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PubMed2007

Thermodynamic characterization of the interaction between CAR-RXR and SRC-1 peptide by isothermal titration calorimetry.

The constitutive androstane receptor (CAR) enhances transcription of specific target genes that regulate several metabolic pathways. CAR functions as an obligate heterodimer (CAR-RXR) with the retinoid X receptor (RXR). Also part of the active receptor complex is the steroid receptor coactivator-1 (SRC-1) which interacts with the receptor complex via specific receptor interaction domains (RIDs). A peptide derived from SRC-1 RID2 is used to study the thermodynamic properties of the interaction with the CAR-RXR ligand binding domain (LBD) complex. In the absence of ligands for both CAR and RXR, binding of coactivator peptide to the CAR-RXR heterodimer is characterized by a favorable enthalpy change and an unfavorable entropy change. The addition of the CAR agonist, TCPOBOP, increases the affinity for coactivator by decreasing the unfavorable entropy and increasing the favorable intrinsic enthalpy of the interaction. The RXR ligand, 9-cis-RA, generates a second SRC-1 site and increases the affinity by improving the entropic component of binding. There is an additional increase in affinity for one of the two sites in the presence of both ligands. The change in heat capacity (deltaCp) is also investigated. A 2-fold difference in deltaCp is observed between liganded and unliganded CAR-RXR. The observed thermodynamic parameters for binding of SRC-1 peptide to liganded and apo CAR-RXR as well as the difference in the deltaCp data provide evidence that the apo CAR-RXR heterodimer is conformationally mobile. The more favorable enthalpic contribution for TCPOBOP-bound CAR-RXR indicates that preformation of the binding site improves the complementarity of the coactivator-receptor interaction.

Alitretinoin↗

PubMed2001

Electrostatic contributions to protein-protein interactions: fast energetic filters for docking and their physical basis.

The methods of continuum electrostatics are used to calculate the binding free energies of a set of protein-protein complexes including experimentally determined structures as well as other orientations generated by a fast docking algorithm. In the native structures, charged groups that are deeply buried were often found to favor complex formation (relative to isosteric nonpolar groups), whereas in nonnative complexes generated by a geometric docking algorithm, they were equally likely to be stabilizing as destabilizing. These observations were used to design a new filter for screening docked conformations that was applied, in conjunction with a number of geometric filters that assess shape complementarity, to 15 antibody-antigen complexes and 14 enzyme-inhibitor complexes. For the bound docking problem, which is the major focus of this paper, native and near-native solutions were ranked first or second in all but two enzyme-inhibitor complexes. Less success was encountered for antibody-antigen complexes, but in all cases studied, the more complete free energy evaluation was able to identify native and near-native structures. A filter based on the enrichment of tyrosines and tryptophans in antibody binding sites was applied to the antibody-antigen complexes and resulted in a native and near-native solution being ranked first and second in all cases. A clear improvement over previously reported results was obtained for the unbound antibody-antigen examples as well. The algorithm and various filters used in this work are quite efficient and are able to reduce the number of plausible docking orientations to a size small enough so that a final more complete free energy evaluation on the reduced set becomes computationally feasible.

Amino Acids↗

PubMed1997

The structure of enzyme IIAlactose from Lactococcus lactis reveals a new fold and points to possible interactions of a multicomponent system.

BACKGROUND: The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is responsible for the binding, transmembrane transport and phosphorylation of numerous sugar substrates. The system is also involved in the regulation of a variety of metabolic and transcriptional processes. The PTS consists of two non-specific energy coupling components, enzyme I and a heat stable phosphocarrier protein (HPr), as well as several sugar-specific multiprotein permeases known as enzymes II. In most cases, enzymes IIA and IIB are located in the cytoplasm, while enzyme IIC acts as a membrane channel. Enzyme IIAlactose belongs to the lactose/cellobiose-specific family of enzymes II, one of four functionally and structurally distinct groups. The protein, which normally functions as a trimer, is believed to separate into its subunits after phosphorylation. RESULTS: The crystal structure of the trimeric enzyme IIAlactose from Lactococcus lactis has been determined at 2.3 A resolution. The subunits of the enzyme, related to each other by the inherent threefold rotational symmetry, possess interesting structural features such as coiled-coil-like packing and a methionine cluster. The subunits each comprise three helices (I, II and III) and pack against each other forming a nine-helix bundle. This helical bundle is stabilized by a centrally located metal ion and also encloses a hydrophobic cavity. The three phosphorylation sites (His78 on each monomer) are located in helices III and their sidechains protrude into a large groove between helices I and II of the neighbouring subunits. A model of the complex between phosphorylated HPr and enzyme IIAlactose has been constructed. CONCLUSIONS: Enzyme IIAlactose is the first representative of the family of lactose/cellobiose-specific enzymes IIA for which a three-dimensional structure has been determined. Some of its structural features, like the presence of two histidine residues at the active site, seem to be common to all enzymes no overall structural homology is observed to any PTS proteins or to any other proteins in the Protein Data Bank. Enzyme IIAlactose shows surface complementarity to the phosphorylated form of HPr and several energetically favourable interactions between the two molecules can be predicted.

Amino Acid Sequence↗

PubMed1995

Glycosylation of the variable region of immunoglobulin G--site specific maturation of the sugar chains.

The structure of the N-linked sugar chains attached to three IgG antibodies, identical in amino acid sequence except for the changes required to introduce the carbohydrate addition sites, has been determined. All three antibodies are specific for dextran but differ in their ability to bind antigen. The heavy chains with a murine variable region (V region) attached to the human gamma 4 constant region were expressed in a murine hybridoma synthesizing the specific light chain. In addition to the glycosylation site in the Fc portion, each antibody has a different glycosylation site in the second complementarity determining region (CDR2) of the heavy chain (Asn54, Asn58, or Asn60). The sugar chains were released from purified Fab and Fc fragments by hydrazinolysis and converted to radioactive oligosaccharides by reduction with sodium borotritide. The structures of these radioactive oligosaccharides were determined by a combination of sequential exoglycosidase digestion and Bio-Gel P-4 and lectin column chromatography. For all three antibodies, the carbohydrate attached to the Fc portion was a mixture of complex-type biantennary sugar chains. The variable region carbohydrate structures attached at Asn54 and Asn58 were also complex-type but more highly sialylated than were the Fc-associated sugars. Moreover, unlike the Fc-associated sugars, a significant population of Fab-associated sugars contained a Gal alpha 1-->3 residue as a non-reducing terminus. In contrast, the carbohydrate attached at Asn60 was a high mannose structure. These results demonstrate that slight changes in the position of carbohydrate attachment within CDR2 of the variable region of the heavy chain can substantially alter carbohydrate processing and that complex-type carbohydrates contained within the same polypeptide chain can have different structures.

Amino Acid Sequence↗

PubMed1999

[Home and outside home food complementarity in Bamako (Mali): nutritional and economic aspects. What is the rationality behind consumers' choices?].

BACKGROUND: Great modifications in social and family relationships and life style come from rapid urbanisation in developing countries. Various types of malnutrition coexist in these towns. Food consumption outside the home is more and more common. This in turn encourages rapid growth in the food informal economic sector which must be taken into account in food and nutrition policy and planning. The aim of this study was to analyse the characteristics and complementarities between home and outside the home food consumption of different kinds of individuals coming from different kinds of families in Bamako, in terms of expenditures and aspects of food and nutritional intakes. METHODS: 366 individuals from 74 families were interviewed. They were chosen according to defined criteria in three districts of Bamako of high, middle and poor socio-economic level. RESULTS: At home the daily food expenditure is 2.27 and 3.79 times greater per individual in rich than in middle income and poor families respectively. Animal proteins are respectively 41%, 19% and 9% of daily protein intake. Energy from lipids is 20 to 30% in rich and middle families. In poor ones it is only 15% which is the lower limit of nutritional recommendations. Moreover, contrary to proteins and carbohydrates, the cost of lipids seems, almost incompressible. Almost everybody eats out of home food, particularly children. Its cost, on an energy basis, is higher than home food. The expense is 19 to 27% of the family food budget. It appears necessary to the satisfaction of nutritional requirements in middle income and poor families. Despite various costs, whatever be the socio-economic level, energy intakes coming from that food are equivalent in absolute terms among various kinds of individuals: children, men and women. CONCLUSION: Families had to adapt their food strategies after the 1994 Franc CFA devaluation. Various hypotheses are presented, linked to intra-family relationships and, within poor families, to insertion in the street food economic sector, in order to understand, the logic of food choices. Such an analysis, where health, nutritional, economic, social and cultural aspects of food are taken into account, allows some concrete orientations for urban food and nutrition policy.

Adolescent↗

PubMed2002

Noncovalent interaction energies in covalent complexes: TEM-1 beta-lactamase and beta-lactams.

The class A beta-lactamase TEM-1 is a key bacterial resistance enzyme against beta-lactam antibiotics, but little is known about the energetic bases for complementarity between TEM-1 and its inhibitors. Most inhibitors form a covalent adduct with the catalytic Ser70, making the measurement of equilibrium constants, and hence interaction energies, technically difficult. This study evaluates noncovalent interactions within covalent complexes by examining the differential stability of TEM-1 and its inhibitor adducts. The thermal denaturation of TEM-1 follows a two-state, reversible model with a melting temperature (T(m)) of 51.6C and a van't Hoff enthalpy of unfolding (DeltaH(VH)) of 146.2 kcal/mol at pH 7.0. The stability of the enzyme changes on forming an inhibitor adduct. As expected, some inhibitors stabilize TEM-1; transition-state analogues increase the T(m) by up to 3.7C (1.7 kcal/mol). Surprisingly, all beta-lactam covalent acyl--enzyme complexes tested destabilize TEM-1 significantly relative to the apo-enzyme. For instance, the clinically used inhibitor clavulanic acid and the beta-lactamase-resistant beta-lactams moxalactam and imipenem destabilize TEM-1 by over 2.6C (1.2 kcal/mol) in their covalent adducts. Based on the structure of the TEM-1/imipenem complex (Maveyraud et al., J Am Chem Soc 1998;120:9748--52), destabilization by moxalactam and imipenem is thought to be caused by a steric clash between the side-chain of Asn132 and the 6(7)-alpha group of these beta-lactams. To test this hypothesis, the mutant enzyme N132A was made. In contrast with wild-type, the covalent complexes between N132A and both imipenem and moxalactam stabilize the enzyme, consistent with the hypothesis. To investigate the structural bases of this dramatic change in stability, the structure of N132A/imipenem was determined by X-ray crystallography. In the complex with N132A, imipenem adopts a very different conformation from that observed in the wild-type complex, and the putative destabilizing interaction with residue 132 is relieved. Studies of several enzymes suggest that beta-lactams, and covalent inhibitors in general, can have either net favorable or net unfavorable noncovalent interaction energies within the covalent complex. In the case of TEM-1, such unfavorable interactions convert substrate analogues into very effective inhibitors.

Amino Acid Substitution↗