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At least 721 records · Page 40Linked to original sources
PubMed2006

Structural model of human endoglin, a transmembrane receptor responsible for hereditary hemorrhagic telangiectasia.

Endoglin is a type I membrane protein expressed as a disulphide-linked homodimer on human vascular endothelial cells whose haploinsufficiency is responsible for the dominant vascular dysplasia known as hereditary hemorrhagic telangiectasia (HHT). Structurally, endoglin belongs to the zona pellucida (ZP) family of proteins that share a ZP domain of approximately 260 amino acid residues at their extracellular region. Endoglin is a component of the TGF-beta receptor complex, interacts with the TGF-beta signalling receptors types I and II, and modulates cellular responses to TGF-beta. Here, we have determined for the first time the three-dimensional structure of the approximately 140 kDa extracellular domain of endoglin at 25 A resolution, using single-particle electron microscopy (EM). This reconstruction provides the general architecture of endoglin, which arranges as a dome made of antiparallel oriented monomers enclosing a cavity at one end. A high-resolution structure of endoglin has also been modelled de novo and found to be consistent with the experimental reconstruction. Each subunit comprises three well-defined domains, two of them corresponding to ZP regions, organised into an open U-shaped monomer. This domain arrangement was found to closely resemble the overall structure derived experimentally and the three modelled de novo domains were tentatively assigned to the domains observed in the EM reconstruction. This molecular model was further tested by tagging endoglin's C terminus with an IgG Fc fragment visible after 3D reconstruction of the labelled protein. Combined, these data provide the structural framework to interpret endoglin's functional domains and mutations found in HHT patients.

Amino Acid Sequence↗
PubMed2005

Folding of the SARS coronavirus spike glycoprotein immunological fragment (SARS_S1b): thermodynamic and kinetic investigation correlating with three-dimensional structural modeling.

Spike glycoprotein of SARS coronavirus (S protein) plays a pivotal role in SARS coronavirus (SARS_CoV) infection. The immunological fragment of the S protein (Ala251-His641, SARS_S1b) is believed to be essential for SARS_CoV entering the host cell through S protein-ACE-2 interaction. We have quantitatively characterized the thermally induced and GuHCl-induced unfolding features of SARS_S1b using circular dichroism (CD), tryptophan fluorescence, and stopped-flow spectral techniques. For the thermally induced unfolding at pH 7.4, the apparent activation energy (E(app)) and transition midpoint temperature (Tm) were determined to be 16.3 +/- 0.2 kcal/mol and 52.5 +/- 0.4 degrees C, respectively. The CD spectra are not dependent on temperature, suggesting that the secondary structure of SARS_S1b has a relatively high thermal stability. GuHCl strongly affected SARS_S1b structure. Both the CD and fluorescent spectra resulted in consistent values of the transition middle concentration of the denaturant (Cm, ranging from 2.30 to 2.45 M) and the standard free energy change (deltaG(o), ranging from 2.1 to 2.5 kcal/mol) for the SARS_S1b unfolding reaction. Moreover, the kinetic features of the chemical unfolding and refolding of SARS_S1b were also characterized using a stopped-flow CD spectral technique. The obvious unfolding reaction rates and relaxation times were determined at various GuHCl concentrations, and the Cm value was obtained, which is very close to the data that resulted from CD and fluorescent spectral determinations. Secondary and three-dimensional structural predictions by homology modeling indicated that SARS_S1b folded as a globular-like structure by beta-sheets and loops; two of the four tryptophans are located on the protein surface, which is in agreement with the tryptophan fluorescence result. The three-dimensional model was also used to explain the recently published experimental results of S1-ACE-2 binding and immunizations.

Amino Acid Sequence↗
PubMed1997

A novel structural model for regulation of clathrin function.

The distinctive triskelion shape of clathrin allows assembly into polyhedral lattices during the process of clathrin-coated vesicle formation. We have used random and site-directed mutagenesis of the yeast clathrin heavy chain gene (CHC1) to characterize regions which determine Chc trimerization and binding to the clathrin light chain (Clc) subunit. Analysis of the mutants indicates that mutations in the trimerization domain at the triskelion vertex, as well as mutations in the adjacent leg domain, frequently influence Clc binding. Strikingly, one mutation in the trimerization domain enhances the association of Clc with Chc. Additional mutations in the trimerization domain, in combination with mutations in the adjacent leg domain, exhibit severe defects in Clc binding while maintaining near normal trimerization properties. The position of these trimerization domain mutations on one face of a putative alpha-helix defines a region on the trimer surface that interacts directly with Clc. These results suggest that Clc extends into the Chc trimerization domain from the adjacent leg, thereby bridging the two domains. On the basis of this conclusion, we propose a new model for the organization of the triskelion vertex which provides a structural basis for regulatory effects of Clc on clathrin function.

Amino Acid Sequence↗
PubMed2003

Synthesis and structure of [Zn(OMe)(L)] x [Zn(OH)(L)] x 2(BPh4), L = cis,cis-1,3,5-tris[(E,E)-3-(2-furyl)acrylideneamino]cyclohexane: structural models of carbonic anhydrase and liver alcohol dehydrogenase.

Direct reaction of [Zn(OH)(L)]+, L = cis,cis-1,3,5-tris[(E,E)-3-(2-furyl)acrylideneamino]cyclohexane, with methanol gives a mixture of the starting material and [Zn(OMe)(L)]+; structural analysis of the complexes shows that they are models of reactive intermediates in the catalytic cycles of the zinc enzymes carbonic anhydrase and liver alcohol dehydrogenase.

Alcohol Dehydrogenase↗
PubMed1997

Development of a structural model for the cytoplasmic domain of an integrin.

The cytoplasmic tails of integrin heterodimers play central roles in controlling the activation states of integrins and in transmitting intracellular signals. Despite their short length, no structure of any integrin cytoplasmic domain has been determined. Therefore, molecular models for the cytoplasmic domain of alpha(IIb)beta3, the major platelet integrin, were generated, including models for the individual cytoplasmic tails, the binary alphaIIb-calcium complex, and the ternary alphaIIb-beta3-calcium complex. Structural analysis of circular dichroism spectra were compiled with data obtained from short homologous sequences within crystallized proteins, and with secondary structural predictions to develop starting models for each subunit. These models were subjected to a series of energy minimization and molecular dynamic simulations to generate final models. AlphaIIb was predicted to be ordered at its N-terminus and its C-terminus could accommodate a cation in a multicoordinated complex. The structure of beta3 was dominated by a beta-turn at its NPXY motif (beta3 744-747). In docking of alphaIIb to different sites within beta3, the conformation of the beta3 juxta-transmembrane (beta3 716-721) was greatly altered. This region was confirmed to be a conformational 'hot-spot' by circular dichroism. The conformational flexibility of this juxta-transmembrane region, which is highly conserved amongst integrins, is ideally located to regulate signaling.

Amino Acid Sequence↗
PubMed2006

Prediction of the mechanism of action of omuralide (clasto-lactacystin beta-lactone) on human cathepsin A based on a structural model of the yeast proteasome beta5/PRE2-subunit/omuralide complex.

Cathepsin A (CathA) is a lysosomal serine carboxypeptidase that exhibits homology and structural similarity to the yeast and wheat serine carboxypeptidases (CPY and CPW) belonging to the alpha/beta-hydrolase fold family. Human CathA (hCathA) and CPW have been demonstrated to be inhibited by a proteasome (threonine protease) inhibitor, lactacystin, and its active derivative, omuralide (clasto-lactacystin beta-lactone), as well as chymostatin. A hCathA/omuralide complex model constructed on the basis of the X-ray crystal structures of the CPW/chymostatin complex and the yeast proteasome beta-subunit (beta5/PRE2)/omuralide one predicted that the conformation of omuralide in the active-site cleft of proteasome beta5/PRE2 should be very similar to that of chymostatin at the S1 catalytic subsites in the hCathA- and CPW-complexes. The relative positions of the glycine residues, i.e., Gly57 in hCathA, Gly53 in CPW, and Gly47 in beta5/PRE2, present in the oxyanion hole of each enzyme were also highly conserved. These results suggest that omuralide might inhibit hCathA and CPW at the S1 subsite in their active-site clefts through direct binding to the active serine residue.

Catalytic Domain↗
PubMed2003

Accuracy of CT-based thickness measurement of thin structures: modeling of limited spatial resolution in all three dimensions.

Measurement of the width of thin structures such as the cortical shell of the vertebral body or femoral neck with computed tomography (CT) is limited by the spatial resolution of the CT system. Limited spatial resolution exists both within the CT image plane and perpendicular to it and can be described by the in-plane point spread function (PSF) and the across-plane slice sensitivity profile (SSP), respectively. The goal of this study was to confirm that errors of thickness measurement of thin structures critically depend on the spatial positioning of the object and the spatial resolution limitations of CT in all three dimensions, and to assess the size of the errors themselves. We compared computer models that incorporated both effects to experimentally assessed cortical thicknesses of the European Spine Phantom. Analysis included varying CT slice width, the orientation of measurement and angle beta of misalignment of longitudinal scanner and phantom axes. Agreement of models with measurements was good in all configurations with an overall error of 0.17 mm. This showed that PSF and SSP are adequate system characteristics to predict deviation of measured values from true widths. Errors between measurements and true cortical thickness values delta(true) averaged to 1.5 mm were strongly positively correlated with slice width d and beta. When the across-plane partial volume effect was eliminated, limited in-plane resolution still accounted for overestimation of delta(true) by 0.68 (137%), 0.27 (27%), and 0.06 mm (4%) for delta(true)=0.5, 1.0, and 1.5 mm, respectively. For delta(true) of 1.0 mm and above, it was shown that although the absolute cortical thickness values might not be accurately measurable, relative differences between two values are reflected in measurement. Implications for cortical thickness measurement are that the spinal cortical shell is too thin, whereas accurate assessment at locations of the femoral neck exhibiting a thicker cortical shell of both difference and absolute values should be possible with CT even for larger misalignment angles, especially when a smaller CT slice width is chosen.

Computer Simulation↗
PubMed2001

Complexation of Cu(2+) by HETPP and the pentapeptide Asp-Asp-Asn-Lys-Ile: a structural model of the active site of thiamin-dependent enzymes in solution.

To obtain structural information on the active site of thiamin-dependent enzymes in solution, we have studied the interactions of Cu(2+) ions with 2-(alpha-hydroxyethyl)thiamin pyrophosphate (HETPP), the pentapeptide Asp-Asp-Asn-Lys-Ile surrounding the thiamin pyrophosphate moiety in the transketolase enzyme, and the tertiary Cu(2+)-pentapeptide-HETPP system in aqueous solutions at various pH values. In the binary Cu(2+)-pentapeptide system around physiological pH, the bonding sites were the terminal NH2 group, the aspartate beta-carboxylates, and a deprotonated peptide nitrogen, while, in the Cu(2+)-HETPP system at the same pH, the Cu(II) was coordinated to the pyrophosphate group and to the pyrimidine N(1') atom. It is found that, in the tertiary system at physiological pH, the peptide bone offers three coordination sites to the metal ion, and the coordination sphere is completed by two additional phosphate oxygens and the nitrogen N(1') of the thiamin coenzyme. The stability constants in the tertiary system are higher than those in the simpler Cu(2+)-HETPP and Cu(2+)-peptide systems. The present data show that the coenzyme adopts the so-called S conformation in solution. The importance of our findings concerning the N(1') coordination and the S conformation in the tertiary system is discussed in conjunction with the role of HETPP as an intermediate of thiamin catalysis.

Binding Sites↗
PubMed1997

Evaluation of comparative protein structure modeling by MODELLER-3.

We evaluate homology-derived 3D models of dihydrofolate reductase (DFR1), phosphotransferase enzyme IIA domain (PTE2A3), and mouse/human UBC9 protein (UBC9(24)) which were submitted to the second Meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP). The DFR1 and PTE2A3 models, based on alignments without large errors, were slightly closer to their corresponding X-ray structures than the closest template structures. By contrast, the UBC9(24) model was slightly worse than the best template due to a misalignment of the N-terminal helix. Although the current models appear to be more accurate than the models submitted to the CASP meeting in 1994, the four major types of errors in side chain packing, position and conformation of aligned segments, position and conformation of inserted segments, and in alignment still occur to almost the same degree. The modest improvement probably originates from the careful manual selection of the templates and editing of the alignment, as well as from the iterative realignment and model building guided by various model evaluation techniques. This iterative approach to comparative modeling is likely to overcome at least some initial alignment errors, as demonstrated by the correct final alignment of the C terminus of DFR.

Amino Acid Sequence↗
PubMed1992

Structural modelling of P-type ion pumps.

Over forty sequences of P-type ion pumps have been determined. They fall into five families showing between 20% and 50% identity in sequence. The conserved residues are concentrated in several regions which are found in all the pumps. All the defined functional sites are associated with conserved segments and provide a basis for subdivision into domains, to which tentative secondary and tertiary structures can be assigned. The domains have been assembled into a structure consisting of a conserved core with variable loops and deletions on the surface, which accommodates site mutants, affinity labels and known epitopes. This model has been correlated with the results of an electron crystallographic study of the Ca++ pump. Two types of crystal have been examined in negative stain and in amorphous ice; thin plates which diffract to 4A and long helical tubes which diffract to 15A. The plates have given a 6A projection map, some of which can be interpreted by difference from the map of the negatively stained crystal, as transmembrane helices. Three dimensional interpretation will require a tilt series. In the meantime, analysis of the tubes has given a 14A 3D map which clearly defines the cytoplasmic domains and their relation to the transmembrane region (Stokes and Toyoshima in preparation). Although it is not yet possible to assign specific functions to the cytoplasmic lobes, the structure at this resolution is consistent with the model.

Animals↗
PubMed1993

HIV-1 proteinase as structural model of intercellular transport proteins of plant viruses.

Intracellular movement of viral infections of plants requires a virus-encoded protein. Alignment of amino acid sequences of central conserved regions of such proteins produced a sequence profile that resembled that of lentiviral proteinases. The known three-dimensional structure of the proteinase encoded by the human immunodeficiency virus-1 (HIV-1) may serve as a model for the three-dimensional structure of the central region of the plant viral proteins. Secondary structures predicted for the plant viral proteins from their amino acid sequences correlate well with those predicted from a proteinase model. In addition, the positions of temperature-sensitive and resistance-breaking mutations in the intercellular transport protein of tobacco mosaic virus are consistent with a structural similarity between the plant viral proteins and the lentiviral proteinases. In a suggested model, the dimeric proteinase-similar domain serves as tether for the attachment of N- and C-terminal domains. The C-terminal domain may be an RNA-binding domain. The similarity was used to assign intercellular transport function to a previously unidentified coding region of the genomes of bacilliform DNA viruses.

Amino Acid Sequence↗
PubMed2006

NMR investigation of DNA primer-template models: structural insights into dislocation mutagenesis in DNA replication.

Slipped frameshift intermediates can occur when DNA polymerase slows or stalls at sites of DNA lesions. However, this phenomenon is much less common when unmodified DNA is replicated. In order to study the effect of templating bases on the alignment of primer-templates, NMR structural investigation has been performed on primer-template oligonucleotide models which mimic the situation that dNTP has just been incorporated opposite template. NMR evidence reveals the occurrence of misalignment when dGTP is incorporated opposite template T with a downstream nucleotide C. Depending on the template sequence, further extension of the primer can lead to realignment.

Base Pair Mismatch↗
PubMed1997

Protein-protein communication: structural model of the repression complex formed by CytR and the global regulator CRP.

The cAMP receptor protein (CRP) and the LacI-related CytR antiactivator bind cooperatively to adjacent DNA sites at or near promoters, an interaction that involves direct protein contacts. Here, we identify a collection of amino acid substitutions in CytR that reestablish protein-protein communication to mutant CRP proteins specifically defective in cooperative binding with wild-type CytR. To assess the location and spatial arrangement of these substitutions, we built a three-dimensional model of CytR based on the recent X-ray structure of the highly homologous PurR repressor bound to DNA. This approach enables us to specify the patch on CytR's surface that contacts CRP. Furthermore, our results permit the construction of a three-dimensional structure of the higher order nucleoprotein complex formed by CytR and CRP.

Alanine↗
PubMed1999

High-resolution autoreactive epitope mapping and structural modeling of the 65 kDa form of human glutamic acid decarboxylase.

The smaller isoform of the GABA-synthesizing enzyme, glutamic acid decarboxylase 65 (GAD65), is unusually susceptible to becoming a target of autoimmunity affecting its major sites of expression, GABA-ergic neurons and pancreatic beta-cells. In contrast, a highly homologous isoform, GAD67, is not an autoantigen. We used homolog-scanning mutagenesis to identify GAD65-specific amino acid residues which form autoreactive B-cell epitopes in this molecule. Detailed mapping of 13 conformational epitopes, recognized by human monoclonal antibodies derived from patients, together with two and three-dimensional structure prediction led to a model of the GAD65 dimer. GAD65 has structural similarities to ornithine decarboxylase in the pyridoxal-5'-phosphate-binding middle domain (residues 201-460) and to dialkylglycine decarboxylase in the C-terminal domain (residues 461-585). Six distinct conformational and one linear epitopes cluster on the hydrophilic face of three amphipathic alpha-helices in exons 14-16 in the C-terminal domain. Two of those epitopes also require amino acids in exon 4 in the N-terminal domain. Two distinct epitopes reside entirely in the N-terminal domain. In the middle domain, four distinct conformational epitopes cluster on a charged patch formed by amino acids from three alpha-helices away from the active site, and a fifth epitope resides at the back of the pyridoxal 5'-phosphate binding site and involves amino acid residues in exons 6 and 11-12. The epitopes localize to multiple hydrophilic patches, several of which also harbor DR*0401-restricted T-cell epitopes, and cover most of the surface of the protein. The results reveal a remarkable spectrum of human autoreactivity to GAD65, targeting almost the entire surface, and suggest that native folded GAD65 is the immunogen for autoreactive B-cells.

Amino Acid Sequence↗
PubMed1995

Modeled structure of the 75-kDa neurotrophin receptor.

Motifs in ligand-binding domains of the neurotrophin (NTR) and lymphotoxin (TNFR-I) receptors define a family of receptors that mediates programmed cell death. We have explored relationships of architecture and function in this family through a molecular model of NTR, also called p75NGFR or LANR. Modeling by homology took advantage of four modular subdomains in the crystal structure of TNFR-I that also occur in NTR. Hypothetical complexes between the model and a ligand structure (for nerve growth factor, NGF) were then examined using docking software. NTR appears to bind in the dimer interface of NGF, making two sets of contacts. NTR subdomains III and IV provide the ligand-contact surfaces, in contrast to TNFR, in which subdomains II and III contact TNF-beta. NTR subdomain II appears to have been evolutionarily modified, potentially contributing to an interface between receptor subunits. These and other specific predictions of the model will require experimental confirmation.

Amino Acid Sequence↗
PubMed2004

Cultural competence among physicians treating Mexican Americans who have diabetes: a structural model.

Latinos, who constitute the fastest growing ethnically distinct US group, experience disproportionately high rates of type 2 diabetes. At the same time, linguistic and economic barriers, differing cultural expectations between patients and physicians, provider reactions based on stereotypes, and managed healthcare shortfalls limit diabetes care. Such trends highlight physicians' need to consider culture in the delivery of effective services. To address these issues we investigated predictors of culturally competent actions among a sample of 134 practicing San Diego County physicians. They provided demographic information and completed questions assessing their cultural knowledge, cultural awareness, and culturally competent actions specific to Mexican Americans with diabetes. We then developed a structural cultural competence model. Results indicated that participation in diverse medical education settings and experience in community clinics predicted cultural knowledge. Participation in diverse educational settings, Latino ethnicity, bilingual skills, and cultural knowledge predicted cultural awareness. An internal medicine specialty predicted less cultural awareness. Culturally competent actions were only predicted by cultural awareness. Goodness-of-fit statistics supported the overall model's acceptability. The number of Mexican Americans physicians see in practice did not predict any tested cultural competence dimension. Our model supports a number of conclusions. First, knowledge of cultural factors per se and simple exposure to Mexican Americans in practice do not directly facilitate culturally competent care. Rather, such care is most strongly predicted by recognition that cultural factors and awareness of personal biases are important. Results further support medical education that does not solely focus on basic information about Mexican Americans but also explores provider biases and preconceptions. Diverse educational experiences appear particularly helpful in this process. Community clinic settings also help practitioners gain cultural knowledge. While Latino ethnicity predicted cultural awareness, results also suggest that all physicians can take steps towards increasing their cultural competence.

Adult↗