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At least 1,621 records · Page 90Linked to original sources
PubMed1992

Interaction of the p85 subunit of PI 3-kinase and its N-terminal SH2 domain with a PDGF receptor phosphorylation site: structural features and analysis of conformational changes.

Circular dichroism and fluorescence spectroscopy were used to investigate the structure of the p85 alpha subunit of the PI 3-kinase, a closely related p85 beta protein, and a recombinant SH2 domain-containing fragment of p85 alpha. Significant spectral changes, indicative of a conformational change, were observed on formation of a complex with a 17 residue peptide containing a phosphorylated tyrosine residue. The sequence of this peptide is identical to the sequence surrounding Tyr751 in the kinase-insert region of the platelet-derived growth factor beta-receptor (beta PDGFR). The rotational correlation times measured by fluorescence anisotropy decay indicated that phosphopeptide binding changed the shape of the SH2 domain-containing fragment. The CD and fluorescence spectroscopy data support the secondary structure prediction based on sequence analysis and provide evidence for flexible linker regions between the various domains of the p85 proteins. The significance of these results for SH2 domain-containing proteins is discussed.

Amino Acid Sequence↗
PubMed1998

p53 mutations in malignant gliomas.

A population-based series of incident cases of malignant glioma were analyzed for mutations in the tumor suppressor gene p53. Exons 4-8 were screened using PCR-single-strand conformation analysis and confirmed through direct sequencing. Of 62 tumors analyzed, 12 (19%) contained mutations in p53: one 18-bp duplication in exon 5, five point mutations in exon 4, three point mutations in exon 7, two point mutations in exon 8, and a splice-site mutation at the exon 6/intron 7 boundary. In contrast to previous studies of malignant glioma, the prevalence of transversion mutations (56%) was higher than transition mutations (33%). A large proportion of transversion mutations occurred in exon 4, a region that is not routinely screened in gliomas. We present here an improved method for screening exon 4 (and other GC-rich regions) of p53 using PCR-single-strand conformation analysis. The high frequency of transversion mutations suggests a role for exogenous carcinogens in the etiology of malignant glioma.

Adolescent↗
PubMed1984

[Two types of tripeptide conformation in collagen. Calculation of the structure of (Gly-Pro-Ser)n and (Gly-Val-Hyp)n polytripeptides].

Conformational analysis of polypeptides (Gly-Pro-Ser)n and (Gly-Val-Hyp)n was carried out for collagen-like triple helical complexes (coiled coils with screw symmetry). The lowest energy structure of the first polymer (helical parameters t 52,8, h 0,282 nm) is very close to that of (Gly-Pro-Hyp)n. The hydroxyl group of a serine residue does not form any intramolecular hydrogen bonds in this structure. (Gly-Val-Hyp)n triple complex is shown to unwind to t 7,7, h 0,297 nm as a result of optimization procedure. These findings confirm the assumption, made earlier on the basis of conformational analysis of (Gly-Pro-Hyp)n, (Gly-Pro-Ala)n, (Gly-Ala-Hyp)n, (Gly-Ala-Ala)n, that the collagen triple helix contains stable wound triplets with proline in the second position, while the absence of imino acid in the 2nd position facilitates the unwinding of the triple helix. Thus, a collagen helix appears to have different parameters for the sites differing in the amino acid sequence. The values measured in the X-ray experiments (h 0,29 nm, t' 36) should be considered as a result of averaging. The model allows to reconcile the X-ray data for collagen and crystalline (Gly-Pro-Pro)10 oligomer.

Collagen↗
PubMed2004

Development of new anti-cancer peptides from conformational energy analysis of the oncogenic ras-p21 protein and its complexes with target proteins.

We have employed a computational approach to design peptides, from known oncogenic proteins, that inhibit tumor growth. This approach has been applied to the ras-p21 protein that becomes oncogenic when single amino acid substitutions occur at critical positions in its polypeptide chain, such as at Gly 12 and Gln 61. In this approach, using two sampling methods, molecular dynamics and the electrostatically driven Monte Carlo (EDMC) method, we have computed the average structures of wild-type and oncogenic forms of ras-p21 alone and bound to a number of its target proteins, such as the ras-binding domain (RBD) of raf, guanine nucleotide exchange protein (GAP) and SOS guanine nucleotide exchange protein (GAP). By superimposing the average structures of the oncogenic forms on those of their wild-type counterparts, we have identified a number of domains that change conformation. These domains are potential effector domains that are involved uniquely in oncogenic ras-p21 signaling. We have therefore synthesized peptides corresponding to these domains and tested them in Xenopus laevis oocytes for their abilities to inhibit oncogenic ras-p21 selectively. Using this approach, we have identified three peptides from ras-p21 and one peptide each from the RBD of raf, GAP and SOS that selectively inhibit oncogenic but not insulin-activated wild-type ras-p21-induced oocyte maturation. We have synthesized the ras-p21 peptides attached to a penetratin leader sequence to enable cell membrane penetration and introduced these peptides into a ras-transformed pancreatic cancer cell line; these peptides, but not an unrelated negative control peptide, cause the cells to undergo complete phenotypic reversion. On the other hand, none of these peptides has any effect on the growth of untransformed pancreatic acinar cells in culture, further suggesting that they may not interfere with normal cell growth. Thus these peptides can be useful agents in the treatment of cancers. We have further used these peptides to demonstrate that oncogenic and wild-type ras-p21 proteins utilize different signal transduction pathways and to identify where these differences occur in cells.

Animals↗
PubMed1996

A thermodynamic analysis of conformational change due to the alpha 2 beta 2 complex formation of tryptophan synthase.

A characteristic property of the tryptophan synthase alpha 2 beta 2 complex is the mutual activation of the alpha and beta subunit upon complex formation. It has been speculated that this mutual activation results from the conformational change due to the alpha/beta subunit interaction. To elucidate this mechanism, we investigated the thermodynamic parameters of association for the various combinations of the alpha and beta subunits from Escherichia coli and Salmonella typhimurium using isothermal titration calorimetry. The negative association enthalpy of the S. typhimurium alpha subunit with the beta subunit from E. coli (or S. typhimurium) was about 20 kJ mol-1 larger than that of the E. coli alpha subunit at 40 degrees C. However, the favorable enthalpy of the S. typhimurium alpha subunit was perfectly compensated by the unfavorable association entropy, therefore, the Gibbs energy of association was similar to that of the E. coli alpha subunit. Furthermore, the site-directed mutagenesis study revealed that a single mutation (K109N; [Asn109] alpha subunit) of the E coli alpha subunit at the subunit interface from E. coli to the S. typhimurium type could change the characteristics of the thermodynamic parameters of association to the S. typhimurium alpha subunit type. The heat-capacity changes of the association of the alpha subunit with the beta subunit were quite great, 6.37-8.21 kJ mol-1 K-1, compared with that due to a decrease in accessible surface area in the subunit interface. The analysis of the thermodynamic parameters of association suggested that the complex formation couples with the folding (rearrangements) of the alpha subunit monomer or/and beta subunit dimer.

Asparagine↗
PubMed2001

Single-strand conformation polymorphism analysis of the glucose transporter gene GLUT1 in maturity-onset diabetes of the young.

Maturity-onset diabetes of the young (MODY), an autosomal dominant, early-onset form of type-2 diabetes, is caused by mutations in five different genes all leading to defect(s) in the pancreatic beta cell. However, some patients with this form of diabetes do not bear a mutation in any of the known (MODY1-MODY5) loci, a notion prompting the search for new MODY genes. Clinical and genetic data point toward a defect in beta cell function in the majority of patients with MODY, and partners of the glucose-sensing device are reasonable functional candidates. The high-capacity glucose transporter GLUT2 has the ideal kinetic features for performing this task. However, complete GLUT2 deficiency in humans leads to hepato-renal glycogenosis (Fanconi-Bickel syndrome), and heterozygous GLUT2 mutations apparently behave in a recessive manner. Furthermore, in the human beta cell GLUT1 mRNA is predominant when compared to GLUT2 and glucose influx appears to be largely mediated by this low-Km transporter. Thus, we looked for the presence of sequence variants by polymerase chain reaction and single-strand conformation polymorphism (PCR-SSCP) within the GLUT1 gene in 90 Italian pedigrees negative at the search for mutations in glucokinase (MODY2) and hepatocyte nuclear factor-1alpha (MODY3), the two genes responsible for about 60% of MODY cases in Italian children. We found three already described silent mutations and a new single base deletion in position -173 of the 5' regulatory region. The -173de1A variant, which was detected in the heterozygous or homozygous state in 30.8% of MODY patients examined and is located in a Nuclear Factor Y binding sequence, is not associated with hyperglycemia in affected relatives of MODY probands. In conclusion, it appears from these results that the glucose transporter gene GLUT1 is unlikely to play a major role in the etiology of MODY diabetes.

Adolescent↗
PubMed1991

Three-dimensional structure of p21 in the active conformation and analysis of an oncogenic mutant.

The three-dimensional structure of the active guanosine triphosphate (GTP)-analogue-containing complex of the H-ras-encoded p21 has been determined. It was necessary to correct the topology of p21 as published earlier. The structure analysis shows all of the interactions between protein and GTP and how the important cofactor Mg2+ is bound. From the oncogenic mutants of p21 crystallized, a Gly12 to Arg mutation has been analyzed in detail. It shows that the overall structure of the mutant is not perturbed and that the side chain of Arg12 is coming close to the gamma-phosphate for an interaction.

Allosteric Regulation↗
PubMed1998

The differentiation of Phytophthora species that are pathogenic on potatoes by an asymmetric PCR combined with single-strand conformation polymorphism analysis.

The goal of this study was to develop a polymerase chain reaction (PCR) capable of differentiating Phytophthora species that are pathogenic on potatoes using a single primer pair. To achieve this objective, primers were derived from conserved regions flanking variable sequences in the internal transcribed spacer 1 (ITS1) of Phytophthora species. One primer pair produced a 140 bp product from P. infestans, P. erythroseptica and P. nicotianae. The PCR products were purified and used in an asymmetric PCR (A-PCR) protocol to generate single-strand DNA (ssDNA). The ssDNA of the Phytophthora potato pathogens reproducibly migrated in non-denaturing polyacrylamide gels in a species-specific manner.

Base Sequence↗
PubMed2004

NIR vibrational overtone spectra of N-methylaniline, N,N-dimethylaniline and N,N-diethylaniline--a conformational structural analysis using local mode model.

In aniline, the lone pair electrons on the nitrogen atom in the amino group interact with the pi electrons of the ring and the mechanical frequency of the ring CH oscillator shows a red shift from that of benzene. This happens because of the parallel orientation of the pi electrons in the two molecules. This effect is observed in N-methylaniline also. But in N,N-dimethylaniline, the addition of two alkyl group to the amino group changes the parallel orientation of pi electrons of the nitrogen. This changes the electron donating nature of the amino substituent and as a result, a blue shift is observed in the mechanical frequency of the ring CH oscillator from that of benzene. The same effect is observed in the ring CH oscillator frequency of N,N-diethylaniline also.

Aniline Compounds↗
PubMed2006

Identification by single-strand conformational polymorphism analysis of known and new mutations of the CYP3A5 gene in a French population.

The cytochrome P450 3A5 (CYP3A5) has been shown to be highly involved in the metabolism of many therapeutic agents. To date, several polymorphisms affecting the CYP3A5 gene have been identified but few studies have shown a complete description of the variability of the CYP3A5 in the French population. Therefore, the extent of CYP3A5 genetic polymorphism was investigated in a French population of 114 patients. The screening of the coding region with their intron-exon boundaries and the proximal flanking regions was performed using a PCR-SSCP strategy. Eighteen polymorphisms were identified, including four new mutations. They correspond to -19 T>C upstream of the exon 1, 7360 T>C in intron 4, 12991 T>C in intron 5 and 29788 delG in exon 12. We also identified 13 alleles including six new alleles. As expected, the most frequent allelic variant is CYP3A5*3, with a frequency of 87% of all alleles. These data confirmed that CYP3A5 gene is highly polymorphic. Furthermore, it will be now interesting to evaluate the impact of this polymorphism on the pharmacokinetic parameters of different drugs.

Cytochrome P-450 CYP3A↗
PubMed2005

The C-terminal tail of the gp41 transmembrane envelope glycoprotein of HIV-1 clades A, B, C, and D may exist in two conformations: an analysis of sequence, structure, and function.

In addition to the major ectodomain, the gp41 transmembrane glycoprotein of HIV-1 is now known to have a minor ectodomain that is part of the long C-terminal tail. Both ectodomains are highly antigenic, carry neutralizing and non-neutralizing epitopes, and are involved in virus-mediated fusion activity. However, data have so far been biologically based, and derived solely from T cell line-adapted (TCLA), B clade viruses. Here we have carried out sequence and theoretically based structural analyses of 357 gp41 C-terminal sequences of mainly primary isolates of HIV-1 clades A, B, C, and D. Data show that all these viruses have the potential to form a tail loop structure (the minor ectodomain) supported by three, beta-sheet, membrane-spanning domains (MSDs). This means that the first (N-terminal) tyrosine-based sorting signal of the gp41 tail is situated outside the cell membrane and is non-functional, and that gp41 that reaches the cell surface may be recycled back into the cytoplasm through the activity of the second tyrosine-sorting signal. However, we suggest that only a minority of cell-associated gp41 molecules - those destined for incorporation into virions - has 3 MSDs and the minor ectodomain. Most intracellular gp41 has the conventional single MSD, no minor ectodomain, a functional first tyrosine-based sorting signal, and in line with current thinking is degraded intracellularly. The gp41 structural diversity suggested here can be viewed as an evolutionary strategy to minimize HIV-1 envelope glycoprotein expression on the cell surface, and hence possible cytotoxicity and immune attack on the infected cell.

Acquired Immunodeficiency Syndrome↗
PubMed1999

Identification of a D579G homozygote cystic fibrosis patient with pancreatic sufficiency and minor lung involvement. Mutations in brief no. 221. Online.

Here we describe the identification of an italian patient homozygote for the D579G mutation affected by a mild form of Cystic Fibrosis with pancreatic sufficiency, minor lung involvement and marked viscosity of the cervical mucous. The D579G mutation causes an A1868G transition, a substitution of an aspartic acid to a glycine residue, generating an important amino acid change (charged to hydrophobic) in the nucleotide-binding domain (NBD). The mutation was first described by Brancolini et al. (1995) on two pancreatic sufficient CF patients, compound heterozygotes for delta508F. Patients were from Southern Italy (Puglia) as the D579G homozygote one, who is a 30 years old woman from Taranto (Puglia), daughter of second cousins born in Bari (Puglia). The identification of a homozygote D579G patient might confirm that this mutation does correlate with pancreatic sufficiency and a mild pulmonary phenotype.

Adult↗
PubMed1996

Development of a model for the delta-opioid receptor pharmacophore: 3. Comparison of the cyclic tetrapeptide, Tyr-c[D-Cys-Phe-D-Pen]OH with other conformationally constrained delta-receptor selective ligands.

We have previously proposed a model of the delta-opioid receptor bound conformation for the cyclic tetrapeptide, Tyr-c[D-Cys-Phe-D-Pen]OH (JOM-13) based on its conformational analysis and from conformation-affinity relationships observed for its analogues with modified first and third residues. To further verify the model, it is compared here with results of conformational and structure-activity studies for other known conformationally constrained delta-selective ligands: the cyclic pentapeptide agonist, Tyr-c[D-Pen-Gly-Phe-D-Phe]OH (DPDPE): the peptide antagonist, Tyr-Tic-Phe-PheOH (TIPP); the alkaloid agonist, 7-spiroindanyloxymorphone (SIOM); and the related alkaloid antagonist, oxymorphindole (OMI). A candidate delta-bound conformer is identified for DPDPE that provides spatial overlap of the functionally important N-terminal NH3+ and C-terminal COO- groups and the aromatic rings of the Tyr and Phe residues in both cyclic peptides. It is shown that all delta-selective ligands considered have similar arrangements of their pharmacophoric elements, i.e., the tyramine moiety and a second aromatic ring (i.e., the rings of Phe3, Phe4, and Tic2 residues in JOM-13, DPDPE, and TIPP, respectively; the indole ring system in OMI, and the indanyl ring system in SIOM). The second aromatic rings, while occupying similar regions of space throughout the analogues considered, have different orientations in agonists and antagonists, but identical orientations in peptide and alkaloid ligands with the same agonistic or antagonistic properties. These results agree with the previously proposed binding model for JOM-13, are consistent with the view that delta-opioid agonists and antagonists share the same binding site, and support the hypothesis of a similar mode of binding for opioid peptides and alkaloids.

Amino Acid Sequence↗
PubMed1998

Design, synthesis, and analysis of conformationally constrained nucleic acids.

In this review I discuss straightforward and general methods to modify nucleic acid structure with disulfide cross-links. A motivating factor in developing this chemistry was the notion that disulfide bonds would be excellent tools to probe the structure, dynamics, thermodynamics, folding, and function of DNA and RNA, much in the way that cystine cross-links have been used to study proteins. The chemistry described has been used to synthesize disulfide cross-linked hairpins and duplexes, higher order structures like triplexes, nonground-state conformations, and tRNAs. Since the cross-links form quantitatively by mild air oxidation and do not perturb either secondary or tertiary structure, this modification should prove quite useful for the study of nucleic acids.

Cross-Linking Reagents↗
PubMed1998

Conformational behavior of the HAV-VP3(110-121) peptidic sequence and synthetic analogs in membrane environments studied by CD and computational methods.

The present study was undertaken to examine the structural features that may be important to explain the immunogenicity of the (110-121) peptide sequence (FWRGDLVFDFQV) of VP3 capsid protein of hepatitis A virus. A conformational analysis of the preferred conformations by CD and molecular mechanics was carried out. Present results suggest that the interaction with liposomes as biomembrane model induces and stabilizes the amphipathic beta-structure of the peptide. To study the contribution of amino acid replacements at the RGD tripeptide as well as the influence of the peptide chain length on peptide conformation, solid-phase peptide synthesis of several peptide analogs was carried out and the peptide conformation was studied using CD spectroscopy. The results show that the RGD sequence is necessary to induce the beta-structure in the presence of liposomes.

Capsid↗
PubMed1999

Circular dichroism spectroscopy analysis of conformational transitions of a 54 base pair DNA duplex composed of alternating CGCGCG and TATATA blocks.

CD spectroscopy was used to analyze conformational properties of a self-complementary 54-mer DNA composed of alternating (CG)3 and (TA)3 hexamers. NaCl induced the Z-form in poly(GC), but the 54-mer remained the B-form under the same conditions. The B-Z transition was induced only after the addition of NiCl2. However, the Z-form was adopted by the whole molecule, not by the (CG)3 blocks alone. Two orders of magnitude higher concentrations of NiCl2 were required to induce the Z-form in poly(AT). The Z-form was also induced in poly(GC) by CsF that switched poly(AT) into the X-form, which seems to be a solution counterpart of D-DNA. Under these conditions the CD spectrum of the 54-mer was consistent with the (TA)3 blocks being in the X-form and the (CG)3 blocks in the B-form. At high concentrations of ethanol or trifluoroethanol, poly(AT) was an A-form, while poly(GC) adopted either Z-form, A-form or Z'-form. At the high trifluoroethanol concentrations the 54-mer cooperatively switched into a conformation whose CD spectrum was most consistent with the A-form in the (TA)3 blocks and the Z'-form in the (CG)3 blocks. This suggests that the base pairs are tilted in the Z'-form as in the A-form. The present article illustrates that CD spectroscopy can provide interesting pieces of information about conformational isomerizations and coexistence of multiple conformations in DNA molecules containing blocks of different simple sequence repeats.

Base Pairing↗
PubMed2002

Conformational studies of cyclic enkephalin analogues with L- or D-proline in position 3.

The conformation of a series of cyclic enkephalin analogues of a general formula X(1)-cyclo[Y(2)-Z(3)-Nal(4)-Leu(5)] (Nal: beta-(2-naphthyl)alanine), where X = Tyr, Phe, or Phe(NO(2)), Y = D-Dab or L-Dab (Dab: 2,4-diaminobutyric acid), and Z = D-Pro or L-Pro, was studied by means of NMR spectroscopy and theoretical conformational analysis with the Empirical Conformational Energy Program for Peptides and Proteins force field plus solvation. The NMR measurements were performed in dimethyl sulfoxide solution. The nuclear Overhauser effect intensities and coupling constants were used to compute the statistical weights of the conformations of the ensemble generated in global conformational searches. The purpose of this study was to determine whether introducing the D- or L-proline residue in position 3 can produce peptides with both rigid backbone and significant separation of the pharmacophore groups in position 1 and 4 (as required for high affinity for the mu-type opioid receptors). It was found that the analogues with D-Dab in position 2 and D-Pro in position 3 possess a stable type II' beta-turn at positions 3 and 4, which rigidifies the cyclic backbone; this finding was confirmed by independent measurements of the temperature coefficients of the amide protons, which indicated very significant screening of the Leu(5) amide proton from the solvent. However, these analogues were found to possess a short interchromophore distance. The analogues containing both Dab and Pro in the L-configuration are characterized by a larger interchromophore distance; however, they do not possess a stable beta-turn and have therefore a higher conformational flexibility. The modifications proposed in this work are therefore not likely to lead to enkephalin analogues with a high affinity for the mu-receptors.

Amino Acid Sequence↗