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PubMed2006

A novel processive mechanism for DNA synthesis revealed by structure, modeling and mutagenesis of the accessory subunit of human mitochondrial DNA polymerase.

Mitochondrial DNA polymerase (pol gamma) is the sole DNA polymerase responsible for replication and repair of animal mitochondrial DNA. Here, we address the molecular mechanism by which the human holoenzyme achieves high processivity in nucleotide polymerization. We have determined the crystal structure of human pol gamma-beta, the accessory subunit that binds with high affinity to the catalytic core, pol gamma-alpha, to stimulate its activity and enhance holoenzyme processivity. We find that human pol gamma-beta shares a high level of structural similarity to class IIa aminoacyl tRNA synthetases, and forms a dimer in the crystal. A human pol gamma/DNA complex model was developed using the structures of the pol gamma-beta dimer and the bacteriophage T7 DNA polymerase ternary complex, which suggests multiple regions of subunit interaction between pol gamma-beta and the human catalytic core that allow it to encircle the newly synthesized double-stranded DNA, and thereby enhance DNA binding affinity and holoenzyme processivity. Biochemical properties of a novel set of human pol gamma-beta mutants are explained by and test the model, and elucidate the role of the accessory subunit as a novel type of processivity factor in stimulating pol gamma activity and in enhancing processivity.

Amino Acid Sequence↗
PubMed1999

A structural model for elongation factor 1 (EF-1) and phosphorylation by protein kinase CKII.

EF-1alpha binds aminoacyl-tRNA to the ribosome with the hydrolysis of GTP; the betagammadelta complex facilitates the exchange of GDP for GTP to initiate another round of elongation. To examine the subunit structure of EF-1 and phosphorylation by protein kinase CKII, recombinant beta, gamma, and delta subunits from rabbit were expressed in E. coli and the subunits were reconstituted into partial and complete complexes and analyzed by gel filtration. To determine the availability of the beta and delta subunits for phosphorylation by CKII, the subunits and the reconstituted complexes were examined as substrates for CKII. Formation of the nucleotide exchange complex increased the rate of phosphorylation of the beta subunit and reduced the Km, while addition of alpha to beta or the betagammacomplex inhibited phosphorylation by CKII. However, alpha had little effect on phosphorylation of delta. Thus, the beta and delta subunits in EF-1 were differentially phosphorylated by CKII, in that phosphorylation of beta was altered by association with other subunits, while the site on delta was always available for phosphorylation by CKII. From the availability of the subunits for phosphorylation by CKII and the composition of the reconstituted partial and complete complexes, a model for the subunit structure of EF-1 consisting of(alpha2betagamma2delta)2 is proposed and discussed.

Amino Acid Sequence↗
PubMed2003

3D structural model of the G-protein-coupled cannabinoid CB2 receptor.

The potential for therapeutic specificity in regulating diseases and for reduced side effects has made cannabinoid (CB) receptors one of the most important G-protein-coupled receptor (GPCR) targets for drug discovery. The cannabinoid (CB) receptor subtype CB2 is of particular interest due to its involvement in signal transduction in the immune system and its increased characterization by mutational and other studies. However, our understanding of their mode of action has been limited by the absence of an experimental receptor structure. In this study, we have developed a 3D model of the CB2 receptor based on the recent crystal structure of a related GPCR, bovine rhodopsin. The model was developed using multiple sequence alignment of homologous receptor sub-types in humans and mammals, and compared with other GPCRs. Alignments were analyzed with mutation scores, pairwise hydrophobicity profiles and Kyte-Doolittle plots. The 3D model of the transmembrane segment was generated by mapping the CB2 sequence onto the homologous residues of the rhodopsin structure. The extra- and intracellular loop regions of the CB2 were generated by searching for homologous C(alpha) backbone sequences in published structures in the Brookhaven Protein Databank (PDB). Residue side chains were positioned through a combination of rotamer library searches, simulated annealing and minimization. Intermediate models of the 7TM helix bundles were analyzed in terms of helix tilt angles, hydrogen-bond networks, conserved residues and motifs, possible disulfide bonds. The amphipathic cytoplasmic helix domain was also correlated with biological and site-directed mutagenesis data. Finally, the model receptor-binding cavity was characterized using solvent-accessible surface approach.

Amino Acid Sequence↗
PubMed1993

Molecular characterization and structural modeling of immunoglobulin variable regions from murine monoclonal antibodies specific for hepatitis B virus surface antigen.

We have characterized structurally the V regions of a set of murine monoclonal antibodies designated A1.2, A3.1, and A2.1, which recognize a group-specific epitope associated with hepatitis B virus surface antigen (HBsAg). The selection of these antibodies for this characterization was based on data which indicated that A1.2 and A3.1 recognize an overlapping epitope, while A2.1 recognizes a different group-specific epitope, on the HBsAg molecule. In addition, a conformation-dependent cross reactive Id is expressed on both A1.2 and A3.1, but not on A2.1. We have determined the primary sequence structures of these three monoclonal antibodies to HBsAg (anti-HBs), and have aligned them to evaluate V region sequence homology and identify potential regions of structural homology which provide a basis for the HBsAg epitope recognition and the cross reactive Id. Both A1.2 and A3.1 express VH regions which are highly homologous to the VH NP gene family (V186-2), both use members of the DSP2 D region gene family and utilize the JH 2 and JH 1 J gene segments, respectively. Alternatively, A2.1 is related to the VH J558 gene family and expresses a fusion of the DFL16.1 and DQ52 D gene regions in conjunction with the MH 1 gene segment. Each of these three monoclonal anti-HBs utilize light chains from the V kappa 21 and the J kappa 4 gene families. Primary amino acid sequence data were employed to construct computer generated models of the A1.2, A3.1, and A2.1 V regions to determine potential antigen combining site structures and the basis for the expression of the cross reactive Id. These results are discussed in terms of potential interaction sites with HBsAg and V region sites involved in Id expression.

Amino Acid Sequence↗
PubMed1984

Xenopus laevis 18S ribosomal RNA: experimental determination of secondary structural elements, and locations of methyl groups in the secondary structure model.

18S ribosomal RNA from X. laevis was subjected to partial digestion with ribonucleases A or T1 under a variety of conditions, and base-paired fragments were isolated. Sequence analysis of the fragments enabled five base-paired secondary structural elements of the 18S RNA to be established. Four of these elements (covering bases 221-256, 713-757, 1494-1555 and 1669-1779) confirm our previous secondary structure predictions, whereas the fifth (comprising bases 1103-1125) represents a phylogenetically conserved "switch" structure, which can also form in prokaryotic 16S RNA. The results are incorporated into a refined model of the 18S RNA secondary structure, which also includes the locations of the many methyl groups in X. laevis 18S RNA. In general the methyl groups occur in non-helical regions, at hairpin loop ends, or at helix boundaries and imperfections. One large cluster of 2'-O-methyl groups occurs in a region of complicated secondary structure in the 5'-one third of the molecule.

Animals↗
PubMed2006

Structural model of silica nanowire assembled from a highly stable (SiO2)8 unit.

The ground-state structures of silica clusters (SiO2)n for n = 1-8 were studied by performing calculations at the B3LYP/6-311+G(d) level of density functional theory. The results indicate that the growth mode of a silica nanowire based on small silica clusters may change at different wire lengths. A linear chain might be assembled from the smallest clusters of rhombic two-membered ring (2MR) with n < or = 5, while the growth motif changes at n = 6 into a more compact form composed of three-membered-rings (3MRs). The 3MR-containing structures become energetically favorable configurations for even longer silica clusters. In particular, the closed molecular ring consisting of 3MRs at n = 8 (i.e., (SiO2)8) with a high symmetry shows extreme energetic stability and relatively high chemical reactivity and thus is considered to be an important building block to assemble into silica nanowires. The relative stability of so-assembled silica nanowires were evaluated and compared with the models of silica nanowires in the literature.

Journal Article↗
PubMed1993

A structural model for the nucleotide binding domains of the flavocytochrome b-245 beta-chain.

NADPH is a system in phagocytic cells that generates O2- and hydrogen peroxide in the endocytic vacuole, both of which are important for killing of the engulfed microbe. Dysfunction of this oxidase results in the syndrome of chronic granulomatous disease, characterized by a profound predisposition to bacterial and fungal infections. A flavocytochrome b is the site of most of the mutations causing this syndrome. The FAD and NADPH binding sites have been located on the beta subunit of this molecule, the C-terminal half of which showed weak sequence similarity to other reductases, including the ferredoxin-NADP reductase (FNR) of known structure. This enabled us to build a model of the nucleotide binding domains of the flavocytochrome using this structure as a template. The model was built initially using a novel automatic modeling method based on distance-matrix projection and then refined using energy minimization with appropriate side-chain torsional constraints. The resulting model rationalized much of the observed sequence conservation and identified a large insertion as a potential regulatory domain. It confirms the inclusion of the neutrophil flavocytochrome b-245 (Cb-245) as a member of the FNR family of reductases and strongly supports its function as the proximal electron transporting component of the NADPH oxidase.

Amino Acid Sequence↗
PubMed1997

Insight into cystic fibrosis by structural modelling of CFTR first nucleotide binding fold (NBF1).

Cystic fibrosis is a human monogenic genetic disease caused by mutations in the cystic fibrosis (CF) gene, which encodes a membrane protein which functions as a channel: the cystic fibrosis transmembrane conductance regulator (CFTR) protein. The most frequent mutation, a deletion of phenylalanine F508 (delta F508), is located in the first nucleotide binding domain of CFTR: NBF1. This mutation leads to a folding defect in NBF1, responsible for an incomplete maturation of CFTR. The absence of CFTR at the surface of epithelial cells causes the disease. Determination of the three-dimensional (3D) structure of NBF1 is a key step to understanding the alterations induced by the mutation. In the absence of any experimental data, we have chosen to build a 3D model for NBF1. This model was built by homology modelling starting from F1-ATPase, the only protein of known 3D structure in the ATP binding cassette (ABC) family. This new model defines the central and critical position of F508, predicted in the hydrophobic core of NBF1. F508 indeed could be involved in hydrophobic interactions to ensure a correct folding pathway. Moreover, this model enables the localization of the LSGGQ sequence (a highly conserved sequence in the ABC family) in a loop, at the surface of the protein. This reinforces the hypothesis of its role for mediation of domain-domain interactions of functional significance for the channel regulation. Finally, the model also allows redefinition of the ends of NBF1 within the CFTR sequence. These extremities are defined by the secondary structure elements that are involved in the NBF1 fold. They lead to reconsideration of the C-terminal limit which was initially defined by the end of exon 12.

Amino Acid Sequence↗
PubMed2005

Structural models for the protein family characterized by gamete surface protein Pfs230 of Plasmodium falciparum.

Ps230 is the largest representative of a 10-member family of proteins found in all Plasmodium species. The family is defined by partially conserved, cysteine-rich double domains that are approximately 350 aa in length and have one to three predicted disulfide bridges in each half. In Plasmodium falciparum, the most dangerous human malaria, Pf12 is the smallest member of the family, comprising just one double domain. Pfs230, with 7 double domains, and Pfs48/45 and Pfs47, with 1.5 double domains each, are found on the gamete surfaces and are thus potential candidates for a transmission-blocking vaccine. Fold prediction analyses of the double domains in Pfs230 reveal structural resemblance to SAG1 (surface antigen 1), a surface protein with a double beta-sandwich structure from another apicomplexan parasite, Toxoplasma gondii. Template-directed modeling onto SAG1 clearly establishes the structural link between SAG1 and Pfs230 and produces positions for the cysteines that accord with the disulfide-bonding arrangement predicted for the Pfs230 family in earlier work. A highly clustered region of polymorphisms within the second double domain in Pfs230 maps to one side of the sandwich surface. This observation suggests that this region may be functional and reinforces the validity of these molecular models for the core domains of the Pfs230 family of proteins.

Animals↗
PubMed1999

[Computerized ribosomal RNA secondary structure modeling of mutants found in Rett syndrome patients and their mothers].

OBJECTIVE: To identify the secondary structure of rRNA mutants, mtDNA2835(C-->T) and mtDNA2706(A-->G) found in Rett syndrome patients and their mothers. METHODS: Both wild type mtDNA sequence of rRNA gene and mutated sequence were input into computer (converted into RNA sequences) and analyzed by the sofware DNASIS v6. 14. The unique prediction size is set 300 bases and the maximum bulge and interior loop size,30 bases. RESULTS: Similar to the positive controls, the mtDNA2835(C-->T) made the 16S rRNA secondary structure totally different,and the energy changes a lot. On the contrary, the mtDNA2706(A-->G) altered little of secondary structure with a small energy shift. CONCLUSION: Computerized folding programs have provided us with a quick prediction of rRNA structure changes induced by these two mutations. Of them, the mtDNA2835(C-->T) might relate to the pathogenesis of Rett syndrome, but the mtDNA2706(A--> G) might be less meaningful.

Computer Simulation↗
PubMed2006

Model structure of the prototypical non-fimbrial adhesin YadA of Yersinia enterocolitica.

Non-fimbrial adhesins, such as Yersinia YadA, Moraxella UspA1 and A2, Haemophilus Hia and Hsf, or Bartonella BadA represent an important class of molecules by which pathogenic proteobacteria adhere to their hosts. They form trimeric surface structures with a head-stalk-anchor architecture. Whereas head and stalk domains are diverse and appear (frequently repetitively) in different combinations, the anchor domains are homologous and display the properties of autotransporters. We have built a molecular model for the prototypical non-fimbrial adhesin, YadA, by combining the crystal structure of the head (PDB:1P9H) with theoretical models for the stalk and the anchor. The head domain is a single-stranded, left-handed beta-helix, connected to the stalk by a conserved trimerization element (the neck). The stalk consists of a right-handed coiled coil, containing ten 15-residue repeats with a C-terminal stutter (insertion of four residues). The stalk continues into the conserved anchor domain, which is formed by four heptads of a left-handed coiled coil, followed by four transmembrane beta-strands. Our model of the YadA coiled coil, generated with the program BeammotifCC, combines these periodicities into a structure that starts with a pronounced right-handed supercoil and ends with a canonical, left-handed conformation. The last two heptads of the coiled coil are located within a 12-stranded beta-barrel, formed by trimerization of the four transmembrane beta-strands in each monomer. We propose that this pore assembles in the outer membrane to form the opening through which the monomer chains exit the cell. After export is completed, the fiber folds and the pore is occluded by the coiled coil. Our model explains how these proteins can act as autotransporters in the absence of any homology to classical, single-chain autotransporters.

Adhesins, Bacterial↗
PubMed2006

Morphologically-structured models of growing budding yeast populations.

It has been well recognized that many key aspects of cell cycle regulation are encoded into the size distributions of growing budding yeast populations due to the tight coupling between cell growth and cell division present in this organism. Several attempts have been made to model the cell size distribution of growing yeast populations in order to obtain insight on the underlying control mechanisms, but most were based on the age structure of asymmetrically dividing populations. Here we propose a new framework that couples a morphologically-structured representation of the population with population balance theory to formulate a dynamic model for the size distribution of growing yeast populations. An advantage of the presented framework is that it allows derivation of simpler models that are directly identifiable from experiments. We show how such models can be derived from the general framework and demonstrate their utility in analyzing yeast population data. Finally, by employing a recently proposed numerical scheme, we proceed to integrate numerically the full distributed model to provide predictions of dynamics of the cell size structure of growing yeast populations.

Cell Cycle↗
PubMed2001

Protein denaturation described by a two-state structural model of liquid water.

Our laboratory has been involved in expounding an outer neighbor molecular-level structural theory for liquid water in the supercooled and ordinary thermodynamic regimes. This theory, which depends on transformations with increasing temperature or pressure, is consistent with all the properties of this substance, including the ten or so "anomalies", and has been recently used to explain the effect that surrounding water has on proteins. For example, the sharp decrease in the hydration entropies of polar groups can be explained through a consideration of the promotion of ice-Ih-type bonding structure at the expense of the less stable ice-II-type bonding structure. These structural transformations occur in the local neighborhood of the polar group. In this paper we discuss this outer neighbor two-state structural theory for liquid water, the role it plays in explaining water's anomalous properties and its description of protein denaturation both as a function of temperature and pressure.

Mathematics↗
PubMed2000

Sequencing and model structure of a Naja naja atra protein fragment.

We report the amino acid sequence of a basic protein isolated from the snake venom of Naja naja atra. An automated Edman sequencer was used to determine the 65-residue sequence, aided by electrospray ionization/mass spectrometry. Online reduction and pyridylethylation of the peptide was performed to identify the cysteine residues. Trypsin, chymotrypsin and aspartic digestions were carried out to derive peptide fragments for further sequencing. Fragmented peptides were overlapped to obtain the complete sequence. Molecular mass measurements of the whole protein and its fragments were used as a countercheck for sequence assignment. Further confirmation of the sequence was indicated by sequence homology to other snake venom neurotoxins. A molecular model of the tertiary structure was constructed based on sequence homology, and was refined by global minimization and extensive quality control algorithms. Electrostatic and hydrophobic surface calculations and molecular dynamics simulations were carried out to determine the functional properties of the molecule.

Amino Acid Sequence↗
PubMed1986

A structural model of the thoracic cage in the cat.

A homogeneous shell model of the mechanical characteristics of the thoracic cage in the cat is presented. The global characterization proposed parallels the characterization--presented elsewhere--of the motor control of the intercostal musculature in terms of a conceptual spatially continuous control function, that underlies the discretely distributed muscular activity and reflects an inferred global dynamic control of the intercostal muscles during breathing. Proposing a static, homogeneous shell characterization of the thoracic cage, which is heterogeneous and composed of an assembly of mobile structures, implies assuming that other elements are indirectly giving this system features that make it resemble, from a structure analysis point of view, a homogeneous, static one. The pattern of the lines of stress along the shell structure proposed as a model compares favourably with the shape of the ribs. In agreement with previous findings, supporting the need for muscular activity to satisfy demands of purely structural character, it is suggested that this global shell-like functional character is achieved by neuromuscular global dynamic integration of the components of the rib cage by the nervous control of the intercostal muscles.

Animals↗
PubMed1988

Structural modeling of the distamycin A-d(CGCGAATTCGCG)2 complex using 2D NMR and molecular mechanics.

The structure of the distamycin A-d(CGCGAATTCGCG)2 complex has been determined through a combination of SKEWSKY and NOESY 2D NMR experiments and molecular mechanics calculations. NMR data provided upper bounds on many proton-proton pairs. The advantage of the SKEWSKY/NOESY method is that small groups of strongly coupled spins can be treated accurately as isolated systems. The AMBER molecular mechanics package, modified to include the NMR constraints, was used in energy refinements. Distamycin A fits snugly into the 5'-AATT-3' minor-groove binding site. Structural analysis revealed van der Waals contacts between A5, A6, and A18 C2H and drug H3 protons, potential three-center hydrogen bonding between drug amide protons and adenine N3 and thymine O2 atoms analogous to the spine of hydration in the crystal structure of the free DNA, and stacking of the sugar O1' atoms of A6-C21, T7-T20, and, T8-T19, over drug pyrrole rings 1, 2, and 3, respectively. In addition to hydrophobic effects, hydrogen bonding, and electrostatic interactions proposed by others, it is suggested that stacking interactions between DNA sugar O1' atoms and the three drug pyrrole rings contribute to the stability of the complex.

Base Composition↗
PubMed2006

Development of a structural model for NF-kappaB inhibition of sesquiterpene lactones using self-organizing neural networks.

A variety of sesquiterpene lactones (SLs) possess considerable anti-inflammatory activity. Several studies have shown that they exert this effect in part by inhibiting the activation of the transcription factor NF-kappaB. In the present study we elaborated on the investigation of a data set of 103 structurally diverse SLs for which we had previously developed several different QSAR equations dependent on the skeletal type. Use of 3D structure descriptors resulted in a single model for the entire data set. In particular, local radial distribution functions (L-RDF) were used that centered on the methylene-carbonyl substructure believed to be the site of attack of cysteine-38 of the p65/NF-kappaB subunit. The model was developed by using a counterpropagation neural network (CPGNN), attesting to the power of this method for establishing structure-activity-relationships. The investigations shed more light onto the influence of the chemical structure on NF-kappaB inhibitory activity.

Lactones↗