sulfate, packs as an asymmetric dimer of 54,000 Da in the crystallographic asymmetric unit. Due to different crystal contacts, peptide 167–180 (the flexible loop of subunit‐1) is an open conformation, whereas in subunit‐2, this peptide (residues 467–480) is in a closed conformation. In the closed conformation, a hydrogen bond exists between the tip of the loop and a well‐defined sulfate ion which is bound to the active site of subunit‐2. Such an active site sulfate is not present in subunit‐1 due to crystal contacts. When the native (2.4 M ammonium sulfate) crystals are transferred to a sulfate‐free mother liquor, the flexible loop of subunit‐2 adopts the open conformation. From a closed starting model, this open conformation was discovered through molecular dynamics refinement without manual intervention, despite involving Cα shifts of up to 7 Å. The tip of the loop, residues 472, 473, 474, and 475, moves as a rigid body. Our analysis shows that in this crystal form the flexible loop of subunit‐2 faces a solvent channel. Therefore the open and the closed conformations of this flexible loop are virtually unaffected by crystal contacts. The actual observed conformation depends only on the absence or presence of a suitable ligand in the active site.
Relaxation data in NMR structure determination: Model calculations for the lysozyme–Gd3+ complex
Authors: Sutcliffe Michael J. , Dobson Christopher M. 
Published: May 2005

AbstractThe effect of including paramagnetic relaxation data as additional restraints in the determination of protein tertiary structures from NMR data has been explored by a systematic series of model calculations. The system used for testing the method was the 2.0 Å resolution tetragonal crystal structure of hen egg white lysozyme (129 amino acid residues) and structures were generated using a version of the hybrid “distance geometry–dynamic simulated annealing” procedure. A limited set of 769 NOEs was used as restraints in all the calculations; the strengths of these were categorized into three classes on the basis of distances observed in the crystal structure. The values of 50 ϕ angles were also restrained on the basis of amide–alpha coupling constants calculated from the X‐ray structure. Five sets of 12 structures were determined using differing sets of paramagnetic relaxation data as restraints additional to those involving the NOE and coupling constant data. The paramagnetic relaxation data were modeled on the basis of the distances of defined protons from the crystallographic binding site of Gd3+ in lysozyme. Analysis of the results showed that the relaxation data significantly improved the correspondence between the set of generated structures and the crystal structure, and that the more well defined the relaxation data, the more significant the improvement in the quality of the structures. The results suggest that the inclusion of paramagnetic relaxation restraints could be of significant value for the experimental determination of protein structures from NMR data.
Modeling conformational change in macromolecules as an elastic deformation
Authors: Andrews Lawrence C. , Harrison Robert W. 
Published: May 2005

AbstractMacromolecules are elastic bodies. Atomic strucutres are available for nucleic acids and proteins in two or more different conformations. It is a common practice to compare two structures by finding the best rigid body superposition of the molecules. This ignores possible deformations. There is useful information in the deviations from the rigid body superposition. If the deviations are considered to be elastic deformations of a common structure than it is possible to extract this information. Results are shown for comparisons of deoxyhemoglobin versus carbonmonoxyhemoglobin and for two different conformations of catabolite gene activator protein.
Secondary structure‐based profiles: Use of structure‐conserving scoring tables in searching protein sequence databases for structural similarities
Authors: Lüthy Roland , McLachlan Andrew D. , Eisenberg David 
Published: May 2005

AbstractThe profile method, for detecting distantly related proteins by sequence comparison, has been extended to incorporate secondary structure information from know X‐ray structures. The sequence of a known structure is aligned to sequences of other members of a given folding class. From the known structure, the secondary structure (α‐helix, β‐strand or “other”) is assigned to each position of the aligned sequences. As in the standard profile method,1 a position‐dependent scoring table, termed a profile, is calculated from the aligned sequences. However, rather than using the standard Dayhoff mutation table in calculating the profile, we use distinct amino acid mutation tables for residues in α‐helices, β‐strands or other secondary structures to calculate the profile. In addition, we also distinguish between internal and external residues. With this new secondary structure‐based profile method, we created a profile for eight‐stranded, antiparallel β barrels of the insecticyanin folding class. It is based on the sequences of retinol‐binding protein, insecticyanin and β‐lactoglobulin. Scanning the sequence database with this profile, it was possible to detect the sequence of avidin. The structure of streptavidin is known, and it appears to be distantly related to the antiparallel β barrels. Also detected is the sequence of complement component C8, which we therefore predict to be a member of this folding class.
Variation of folded polypeptide surface area with probe size
Authors: Islam Suhail A. , Weaver David L. 
Published: May 2005

AbstractThree types of polypeptide surface area (contact, accessible, and molecular) have been studied as a function of the radius of a probe sphere used to map the surface. The surfaces are: (1) three α‐helices, the H‐helix of myoglobin, the E‐helix of leghemoglobin, and an artificial polyalanine helix, each with 26 residues; (2) two globins, myoglobin and leghemoglobin, each with 153 residues: and (3) a two center model system for which the three types of surface area have been calculated analytically. The two globin helices have almost identical surface areas as a function of probe size as do the two globins. The polyalanine helix surface area is smaller but similar in shape to the globin helix areas. All three helix contact areas tend to the same limit as the probe size increases, and the globin contact areas behave similarly. Fractal dimensions were calculated for the helix and globin contact and molecular surfaces. All fractal dimensions showed strong dependence on probe size. The contact fractal dimension peaks at larger values for both the helices and globins. Most residues do not make contact with large probes (15 Å).
Molecular dynamics simulations of the cytochrome c3–rubredoxin complex from Desulfovibrio vulgaris
Authors: Stewart David E. , Wampler John E. 
Published: May 2005

AbstractMolecular dynamics simulations have been carried out on the complex formed between the tetraheme cytochrome c3 and the iron protein rubredoxin from the sulfate‐reducing bacterium Desulfovibrio vulgaris. These simulations were performed both with explicit solvent water molecules included, and without solvent molecules using a distance‐dependent dielectric constant to approximate the screening effects of solvent. The results of both simulations are strikingly different, indicating that the representation of environmental effects is important in such simulations. For example, a striking adaptation of the two proteins seen in the nonsolvated simulation is not seen when explicit solvent water is included; in fact, the complex appears to become weaker in the solvated simulation. Nonetheless, the iron–iron distance decreases more significantly in the solvated simulation than in the nonsolvated simulation. It was found that in both cases molecular dynamics optimized the structures further than energy minimization alone.
A 175‐psec molecular dynamics simulation of camphor‐bound cytochrome P‐450cam
Authors: Paulsen Mark D. , Ornstein Rick L. 
Published: May 2005

AbstractThe structure and internal motions of cytochrome P‐450cam, a monooxygenase heme enzyme with 414 amino acid residues, with camphor bound at the active site have been evaluated on the basis of a 175‐psec molecular dynamics simulation carried out at 300 K. All hydrogen atoms were explicitly modeled, and 204 crystallographic waters were included in the simulation. Based on an analysis of the time course of the trajectory versus potential energy, root mean square deviation, radius of gyration, and hydrogen bonding, the simulation was judged to be stable and representative of the average experimental structure. The averaged structural properties of the enzyme were evaluated from the final 135 psec of the simulation. The average atomic displacement from the X‐ray structure was 1.39 Å for all heavy atoms and 1.17 Å for just C‐α atoms. The average root‐mean‐square (rms) fluctuations of all heavy atoms and backbone atoms were 0.42 and 0.37 Å, respectively. The computed rms fluctuations were in reasonable agreement with the experimentally determined temperature factors. All 13 segments of α‐helix and 5 segments of β‐sheet were well preserved with the exception of the N‐terminal half of halix F which alternated between an α‐helix and a 310‐helix. In addition there were in general only small variations in the relative orientation of adjacent α‐helices. The rms fluctuations of the backbone dihedral angles in the secondary structure elements were almost uniformly smaller, with the fluctuation in α‐helices and β‐sheets, 31 and 10% less, respectively, than those in nonsecondary structure regions. The reported crystal structure contains kinks in both helices C and I. In the simulation, both of these regions showed high mobility and large deviations from their starting positions. Since the kink in the I helix is at the oxygen binding site, these motions may have mechanistic implications.
Structure–function relationships of the hematopoietic growth factors
Authors: Kaushansky Kenneth 
Published: May 2005

AbstractThe hematopoietic growth factors are a family of glycoproteins involved in the production of blood cells from their bone marrow precursors and in the activation of mature blood cells. Much has been learned about the structural features of these molecules responsible for their characteristic biological activities. Most studies have been based upon mutagenesis strategies of intact polypeptides and on epitope mapping of informative monoclonal antibodies to the growth factors. A more limited amount of physical data is available. This review will summarize these findings, highlight the growing body of evidence suggesting that many of these proteins share common evolutionary origins and structural elements, and hopefully point to the directions being taken for further investigations of these scientifically informative and clinically useful group of proteins.
CLIX: A search algorithm for finding novel ligands capable of binding proteins of known three‐dimensional structure
Authors: Lawrence Michael C. , Davis Paul C. 
Published: May 2005

AbstractA computer algorithm, CLIX, capable of searching a crystallographic database of small molecules for candidates which have both steric and chemical likelihood of binding a protein of known three‐dimensional structure is presented. The algorithm is a significant advance over previous strategies which consider solely steric or chemical requirements for binding. The algorithm is shown to be capable of predicting the correct binding geometry of sialic acid to a mutant influenzavirus hemagglutinin and of proposing a number of potential new ligands to this protein.
Effects of eglin‐c binding to thermitase: Three‐dimensional structure comparison of native thermitase and thermitase eglin‐c complexes
Authors: Gros Piet , Teplyakov Alex V. , Hol Wim G. J. 
Published: May 2005

AbstractThermitase is a thermostable member of the subtilisin family of serine proteases. Four independently determined crystal structures of the enzyme are compared in this study: a high resolution native one and three medium resolution complexes of thermitase with eglin‐c, grown from three different calcium concentrations. It appeared that the B‐factors of the thermitase eglin complex obtained at 100 mM CaCl2 and elucidated at 2.0 Å resolution are remarkably similar to those of the 1.4 Å native structure: the main chain atoms have an rms difference of only 2.3 Å2; for all atoms this difference is 4.6 Å2. The rms positional differences between these two structures of thermitase are 0.31 Å for the main chain atoms and 0.58 Å for all atoms. There results show that not only atomic positions but also temperature factors can agree well in X‐ray structures determined entirely independently by procedures which differ in virtually every possible technical aspect.A detailed comparison focussed on the effects of eglin binding on the structure of thermitase. Thermitase can be considered as consisting of (1) a central core of 94 residues, plus (2) four segments of 72 residues in total which shift as rigid bodies with respect to the core, plus (3) the remaining 113 residues which show small changes but, however, cannot be described as rigid bodies. The central cores of native thermitase and the 100 mM CaCl2 thermitase:eglin complex have an rms deviation of 0.13 Å for 376 main chain atoms. One of the segments, formed by loops of the strong calcium binding site, shows differences up to 1.0 Å in Cα positions. These are probably due to crystal packing effects.The three other segments, comprising 51 residues, are affected conformational changes upon eglin binding so that the P1 to P3 binding pockets of thermitase broaden by 0.4 to 0.7 Å. The residues involved in these changes correspond with residues which change position upon inhibitor binding in other subtilisins. This suggests that an induced fit mechanism is operational during substrate recognition by subtilisins.
Redesigning the DNA‐binding specificity of a zinc finger protein: A data base‐guided approach
Authors: Desjarlais John R. , Berg Jeremy M. 
Published: May 2005

AbstractA peptide corresponding to the three zinc finger domains of the human transcription factor Sp1 has been expressed and found to bind a consensus Sp1 binding site with the sequence 5′‐GGGGCGGGG‐3′. Examination of the amino acid distributions within a large zinc finger sequence data base and chemical arguments suggested that a particular Arg to Gln sequence change might convert binding specificity to 5′‐GGGGCAGGG‐3′. Experimental tests of this hypothesis revealed that such a change could be induced only when two other sequence changes, deduced from examination of sequence correlations, were made as well. These results provide the most direct information to date about how zinc finger proteins might recognize adenine‐containing binding sites and bear on the existence and nature of any code between zinc finger protein and binding site sequences.