bluuebunny/crossref_metadata_2025_split huggingface dataset:
An insight into the general relationship between the three dimensional structures of enzymes and their electronic wave functions: Implication for the prediction of functional sites of enzymes
Authors: Fukushima K. , Wada M. , Sakurai M. 
Published: January 2008

AbstractIn this study, we explored the general relationship between the three‐dimensional (3D) structures of enzymes and their electronic wave functions. Furthermore, we developed a method for the prediction of their functionally important sites. For this purpose, we first performed linear‐scaling molecular orbital calculations for 112 nonredundant, non‐homologous enzymes with known structure and function. In consequence, we showed that the canonical molecular orbitals (MOs) of the enzymes could be classified into three groups according to the degree of electron delocalization: highly localized orbitals (Group A), highly delocalized orbitals whose electrons are distributed over almost the whole molecule (Group B), and moderately delocalized orbitals (Group C). The MOs belonging to Group A are located near the HOMO‐LUMO band gap, and thereby include the frontier orbitals of a given enzyme. We inferred that the MOs of Group B play a role in stabilizing the 3D structure of the enzyme, while those of Group C contribute to constructing the covalent bond framework of the enzyme. Next, we investigated whether the frontier orbitals of enzymes could be used for identifying their potential functional sites. As a result, we found that the frontier orbitals of the 112 enzymes have a high propensity to be colocalized with the known functional sites, especially when the enzymes are hydrated. Such a propensity is shown to be remarkable when Glu or Asp is a functional site residue. On the basis of these results, we finally propose a protocol for the prediction of functional sites of enzymes. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Stacking efficiency and flexibility analysis of aromatic amino acids in cap‐binding proteins
Authors: Worch Remigiusz , Stolarski Ryszard 
Published: January 2008

AbstractRecognition of the ribonucleic acid 5′ termini (RNA 5′ cap) by a wide class of cap‐binding proteins is largely accomplished by cation‐π stacking that involves the positively charged 7‐methylguanine ring and aromatic amino acid side chains. Quantum calculations of the stacking energy were performed by means of MP2 perturbation method for binary and ternary associates composed of the 7‐methylguanine moiety and tryptophan, tyrosine, or phenylalanine, in their spatial orientations known from the crystalline cap‐protein complexes. The results clearly pointed to an enhancement of the stacking energy due to a net positive charge in the cap guanine moiety and allowed analysis of a role of various amino acids in stabilization of the complexes. Conformational flexibility of the aromatic amino acids taking part in binding ligands to a wide class of RNA‐recognizing proteins, including the cap‐binding proteins, was determined by regional order neural network (RONN) algorithm that provides results close to those of the crystallographic B‐factors analysis. Interestingly, some of the tyrosines that are classified in general as “rigid” showed high flexibility when engaged in binding the cap to nuclear cap‐binding protein complex CBC and to viral methyltransferase VP39. Parallel analyses of the binding energy and flexibility of the protein fragments engaged in the binding leads to understanding differences in molecular mechanisms of the cap recognition by various proteins, CBC compared with the eukaryotic initiation factor eIF4E, and enzymes vs. other protein factors. Proteins 2008. © 2008 Wiley‐Liss, Inc.
A phospho‐sugar binding domain homologous to NagB enzymes regulates the activity of the central glycolytic genes repressor
Authors: Doan Thierry , Martin Laetitia , Zorrilla Silvia , Chaix Denis , Aymerich Stéphane , Labesse Gilles , Declerck Nathalie 
Published: January 2008

AbstractCggR belongs to the SorC family of bacterial transcriptional regulators which control the expression of genes and operons involved in carbohydrate catabolism. CggR was first identified in Bacillus subtilis where it represses the gapA operon encoding the five enzymes that catalyze the central part of glycolysis. Here we present a structure/function study demonstrating that the C‐terminal region of CggR regulates the DNA binding activity of this repressor in response to binding of a phosphorylated sugar. Molecular modeling of CggR revealed a winged‐helix DNA‐binding motif followed by a C‐terminal domain presenting weak but significant homology with glucosamine‐6‐phosphate deaminases from the NagB family. In silico ligand screening suggested that the CggR C‐terminal domain would bind preferentially bi‐phosphorylated compounds, in agreement with previous studies that proposed fructuose‐1,6‐biphosphate (FBP) as the inducer metabolite. In vitro, FBP was the only sugar compound capable of interfering with CggR cooperative binding to DNA. FBP was also found to protect CggR against trypsin degradation at two arginine residues predicted to reside in a mobile loop forming the active site lid of the NagB enzymes. Replacement of residues predicted to interact with FBP led to mutant CggR with altered repressor activity in vivo but retaining their structural integrity and DNA binding activity in vitro. Interestingly, some of the mutant repressors responded with different specificity towards mono‐ and di‐phospho‐fructosides. Based on these results, we propose that the activity of the CggR‐like repressors is controlled by a phospho‐sugar binding (PSB) domain presenting structural and functional homology with NagB enzymes. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Structural basis for the cold adaptation of psychrophilic M37 lipase fromPhotobacterium lipolyticum
Authors: Jung Suk‐Kyeong , Jeong Dae Gwin , Lee Mi Sook , Lee Jung‐Kee , Kim Hyung‐Kwoun , Ryu Seong Eon , Park Byoung Chul , Kim Jae Hoon , Kim Seung Jun 
Published: January 2008

AbstractThe M37 lipase from Photobacterium lipolyticum shows an extremely low activation energy and strong activity at low temperatures, with optimum activity seen at 298 K and more than 75% of the optimum activity retained down to 278 K. Though the M37 lipase is most closely related to the filamentous fungal lipase, Rhizomucor miehei lipase (RML) at the primary structure level, their activity characteristics are completely different. In an effort to identify structural components of cold adaptation in lipases, we determined the crystal structure of the M37 lipase at 2.2 Å resolution and compared it to that of nonadapted RML. Structural analysis revealed that M37 lipase adopted a folding pattern similar to that observed for other lipase structures. However, comparison with RML revealed that the region beneath the lid of the M37 lipase included a significant and unique cavity that would be occupied by a lid helix upon substrate binding. In addition, the oxyanion hole was much wider in M37 lipase than RML. We propose that these distinct structural characteristics of M37 lipase may facilitate the lateral movement of the helical lid and subsequent substrate hydrolysis, which might explain its low activation energy and high activity at low temperatures. Proteins 2008. © 2008 Wiley‐Liss, Inc.
The solution structure of the outer membrane lipoprotein OmlA from Xanthomonas axonopodis pv. citri reveals a protein fold implicated in protein–protein interaction
Authors: Vanini Marina Marques Teixeira , Spisni Alberto , Sforça Maurício Luis , Pertinhez Thelma Aguiar , Benedetti Celso Eduardo 
Published: January 2008

AbstractThe outer membrane lipoprotein A (OmlA) belongs to a family of bacterial small lipoproteins widely distributed across the beta and gamma proteobacteria. Although the role of numerous bacterial lipoproteins is known, the biological function of OmlA remains elusive. We found that in the citrus canker pathogen, Xanthomonas axonopodis pv. citri (X. citri), OmlA is coregulated with the ferric uptake regulator (Fur) and their expression is enhanced when X. citri is grown on citrus leaves, suggesting that these proteins are involved in plant‐pathogen interaction. To gain insights into the function of OmlA, its conformational and dynamic features were determined by nuclear magnetic resonance. The protein has highly flexible N‐ and C‐ termini and a structurally well defined core composed of three β‐strands and two small α‐helices, which pack against each other forming a two‐layer alpha/beta scaffold. This protein fold resembles the domains of the β‐lactamase inhibitory protein BLIP, involved in protein–protein binding. In conclusion, the structure of OmlA does suggest that this protein may be implicated in protein–protein interactions required during X. citri infection. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Development of new laccases by directed evolution: Functional and computational analyses
Authors: Festa Giovanna , Autore Flavia , Fraternali Franca , Giardina Paola , Sannia Giovanni 
Published: January 2008

AbstractLaccases are blue multicopper oxidases that couple the four‐electron reduction of oxygen with the oxidation of a broad range of aromatic substrates. These fungal enzymes can be used for many applications such as bleaching, organic synthesis, bioremediation, and in laundry detergents. Laccases from Pleurotus ostreatus have been successfully heterologously expressed in yeasts. The availability of established recombinant expression systems has allowed the construction of mutated, “better performing” enzymes through molecular evolution techniques. In the present work, random mutagenesis experiments on poxc and poxa1b cDNAs, using error prone PCR (EP‐PCR) have been performed. By screening a library of 1100 clones the mutant 1M9B was selected, it shows a single mutation (L112F) leading to an enzyme more active but less stable with respect to the wild‐type enzyme (POXA1b) in all the analyzed conditions. This mutant has been used as a template for a second round of EP‐PCR. From this second generation library of 1200 clones, three mutants have been selected. Properties of the four mutants, 1M9B screened from the first library, and 1L2B, 1M10B, and 3M7C from the second library, were analyzed. The better performing mutant 3M7C presents, besides L112F, only one substitution (P494T) responsible both for the significantly increased stability and for the exhibited higher activity of this mutant. Molecular dynamics simulations have been performed on three‐dimensional models of POXA1b, 1M9B, and 3M7C, and hypotheses on the structure–function relationships of these proteins have been formulated. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Crystal structure and stereochemical studies of KD(P)G aldolase from Thermoproteus tenax
Authors: Pauluhn Anuschka , Ahmed Hatim , Lorentzen Esben , Buchinger Sebastian , Schomburg Dietmar , Siebers Bettina , Pohl Ehmke 
Published: January 2008

AbstractCarbon–carbon bond forming enzymes offer great potential for organic biosynthesis. Hence there is an ongoing effort to improve their biocatalytic properties, regarding availability, activity, stability, and substrate specificity and selectivity. Aldolases belong to the class of CC bond forming enzymes and play important roles in numerous cellular processes. In several hyperthermophilic Archaea the 2‐keto‐3‐deoxy‐(6‐phospho)‐gluconate (KD(P)G) aldolase was identified as a key player in the metabolic pathway. The carbohydrate metabolism of the hyperthermophilic Crenarchaeote Thermoproteus tenax, for example, has been found to employ a combination of a variant of the Embden–Meyerhof–Parnas pathway and an unusual branched Entner–Doudoroff pathway that harbors a nonphosphorylative and a semiphosphorylative branch. The KD(P)G aldolase catalyzes the reversible cleavage of 2‐keto‐3‐deoxy‐6‐phosphogluconate (KDPG) and 2‐keto‐3‐deoxygluconate (KDG) forming pyruvate and glyceraldehyde 3‐phosphate or glyceraldehyde, respectively. In T. tenax initial studies revealed that the pathway is specific for glucose, whereas in the thermoacidophilic Crenarchaeote Sulfolobus solfataricus the pathway was shown to be promiscuous for glucose and galactose degradation. The KD(P)G aldolase of S. solfataricus lacks stereo control and displays additional activity with 2‐keto‐3‐deoxy‐6‐phosphogalactonate (KDPGal) and 2‐keto‐3‐deoxygalactonate (KDGal), similar to the KD(P)G aldolase of Sulfolobus acidocaldarius. To address the stereo control of the T. tenax enzyme the formation of the two C4 epimers KDG and KDGal was analyzed via gas chromatography combined with mass spectroscopy. Furthermore, the crystal structure of the apoprotein was determined to a resolution of 2.0 Å, and the crystal structure of the protein covalently linked to a pathway intermediate, namely pyruvate, was determined to 2.2 Å. Interestingly, although the pathway seems to be specific for glucose in T. tenax the enzyme apparently also lacks stereo control, suggesting that the enzyme is a trade‐off between required catabolic flexibility needed for the conversion of phosphorylated and nonphosphorylated substrates and required stereo control of cellular/physiological enzymatic reactions. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Molecular dynamics simulations of the active matrix metalloproteinase‐2: Positioning of the N‐terminal fragment and binding of a small peptide substrate
Authors: Díaz Natalia , Suárez Dimas 
Published: January 2008

AbstractHerein we use different computational methods to study the structure and energetic stability of the catalytic domain of the active MMP‐2 enzyme considering two different orientations of its N‐terminal coil. The first orientation is largely solvent accessible and corresponds to that observed in the 1CK7 crystal structure of the proenzyme. In the second orientation, the N‐terminal coil is packed against the Ω‐loop and the α3‐helix of the MMP‐2 enzyme likewise in the so‐called “superactivated” form of other MMPs. Binding to the MMP‐2 catalytic domain of a short peptide substrate, which mimics the sequence of the α1 chain of collagen type I, is also examined considering again the two configurations of the N‐terminal coil. All these MMP‐2 models are subject to 20 ns molecular dynamics (MD) simulations followed by MM‐PBSA (Molecular Mechanics Poisson‐Boltzmann Surface Area) calculations. The positioning of the N‐terminal coil in the “superactivated” form is found to be energetically favored for the MMP‐2 enzyme. Moreover, this configuration of the N‐terminal moiety can facilitate the binding of peptide substrates. Globally, the results obtained in this study could be relevant for the structural‐based design of specific MMP inhibitors. Proteins 2008. © 2008 Wiley‐Liss, Inc.
The X‐ray structure ofN‐methyltryptophan oxidase reveals the structural determinants of substrate specificity
Authors: Ilari Andrea , Bonamore Alessandra , Franceschini Stefano , Fiorillo Annarita , Boffi Alberto , Colotti Gianni 
Published: January 2008

AbstractThe X‐ray structure of monomeric N‐methyltryptophan oxidase from Escherichia coli (MTOX) has been solved at 3.2 Å resolution by molecular replacement methods using Bacillus sp. sarcosine oxidase structure (MSOX, 43% sequence identity) as search model. The analysis of the substrate binding site highlights the structural determinants that favour the accommodation of the bulky N‐methyltryptophan residue in MTOX. In fact, although the nature and geometry of the catalytic residues within the first contact shell of the FAD moiety appear to be virtually superposable in MTOX and MSOX, the presence of a Thr residue in position 239 in MTOX (Met245 in MSOX) located at the entrance of the active site appears to play a key role for the recognition of the amino acid substrate side chain. Accordingly, a 15 fold increase in kcatand 100 fold decrease in Kmfor sarcosine as substrate has been achieved in MTOX upon T239M mutation, with a concomitant three‐fold decrease in activity towards N‐methyltryptophan. These data provide clear evidence for the presence of a catalytic core, common to the members of the methylaminoacid oxidase subfamily, and of a side chain recognition pocket, located at the entrance of the active site, that can be adjusted to host diverse aminoacids in the different enzyme species. The site involved in the covalent attachment of flavin has also been addressed by screening degenerate mutants in the relevant positions around Cys308‐FAD linkage. Lys341 appears to be the key residue involved in flavin incorporation and covalent linkage. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Ordered conformational change in the protein backbone: Prediction of conformationally variable positions from sequence and low‐resolution structural data
Authors: Kuznetsov Igor B. 
Published: January 2008

AbstractOrdered conformational changes are an important structural property of proteins and are involved in a variety of fundamental biological activities. Large‐scale analyses of the implications of such changes for protein function and dysfunction require efficient methods for automated recognition of conformationally variable residue positions. The goal of this work was to study sequence and low‐resolution structural properties of residue positions that change backbone conformation upon changes in protein environment and the utility of these properties for automated recognition of such conformationally variable positions. This study was performed using a large nonredundant set of experimentally characterized proteins that undergo ordered conformational transitions obtained from the Database of Macromolecular Movements. The results of this study show that ordered changes in backbone conformation are not limited to solvent accessible loop regions. A considerable fraction of conformationally variable positions is observed in helices and strands, and in buried positions. Conformationally variable positions are less conserved in evolution. Local patterns of (a) sequence neighbors, (b) evolutionary conservation, and (c) solvent accessibility can be used to predict conformationally variable positions with balanced sensitivity and specificity, albeit with large variance at the level of individual proteins. However, including a pattern of secondary structure into the prediction scheme results in a highly unbalanced performance when all conformationally variable positions located in regular secondary structure are misclassified. Application of the present methodology to the prion protein (PrP) shows that conformationally variable positions predicted in its ordered C‐terminal domain are located within segments presumed to be involved in refolding of PrP. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Sequence–structure–function analysis of the bifunctional enzyme MnmC that catalyses the last two steps in the biosynthesis of hypermodified nucleoside mnm5s2U in tRNA
Authors: Roovers Martine , Oudjama Yamina , Kaminska Katarzyna H. , Purta Elzbieta , Caillet Joël , Droogmans Louis , Bujnicki Janusz M. 
Published: January 2008

AbstractMnmC catalyses the last two steps in the biosynthesis of 5‐methylaminomethyl‐2‐thiouridine (mnm5s2U) in tRNA. Previously, we reported that this bifunctional enzyme is encoded by theyfcKopen reading frame in theEscherichia coliK12 genome. However, the mechanism of its activity, in particular the potential structural and functional dependence of the domains responsible for catalyzing the two modification reactions, remains unknown. With the aid of the protein fold‐recognition method, we constructed a structural model of MnmC in complex with the ligands and target nucleosides and studied the role of individual amino acids and entire domains by site‐directed and deletion mutagenesis, respectively. We found out that the N‐terminal domain contains residues responsible for binding of the S‐adenosylmethionine cofactor and catalyzing the methylation of nm5s2U to form mnm5s2U, while the C‐terminal domain contains residues responsible for binding of the FAD cofactor. Further, point mutants with compromised activity of either domain can complement each other to restore a fully functional enzyme. Thus, in the conserved fusion protein MnmC, the individual domains retain independence as enzymes. Interestingly, the N‐terminal domain is capable of independent folding, while the isolated C‐terminal domain is incapable of folding on its own, a situation similar to the one reported recently for the rRNA modification enzyme RsmC. Proteins, 2008. © 2008 Wiley‐Liss, Inc.
On defining the dynamics of hydrophobic patches on protein surfaces
Authors: Lijnzaad Philip , Feenstra K. Anton , Heringa Jaap , Holstege Frank C. P. 
Published: January 2008

AbstractWe present a simple and efficient method called PATCHTRACK, for studying the dynamics of hydrophobic surface patches. It tracks the patches on snapshot structures taken from a Molecular Dynamics simulation. They are connected into so‐called patch runs, which are subsequently clustered into so‐called recurrent patches. The method is applied to simulations of three different proteins. Protein motion causes addition and removal of one or more atoms to a patch, resulting in size fluctuations of around 25%. The fluctuations eventually lead to the break‐up of a patch, and their average life span is therefore remarkably short at around 4 ps. However, some patch runs are much more stable, lasting hundreds of picoseconds. One such case is the largest patch in amicyanin that is known to be biologically relevant. Another case, previously not reported, is found in phospholipase A2, where the functional significance of a large recurrent patch formed by Leu58 and Phe94 seems likely. This patch appears to have been overlooked as it is relatively small in the X‐ray structure, demonstrating the utility of the current method. The most frequently occurring patch size is 40–60 Å2, but sizes of up to 500 Å2 are also observed. There is no clear relation between patch run durations and their average size. However, long‐lasting patch runs tend not to have large fluctuations. The recurrent patches have alternating periods of “liveness” and “dormancy”; around 25% of them is predominantly in the live state. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Four new forms of the contracted Schrödinger equation and their connection with the second‐order hypervirial condition
Authors: Valdemoro C. , Tel L. M. , Pérez‐Romero E. , Alcoba D. R. 
Published: January 2008

AbstractThrough the use of an important property of a fourth‐order correlation matrix previously reported (Valdemoro, C.; Tel, L. M.; Alcoba, D. R.; Perez‐Romero, E.; Casquero, F. J. Int J Quantum Chem 2002, 90, 1555; Alcoba, D. R.; Valdemoro, C. Phys Rev A 2001, 64, 062105) four new equivalent forms of the second‐order contracted Schrödinger equation (2‐CSE) are obtained. The role played by the energy terms involving these correlation matrices is crucial in the solution of these equations. The relations linking the Hermitian (Yasuda, K. Phys Rev A 1999, 59, 4133) and antiHermitian parts (Mazziotti, D. A. Phys Rev Lett 2006, 97, 142002) of the 2‐CSE with these correlation energy terms are analyzed in detail. A discussion of the second‐order hypervirial condition is also given here. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008