bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coiled‐coil stutter and link segments in keratin and other intermediate filament molecules: A computer modeling study
Authors: North Anthony C. T. , Steinert Peter M. , Parry David A. D. 
Published: May 2005

AbstractStructural discontinuities have previously been identified in four regions of the coiled‐coil rod domain structure present in intermediate filament (IF) protein molecules. These include a point at which a phase shift occurs in the heptad periodicity characteristic of the sequence of polar and apolar residues in α‐helical coiled‐coils, and three links that lack a heptad substructure. We have studied these regions by computer‐based molecular modeling and comparative sequence analysis and conclude that the phasing discontinuity can be accommodated without significant distortion of the overall double‐helical chain conformation; the L2 link has a similar conformation in all different types of IF molecules, a favorable conformation being one in which the two strands wrap tightly around each other; the L12 links vary in length between different IF types but contain important sequence similarities suggestive of a partial β structure; the L1 links show larger variations in length, a lower degree of similarity, and probably diverse structures. Variations in the overall charges of the different links suggest that ionic interactions may playa significant role in filament assembly. The results also have general significance for other α‐fibrous proteins in which either the characteristic heptad phasing undergoes a discontinuity or where a short non‐coiled‐coil sequence occurs within a coiled‐coil rod domain structure. © 1994 Wiley‐Liss, Inc.
Intrinsic secondary structure propensities of the amino acids, using statistical ϕ–ψ matrices: Comparison with experimental scales
Authors: Muñoz Victor , Serrano Luis 
Published: May 2005

AbstractToday there are several different experimental scales for the intrinsic α‐helix as well as β‐strand, propensities of the 20 amino acids obtained from the thermodynamic analysis of various model systems. These scales do not compare well with those extracted from statistical analysis of three‐dimensional structure databases. Possible explanations for this could be the limited size of the databases used, the definitions of intrinsic propensities, or the theoretical approach. Here we report a statistical determination of α‐helix and β‐strand propensities derived from the analysis of a database of 279 three‐dimensional structures. Contrary to what has been generally done, we have considered a particular residue as in α‐helix or β‐strand conformation by looking only at its dihedral angles (ϕ–ψ matrices). Neither the identity nor the conformation of the surrounding residues in the amino acid sequence has been taken into consideration. Pseudoenergy empirical scales have been calculated from the statistical propensities. These scales agree very well with the experimental ones in relative and absolute terms. Moreover, its correlation with the average of the experimental scales for α‐helix or β‐strand is as good as the correlations of the individual experimental scales with the average. These results show that by using a large enough database and a proper definition for the secondary structure propensities, it is possible to obtain a scale as good as any of experimental origin. Interestingly the ϕ–ψ analysis of the Ramachandran plot suggests that the amino acids could have different β‐strand propensities in different subregions of the β‐strand area. © 1994 Wiley‐Liss, Inc.
Hydrophobic docking: A proposed enhancement to molecular recognition techniques
Authors: Vakser Ilya A. , Aflalo Claude 
Published: May 2005

AbstractIn the classical procedures for predicting the structure of protein complexes two molecules are brought in contact at multiple relative positions, the extent of complementarity (geometric and/or energy) at the surface of contact is assessed at each position, and the best fits are retrieved. In view of the higher occurrence of hydrophobic groups at contact sites, their contribution results in more intermolecular atom–atom contacts per unit area for correct matches than for false positive fits. The hydrophobic groups are also potentially less flexible at the surface. Thus, from a practical point of view, a partial representation of the molecules based on hydrophobic groups should improve the quality of the results in finding molecular recognition sites, as compared to full representation. We tested this proposal by applying the idea to an existing geometric fit procedure and compared the results obtained with full vs. hydrophobic representations of molecules in known molecular complexes. The hydrophobic docking yielded distinctly higher signal‐to‐noise ratio so that the correct match is discriminated better from false positive fits. It appears that nonhydrophobic groups contribute more to false matches. The results are discussed in terms of their relevance to molecular recognition techniques as compared to energy calculations. © 1994 Wiley‐Liss, Inc.
A P‐loop‐like motif in a widespread ATP pyrophosphatase domain: Implications for the evolution of sequence motifs and enzyme activity
Authors: Bork Peer , Koonin Eugene V. 
Published: May 2005

AbstractA conserved amino acid sequence motif was identified in four distinct groups of enzymes that catalyze the hydrolysis of the α–β phosphate bond of ATP, namely GMP synthetases, argininosuccinate synthetases, asparagine synthetases, and ATP sulfurylases. The motif is also present in Rhodobacter capsulata AdgA, Escherichia coli NtrL, and Bacillus subtilis OutB, for which no enzymatic activities are currently known. The observed pattern of amino acid residue conservation and predicted secondary structures suggest that this motif may be a modified version of the P‐loop of nucleotide binding domains, and that it is likely to be involved in phosphate binding. We call it PP‐motif, since it appears to be a part of a previously uncharacterized ATP pyrophophatase domain. ATP sulfurylases, NtrL, and OutB consist of this domain alone. In other proteins, the pyrophosphatase domain is associated with amidotransferase domains (type I or type II), a putative citrulline‐aspartate ligase domain or a nitrilase/amidase domain. Unexpectedly, statistically significant overall sequence similarity was found between ATP sulfurylase and 3′‐phosphoadenosine 5′‐phosphosulfate (PAPS) reductase, another protein of the sulfate activation pathway. The PP‐motif is strongly modified in PAPS reductases, but they share with ATP sulfurylases another conserved motif which might be involved in sulfate binding. We propose that PAPS reductases may have evolved from ATP sulfurylases; the evolution of the new enzymatic function appears to be accompanied by a switch of the strongest functional constraint from the PP‐motif to the putative sulfate‐binding motif. © 1994 Wiley‐Liss, Inc.
Thermodynamic genetics of the folding of the B1 immunoglobulin‐binding domain from streptococcal protein G
Authors: O'Neil Karyn T. , Hoess Ronald H. , Raleigh Daniel P. , DeGrado William F. 
Published: May 2005

AbstractA method has been developed to select proteins that are thermodynamically destabilized yet still folded and functional. The DNA encoding the B1 IgG‐binding domain from Group G Streptococcus (Strp G) has been fused to gene III of bacteriophage M13. The resulting fusion protein is displayed on the surface of the phage thus enabling the phage to bind to IgG molecules. In addition, these phage exhibit a small plaque phenotype that is reversed by mutations that destabilize the Strp G domain. By selecting phage with large plaque morphology that retain their IgG‐binding function, it is possible to identify mutants that are folded but destabilized compared with wild‐type Strp G. Such mutants can be divided into three general categories: (1) those that disrupt packing of hydrophobic side chains in the protein interior; (2) those that destabilize secondary structure; and (3) those that alter specific hydrogen bonds involving amino acid side chains. A number of the mutants have been physically characterized by circular dichroism and nuclear magnetic resonance and have been shown to have structures similar to wild‐type Strp G but stabilities that were decreased by 2–5 kcal/mol. © 1995 Wiley‐Liss, Inc.
A vector projection method for predicting the specificity of GalNAc‐transferase
Authors: Chou Kuo‐Chen , Zhang Chun‐Ting , Kézdy Ferenc J. , Poorman Roger A. 
Published: May 2005

AbstractThe specificity of UDP‐Gal‐NAc:polypeptide N‐acetylgalactosaminytransferase (GalNAc‐transferase) is consistent with the existence of an extended site composed of nine subsites, denoted by P4, P3, P2, P1, P0, P1′, P2′, P3′, and P4′, where the acceptor at P0 is being either Ser or Thr. To predict whether a peptide will react with the enzyme to form a Ser‐ or Thr‐conjugated glycopeptide, a vector projection method is proposed which uses a training set of amino acid sequences surrounding 90 Ser and 106 Thr O‐glycosylation sites extracted from the National Biomedical Research Foundation Protein Database. The model postulates independent interactions of the 9 amino acid moieties with their respective binding sites. The high ratio of correct predictions vs. total predictions for the data in both the training and the testing sets indicates that the method is self‐consistent and efficient. It provides a rapid means for predicting O‐glycosylation and designing effective inhibitors of GalNAc‐transferase. © 1995 Wiley‐Liss, Inc.
Structural studies of a synthetic peptide derived from the carboxyl‐terminal domain of RNA polymerase II
Authors: Cagas Perseveranda M. , Corden Jeffry L. 
Published: May 2005

AbstractThe conformation of the repeating heptapeptide unit of the carboxyl‐terminal domain of RNA Polymerase II, Y1S2P3T4S5P6S7 has been examined using nuclear magnetic resonance spectroscopy and circular dichroism. Nuclear Overhauser effects and CD spectra for the synthetic 56‐residue peptide H2N‐(S2P3T4S5P6S7Yl)8‐COOH in water indicate that the peptide is largely unordered. A small population of folded molecules is observed to contain β‐turns located at Ser2‐Pro3‐Thr4‐Ser5 (SPTS) and Ser5‐Pro6‐Ser7‐Tyr1 (SPSY). CD and NMR results in 90% TFE also indicate an equilibrium population of structures, but the fraction of turns is higher. Similarities of nuclear Overhauser effects in water and in 90% TFE suggest that the structures in TFE are biologically relevant. Based on these observations, the average structure of a single conformer of the heptapeptide repeat in 90% TFE was obtained by a distance geometry‐simulated annealing method, using distance restraints extracted from nuclear Overhauser data. NMR spectra of the 56‐mer show signals corresponding to only one repeat indicating that each repeat is in an identical environment. Thus it is possible to obtain an average structure of the heptapeptide repeat from NOE data on the 56‐mer. Twenty‐seven final structures were calculated and the root mean square deviations between the 27 structure and the mean coordinates was 1.52 Å for the backbone and 2.2 Å for all nonhydrogen atoms. The heptapeptide repeat consists of two overlapping β‐turns which are potentially stabilized by hydrogen bonds. The hydroxyl side chains of Ser2, Ser5, Thr4, and Ser7 all appear to be equally exposed for potential phosphorylation. The tyrosyl side chain of each repeat is folded inwards to the backbone and can potentially hydrogen bond to the carbonyl oxygen of the tyrosine in the preceding repeat. Iteration of the average structure of the heptapeptide repeat results in a model of the carboxyl‐terminal domain with a regular but unusual secondary structure consisting of a series of staggered β‐turns. © 1995 Wiley‐Liss, Inc.
Computational approaches to study protein unfolding: Hen egg white lysozyme as a case study
Authors: Hünenberger P. H. , Mark A. E. , van Gunsteren W. F. 
Published: May 2005

AbstractFour methods are compared to drive the unfolding of a protein: (1) high temperature (T‐run), (2) high pressure (P‐run), (3) by imposing a gradual increase in the mean radius of the protein using a penalty function added to the physical interaction function (F‐run, radial force driven unfolding), and (4) by weak coupling of the difference between the temperature of the radially outward moving atoms and the radially inward moving atoms to an external temperature bath (K‐run, kinetic energy driven unfolding). The characteristic features of the four unfolding pathways are analyzed in order to detect distortions due to the size or the type of the applied perturbation, as well as the features that are common to all of them. Hen egg white lysozyme is used as a test system. The simulations are analyzed and compared to experimental data like 1H‐NMR amide proton exchange‐folding competition, heat capacity, and compressibility measurements. © 1995 Wiley‐Liss, Inc.
A model for the LexA repressor DNA complex
Authors: Knegtel Ronald M. A. , Fogh Rasmus H. , Boelens Rolf , Kaptein Robert , Ottleben Gunnar , Rüterjans Heinz , Dumoulin Pascal , Schnarr Manfred 
Published: May 2005

AbstractA structural model for the interaction of the LexA repressor DNA binding domain (DBD) with operator DNA is derived by means of Monte Carlo docking. Protein–DNA complexes were generated by docking the LexA repressor DBD NMR solution structure onto both rigid and bent B‐DNA structures while giving energy bonuses for contacts in agreement with experimental data. In the resulting complexes, helix III of the LexA repressor DBD is located in the major groove of the DNA and residues Asn‐41, Glu‐44, and Glu‐45 form specific hydrogen bonds with bases of the CTGT DNA sequence. Ser‐39, Ala‐42, and Asn‐41 are involved in a hydrophobic interaction with the methyl group of the first thymine base. Residues in the loop region connecting the two β‐sheet strands are involved in nonspecific contacts near the dyad axis of the operator. The contacts observed in the docked complexes cover the entire consensus CTGT half‐site DNA operator, thus explaining the specificity of the LexA repressor for such sequences. In addition, a large number of nonspecific interactions between protein and DNA is observed. The agreement between the derived model for the LexA repressor DBD/DNA complex and experimental biochemical results is discussed. © 1995 Wiley‐Liss, Inc.
The first solvation shell of magnesium ion in a model protein environment with formate, water, and X‐NH3, H2S, imidazole, formaldehyde, and chloride as ligands: An ab initio study
Authors: Deerfield David W. , Fox Douglas J. , Head‐Gordon Martin , Hiskey Richard G. , Pedersen Lee G. 
Published: May 2005

AbstractThe first coordination shell of an Mg(II) ion in a model protein environment is studied. Complexes containing a model carboxylate, an Mg(II) ion, various ligands (NH3, H2S, imidazole, and formaldehyde) and water of hydration about the divalent metal ion were geometry optimized. We find that for complexes with the same coordination number, the unidentate carboxylate–Mg(II) ion is greater than 10 kcal mol−1 more stable than the bidentate orientation. Imidazole was found to be the most stable ligand, followed in order by NH3 formaldehyde, H2O, and H2S. © 1995 Wiley‐Liss, Inc.
LINUS: A hierarchic procedure to predict the fold of a protein
Authors: Srinivasan Rajgopal , Rose George D. 
Published: May 2005

AbstractWe describe LINUS, a hierarchic procedure to predict the fold of a protein from its amino acid sequence alone. The algorithm, which has been implemented in a computer program, was applied to large, overlapping fragments from a diverse test set of 7 X‐ray‐elucidated proteins, with encouraging results. For all proteins but one, the overall fragment topology is well predicted, including both secondary and supersecondary structure. The algorithm was also applied to a molecule of unknown conformation, groES, inwhich X‐ray structure determination is presently ongoing. LINUS is an acronym for Local Independently Nucleated Units of Structure. The procedure ascends the folding hierarchy in discrete stages, with concomitant accretion of structure at each step. The chain is represented by simplified geometry and folds under the influence of a primitive energy function. The only accurately described energetic quantity in this work is hard sphere repulsion–the principal forceinvolved in organizing protein conformation [Richards, F. M. Ann. Rev. Biophys. Bioeng. 6:151–176, 1977]. Among other applications, the method is a natural tool for use in the human genome initiative. © 1995 Wiley‐Liss, Inc.
Structural model of the photosynthetic reaction center of Rhodobacter capsulatus
Authors: Foloppe Nicolas , Ferrand Michel , Breton Jacques , Smith Jeremy C. 
Published: May 2005

AbstractThe reaction center (RC) from the photosynthetic bacterium Rhodobacter (Rb.) capsulatus has been the subject of a considerable amount of molecular biological and spectroscopic work aimed at improving our understanding of the primary steps of photosynthesis. However, no three‐dimensional structure is available for this protein. We present here a model obtained by combining information from the structure of the highly homologous RC from Rhodopseudomonas (Rps.) viridis with molecular mechanics and simulated annealing calculations. In the Rb. Capsulatus model the orientations of the bacteriochlorophyll monomer and the bacteriopheophytin on the branch inactive in electron transfer differ significantly from those in the RCs of Rps. Viridis and Rb. Sphaeroides. The bacteriopheophytin orientational difference is in good accord with previous linear dichroism measurements. A comparison is made of interactions between the pigments and the protein environment that may be of functional significance in Rps. viridis, Rb. sphaeroides, and Rb. capsulatus. © 1995 Wiley‐Liss, Inc.
Cloning and expression of the uracil–DNA glycosylase inhibitor (UGI) from bacteriophage PBS‐1 and crystallization of a uracil–DNA glycosylase–UGI complex
Authors: Savva Renos , Pearl Laurence H. 
Published: May 2005

AbstractThe uracil‐DNA glycosylase inhibitory protein (UGI) from the bacterio‐phage PBS‐l has been cloned and overexpressed. The nucleotide sequence is identical to that for the previously described PBS‐2 inhibitor. The recombinant PBS‐l UGI inhibits the uracil‐DNA glycosylase from herpes simplex virus type‐l (HSV‐l UDGase), and a complex between the HSV‐l UDGase and PBS‐l UGI has been crystallized. The crystals have unit cell dimensions a = 143.21 Å, c = 40.78 Å and are in a polar hexagonal space group. There is a single complex in the asymmetric unit with a solvent content of 62% by volume and the crystals diffract to 2.5Å on a synchrotron radiation source. © 1995 Wiley‐Liss, Inc.
Crystallization and preliminary X‐ray analysis of the cytoplasmic domain of human erythrocyte band 3
Authors: Kiyatkin Anatoly B. , Natarajan Padmaja , Munshi Sanjeev , Minor Wladyslaw , Johnson John E. , Low Philip S. 
Published: May 2005

AbstractA cytoplasmic domain of the human erythrocyte membrane protein band 3 (Mr = 42,500), residues 1–379, expressed in and purified from E. coli, has been crystallized by the method of vapor diffusion in sitting drops with subsequent streak‐seeding at room temperature. Initial crystals were grown from solutions containing 65–68% saturated ammonium sulfate at pH 4.9 and 2 mg/ml protein. Subsequent streak‐seeding into solutions of 50–53% ammonium sulfate at pH 4.9 and 7 mg/ml protein produced single crystals suitable fur X‐ray analysis, which contained pure protein as revealed by gel electrophoresis. The crystals belong to the monoclinic space group C2 with cell dimensions of a = 178.8 Å, b = 90.5 Å, c = 122.1 Å, and β = 131.3° and diffract at least to 2.7 Å resolution (at 100 K). A self‐rotation function shows the presence of approximate 222 local symmetry. © 1995 Wiley‐Liss, Inc.
A predicted consensus structure for the protein kinase C2 homology (C2H) domain, the repeating unit of synaptotagmin
Authors: Gerloff Dietlind L. , Chelvanayagam Gareth , Benner Steven A. 
Published: May 2005

AbstractA secondary structure has been predicted for the protein kinase C2 regulatory domain found in homologous form in synaptotagmin, some phospholipases, and some GTP activated proteins. The proposed structure is built from seven consecutive beta strands followed by a terminal alpha helix. Considerations of overall surface exposure of individual secondary structural elements suggest that these are packed into a 2‐sheet beta sandwich structure, with one of only three of the many possible folds being preferred. © 1995 Wiley‐Liss, Inc.
Effects of pH and high ionic strength on the adsorption and activity of native and mutated cellobiohydrolase I from Trichoderma reesei
Authors: Reinikainen Tapani , Teleman Olle , Teeri Tuula T. 
Published: May 2005

AbstractCellobiohydrolase I (CBHI) is the major cellulase of Trichoderma reesei. The enzyme contains a discrete cellulose‐binding domain (CBD), which increases its binding and activity on crystalline cellulose. We studied cellulase‐cellulose interactions using site‐directed mutagenesis on the basis of the three‐dimensional structure of the CBD of CBHI. Three mutant proteins which have earlier been produced in Saccharomyces cerevisiae were expressed in the native host organism. The data presented here support the hypothesis that a conserved tyrosine (Y492) located on the flat and more hydrophilic surface of the CBD is essential for the functionality. The data also suggest that the more hydrophobic surface is not directly involved in the CBD function. The pH dependence of the adsorption revealed that electrostatic repulsion between the bound proteins may also control the adsorption. The binding of CBHI to cellulose was significantly affected by high ionic strength suggesting that the interaction with cellulose includes a hydrophobic effect. High ionic strength increased the activity of the isolated core and of mutant proteins on crystalline cellulose, indicating that once productively bound, the enzymes are capable of solubilizing cellulose even with a mutagenized or with no CBD. © 1995 Wiley‐Liss, Inc.
Activation of blood coagulation factor VIIa with cleaved tissue factor extracellular domain and crystallization of the active complex
Authors: Kirchhofer Daniel , Guha Arabinda , Nemerson Yale , Konigsberg William H. , Vilbois Francis , Chène Christiane , Banner David W. , D'Arcy Allan 
Published: May 2005

AbstractExposure of blood to tissue factor leads to the formation of a high affinity tissue factor/factor VIIa complex which initiates blood coagulation. As a first step toward obtaining structural information of this enzyme system, a complex of active‐site inhibited factor VIIa (F.VIIai) and soluble tissue factor (sTF) was prepared for crystallization. Crystals were obtained, but only after long incubation times. Analysis by SDS‐PAGE and mass spectrometry indicated the presence of sTF fragments similar to those formed by proteolytic digestion with subtilisin (Konigsberg, W., Nemerson, Y., Fang, C., Lin, T.‐C. Thromb. Haemost. 69:1171, 1993). To test the hypothesis that limited proteolysis of sTF facilitated the crystallization of the complex, sTF fragments were generated by subtilisin digestion and purified. Analysis by tandem mass spectrometry showed the presence of nonoverlapping N‐ and C‐terminal sTF fragments encompassing more than 90% of the tissue factor extracellular domain. Enzymatic assays and binding studies demonstrated that an equimolar mixture of N‐ and C‐terminal fragments bound to factor VIIa and fully restored cofactor activity. A complex of F.VIIai and sTF fragments was prepared for crystallization. Crystals were obtained using microseeding techniques. The best crystals had maximum dimensions of 0.12 × 0.12 × 0.6 mm and showed diffraction to a resolution of 3 Å. © 1995 Wiley‐Liss, Inc.