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PubMed2001

Structural model of a voltage-gated potassium channel based on spectroscopic data.

It is estimated that membrane proteins comprise as much as 30% of most genomes. Yet our knowledge of membrane-protein folding is still in its infancy. Consequently, there is a great need for developing approaches that can further advance our understanding of how peptides and proteins interact with membranes and thereby attain their folded structure. An approach that we have been exploring involves dissecting voltage-gated ion channels into simple peptide domains for the purpose of determining their structure in different media using physical techniques. We have synthesized peptides corresponding to the six membrane-spanning segments, as well as the pore domain, of the Shaker channel and characterized their secondary structures. From these studies we have developed a model for the transmembrane structure of the Shaker potassium channel that is constructed from alpha-helices. The hard structural data obtained from these studies lends support to the recent theoretical models of this channel protein that have been developed by others.

Models, Molecular↗

PubMed1992

A structural model for human dihydrolipoamide dehydrogenase.

The hypothesis that dihydrolipoamide dehydrogenases (E3s) have tertiary structures very similar to that of human glutathione reductase (GR) was tested in detail by three separate criteria: (1) by analyzing each putative secondary structural element for conservation of appropriate polar/nonpolar regions, (2) by detailed comparison of putative active site residues in E3s with their authentic counterparts in human GR, and (3) by comparison of residues at the putative dimeric interface of the E3s with the authentic residues in GR. All three criteria are satisfied in a convincing way for the 7 E3s that were considered, supporting the conclusion that the structural scaffolding and the overall tertiary structure (which determines the location of functional sites and residues) are remarkably similar for the E3s and for GR. These analyses together with the crystal structures of human erythrocyte GR formed the basis for construction of a molecular model for human E3. The cofactor FAD and the substrates NAD and lipoic acid were also included in the model. Unexpectedly, the surface residues in the cleft that holds the lipoamide were found to be highly charged and predominantly acidic, allowing us to predict that the region around the lipoamide in the subunit should be basic in nature. The molecular model can be tested by site-directed mutagenesis of residues predicted to be in the dihydrolipoamide acetyltransferase subunit binding cleft.

Amino Acid Sequence↗

PubMed1977

A structural model for the cholesterol-phosphatidylcholine complexes in bilayer membranes.

Based on the structural properties of phospholipid and cholesterol molecules, and making use of the known structural and motional effects of cholesterol and its analogs on phospholipid bilayers, a model for the cholesterol-phosphatidylcholine complex is proposed. In this model, the 3beta-hydroxyl group of cholesterol is assumed to engage in hydrogen bonding with the carbonyl oxygen of the fatty acyl groups in phospholipids. Some specific configurations of the saturated and unsaturated fatty acyl chains of the phospholipid are suggested to participate in van der Waals attractive interactions with the apha and beta surface of the steroid nucleus.

Binding Sites↗

PubMed1997

X-ray structure of Tyr-D-Tic-Phe-Phe-NH2 (D-TIPP-NH2), a highly potent mu-receptor selective opioid agonist. Comparison with proposed model structures.

Tyr-D-Tic-Phe-Phe-NH2 (D-TIPP), a linear tetrapeptide containing the conformationally restricted Tic residue (tetrahydroisoquinoline-3-carboxylic acid), is an opioid agonist which exhibits high affinity and selectivity for the mu-receptor. Its conformational features have been studied using a combination, a solid-state (X-ray) and modeling (molecular mechanics and Monte Carlo simulations) methods. The results of the X-ray study showed two distinct conformers for D-TIPP, with the main differences lying in the orientation of the Tyr side-chain and the presence of both D-Tic(+) and D-Tic(-) conformations for the D-Tic residue. The peptide backbone is folded and stabilized by the formation of one intramolecular hydrogen bond. The modeling results also indicated a folded backbone for the peptide and both cis and trans conformers for the D-Tic residue are found in the lowest-energy structures. Comparison of the X-ray and modeling results shows many similarities especially around the D-Tic residue.

Crystallography, X-Ray↗

PubMed2005

Unique features of the structural model of 'hard' cuticle proteins: implications for chitin-protein interactions and cross-linking in cuticle.

Cuticular proteins are one of the determinants of the physical properties of cuticle. A common consensus region (extended R&R Consensus) in these proteins binds to chitin, the other major component of cuticle. We previously predicted the preponderance of beta-pleated sheet in the consensus region and proposed its responsibility for the formation of helicoidal cuticle (Iconomidou et al., Insect Biochem. Mol. Biol. 29 (1999) 285). Subsequently, we verified experimentally the abundance of antiparallel beta-pleated sheet in the structure of cuticle proteins (Iconomidou et al., Insect Biochem. Mol. Biol. 31 (2001) 877). Homology modelling of soft (RR-1) cuticular proteins using bovine plasma retinol binding protein (RBP) as a template revealed an antiparallel beta-sheet half-barrel structure as the basic folding motif (Hamodrakas et al., Insect Biochem. Molec. Biol. 32 (2002) 1577). The RR-2 proteins characteristic of hard cuticle, have a far more conserved consensus and frequently more histidine residues. Extension of modelling to this class of consensus, in this work, reveals in detail several unique features of the proposed structural model to serve as a chitin binding structural motif, thus providing the basis for elucidating cuticle's overall architecture and chitin-protein interactions in cuticle.

Amino Acid Sequence↗

PubMed2004

[Reliability of students' evaluations of university teaching: an analysis of four-facet data by a generalized model and structural equation modeling].

In our study, we examined the reliability of students' evaluation of university teaching. First, we analyzed four-facet data (teacher x rater x viewpoint x order) by the generalizability theory approach, and estimated the variance components for the facets as a G study. Then, we evaluated the reliability from the point of view of the generalizability coefficient (a reliability-like coefficient that is used when a decision concerns the relative ordering of individuals) and the index of dependability (an index that is used when a decision focuses on the absolute level of an individual's performance independent of others' performance), and examined how those indices change as the number of raters and viewpoints are changed. With these analyses we found conditions needed to maintain sufficient reliability of the evaluation for various situations. We also introduced a new method to evaluate the reliability at each level of facet by using structural equation modeling. By this method, one can examine the reliability of students' evaluation of university teaching more specifically.

Adult↗

PubMed1994

Structural modeling and electrostatic properties of aspartate transcarbamylase from Saccharomyces cerevisiae.

In Saccharomyces cerevisiae the first two reactions of the pyrimidine pathway are catalyzed by a multifunctional protein which possesses carbamylphosphate synthetase and aspartate transcarbamylase activities. Genetic and proteolysis studies suggested that the ATCase activity is carried out by an independently folded domain. In order to provide structural information for ongoing mutagenesis studies, a model of the three-dimensional structure of this domain was generated on the basis of the known X-ray structure of the related catalytic subunit from E. coli ATCase. First, a model of the catalytic monomer was built and refined by energy minimization. In this structure, the conserved residues between the two proteins were found to constitute the hydrophobic core whereas almost all the mutated residues are located at the surface. Then, a trimeric structure was generated in order to build the active site as it lies at the interface between adjacent chains in the E. coli catalytic trimer. After docking a bisubstrate analog into the active site, the whole structure was energy minimized to regularize the interactions at the contact areas between subunits. The resulting model is very similar to that obtained for the E. coli catalytic trimer by X-ray crystallography, with a remarkable conservation of the structure of the active site and its vicinity. Most of the interdomain and intersubunit interactions that are essential for the stability of the E. coli catalytic trimer are maintained in the yeast enzyme even though there is only 42% identity between the two sequences. Free energy calculations indicate that the trimeric assembly is more stable than the monomeric form. Moreover an insertion of four amino acids is localized in a loop which, in E. coli ATCase, is at the surface of the protein. This insertion exposes hydrophobic residues to the solvent. Interestingly, such an insertion is present in all the eukaryotic ATCase genes sequences so far, suggesting that this region is interacting with another domain of the multifunctional protein.

Amino Acid Sequence↗

PubMed2002

A structural model for force regulated integrin binding to fibronectin's RGD-synergy site.

The synergy site on fibronectin's FN-III(9) module, located approximately 32 A away from the RGD-loop on FN-III(10), greatly enhances integrin alpha(5)beta(1) mediated cell binding. Since fibronectin is exposed to mechanical forces acting on the extracellular matrix in vivo, we used steered molecular dynamics to study how mechanical stretching of FN-III(9-10) affects the relative distance between these two synergistic sites. Our simulations predict the existence of an intermediate state prior to unfolding. In this state, the synergy-RGD distance is increased from 32 A to approximately 55 A, while the conformations of both sites remain unperturbed. This distance is too large for both sites to co-bind the same receptor, as indicated by experiments that confirm that increasing the length of the linker chain between FN-III(9) and FN-III(10) reduces alpha(5)beta(1) binding. Our simulations thus suggest that increased alpha(5)beta(1)-binding attributed to the synergy site, along with the associated downstream cell-signaling events, can be turned off mechanically by stretching FN-III(9-10) into this intermediate state. The potential physiological implications are discussed.

Computer Simulation↗

PubMed2006

Standard errors in covariance structure models: asymptotics versus bootstrap.

Commonly used formulae for standard error (SE) estimates in covariance structure analysis are derived under the assumption of a correctly specified model. In practice, a model is at best only an approximation to the real world. It is important to know whether the estimates of SEs as provided by standard software are consistent when a model is misspecified, and to understand why if not. Bootstrap procedures provide nonparametric estimates of SEs that automatically account for distribution violation. It is also necessary to know whether bootstrap estimates of SEs are consistent. This paper studies the relationship between the bootstrap estimates of SEs and those based on asymptotics. Examples are used to illustrate various versions of asymptotic variance-covariance matrices and their validity. Conditions for the consistency of the bootstrap estimates of SEs are identified and discussed. Numerical examples are provided to illustrate the relationship of different estimates of SEs and covariance matrices.

Adolescent↗

PubMed2006

Refinement of the structural model for the Photosystem II supercomplex of higher plants.

Recent X-ray structures determined for the Photosystem II (PSII) core complex isolated from cyanobacteria have provided important information for understanding the functionality of this photosynthetic enzyme including its water splitting activity. As yet, no high-resolution structure is available for PSII of plants or eukaryotes in general. However, crystal structures have been determined for some components of plant PSII which together with the cyanobacterial structure can be used to interpret lower resolution structures of plant PSII derived from electron cryomicroscopy (cryo-EM). Here, we utilise the published X-ray structures of a cyanobacterial PSII core, Light Harvesting Complex II (LHCII), PsbP and PsbQ proteins to construct a model of the plant LHCII-PSII supercomplex using a 17 A resolution 3D electron density map of the spinach supercomplex determined by cryo-EM and single particle analysis. In so doing, we tentatively identify the relative positioning of the chlorophylls within the supercomplex and consider energy transfer pathways between the different subunits. The modelling has also allowed density to be assigned to the three extrinsic proteins of plant PSII, PsbO, PsbP and PsbQ associated with the water splitting centre and concluded that although the position of PsbO is the same as in cyanobacteria, PsbP and PsbQ are located in different positions to the cyanobacterial extrinsic PsbU and PsbV proteins.

Chlorophyll↗

PubMed2001

A structural model for the ternary cleavable complex formed between human topoisomerase I, DNA, and camptothecin.

Using the X-ray crystal structure of the human topoisomerase I (TOP1)-DNA cleavable complex, we have developed a general model for the ternary drug-DNA-TOP1 cleavable complex formed with camptothecin (CPT) and its analogues. This model has the drug intercalated between the -1 and +1 base pairs, with the E-ring pointing into the minor groove and the A-ring directed toward the major groove. The ternary complex is stabilized by an array of hydrogen bonding and hydrophobic interactions between the drug and both the enzyme and the DNA. Significantly, the proposed model is consistent with the current body of experimental mutation, cross-linking, and structure-activity data. In addition, the model reveals potential sites of interaction that can provide a rational basis for the design of next generation compounds as well as for de novo drug design.

Antineoplastic Agents, Phytogenic↗

PubMed2004

Secondary structure models of the 3' untranslated regions of diverse R2 RNAs.

The RNA structure of the 3' untranslated region (UTR) of the R2 retrotransposable element is recognized by the R2-encoded reverse transcriptase in a reaction called target primed reverse transcription (TPRT). To provide insight into structure-function relationships important for TPRT, we have created alignments that reveal the secondary structure for 22 Drosophila and five silkmoth 3' UTR R2 sequences. In addition, free energy minimization has been used to predict the secondary structure for the 3' UTR R2 RNA of Forficula auricularia. The predicted structures for Bombyx mori and F. auricularia are consistent with chemical modification data obtained with beta-ethoxy-alpha-ketobutyraldehyde (kethoxal), dimethyl sulfate, and 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide metho-p-toluene sulfonate. The structures appear to have common helices that are likely important for function.

3' Untranslated Regions↗

PubMed2001

Initiation of HIV-2 reverse transcription: a secondary structure model of the RNA-tRNA(Lys3) duplex.

Human immunodeficiency virus type 2 (HIV-2) reverse transcription is initiated from cellular tRNA(Lys3) partially annealed to the RNA viral genome at the primer binding site (PBS). This annealing involves interactions between two highly structured RNA molecules. In contrast to HIV-1, in which the reverse transcription initiation complex has been thoroughly studied, there is still little information regarding a possible model to describe the secondary structure of the template-primer complex in HIV-2. To determine whether HIV-2 RNA sequences flanking the PBS may specifically interact with the natural primer tRNA, we performed site-directed mutagenesis and enzymatic footprinting. An RNA fragment corresponding to the HIV-2 U5 RNA domain and tRNA(Lys3) were probed either in their free form or in the binary complex. Important reactivity changes to nucleases were obtained upon complex formation. In addition to the canonical contacts between the viral PBS and the 3' end acceptor stem of tRNA(Lys3), we identified two additional interacting domains: (i) the U-rich region of the anticodon loop with the A-rich sequence of the internal loop within the U5-prePBS region; (ii) nucleotides 48-54 from the TPsiC domain of tRNA(Lys3) and the 240-247 region of viral U5-RNA. In view of these experimental data and sequence comparison between different HIV-2 isolates, we propose a model for the secondary structure of the HIV-2 template-primer initiation complex.

Anticodon↗

PubMed1999

Correlating Atomic Scale Experimental Observations to Develop Three-Dimensional Structural Models for Grain Boundaries in Oxides.

: Determining the three-dimensional atomic structure of grain boundaries is a crucial first step toward understanding how these defects control the overall bulk properties of materials. In this report we discuss the correlation of experimental atomic resolution Z-contrast images and electron energy loss spectrometry (EELS) to achieve this goal. Initial structural analysis is afforded through empirical bond-valence potentials. This structure is then refined using multiple scattering analysis of the energy loss spectra. These techniques are demonstrated in the analysis of a 27 degrees MgO [001] tilt grain boundary. Through this analysis, we were able to determine specific atomic locations of Ca dopants found present at this grain boundary.

Journal Article↗

PubMed2006

Structure modeling of all identified G protein-coupled receptors in the human genome.

G protein-coupled receptors (GPCRs), encoded by about 5% of human genes, comprise the largest family of integral membrane proteins and act as cell surface receptors responsible for the transduction of endogenous signal into a cellular response. Although tertiary structural information is crucial for function annotation and drug design, there are few experimentally determined GPCR structures. To address this issue, we employ the recently developed threading assembly refinement (TASSER) method to generate structure predictions for all 907 putative GPCRs in the human genome. Unlike traditional homology modeling approaches, TASSER modeling does not require solved homologous template structures; moreover, it often refines the structures closer to native. These features are essential for the comprehensive modeling of all human GPCRs when close homologous templates are absent. Based on a benchmarked confidence score, approximately 820 predicted models should have the correct folds. The majority of GPCR models share the characteristic seven-transmembrane helix topology, but 45 ORFs are predicted to have different structures. This is due to GPCR fragments that are predominantly from extracellular or intracellular domains as well as database annotation errors. Our preliminary validation includes the automated modeling of bovine rhodopsin, the only solved GPCR in the Protein Data Bank. With homologous templates excluded, the final model built by TASSER has a global C(alpha) root-mean-squared deviation from native of 4.6 angstroms, with a root-mean-squared deviation in the transmembrane helix region of 2.1 angstroms. Models of several representative GPCRs are compared with mutagenesis and affinity labeling data, and consistent agreement is demonstrated. Structure clustering of the predicted models shows that GPCRs with similar structures tend to belong to a similar functional class even when their sequences are diverse. These results demonstrate the usefulness and robustness of the in silico models for GPCR functional analysis. All predicted GPCR models are freely available for noncommercial users on our Web site (http://www.bioinformatics.buffalo.edu/GPCR).

Algorithms↗

PubMed1989

Cloning and sequence analysis of the 18 S ribosomal RNA gene of tomato and a secondary structure model for the 18 S rRNA of angiosperms.

The gene of a cytoplasmic 18 S ribosomal RNA (18 S rDNA) of the dicotyledonous plant tomato (Lycopersicon esculentum) cv. Rentita has been cloned, and its complete primary structure has been determined. The tomato 18 S rDNA is 1805 bp long with a G + C content of 49.6%. Its sequence exhibits 94%-96% positional identity when it is colinearly aligned with the previously reported sequences of the 17-18 S rDNAs of the dicot soybean and the monocots maize and rice. A model of the secondary structure of the 18 S rRNA of angiosperms is presented and its genera-specific structural features are compared with a current eukaryotic 18 S rRNA consensus model.

Base Sequence↗

PubMed1991

Structural model of the nucleotide-binding conserved component of periplasmic permeases.

The amino acid sequences of 17 bacterial membrane proteins that are components of periplasmic permeases and function in the uptake of a variety of small molecules and ions are highly homologous to each other and contain sequence motifs characteristic of nucleotide-binding proteins. These proteins are known to bind ATP and are postulated to be the energy-coupling components of the permeases. Several medically important eukaryotic proteins, including the multidrug-resistance transporters and the protein encoded by the cystic fibrosis gene, are also homologous to this family. By multiple sequence alignment of these 17 proteins, the consensus sequence, secondary structure, and surface exposure were predicted. The secondary structural motifs that are conserved among nucleotide-binding proteins were identified in adenylate kinase, p21ras, and elongation factor Tu by superposition of their known tertiary structures. The equivalent secondary structural elements in the predicted conserved component were located. These, together with sequence information, served as guides for alignment with adenylate kinase. A model for the structure of the ATP-binding domain of the permease proteins is proposed by analogy to the adenylate kinase structure. The characteristics of several permease mutations and biochemical data lend support to the model.

Adenylate Kinase↗

PubMed2005

The modeled structure of the RNA dependent RNA polymerase of GBV-C virus suggests a role for motif E in Flaviviridae RNA polymerases.

BACKGROUND: The Flaviviridae virus family includes major human and animal pathogens. The RNA dependent RNA polymerase (RdRp) plays a central role in the replication process, and thus is a validated target for antiviral drugs. Despite the increasing structural and enzymatic characterization of viral RdRps, detailed molecular replication mechanisms remain unclear. The hepatitis C virus (HCV) is a major human pathogen difficult to study in cultured cells. The bovine viral diarrhea virus (BVDV) is often used as a surrogate model to screen antiviral drugs against HCV. The structure of BVDV RdRp has been recently published. It presents several differences relative to HCV RdRp. These differences raise questions about the relevance of BVDV as a surrogate model, and cast novel interest on the "GB" virus C (GBV-C). Indeed, GBV-C is genetically closer to HCV than BVDV, and can lead to productive infection of cultured cells. There is no structural data for the GBV-C RdRp yet. RESULTS: We show in this study that the GBV-C RdRp is closest to the HCV RdRp. We report a 3D model of the GBV-C RdRp, developed using sequence-to-structure threading and comparative modeling based on the atomic coordinates of the HCV RdRp structure. Analysis of the predicted structural features in the phylogenetic context of the RNA polymerase family allows rationalizing most of the experimental data available. Both available structures and our model are explored to examine the catalytic cleft, allosteric and substrate binding sites. CONCLUSION: Computational methods were used to infer evolutionary relationships and to predict the structure of a viral RNA polymerase. Docking a GTP molecule into the structure allows defining a GTP binding pocket in the GBV-C RdRp, such as that of BVDV. The resulting model suggests a new proposition for the mechanism of RNA synthesis, and may prove useful to design new experiments to implement our knowledge on the initiation mechanism of RNA polymerases.

Binding Sites↗